Daily Archives: November 7, 2019

Researchers in Germany have discovered the fossilized bones of a previously unknown species of ape that appeared to walk upright, according to a study published yesterday (November 6) in Nature. The bones, which the team dated to nearly 12 million years ago, suggest that bipedalism might have evolved in a common ancestor of humans and other great apes living in Europe, and not in more-recent human ancestors in Africa as many researchers had assumed.

The finding changes the why, when and where of evolution of bipedality dramatically, study coauthor Madelaine Bhme, a paleobiologist at the University of Tbingen in Germany, tells Reuters.

There are many theories about the evolution of bipedalism, but many assumed that upright walking appeared in our ancestors about 6 million to 8 million years agopossibly as an adaptation to a reduction in forest cover occurring in East Africa around the same time.

The new set of bones, unearthed from a clay pit in Bavaria between 2015 and 2018, are around 11.62 million years old and belong to several baboon-size apes, members of a species researchers have named Danuvius guggenmosi.The limbs show an unusual combination of anatomical features indicative of an ability to move both by swinging through trees and by walking upright.

It was astonishing for us to realise during the process of research how similar certain bones were to humans, as opposed to great apes, Bhme says in a statement, The Guardianreports.

Researchers found 21 bones from a single Danuvius guggenmosiindividual at the site.

CHRISTOPH JCKEL

Together, the mosaic features of D. guggenmosi arguably provide the best model yet of what a common ancestor of humans and African apes might have looked like, writes Tracy Kivell, a paleoanthropologist at the University of Kent who was not involved in the work, in an accompanying commentary in Nature. It offers something for everyone: the forelimbs suited to life in the trees that all living apes, including humans, still have, and lower limbs suited to extended postures like those used by orangutans during bipedalism in the trees.

The fossils could help researchers study hominid evolution more generally, the authors write in their paper. With a broad thorax, long lumbar spine and extended hips and knees, as in bipeds, and elongated and fully extended forelimbs, as in all apes (hominoids), Danuvius combines the adaptations of bipeds and suspensory apes, and provides a model for the common ancestor of great apes and humans.

Catherine Offord is an associate editor atThe Scientist. Email her atcofford@the-scientist.com.

Go here to read the rest:

Ape Fossils Shed New Light on Evolution of Bipedalism - The Scientist

A billion years ago, an ancestral algal species split in two, starting the evolution of green plants that has led to the nearly half million diverse species we have today. Now, an international consortium of plant scientists has generated thousands of gene sequences from each of more than 1,100 plant species, providing the most data-rich framework to date for understanding the evolutionary history of this green tree of life.

Norman Wickett, a conservation scientist at Northwestern University and the Chicago Botanic Garden, is a longtime member of the One Thousand Plant Transcriptomes Initiative (1KP), the consortium of close to 200 researchers that conducted the nine-year study.

The researchers sequenced tens of thousands of genes for species distributed across all major groups of land plants and their green algal relatives. Their findings were published as the cover article in the Oct. 31 print issue of the journal Nature.

One key finding of the study is that fundamental events in evolutionary history, such as the colonization of land by plants, may have followed a different set of steps than was previously thought. Another important discovery is that gene and genome duplications may have been important for the challenge of colonizing land and for adapting to new environments as the environments on land changed over time.

Determining how plants -- or any organisms -- are related to each other provides the foundation for understanding the timing and significance of major events in the history of life on Earth, said Wickett, a co-author of the study. The more data we have to figure out these relationships, the more precisely we can do this. Our project gave us an unprecedented data set for not only putting together the evolutionary tree of plants but also for understanding the diversity and evolutionary complexity of genes at different times in their history.

Wickett is an adjunct professor in the Program in Plant Biology and Conservation in Northwesterns Weinberg College of Arts and Sciences and an associate conservation scientist at the Chicago Botanic Garden. His contributions to the 1KP study include helping determine how todays plants and algae are related to one another and developing certain data processing methods necessary for making comparisons that use such a large amount of data.

