Catastrophic desert formation in Daisyworld

Feedback between life and its environment is ubiquitous but the strength of coupling and its global implications remain hotly debated. Abrupt changes in the abundance of life for small changes in forcing provide one indicator of regulation, for example, when vegetation-climate feedback collapses in the formation of a desert. Here we use a two-dimensional "Daisyworld" model with curvature to show that catastrophic collapse of life under gradual forcing provides a testable indicator of environmental feedback. When solar luminosity increases to a critical value, a desert forms across a wide band of the planet. The scale of collapse depends on the strength of feedback. The efficiency of temperature regulation is limited by mutation rate in an analogous manner to the limitation of adaptive fitness in evolutionary theories. The final state of the system emerging from single-site rules can be described by two global quantities: optimization of temperature regulation and maximization of diversity, which are mathematically analogous to energy and entropy in thermodynamics.     

Symbiotic physiology promotes homeostasis in Daisyworld

A connection is hypothesized between the physiological consequences of mutualistic symbiosis and life's average long-term impact on certain highly biologically conserved environmental variables. This hypothesis is developed analytically and with a variant of the Daisyworld model. Biological homeostasis is frequently effective due to co-ordination between opposing physiological “rein” functions, which buffer an organism in response to an external (often environmental) perturbation. It is proposed that during evolutionary history the pooling of different species' physiological functions in mutualistic symbioses increased the range of suboptimal environmental conditions that could be buffered against—a mutual tolerance benefit sometimes sufficient to outweigh the cost of cooperation. A related argument is that for a small number of biologically-crucial physical variables (i) the difference between organism interiors and the life-environment interface is relatively low, and (ii) the biologically optimum level of that variable is relatively highly conserved across different species. For such variables, symbiosis tends to cause (at a cost) an increase in the number of environmental buffering functions per unit of selection, which in turn biases the overall impact of the biota on the state of the variable towards the biological optimum. When a costly but more temperature-tolerant and physiologically versatile symbiosis between one black (warming) and one white (cooling) “daisy” is added to the (otherwise unaltered) Daisyworld parable, four new results emerge: (1) The extension of habitability to a wider luminosity range, (2) resistance to the impact of “cheater” white daisies with cold optima, that derive short-term benefit from environmental destabilisation, (3) the capacity to maintain residual, oscillatory regulation in response to forcings that change more rapidly than allele frequencies and (crucially) (4) “succession”-type dynamics in which the tolerant symbiosis colonises and to an extent makes habitable an otherwise lifeless environment, but is later displaced by free-living genotypes that have higher local fitness once conditions improve. The final result is arguably analogous to lichen colonisation of the Neoproterozoic land surface, followed by the Phanerozoic rise of vascular plants. Caution is necessary in extrapolating from the Daisyworld parable to real ecology/geochemistry, but sufficiently conserved variables may be water potential, macronutrient stoichiometry and (to a lesser extent) the temperature window for metabolic activity.     

A fitness based analysis of Daisyworld

The Gaia hypothesis [Lovelock, J., Margulis, L., 1974. Atmospheric homeostasis: the Gaia hypothesis. Tellus 26, 1], that the earth functions as a self-regulating system, has never sat particularly comfortably with ideas in mainstream biology [Anon, 2002. In pursuit of arrogant simplicities. Nature 416, 247]. A lack of any clear role for evolution in the model has led to claims of teleology-that self-regulation emerges because it is pre-ordained to do so [Doolittle, W.F., 1981. Is nature really motherly? CoEvol. Q. 58-63; Dawkins, R., 1979. The Extended Phenotype. Oxford University Press, Oxford]. The Daisyworld parable [Watson, A.J., Lovelock, J.E., 1983. Biological homeostasis of the global environment--the parable of Daisyworld. Tellus B 35, 284], a simple mathematical illustration of Gaia, went some way to addressing these critiques but, despite recent success in incorporating natural selection [Stocker, S.,1995. Regarding mutations in Daisyworld models. J. Theor. Biol. 175, 495; Lenton, T.M., 1998. Gaia and natural selection. Nature 394, 439; Lenton, T.M., Lovelock, J.E., 2001. Daisyworld revisited: quantifying biological effects on planetary self-regulation. Tellus B 53, 288; Wood, A.J., Ackland, G.J., Lenton, T.M., 2006. Mutation of albedo and growth response leads to oscillations in a spatial Daisyworld. J. Theor. Biol. 242, 188], it remains a widely held view that the ideas are inconsistent with biological principles. We show that standard methodology from quantitative genetics can be used to predict the stationary states and dynamic behaviour of Daisyworlds. The system regulates its temperature due to the low-level evolutionary dynamics of competition between the thermally coupled daisies, no higher level principle is invoked. A reconciliation of Gaia with evolutionary theory may allow further development of evolutionary arguments for the existence of global self-regulatory systems.     

