Tree of life

Here: Interactive Tree Of Life is an online tool for the display, annotation and management of phylogenetic trees. Explore your trees directly in the browser, and annotate them with various types of data. More. This is absolutely not a tree. Not the remotest resemblance to a tree. Just sayin’ is all. How about a rotunda of life with many alcoves? See also: Tree of life problematic The tree of life is mostly a complete mystery (so then how do we know it’s a tree?) Kirk Durston on the new tree of life Tree of life morphs into … leaf? Maybe the Tree of Life is more of an art exhibit than a science pursuit? Follow UD News at Twitter!

Former Templeton Fellow John Fellow asserts: Why Teleology Isn’t Dead

Conway Morris argues that in the grand scheme, evolution will not be reduced to chance: constraints built into life at the most fundamental level guarantee that life is going to follow the same evolutionary pathways to achieve limbs, respiration, vision, balance, an immune system, indeed all the remarkable features we associate with living things across the great spectrum of life.

Morris begs the question by assuming a stochastic origin of these “constraints built into life”. Read More ›

It was multicellular, not unicellular, a predicted. From Nature News: A mysterious deep-ocean seaweed diverged from the rest of the green-plant family around 540 million years ago, developing a large body with a complex structure independently from all other sea or land plants. All of the seaweed’s close relatives are unicellular plankton. The finding, published today in Scientific Reports, upends conventional wisdom about the early evolution of the plant kingdom. “People have always assumed that within the green-plant lineage, all the early branches were unicellular,” says Frederik Leliaert, an evolutionary biologist at Ghent University in Belgium. “It is quite surprising that among those, a macroscopic seaweed pops up.” … “We still need to do a lot more sampling of those Read More ›

From One Zoom Tree of life software: OneZoom is a vivid and interactive guide to the relationships between all life on earth. You can marvel at a stunning variety of species and discover your favourites among them on our tree of life. More. Click on human for some fun. The problem with a “”tree of life” is that a normal tree does not change much from branch to branch, but the history of jellyfish, water bears, and weasels is just so different that the connection is possibly better seen as a river flowing through many landscapes than as a tree. In fact, the tree is beginning to look more like a river all the time. Great show here too. See Read More ›

Open access paper, too, from PLOS: A universal Tree of Life (TOL) has long been a goal of molecular phylogeneticists, but reticulation at the level of genes and possibly at the levels of cells and species renders any simple interpretation of such a TOL, especially as applied to prokaryotes, problematic. … So, even a tree of cellular lineages is not an unproblematic concept. Students of animals and plants have long accepted that incomplete lineage sorting, introgression, and full-species hybridization pose difficulties for the sorts of trees that Darwin might have had us draw. But it is microbes, with their promiscuous willingness to exchange genes between widely separated branches of any “tree,” that have most seriously jeopardized the neo-Darwinian synthesis, in Read More ›

From Ed Yong at the Atlantic: “This is humbling,” says Jonathan Eisen from the University of California, Davis, “because holy **#$@#!, we know virtually nothing right now about the biology of most of the tree of life.”More. Which makes the dogmatism of the Darwinians all the more curious. And who would ever have thought of calling it a tree anyway, but for past beliefs? See also: Tree of life morphs into … leaf? and Kirk Durston on the new tree of life Classic Darwinian fundamentalism: Follow UD News at Twitter!

Biophysicist Kirk Durston of Contemplations writes, re Tree of life morphs into … leaf?: I studied that new tree of life for a while. It leaves me wondering how much is empirical observation and how much is conjecture. I would much rather see the imaginary parts removed and only the dots plotted. As one involved in bioinformatics, I know that one must be very careful to avoid ‘fitting’ the dots into a pre-conceived pattern. Would could just as easily (perhaps even more easily) fit the dots into clusters representing the various ‘kinds’ of life. My own perspective is that life should be mapped out in clusters of dots; leave out everything else for which there is no empirical evidence for. Read More ›

From ScienceDaily: Scientists have dramatically expanded the tree of life, which depicts the variety and evolution of life on Earth, to account for thousands of new microscopic life forms discovered over the past 15 years. The expanded view finally gives bacteria and Archaea their due, showing that about two-thirds of all diversity on Earth is bacterial — half bacteria that cannot be isolated and grown in the lab — while nearly one-third is Archaeal. This is great but no way is it a tree. Readers, what would you call it? One striking aspect of the new tree of life is that a group of bacteria described as the “candidate phyla radiation” forms a very major branch. Only recognized recently, and Read More ›

Error found in study of first ancient African genome

“Finding that much of Africa has Eurasian ancestry was mistaken.” . . .