Gane Ka-Shu Wong, a professor at the University of Alberta, is the collaborations lead investigator and a co-corresponding author of the study. The other co-corresponding author is James Leebens-Mack, a professor of plant biology at the University of Georgia.

In the tree of life, everything is interrelated, Wong said. And if we want to understand how the tree of life works, we need to examine the relationships between species. Thats where genetic sequencing comes in.

The findings reveal the timing of whole genome duplications and the origins, expansions and contractions of gene families contributing to fundamental genetic innovations enabling the evolution of green algae, mosses, ferns, conifer trees, flowering plants and all other green plant lineages. The history of how and when plants secured the ability to grow tall and make seeds, flowers and fruits provides a framework for understanding plant diversity around the planet, including annual crops and long-lived forest tree species.

Our inferred relationships among living plant species inform us that over the billion years since an ancestral green algal species split into two separate evolutionary lineages, one including flowering plants, land plants and related algal groups and the other comprising a diverse array of green algae, plant evolution has been punctuated with innovations and periods of rapid diversification, Leebens-Mack said.

In order to link what we know about gene and genome evolution to a growing understanding of gene function in flowering plant, moss and algal organisms, we needed to generate new data to better reflect gene diversity among all green plant lineages, Leebens-Mack said.

The study inspired a community effort to gather and sequence diverse plant lineages derived from terrestrial and aquatic habitats on a global scale. More than 100 taxonomic specialists contributed material from field and living collections that include the Central Collection of Algal Cultures, Royal Botanic Gardens, Kew, Royal Botanic Garden Edinburgh, Atlanta Botanical Garden, New York Botanical Garden, Fairylake Botanical Garden, Shenzhen, The Florida Museum of Natural History, Duke University, University of British Columbia Botanical Garden and The University of Alberta.

By sequencing and analyzing genes from a broad sampling of plant species, researchers are better able to reconstruct gene content in the ancestors of all crops and model plant species and gain a more complete picture of the gene and genome duplications that enabled evolutionary innovations.

The massive scope of the project demanded development and refinement of new computational tools for sequence assembly and phylogenetic analysis.

New algorithms were developed by software engineers at BGI to assemble the massive volume of gene sequence data generated for this project, Wong explained.

Founder professor of computer science Tandy Warnow, of the University of Illinois at Urbana-Champaign, and Siavash Mirarab, assistant professor of electrical and computer engineering at the University of California San Diego, developed new algorithms for inferring evolutionary relationships from hundreds of gene sequences for more than 1,000 species, addressing substantial heterogeneity in evolutionary histories across the genomes.

The timing of 244 whole genome duplications across the green plant tree of life was one of the interrelated research foci of the project.

Perhaps the biggest surprise of our analyses was the near absence of whole genome duplications in the algae, said Mike Barker, associate professor of ecology and evolutionary biology at the University of Arizona.

Building on nearly 20 years of research on plant genomes, we found that the average flowering plant genome has nearly four rounds of ancestral genome duplication dating as far back as the common ancestor of all seed plants more than 300 million years ago, he said. We also find multiple rounds of genome duplication in fern lineages, but there is little evidence of genome doubling in algal lineages.

In addition to genome duplications, the expansion of key gene families has contributed to the evolution of multicellularity and complexity in green plants.

Gene family expansions through duplication events catalyzed diversification of plant form and function across the green tree of life, said co-author Marcel Quint, professor of crop physiology at Halle University, Germany. Such expansions unleashed during terrestrialization, or even before, set the stage for evolutionary innovations including the origin of the seed and, later, the origin of the flower.

The view of evolutionary relationships provided by 1KP has led to new hypotheses about the origins of key structures and processes in green plants, said co-author Pam Soltis, of the Florida Museum of Natural History,University of Florida.

Nearly a decade ago, Wong organized private funding through the Somekh Family Foundation as well as support from the Government of Alberta and a sequencing commitment from BGI in Shenzhen, China, to launch 1KP. Once the project was operational, additional resources came from other ongoing projects, including iPlant (now CyVerse) funded by the U.S. National Science Foundation.