Temperature breaks in Arrhenius plots: a thermodynamic consequence of a phase change

Temperature “breaks” in Arrhenius plots of biological data are real and can be explained as a consequence of a phase change in the system.     

Non-local thermodynamic effects and efficiency of oxidative phosphorylation

A non-equilibrium thermodynamic model of oxidative phosphorylation is formulated, which allows us to take into account some non-local effects. In this way, we compute the influence of the tangential resistivity of the inner mitochondrial membrane to proton current, as well as that of the distance between active sites, on the stoichiometry and efficiency of energy conversion.     

Seasonal variation of maximum photochemical efficiency in boreal Norway spruce stands

 The seasonal variation in maximum photochemical efficiency of photosystem II (F_v/F_m) and the relationship between F_v/F_m and climatic factors such as irradiance, frost-nights and daily mean temperature was studied in young Norway spruce trees for 4 years in northern Sweden. As a result of night frost, the F_v/F_m-ratio gradually decreased during the autumn. There was between-year variation in the pattern of F_v/F_m in fully exposed shoots during autumn and spring, largely as an effect of differing temperature conditions. During spring, there was a strong apparent relationship between daily mean temperature and F_v/F_m within the temperature range –3 to 12°C. The light regime to which the needles were exposed during winter affected F_v/F_m, and moderately shaded shoots from the bottom of the canopy generally had a higher F_v/F_m-ratio than fully exposed shoots from the top of the canopy. Received: 1 October 1997 / Accepted: 16 June 1998     

Clinorotation effect on thermodynamic efficiency of energy transformation in chloroplasts of higher plants

The aim of the work was to estimate the effect of clinorotation on thermodynamic coupling and efficiency of the process of photosynthetic energy transformation in chloroplasts using nonequilibrium thermodynamics approach. These parameters were calculated from experimentally determined net photosynthetic oxygen evolution at static head [(Je)sh], uncoupled rate of the oxygen evolution (Jo)unc and net rate of ATP production. It was found that in chloroplasts isolated from control and clinorotated pea plants coefficient of thermodynamic coupling of photophosphorylation (q) was 0.94 and 0.91 respectively. Optimal thermodynamic efficiency (eta opt) of the systems were calculated as 0.64 and 0.6 for control and clinorotation plants. Thus the data of the work show that thermodynamic efficiency of light energy transformation in higher plants is under influence of imitated weightlessness conditions.     

Property and efficiency of the maximum likelihood method for molecular phylogeny

Summary The maximum likelihood (ML) method for constructing phylogenetic trees (both rooted and unrooted trees) from DNA sequence data was studied. Although there is some theoretical problem in the comparison of ML values conditional for each topology, it is possible to make a heuristic argument to justify the method. Based on this argument, a new algorithm for estimating the ML tree is presented. It is shown that under the assumption of a constant rate of evolution, the ML method and UPGMA always give the same rooted tree for the case of three operational taxonomic units (OTUs). This also seems to hold approximately for the case with four OTUs. When we consider unrooted trees with the assumption of a varying rate of nucleotide substitution, the efficiency of the ML method in obtaining the correct tree is similar to those of the maximum parsimony method and distance methods. The ML method was applied to Brown et al.'s data, and the tree topology obtained was the same as that found by the maximum parsimony method, but it was different from those obtained by distance methods.     

