Lifeboat Foundation

For three years, anthropologist Alan Rogers has attempted to solve an evolutionary puzzle. His research untangles millions of years of human evolution by analyzing DNA strands from ancient human species known as hominins. Like many evolutionary geneticists, Rogers compares hominin genomes looking for genetic patterns such as mutations and shared genes. He develops statistical methods that infer the history of ancient human populations.

In 2017, Rogers led a study which found that two lineages of ancient humans, Neanderthals and Denisovans, separated much earlier than previously thought and proposed a bottleneck population size. It caused some controversy—anthropologists Mafessoni and Prüfer argued that their method for analyzing the DNA produced different results. Rogers agreed, but realized that neither method explained the genetic data very well.

“Both of our methods under discussion were missing something, but what?” asked Rogers, professor of anthropology at the University of Utah.

Life is usefully defined on the basis of process: Any set of entities that participates in the process of evolution by natural selection is alive. But how does evolution by natural selection—and thus life—get started? The answer is far from obvious. Lack of insight haunts origins of life research and plagues understanding of the major evolutionary transitions, including the transition from cells to multicellular life.

In a new paper published in Nature Ecology & Evolution, a team led by Paul Rainey at ESPCI Paris and the Max Planck Institute for Evolutionary Biology provides a solution. Adopting a theoretical approach inspired from earlier and on-going experiments, Rainey and his team show how ecological circumstances can kick-start life, both from the get-go, and also at each of the major evolutionary transitions.

For entities to participate in the process of evolution by natural selection, entities need to be discreet and vary one to another, entities must replicate and offspring must resemble parental types. These basic Darwinian properties (variation, reproduction and heredity) are such fundamental features of life that it is easy to take their existence for granted. But as Black et al point out, Darwinian properties are derived and require evolutionary explanation. In the absence of any manifestation of heritable variance in fitness evolution is governed by chance alone and the road out of randomness difficult to conceive.

Wall Street’s Biotech Investment Wizard — On this most recent ideaXme (http://radioideaxme.com/) episode, I was honored to be joined by my friend, and biotech / pharma / healthcare investment banker extraordinaire, Frederick Frank, to talk about his 50-year career history behind the industry’s mega-deals — #Ideaxme #Biopharma #Biotech #WallStreet #Mergers #Acquisitions #VentureCapital #Genentech #Roche #BristolMyersSquibb #PrivateEquity #Health #Wellness #Longevity #Regeneration #LifeExtension #Aging #IraPastor #Bioquark #Regenerage

Ira Pastor, ideaXme exponential health ambassador, interviews Fred Frank, Founder and Chair of Evolution Life Science Partners, an investment bank focused on the needs of life sciences and healthcare companies.

Continue reading “Biotech’s Wizard Of Wall Street : Fred Frank At The Forefront of Investment” »

People who understand evolution are more likely to accept it, study shows. #DarwinDay

O.o!

The first sequenced genome was that of the 3569-nucleotide single-stranded RNA (ssRNA) bacteriophage MS2. Despite the recent accumulation of vast amounts of DNA and RNA sequence data, only 12 representative ssRNA phage genome sequences are available from the NCBI Genome database (June 2019). The difficulty in detecting RNA phages in metagenomic datasets raises questions as to their abundance, taxonomic structure, and ecological importance. In this study, we iteratively applied profile hidden Markov models to detect conserved ssRNA phage proteins in 82 publicly available metatranscriptomic datasets generated from activated sludge and aquatic environments. We identified 15,611 nonredundant ssRNA phage sequences, including 10¹⁵ near-complete genomes. This expansion in the number of known sequences enabled us to complete a phylogenetic assessment of both sequences identified in this study and known ssRNA phage genomes. Our expansion of these viruses from two environments suggests that they have been overlooked within microbiome studies.

Viruses, particularly bacteriophages targeting prokaryotes, are the most diverse biological entities in the biosphere (1, 2). Currently, there are 11,489 genome sequences available in the NCBI (National Center for Biotechnology Information) Viral RefSeq database (version 94). The vast majority of known phage have a double-stranded DNA (dsDNA) genome (3, 4). Recent metagenomic analysis of 145 marine virome sampling sites identified 195,728 DNA viral populations, highlighting that only a fraction of Earth’s viral diversity has been characterized (5). An additional expansion of known phage populations by Roux et al. (6) revealed that not only dsDNA phages but also single-stranded DNA Inoviridae are far more diverse than previously considered. The rapid expansion in viral discovery through metagenomics is enabling a greater understanding of their roles within environments and their evolutionary relationships, which is subsequently causing a revolution in phage taxonomy (7).