The paper is titled One Thousand Plant Transcriptomes and Phylogenomics of Green Plants and was published online Oct. 23 in Nature. Sequences, sequence alignments and tree data are available through the CyVerse Data Commons.

More here:

Study provides strong framework for 1 billion years of green plant evolution - Northwestern University NewsCenter

A population of red deer on a Scottish island are providing scientists with the first evidence of wild animals evolving differently due to man-made climate change.

A new study into the deer living on the small Hebridean island of Rum reveals genetic changes believed to be related to a warming climate mean the animals are giving birth slightly earlier each year.

Using data from previous research going back to the 1970s, the team, which includes scientists from the University of Edinburgh, found average birth dates were getting earlier at a rate of about three days per decade, partly due to the effects of warmer temperatures on the deers behaviour and physiology.

Sharing the full story, not just the headlines

Now, scientists have revealed that genetic changes caused by natural selection the theory of evolution developed by Charles Darwin are also involved.

Female red deer called hinds give birth to a single calf each year, and those that reproduce earlier in the year have more offspring over their lifetime, researchers say.

The moment by Yongqing Bao, China

Yongqing Bao/Wildlife Photographer of the Year

Night glow by Cruz Erdmann, New Zealand

Cruz Erdmann/Wildlife Photographer of the Year

Tapestry of life by Zorica Kovacevic, Serbia/USA

Zorica Kovacevic/Wildlife Photographer of the Year

Land of the eagle by Audun Rikardsen, Norway

Audun Rikardsen/Wildlife Photographer of the Year

Snow exposure by Max Waugh, USA

Max Waugh/Wildlife Photographer of the Year

The equal match by Ingo Arndt, Germany

Ingo Arndt/Wildlife Photographer of the Year

Creation by Luis Vilario Lopez, Spain

Luis Vilario Lopez/Wildlife Photographer of the Year

The huddle by Stefan Christmann, Germany

Stefan Christmann/Wildlife Photographer of the Year

Humming surprise by Thomas Easterbrook, UK

Thomas Easterbrook/Wildlife Photographer of the Year

Another barred migrant by Alejandro Prieto, Mexico

Alejandro Prieto/Wildlife Photographer of the Year

Frozen moment by Jrmie Villet, France

Jrmie Villet/Wildlife Photographer of the Year

Early riser by Riccardo Marchgiani, Italy

Riccardo Marchegiani/Wildlife Photographer of the Year

Pondworld by Manuel Plaickner, Italy

Manuel Plaickner/Wildlife Photographer of the Year

Face of deception by Ripan Biswas, India

Ripan Biswas/Wildlife Photographer of the Year

Snow-plateau nomads by Shangzhen Fan, China

Shangzhen Fan/Wildlife Photographer of the Year

The moment by Yongqing Bao, China

Yongqing Bao/Wildlife Photographer of the Year

Night glow by Cruz Erdmann, New Zealand

Cruz Erdmann/Wildlife Photographer of the Year

Tapestry of life by Zorica Kovacevic, Serbia/USA

Zorica Kovacevic/Wildlife Photographer of the Year

Land of the eagle by Audun Rikardsen, Norway

Audun Rikardsen/Wildlife Photographer of the Year

Snow exposure by Max Waugh, USA

Max Waugh/Wildlife Photographer of the Year

The equal match by Ingo Arndt, Germany

Ingo Arndt/Wildlife Photographer of the Year

Creation by Luis Vilario Lopez, Spain

Luis Vilario Lopez/Wildlife Photographer of the Year

The huddle by Stefan Christmann, Germany

Stefan Christmann/Wildlife Photographer of the Year

Humming surprise by Thomas Easterbrook, UK

Thomas Easterbrook/Wildlife Photographer of the Year

Another barred migrant by Alejandro Prieto, Mexico

Alejandro Prieto/Wildlife Photographer of the Year

Frozen moment by Jrmie Villet, France

Jrmie Villet/Wildlife Photographer of the Year

Early riser by Riccardo Marchgiani, Italy

Riccardo Marchegiani/Wildlife Photographer of the Year

Pondworld by Manuel Plaickner, Italy

Manuel Plaickner/Wildlife Photographer of the Year

Face of deception by Ripan Biswas, India

Ripan Biswas/Wildlife Photographer of the Year

Snow-plateau nomads by Shangzhen Fan, China

Shangzhen Fan/Wildlife Photographer of the Year

Their findings show that this is partly because of an association between the genes that make hinds give birth earlier and higher overall reproductive success. As a result, genes for breeding earlier have become more common in the Rum deer population over time.

