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Tree of life

Many plankton behave like both plants and animals, challenging biological concepts

Tales from the Tree Bundle of Seedlings, or maybe best called Web of Life: Traditionally, marine microplankton had been divided similarly to species on land. You had plant-like phytoplankton, such as algae, and animal-like zooplankton that ate the phytoplankton. What Stoecker found was that some of these organisms were somewhere in the middle: They could eat like animals when food was present and photosynthesize like plants in the light. “If you think about it, it can be the best of both worlds,” says marine ecologist Dave A. Caron of the University of Southern California. Today, there’s growing realization that these in-between beasties — dubbed mixotrophs — are not only widespread but also play vital roles in the ecology of the Read More ›

New kingdoms of life: The “Tree of Life” is a hard concept to get past

The recent find of a probable new kingdom of life in a routine dirt sample in Nova Scotia (an east coast province of Canada) raises an obvious question: How much more is there out there that is underfoot, so to speak, that does not fit our tidy categories? Just yesterday, we were looking at the vast newly discovered array of subterranean microorganisms, many of which won’t turn out to be very tidy either, including those that live for millennia rather than twenty minutes. One writer describes the hemimastigotes above as the latest (and most profound) of additions quietly and routinely added to the “tree of life,” (as if nothing is changing?): To understand how evolutionarily distinct the hemimastigote lineage is, Read More ›

Podcast: Winston Ewert on the Dependency Graph vs. Darwin’s Tree of Life, Part 1

Here: On this episode of ID the Future, guest host Robert J. Marks talks with Dr. Winston Ewert about Ewert’s groundbreaking new hypothesis challenging Darwin’s common descent tree of life. The new model is based on the well-established technique of repurposing software code in different software projects. Ewert, a senior researcher at Biologic and the Evolutionary Informatics Lab, describes the nested hierarchical pattern of life and how any credible theory of life’s origin and diversity must explain it. He then describes how Darwin’s basic theory fits, and doesn’t fit, the pattern, and the various ancillary mechanisms invoked to close the gaps. These patches include horizontal gene transfer, convergent evolution, and incomplete lineage sorting. Ewert then cues up what he argues Read More ›

Acknowledged: Claims of well-established patterns in evolution may be “remarkable bias”

From ScienceDaily: How do the large-scale patterns we observe in evolution arise? A new paper in the journal Evolution by researchers at Uppsala University and University of Leeds argues that many of them are a type of statistical artefact caused by our unavoidably recent viewpoint looking back into the past. As a result, it might not be possible to draw any conclusions about what caused the enormous changes in diversity we see through time. The diversity of life through time shows some striking patterns. For example, the animals appear in the fossil record about 550 million years ago, in an enormous burst of diversification called the “Cambrian Explosion.” Many groups of organisms appear to originate like this, but later on Read More ›

Winston Ewert on his dependency graph model of the relationship of life forms

Programmer Winston Ewert has developed a dependency graph, as an alternative to the Darwinian “tree of life,” to understand relationships among life forms. Here he discusses it with Jonathan McLatchie: Dr. Winston Ewert … proposes an alternative model to common descent to explain the hierarchical classification of life. Based on his paper published in Bio-Complexity, available here. Note: Winston Ewert, who works at the Evolutionary Informatics Lab, is an author of Introduction to Evolutionary Informatics See also: Evolutionary informatics: A simplified explanation of Winston Ewert’s dependency graph and New “fixed” bacterial Tree of Life looks like a cityscape seen from below

New “fixed” bacterial Tree of Life looks like a cityscape

Seen from below: Professor Hugenholtz said the scientific community generally agrees that evolutionary relationships are the most natural way to classify organisms, but bacterial taxonomy is riddled with errors, due to historical difficulties. “This is mainly because microbial species have very few distinctive physical features, meaning that there are thousands of historically misclassified species,” he said. “It’s also compounded by the fact that we can’t yet grow the great majority of microorganisms in the laboratory, so have been unaware of them until quite recently.” Dr. Donovan Parks, the lead software developer on the project, is excited about the recent advancement of genome sequencing technology, and how it’s helping reconstruct the bacterial tree of life. … The research team then used Read More ›

Find deepens mystery of turtle’s origins

From ScienceDaily: There are a couple of key features that make a turtle a turtle: its shell, for one, but also its toothless beak. A newly-discovered fossil turtle that lived 228 million years ago is shedding light on how modern turtles developed these traits. It had a beak, but while its body was Frisbee-shaped, its wide ribs hadn’t grown to form a shell like we see in turtles today. “This creature was over six feet long, it had a strange disc-like body and a long tail, and the anterior part of its jaws developed into this strange beak,” says Olivier Rieppel, a paleontologist at Chicago’s Field Museum and one of the authors of a new paper in Nature. “It probably Read More ›

