Lifeboat Foundation

Maximizing the protection of life on Earth requires knowledge of the global patterns of biodiversity at multiple dimensions, from genetic diversity within species, to species and ecosystem diversity. Yet, the lack of genetic sequences with geographic information at global scale has so far hindered our ability to map genetic diversity, an important, but hard to detect, biodiversity dimension.

In a new study, researchers from the Universities of Copenhagen and Adelaide have collected and georeferenced a massive amount of genetic data for terrestrial mammals and evaluated long-standing theories that could explain the global distribution of genetic diversity. They found that regions of the world rich in deep evolutionary history, such as Northern Andes, the Eastern Arc Mountains, Amazonia, the Brazilian Atlantic forest, the central America jungles, sub-Saharan Africa and south-eastern Asia are also strongholds of genetic diversity. They also show that the relatively stable climate in these regions during the past 21’000 years contributes significantly to this intraspecific richness.

“Genetic diversity within species is a critical component of biodiversity, playing two important roles at the same time. It reflects species evolutionary history and defines their capacity to adapt under future environmental change. However, and despite the predictions of major biodiversity theories, the actual global distribution of genetic diversity remained, so far, a mystery. Recent collective efforts to populate public databases with genetic sequences and their localities allowed us to evaluate these theories and generate the first global maps of genetic diversity in terrestrial mammal assemblages”, says Spyros Theodoridis, Postdoctoral Researcher at the Center for Macroecology, Evolution and Climate, GLOBE Institute, and lead author of the study.

I always enjoy the perspective of David Wood, and in this session of the London Futurists there is a panel discussion about genetic engineering in the future.

Our DNA is becoming as readable, writable, and hackable as our information technology. The resulting genetic revolution is poised to transform our healthcare, our choices for the characteristics of the next generation, and our evolution as a species. The future could bring breathtaking advances in human well-being, but it could also descend into a dangerous genetic arms race.

Continue reading “Hacking Darwin: Genetic Engineering and the Future of Humanity” »

Circa 2018

CRISPR-Cas adaptive immune systems of bacteria and archaea have catapulted into the scientific spotlight as genome editing tools. To aid researchers in the field, we have developed an automated pipeline, named CRISPRdisco (CRISPR discovery), to identify CRISPR repeats and cas genes in genome assemblies, determine type and subtype, and describe system completeness. All six major types and 23 currently recognized subtypes and novel putative V-U types are detected. Here, we use the pipeline to identify and classify putative CRISPR-Cas systems in 2,777 complete genomes from the NCBI RefSeq database. This allows comparison to previous publications and investigation of the occurrence and size of CRISPR-Cas systems. Software available at http://github.com/crisprlab/CRISPRdisco provides reproducible, standardized, accessible, transparent, and high-throughput analysis methods available to all researchers in and beyond the CRISPR-Cas research community. This tool opens new avenues to enable classification within a complex nomenclature and provides analytical methods in a field that has evolved rapidly.

CRISPR-Cas^* bacterial and archaeal immune systems remain of high interest across many domains of the life sciences, including food science, molecular biology, prokaryotic evolution, and as a technology from pharma to next-generation crops.^1–4 The unifying interest in CRISPR is the tremendous wealth of applications this technology affords. While application and tool development using a handful of characterized CRISPR-Cas systems has exploded, the annotation and discovery of systems remains an ongoing challenge for microbiologists and bioinformaticians to solve. The ability to identify CRISPR-Cas systems can benefit the greater scientific community, from microbiologists attempting to learn about adaptive immunity in prokaryotes, to molecular biologists interested in harnessing the nucleic acid-targeting functions of various Cas proteins.

face_with_colon_three circa 2015 this guppy could lead to rapid biological singularity.

Some species are evolving far more quickly than Darwin ever imagined.