A red deer calf on the Isle of Rum, Scotland (J Pemberton/University of Edinburgh)

Dr Timothee Bonnet, of the Australian National University, who led the study, said: This is one of the few cases where we have documented evolution in action, showing that it may help populations adapt to climate warming.

Professor Josephine Pemberton, of the University of Edinburghs School of Biological Sciences, who was also involved in the study, said: Long-term studies of individual lifetimes are one of the few ways to understand how populations respond to environmental change and how to manage its effects.

Sally Thomas, Scottish Natural Heritages director of people and nature, said: These findings are a fascinating example of the impact climate change may be having on wildlife. More and more research is demonstrating climate change is influencing species across the UK and the world.

The research is published in the journal PLOSBiology.

Follow this link:

Red deer show first evidence of animal evolution in response to climate change, study reveals - The Independent

Its become increasingly clear as we reach its limits that deep learning a specific subset of AI technology isnt going to magically lead to human-level artificial intelligence.

If we want robots that can think like us, weve got to stop giving them all the answers. Curiosity and exploration are the two key components of the human intellect that deep learning simply doesnt provide.

In a recent article in Quanta Magazine, writer Matthew Hutson describes the work of computer scientist Kenneth Stanley, who is currently working at Ubers AI lab. Stanleys pioneering work in the field of neuroevolution has paved the way for a new artificial intelligence paradigm that eschews traditional objective-based training models in favor of AI models that have no purpose but to explore and be creative.

Hutson writes:

Biological evolution is also the only system to produce human intelligence, which is the ultimate dream of many AI researchers. Because of biologys track record, Stanley and others have come to believe that if we want algorithms that can navigate the physical and social world as easily as we can or better! we need to imitate natures tactics.

Instead of hard-coding the rules of reasoning, or having computers learn to score highly on specific performance metrics, they argue, we must let a population of solutions blossom. Make them prioritize novelty or interestingness instead of the ability to walk or talk. They may discover an indirect path, a set of steppingstones, and wind up walking and talking better than if theyd sought those skills directly.

Standard deep learning models use a black box a set of weights and parameters that, ultimately, become too complex for developers to describe individually to brew up machine learning algorithms and tweak them until they spit out the right data. This isnt intelligence, its prestidigitation.

If AI could evolve its own solutions and combine those parameters with deep learning, itd be closer to imitating human-level problem solving. At least, thats what Stanley argues.

His research involves building evolutionary algorithms that can function in tandem with deep learning systems. In essence, rather than teaching an AI to solve a problem, he develops algorithms that sort of meander about seeing what theyre capable of. These systems arent rewarded for solving a problem like normal AI paradigms. They just go until something happens. Whats remarkable is that, without a problem to solve, they still manage to solve many kinds of problems far more efficiently than traditional deep learning models.

More from Hutsons article in Quanta:

In one test, they [Stanley and researcher Joel Lehman] placed virtual wheeled robots in a maze and evolved the algorithms controlling them, hoping one would find a path to the exit. They ran the evolution from scratch 40 times. A comparison program, in which robots were selected for how close (as the crow flies) they came to the exit, evolved a winning robot only 3 out of 40 times. Novelty search, which completely ignored how close each bot was to the exit, succeeded 39 times. It worked because the bots managed to avoid dead ends.

Deep learning AI doesnt know what to do when it hits a wall. Once the machine gets stuck, it has to start over again thats why it takes millions of training cycles to teach an AI how to accomplish a task successfully. With Stanleys evolutionary algorithm-based hybrid model, the AI isnt trying to find the exit, its basically just doing stuff and then trying to find more stuff to do. The machines curiosity forces it through the entire maze almost every time because its bent on exploring.