At New York Times: Darwin skeptic Carl Woese “effectively founded a new branch of science”

David Quammen, author of The Tangled Tree:A Radical New History of Life, a biography of Darwin skeptic Carl Woese, who discovered the Archaea, offers a long reflection at the New York Times on how biology is moving away from Darwinism: Woese was a rebel researcher, obscure but ingenious, crotchety, driven. He had his Warholian 15 minutes of fame on the front page of The Times, and then disappeared back into his lab in Urbana, scarcely touched by popular limelight throughout the remaining 35 years of his career. But he is the most important biologist of the 20th century that you’ve never heard of. He asked profound questions that few other scientists had asked. He created a method — clumsy and Read More ›

Life should be classified not as a tree but as a dependency graph, says researcher

Winston Ewert, one of the authors of Introduction to Evolutionary Informatics has a new paper at BIO-Complexity: Abstract: The hierarchical classification of life has been claimed as compelling evidence for universal common ancestry. However, research has uncovered much data which is not congruent with the hierarchical pattern. Nevertheless, biological data resembles a nested hierarchy sufficiently well to require an explanation. While many defenders of intelligent design dispute common descent, no alternative account of the approximate nested hierarchy pattern has been widely adopted. We present the dependency graph hypothesis as an alternative explanation, based on the technique used by software developers to reuse code among different software projects. This hypothesis postulates that different biological species share modules related by a dependency Read More ›

Molecular biologist: Speculation re the last universal common ancestor is not helping science

From molecular biologist Mike Klymkowsky at The Scientist There is a pernicious temptation in science to speak authoritatively about topics that are beyond scientific exploration and certainty. This has led some theoretical physicists to advocate for a “post-empirical” form of science. That is the idea that theories need not be judged on their ability to make new and testable predictions about the observable universe, in some cases, the absence of a plausible alternative is sufficient. … Klymkowsky is certain that there was a single Last Universal Common Ancestor (LUCA)* but before that? But what came before and the exact steps leading to LUCA are unknowable. Moreover, the billions of years that have elapsed since LUCA’s origin and the active nature Read More ›

Startling Result–90% of Animals Less than 200 kya

From PhysOrg this morning, in a study using “DNA bar-codes” (mitochondrial DNA, using a specific gene COI) and conducted around the world, here’s the verdict: The study’s most startling result, perhaps, is that nine out of 10 species on Earth today, including humans, came into being 100,000 to 200,000 years ago. “This conclusion is very surprising, and I fought against it as hard as I could,” Thaler told AFP. The scientists can’t figure out what might have caused this. They ask: Was there some catastrophic event 200,000 years ago that nearly wiped the slate clean? Maybe a “flood”? About “bar-codes” there’s this: On the one hand, the COI gene sequence is similar across all animals, making it easy to pick Read More ›

Phylogenetics of plants is a mess

From Douglas E. Soltis, Michael J. Moore, Emily B. Sessa, Stephen A. Smith, and Pamela S. Soltis, Using and navigating the plant tree of life, at Amerian Journal of Botany 7 April 2018 https://doi.org/10.1002/ajb2.1071 (open access) : The “tree of life” has become a metaphor for the interconnectivity and breadth of all life on Earth. It also has come to symbolize the broad investigation of biodiversity, including both the reconstruction of phylogeny and the numerous downstream analyses that are possible with a firm phylogenetic underpinning. … Accompanying these exciting advances are equally significant challenges that remain for the construction of a better and more complete picture of the evolution of plant lineages. In addition to the computational challenges of larger Read More ›

Giant virus shares genes (core histones) with complex life forms. But what exactly does that imply?

From ScienceDaily: “It’s exciting and significant to find a living family of giant viruses with eukaryote-specific genes in a form that predates the latest common ancestor of all eukaryotes,” says Albert Erives, associate professor in the Department of Biology. “These viruses are like time machines that tell us more about how life on our planet came to be.” In the study, Erives analyzed the genome of a virus family called Marseilleviridae and found it shares a similar set of genes, called core histones, with eukaryotes. That places Marseilleviridae, and perhaps its viral relatives, somewhere along eukaryotes’ evolutionary journey. “We now know that eukaryotes are more closely related to viruses,” says Erives, “and the reason is because they share core histones, Read More ›