High-fidelity modelling of nanosecond repetitively pulsed discharges (NRPDs) is burdened by the multiple time and length scales and large chemistry mechanisms involved, which prohibit detailed analyses and parametric studies. In the present work, we propose a ‘frozen electric-field’ modelling approach to expedite the NRPD simulations without adverse effects on the solution accuracy. First, a burst of nanosecond voltage pulses is simulated self-consistently until the discharge reaches a stationary state. The calculated spatial distributions and temporal evolution of the electric field, electron density and electron energy during the last pulse are then stored in a library and the electrical characteristics of subsequent pulses are frozen at these values. This strategy allows the timestep for numerical integration to be increased by four orders of magnitude (from 10⁻¹³ to 10⁻⁹ s), thereby significantly improving the computational efficiency of the process. Reduced calculations of a burst of 50 discharge pulses show good agreement with the predictions from a complete plasma model (electrical characteristics calculated during each pulse). The error in species densities is less than 20% at the centre of the discharge volume and about 30% near the boundaries. The deviations in temperature, however, are much lower, at 5% in the entire domain. The model predictions are in excellent agreement with measured ignition delay times and temperatures in H₂–air mixtures subject to dielectric barrier NRPD over a pressure range of 54–144 Torr with equivalence ratios of 0.7–1.2. The OH density increases with pressure and triggers low-temperature fuel oxidation, which leads to rapid temperature rise and ignition. The ignition delay decreases by a factor of 2, with an increase in pressure from 54 to 144 Torr. In contrast, an increase in the H₂–air equivalence ratio from 0.7 to 1.2 marginally decreases the ignition delay by about 20%. This behaviour is attributed to the insensitivity of OH production rates to the variation in the equivalence ratio.

Despite the traditional view that species do not exchange genes by hybridisation, recent studies show that gene flow between closely related species is more common than previously thought. A team of scientists from Uppsala University and Princeton University now reports how gene flow between two species of Darwin’s finches has affected their beak morphology. The study is published today in Nature Ecology and Evolution.

Darwin’s finches on the Galápagos Islands are an example of a rapid adaptive radiation in which 18 species have evolved from a common ancestral species within a period of 1–2 million years. Some of these species have only been separated for a few hundred thousand years or less.

Rosemary and Peter Grant of Princeton University, co-authors of the new study, studied populations of Darwin’s finches on the small island of Daphne Major for 40 consecutive years and observed occasional hybridisation between two distinct species, the common cactus finch and the medium ground finch. The cactus finch is slightly larger than the medium ground finch, has a more pointed beak and is specialised to feed on cactus. The medium ground finch has a blunter beak and is specialised to feed on seeds.

Quantitative biologists David McCandlish and Juannan Zhou at Cold Spring Harbor Laboratory have developed an algorithm with predictive power, giving scientists the ability to see how specific genetic mutations can combine to make critical proteins change over the course of a species’ evolution.

Described in Nature Communications, the algorithm called “minimum epistasis interpolation” results in a visualization of how a protein could evolve to either become highly effective or not effective at all. They compared the functionality of thousands of versions of the protein, finding patterns in how mutations cause the protein to evolve from one functional form to another.

Continue reading “Algorithm Developed to Predict the Evolution of Genetic Mutations” »

The McGill University paleontologist, who died from COVID-19, was known for using multidisciplinary methods to explore the origins of amphibians, birds, and mammals.

Water spliting got cheaper.

Alkaline anion exchange membrane (AEM) electrolysers to produce hydrogen from water are still at an early stage of development, and their performance is far lower than that of systems based on proton exchange membranes. Here, we report an ammonium-enriched anion exchange ionomer that improves the performance of an AEM electrolyser to levels approaching that of state-of-the-art proton exchange membrane electrolysers. Using rotating-disk electrode experiments, we show that a high pH (13) in the electrode binder is the critical factor for improving the activity of the hydrogen- and oxygen-evolution reactions in AEM electrolysers. Based on this observation, we prepared and tested several quaternized polystyrene electrode binders in an AEM electrolyser. Using the binder with the highest ionic concentration and a NiFe oxygen evolution catalyst, we demonstrated performance of 2.7 A cm⁻² at 1.8 V without a corrosive circulating alkaline solution. The limited durability of the AEM electrolyser remains a challenge to be addressed in the future.