Evolutionary algorithms arent new, but the vein of research surrounding them has been largely swept to the side in favor of more immediately-lucrative development opportunities in standard deep learning technology the kind that fuels B2B and B2C sales. And theyre also under-explored because theyre expensive. Its takes a lot less power to train a narrow-minded AI than it does to run evolutionary algorithms. But the payoff could be huge.

The big idea here is to backdoor human-level intelligence on accident by letting AI evolve its own algorithms though unfettered exploration. Stanley and others believe its possible that AGI could manifest as a byproduct of machine curiosity, just like human consciousness occurred as aresult of biological evolution.

Computers Evolve a New Path Toward Human Intelligence on Quanta Magazine

Link:

Why the quickest path to human-level AI may be letting it evolve on its own - The Next Web

Editors note: Phillip E. Johnson, Berkeley law professor and author ofDarwin on Trialand other books,died on November 2.Evolution Newsis sharing remembrances from Fellows of Discovery Institute. Dr. Behes most recent book isDarwin Devolves. Thefollowing essay appeared originally as the Foreword to the 20th Anniversary edition of Darwin on Trial.

Twenty years can be a virtual eternity in modern science, so rapidly do new discoveries accumulate. Twenty years ago the idea of determining the entire DNA sequence of even a tiny living organism such as a bacterium, let alone the genetic endowment of a large animal such as a mammal, seemed a dream. Yet shortly before I wrote this foreword, the 1000th kind of bacterial genome was sequenced. The DNA code of humans was completed a decade ago. That of other familiar creatures, such as dog, rice, mosquito, and more, are also now public knowledge.

Its not only the genome sequences of organisms that has been brought to light in the past two decades. DNA is the instruction manual that tells cells how to go about building pieces of molecular machinery that actually run the cell. But, like trying to picture the end result of an instruction manual written in a foreign language, it is usually not very straightforward for a scientist to determine what kind of machines are going to result simply by looking at the DNA instructions. However, by performing clever laboratory experiments, investigators can probe the machinery directly. In the past two decades whole new classes of molecular machines have been discovered. One of the most interesting is a class of RNA molecules that helps regulate DNA. RNA (as you of course remember from your high school biology class) is a chemical cousin of DNA, and an intermediate between the information coded in DNA and its translation into proteins, which are the usual components of molecular machines. But other roles have been discovered for RNA including, most surprisingly, the ability to decide when some DNA genes are turned on and off.

In other areas of biology besides the micro-world, too, discoveries have been pouring in. New fossil finds, new ways that the brain communicates, and more, have dazzled the scientific community and the world.

Twenty years can be a virtual eternity in modern science but in logic, not so much. Arguments that rest on faulty premises and strained reasoning are not helped at all by the passage of time. It is the brilliance of Phillip Johnson, Jefferson E. Peyser Professor of Law, Emeritus, at the University of California Berkeley and an expert in the way arguments are framed and the unspoken premises they rest on, to have written a book, Darwin on Trial, that, despite the intervening years and progress of science, is as fresh and relevant today as when it was first printed.

Johnsons classic masterpiece came about rather serendipitously. While on sabbatical in England over two decades ago, he chanced to pick up two books concerning evolution. The first was The Blind Watchmaker by Oxford biologist and world-renowned atheist Richard Dawkins. Dawkinss book is widely acknowledged even today to be the most vigorous defense of Darwinian evolution available for a general readership. The second book was the less well-known, but soon-to-be-influential, Evolution: A Theory in Crisis, by an English geneticist, Michael Denton, who at the time was working in Australia. Denton, an agnostic, was fed-up with the claims Darwinists made for their theory when he saw many problems with it. In the book he detailed his scientific criticisms of Darwinism with nary a single Bible verse to bolster them.

Reading side-by-side books by knowledgeable, secular scientists alternately criticizing and extolling the dominant scientific theory of our age, Johnson was enchanted. Clearly, he realized, something more than just the undisputed facts entered into the weighing of the evidence. And when a large theory such as evolution cuts across many disciplines, no one can claim to be expert in all of the evidence. Rather, the evidence is much better evaluated by a generalist trained to evaluate the logic of arguments and the assumptions lying behind them, as Johnson himself was exquisitely qualified to do.