Mutation of albedo and growth response produces oscillations in a spatial Daisyworld

We extended a two-dimensional cellular automaton (CA) Daisyworld to include mutation of optimal growth temperature as well as mutation of albedo. Thus, the organisms (daisies) can adapt to prevailing environmental conditions or evolve to alter their environment. We find the resulting system oscillates with a period of hundreds of daisy generations. Weaker and less regular oscillations exist in previous daisyworld models, but they become much stronger and more regular here with mutation in the growth response. Despite the existence of a particular combination of mean albedo and optimum individual growth temperature which maximises growth, we find that this global state is unstable with respect to mutations which lower absolute growth rate, but increase marginal growth rate. The resulting system oscillates with a period that is found to decrease with increasing death rate, and to increase with increasing heat diffusion and heat capacity. We speculate that the origin of this oscillation is a Hopf bifurcation, previously predicted in a zero-dimensional system.     

The consequence of PRELP overexpression on skin.

PRELP is a member of the small leucine-rich repeat proteoglycan family that is abundantly expressed in many cartilages compared to other connective tissues. To study the consequence of PRELP overexpression in tissues where it is normally expressed at low abundance, transgenic mice were generated in which the human PRELP transgene was placed under control of the CMV promoter. A connective tissue phenotype was observed in the skin, where the organization of collagen fibrils in the dermis was perturbed and the thickness of the hypodermal fat layer was diminished.     

The thermodynamic principles of isochoric cryopreservation

The goal of this study is to introduce the fundamental thermodynamic principles of isochoric (constant volume) cryopreservation for low temperature preservation of biological materials. Traditionally, cryopreservation is performed in an isobaric process (constant pressure) at 1 atm, because this is our natural environment and it is most convenient experimentally. More than half a century of studies on cryopreservation shows that the major mechanism of damage during isobaric cryopreservation is the increase in intracellular ionic concentration during freezing, which presumably causes chemical damage to the components of cells. Cryoprotectants as well as hyperbaric pressures have been developed as methods to reduce the extent of chemical damage during freezing. The theoretical studies in this paper show that in isochoric cryopreservation, the increase in solution concentration during freezing is lower at each temperature by almost an order of magnitude from that in isobaric cryopreservation. This suggests that isochoric cryopreservation could be a preferential alternative to isobaric cryopreservation. The technology for isochoric cryopreservation is very simple; freezing in a constant volume chamber. Using a simple isochoric cryopreservation device, we confirm the theoretical thermodynamic predictions.     

The consequence of natural selection on genetic variation in the mouse

Laboratory mouse strains are known to have emerged from recent interbreeding between individuals of Mus musculus isolated populations. As a result of this breeding history, the collection of polymorphisms observed between laboratory mouse strains is likely to harbor the effects of natural selection between reproductively isolated populations. Until now no study has systematically investigated the consequences of this breeding history on gene evolution. Here we have used a novel, unbiased evolutionary approach to predict the founder origin of laboratory mouse strains and to assess the balance between ancient and newly emerged mutations in the founder subspecies. Our results confirm a contribution from at least four distinct subspecies. Additionally, our method allowed us to identify regions of relaxed selective constraint among laboratory mouse strains. This unique structure of variation is likely to have significant consequences on the use of mouse to find genes underlying phenotypic variation.     