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Re “Dreadful row breaks out re cladistics” (Darwin’s Tree of Life) , physicist Rob Sheldon offers, It is about the relative merits of using parsimony (Occam’s Razor) versus Bayesian (likelihood) analysis in cladistics. The first is more causal, more deterministic, more rational while the second allows priors and opinions and “other stuff” to influence the output. The Darwinian priors can be used in the 2nd, but are excluded from the 1st. So you would think Darwinians would like Bayesian, but they don’t; they seem to prefer parsimony. On the other hand, many have pointed out that parsimony merely looks deterministic, but smuggles in a lot of assumptions. So perhaps the debate is between implicit versus explicit Darwinists–because as long as Read More ›

Teapots bust. From a story at Wired: Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud The editorial in the February issue of the scientific journal Cladistics didn’t exactly drop with a bang. Cladistics has around 600 subscribers—almost half of which are libraries or other institutions—and it’s aimed at “scientists working in the research fields of evolution, systematics and integrative biology,” as the journal’s summary says. It’s a journal about building evolutionary trees of life, basically. Important, but harmless, right? … the editors of Cladistics were insisting that anyone trying to build those trees of life had to use a method called parsimony—that, in fact, anyone who didn’t use parsimony wasn’t doing real science. Science Twitter caught fire pretty fast after Read More ›

So whose dictation is it taking? From ScienceDaily: Looking Back 3.8 Billion Years Into the Root of the ‘Tree of Life’ … NASA-funded researchers at the Georgia Institute of Technology are tapping information found in the cells of all life on Earth, and using it to trace life’s evolution. They have learned that life is a master stenographer — writing, rewriting and recording its history in elaborate biological structures. Nw her is an interesting admission: “The ribosome recorded its history,” said Williams. “It accreted and got bigger and bigger over time. But the older parts were continually frozen after they accreted, just like the rings of a tree. As long as that tree lives, the inner rings will not change. Read More ›

  From ScienceDaily: ‘Tree of life’ for 2.3 million species released Presumably, “tree of life” is placed in quotation marks because it so little resembles a tree. Didn’t it used to be capped, as Tree of Life? 😉 The new style is probably a good sign. The first draft of the tree of life for all 2.3 million named species of animals, plants, fungi and microbes has been released. Thousands of smaller trees have been published over the years for select branches, but this is the first time those results have been combined into a single tree. The end result is a digital resource that is available online for anyone to use or edit, much like a ‘Wikipedia’ for evolutionary Read More ›

Honest.* Further to Researchers: Jumping genes make the Tree of Life a bush (For instance, a cuckoo can be more closely related to a hummingbird than a pigeon in a certain part of its genome, while the opposite holds true in another part), from Science News: Schoolroom kingdoms are taking a backseat to life’s supergroups Since a radial diagram based on 1990s genetics inspired a rush for tree-of-life tattoos, technical diagrams of life’s ancestral connections have been redrawn. And the simplified version of the tree of life memorized by schoolchildren for decades lags far behind what researchers depict today. … In the new vision — based on increasingly sophisticated genetic analyses — people and other animals are closer cousins to Read More ›

As opposed to a circle, or in the case of prokaryotes, a forest? Matchwood? From ScienceDaily: Less than a year ago, a consortium of some hundred researchers reported that the relationship between all major bird clades had been mapped out by analysing the complete genome of around 50 bird species. This included the exact order in which the various lineages had diverged. Since then, two of the members of the consortium, Alexander Suh and Hans Ellegren at the Uppsala University Evolutionary Biology Centre, have expanded upon this model by analysing the avian genome through a new method, which hinges on so-called ‘jumping genes’. Their results paint a partially contrasting picture of the kinship between the various species. … By using Read More ›