If you thought tendentious theories and outlandish alibis were confined to courtroom shenanigans, Johnson will quickly disabuse you. Partisan strategies find their way into even the most abstruse scientific arguments. Johnson argues that Darwins theory of evolution relies heavily on the highly tendentious, usually unstated, assumption of materialism: the idea that the only things that really exist are matter and energy in the physical universe. If one begins with that assumption, then one has neatly gotten rid of the chief rival to evolution which has seemed much more plausible to the greatest minds throughout history: that a supernatural entity, God, possessed of great power and intellect, designed the cosmos and the life it contains. If, by postulate, no such Being exists, then something like evolution pretty much has to be true. The universe alone exists, so the universe alone must have produced life.

A neat little trick, and one which saves an awful lot of scientific work. If a scientist can beguile the world into thinking that his theory must be true by definition, and that others must be ruled out from the start, then evidence becomes decidedly secondary, and no rival theories need apply.

But what if one is unwilling to concede that postulate? What if one suspects that there may indeed be a Mind beyond the universe, capable of affecting it, as the overwhelming number of people throughout history have thought? In that case, Johnson argues persuasively, the typical evidence brought forward for Darwinian evolution looks far less compelling than its boosters make it out to be. If Darwinism simply has to be true, then two breeds of finches with slightly different beak shapes seems like stunning confirmation of the theory. If it doesnt have to be true, then you just have two birds with slightly different beaks, and the question of what formed finches in the first place stands. Soon the skeptic of Darwinism comes to the conclusion that a large part of the modern worldview is built not on solid scientific evidence, but on philosophical bias enforced with sociological prejudice.

Make no mistake, however that sociological prejudice has teeth. From ridicule to shunning to dismissal from a job, a variety of unpleasant consequences can be brought to bear on folks in vulnerable situations who dont get with the Darwinian program. You are about to read a dangerous book.

Thats what happened to me. When it first came out in 1991 I saw an advertisement for Darwin on Trial, ordered a copy, and devoured it in two days. Having earlier read Dentons Evolution: A Theory in Crisis (the same book that Johnson read on his sabbatical in London), I realized that Darwins theory had a lot of problems. But Phils book got me to see why it was popular with scientists nonetheless: it was the only game in town the only slightly plausible explanation for life that did not invoke intelligent causes. Then one fine day in 1991 I was strolling through the department office and noticed the latest edition of Science magazine. I stopped to look at the table of contents and noticed there was a news item on an anti-evolution book from an unusual source a U.C. Berkeley professor. I read the item and saw it wasnt so much a story as a warning to faculty to keep their students away from this book it might confuse them.

Im half Irish on my mothers side, so when I see such blatant tendentiousness I get ticked off. I fired off a letter to the editor of Science pointing out that this Johnson fellow seemed pretty bright, noticed grand claims being made for evolution with little data, and was likely to make up his own mind about Darwins theory, thank you very much. A person like that, I wrote, should be argued with, not condescended to. Much to my surprise, Science printed the letter, and to my further surprise a few days later I got a letter in the mail from Phil, thanking me for writing the letter.

Little did I know it at the time, but I was now in the circle of Phil Johnsons useful contacts. Over the years, more academics gathered in Phils circle and joined the high intellectual adventure of battling a decrepit idea that had managed to hang on through a combination of bad science and bad philosophy. Over the years we had our victories and defeats, but because of Phillip Johnsons leadership no informed person will ever again honestly say that Darwins theory flows straight from the data.

In Darwin on Trial Phillip Johnson discusses a number of strands of scientific evidence that in the 1990s purportedly supported Darwins theory, and he neatly shows they are at best inadequate, at worst contradictory. Lets revisit several of these topics and see if the intervening years have been kinder to Darwin. The three areas Ill briefly discuss are, in turn, mutations, fossils, and the origin of life.