The turbidity maximum in the Tamar estuary

Many estuaries of medium to high tidal range exhibit an accumulation of fine cohesive material in their upper reaches in the region of the limit of saline intrusion. Much, or all, of this material is suspended each tidal cycle and the entire region undergoes a seasonal variation which appears to depend on fluvial input. Two factors which are throught to influence the formation and maintenance of turbidity maxima are the differing magnitudes of the bed shear stress (τ₀) on flood and ebb tides and the large vertical density gradient which developes on the ebb tide. Crucial to the importance of the first factor is that τ₀ exceeds a critical value, at which erosion occurs, for a greater period on the flood than on the ebb. The effect of the density gradient is that upward propagation of bed generated eddies is inhibited and the sediment is not transported into the upper part of the flow where it will be most effectively transported. It is not clear which, if either, of these mechanisms is dominant. Data consisting of vertical profiles of velocity, salinity and suspended solids were collected at four stations in the Tamar estuary during a high range tidal cycle. One station, at which the depth mean salinity (S _d ) varied from 0.0 to ∼ 12.0‰, was occupied permanently. The other stations were occupied such that data were collected asS _d varied in the range 0.0 to ∼ 4.0‰. In this way each station was occupied for a period of time on the ebb and flood tide. Observations show that during the early ebb, when the flow is relatively deep and slow, stratification persist untilS _d ∼ 0.0‰ and that no significant transport occurs while the flow is saline but that there is a rapid increase in suspended solids concentrations after this time. During the later ebb the shallower faster flow allowed the density gradient to be erode and significant transport was observed atS _d ∼ 5.0‰. On the flood tide the flow in the low salinity region is well-mixed troughout. Computation of the fluxes and total transport per unit breath of estuary show that on the ebb tide the quantity of solid material being transported by the low salinity (0–3‰) region remains nearly constant as this region of the flow is advebted seaward. On the flood tide, however, as the same region is advected landward the quantity of material being transported increases. It is concluded that in the Tamar estuary the early ebb tide stratification contributed to the formation and maintenance of a turbidity maximum which is strongly associated with the low salinity region of the flow. It is also speculated that the differences in the ebb and flood tide transport are caused by differences in the availability of mobile material on the bed at different stages of the tidal cycle.     

Sex preselection: high-speed flow cytometric sorting of X and Y sperm for maximum efficiency

Sex preselection that is based on flow-cytometric measurement of sperm DNA content to enable sorting of X- from Y-chromosome-bearing sperm has proven reproducible at various locations and with many species at greater than 90% purity. Offspring of the predetermined sex in both domestic animals and human beings have been born using this technology since its introduction in 1989. The method involves treating sperm with the fluorescent dye, Hoechst 33342, which binds to the DNA and then sorting them into X- and Y-bearing-sperm populations with a flow cytometer/cell sorter modified specifically for sperm. Sexed sperm are then used with differing semen delivery routes such as intra-uterine, intra-tubal, artificial insemination (deep-uterine and cervical), in vitro fertilization and embryo transfer, and intra-cytoplasmic sperm injection (ICSI). Offspring produced at all locations using the technology have been morphologically normal and reproductively capable in succeeding generations. With the advent of high-speed cell sorting technology and improved efficiency of sorting by a new sperm orienting nozzle, the efficiency of sexed sperm production is significantly enhanced. This paper describes development of the these technological improvements in the Beltsville Sexing Technology that has brought sexed sperm to a new level of application. Under typical conditions the high-speed sperm sorter with the orienting nozzle (HiSON) results in purities of 90% of X- and Y-bearing sperm at 6 million sperm per h for each population. Taken to its highest performance level, the HiSON has produced X-bearing-sperm populations at 85 to 90% purity in the production of up to 11 million X-bearing-sperm per h of sorting. In addition if one accepts a lower purity (75 to 80%) of X, nearly 20 million sperm can be sorted per h. The latter represents a 30 to 60-fold improvement over the 1989 sorting technology using rabbit sperm. It is anticipated that with instrument refinements the production capacity can be improved even further. The application of the current technology has led to much wider potential for practical usage through conventional and deep-uterine artificial insemination of many species, especially cattle. It also opens the possibility of utilizing sexed sperm for artificial insemination in swine once low-sperm-dose methods are perfected. Sexed sperm on demand has become a reality through the development of the HiSON system.