Continue reading “Expansion of known ssRNA phage genomes: From tens to over a thousand” »

Evolutionary Medicine — Linking human pathology with our past, present, and future evolutionary trajectories — ideaXme (http://radioideaxme.com/) welcomes Prof. Dr. Frank Rühli, Director of the Institute of Evolutionary Medicine, University of Zurich — #Ideaxme #EvolutionaryMedicine #Evolution #Microevolution #Paleopathology #BiologicalAnthropology #ComparativeAnatomy #Mummies #Mummy #Hypercholesterinemia #Diabetes #DrugAddiction #Health #Wellness #Regeneration #Longevity #Aging #IraPastor #Bioquark #Regenerage

Ira Pastor, ideaXme exponential health ambassador, interviews Professor Dr. Frank Rühli, Director of the Institute of Evolutionary Medicine and on the Medical Faculty of University of Zurich, and Founding Director, Chair, Full Professor of Evolutionary Medicine.

Continue reading “The Health Past Of Mummies: Evolutionary Medicine Insights For Human Diseases Now” »

The Tasmanian devil (Sarcophilus harrisii), the largest marsupial carnivore, is endangered due to a transmissible facial cancer spread by direct transfer of living cancer cells through biting. Here we describe the sequencing, assembly, and annotation of the Tasmanian devil genome and whole-genome sequences for two geographically distant subclones of the cancer. Genomic analysis suggests that the cancer first arose from a female Tasmanian devil and that the clone has subsequently genetically diverged during its spread across Tasmania. The devil cancer genome contains more than 17,000 somatic base substitution mutations and bears the imprint of a distinct mutational process. Genotyping of somatic mutations in 104 geographically and temporally distributed Tasmanian devil tumors reveals the pattern of evolution and spread of this parasitic clonal lineage, with evidence of a selective sweep in one geographical area and persistence of parallel lineages in other populations.

Circa 2013

In a feat of “molecular time travel,” the researchers resurrected and analyzed the functions of the ancestors of genes that play key roles in modern human reproduction, development, immunity and cancer. By re-creating the same DNA changes that occurred during those genes’ ancient history, the team showed that two mutations set the stage for hormones like estrogen, testosterone and cortisol to take on their crucial present-day roles.

“Changes in just two letters of the genetic code in our deep evolutionary past caused a massive shift in the function of one protein and set in motion the evolution of our present-day hormonal and reproductive systems,” said Joe Thornton, PhD, professor of human genetics and ecology & evolution at the University of Chicago, who led the study.

“If those two mutations had not happened, our bodies today would have to use different mechanisms to regulate pregnancy, libido, the response to stress, kidney function, inflammation, and the development of male and female characteristics at puberty,” Thornton said.

Circa 2011 essentially cancer could help with evolution as it can challenge the immune system to be more strong. Essentially a symbiotic relationship to evolve with it and grow stronger with it then like it can be used as a good thing to make sure that evolution has stronger genetic code.

Evolutionary theories are critical for understanding cancer development at the level of species as well as at the level of cells and tissues, and for developing effective therapies. Animals have evolved potent tumor suppressive mechanisms to prevent cancer development. These mechanisms were initially necessary for the evolution of multi-cellular organisms, and became even more important as animals evolved large bodies and long lives. Indeed, the development and architecture of our tissues were evolutionarily constrained by the need to limit cancer. Cancer development within an individual is also an evolutionary process, which in many respects mirrors species evolution. Species evolve by mutation and selection acting on individuals in a population; tumors evolve by mutation and selection acting on cells in a tissue. The processes of mutation and selection are integral to the evolution of cancer at every step of multistage carcinogenesis, from tumor genesis to metastasis. Factors associated with cancer development, such as aging and carcinogens, have been shown to promote cancer evolution by impacting both mutation and selection processes. While there are therapies that can decimate a cancer cell population, unfortunately, cancers can also evolve resistance to these therapies, leading to the resurgence of treatment-refractory disease. Understanding cancer from an evolutionary perspective can allow us to appreciate better why cancers predominantly occur in the elderly, and why other conditions, from radiation exposure to smoking, are associated with increased cancers. Importantly, the application of evolutionary theory to cancer should engender new treatment strategies that could better control this dreaded disease.

We expect that the public generally views evolutionary biology as a science about the past, with stodgy old professors examining dusty fossils in poorly lit museum basements. Evolution must certainly be a field well-separated from modern medicine and biomedical research, right? If the public makes a connection between evolution and medicine, it is typically in the example of bacteria acquiring antibiotic resistance. But what does evolution have to do with afflictions like heart disease, obesity, and cancer? As it turns out, these diseases are intricately tied to our evolutionary histories, and understanding evolution is essential for preventing, managing and treating these diseases (1, 2). This review will focus on cancer: how evolutionary theories can be used to understand cancer development at the level of species as well as at the level of cells and tissues. We will also discuss the implications and benefits of an evolutionary perspective towards cancer prevention and therapies.

Continue reading “How cancer shapes evolution, and how evolution shapes cancer” »