Ultimately the fodder for Darwinian evolution is random mutation. Deep in the genetic endowment of some creature a change occurs that makes it genetically different from its parents. Since the DNA of living creatures is highly functional, usually the change is for the worse. The poor creature thus finds itself at a disadvantage in the struggle for life and its line quickly dies out in the process of natural selection. But on rare occasions, the mutation is actually for the better. The lucky creature has an advantage over its brothers and sisters, and its offspring over theirs. Over time the offspring of the fortunate mutant come to dominate the population. Repeat this scenario over and over again, and the result is Darwinian evolution. Or so the story goes.

In Darwin on Trial Johnson discussed what was know about mutation up until the early 1990s, which was mostly speculative. But since that time, with the newly developed easy ability to sequence DNA, evolution experiments can actually be done in real time in the laboratory, and the exact mutations that give organisms an advantage can be tracked down. What have these experiments shown? Just about the time Darwin on Trial was being written a scientist named Richard Lenski at Michigan State University began the largest laboratory evolution experiment ever. Lenski, a microbiologist, decided to grow cultures of the common bacterium E. coli in his lab. Because it is so small, the bacterium can reproduce very quickly (in less than an hour) and grow to enormous numbers (billions in a single test tube). Once the growing bacteria had exhausted the food in one test tube, Lenski and his colleagues would transfer a small portion of them to a fresh test tube. When that test tube became saturated with bacteria, they would transfer another small portion to another fresh tube. They have been repeating this procedure for decades, which in bacterial terms is upward of 50,000 generations and a cumulative population size of hundreds of trillions! This is roughly the number of generations and population size that it supposedly took for some primate ancestor to evolve into modern humans.

Along the way Lenski saw that his bacteria were improving they could grow faster than the starting bacteria could. However, the big surprise came when he and his coworkers tracked down the beneficial mutations. It turned out that mutations in the improved bacteria had broken a lot of genes and thrown others away. In other words, just as it may be beneficial to throw sophisticated-but-heavy computers and machinery off a sinking ship, it was beneficial for the bacteria to toss out sophisticated genes that normally were useful. That actually made the mutant bacteria grow faster than their relatives, but it hardly answers the question of where sophisticated genes come from in the first place. In the end, after 50,000 generations, not only did a new kind of organism not evolve, but rather the original organism was degraded. This is currently our best evidence of what random mutation is capable of: Most mutations are harmful, and the few that are beneficial break genes.

In Darwin on Trial Phillip Johnson criticizes the state of the fossil record circa 1990, and shows that it is not at all what Darwin expected it to turn out to be when he wrote The Origin of Species in 1859. The scarcity of transitional forms, frequency of punctuated equilibrium, the Cambrian explosion, the ever-shifting categorization of, and scandals over, supposedly human-ancestral fossils all gave the skeptic strong reason to think that Darwinism was less of a scientific citadel than a scientific Potemkin village. Yet anyone who glances at a newspaper or watches TV knows that major new fossil finds have been announced about every month or so for the past few decades. Do they make Johnsons argument outdated?

No, they re-enforce it. Lets look at just two fossils that have been among the more prominently publicized recently. In the mid 2000s several fossils were discovered in northern Canada of a strange fish-like creature dubbed Tiktaalik. The fossils were dated to hundreds of millions of years ago, to a time when there were thought to be fish but no vertebrate land animals, or tetrapods. On close examination the fossils were seen to have structures in particular, bones that resembled wrists that were thought to make them good candidates for transitional forms between fish and tetrapods. For several years Tiktaalik was hailed as the missing link between fish and land vertebrates. But its moment of fame was cut short in early 2010 with the discovery of fossil footprints in Poland of true tetrapods which were at least ten million years older than Tiktaalik. At a stroke, the Canadian fossil could no longer be a transitional form, since it appeared later in the fossil record than its supposed descendants. Thus, as Johnson argued in 1991, it continues to be true that fossils dont tell their own stories, and the tale of ancestors being modified into descendants still relies on Darwinian theory to fill in 99 percent of the details. Question the theory and the hard evidence is much less impressive.

In Chapter Six of Darwin on Trial Johnson describes a preview in 1984 for a group of anthropologists of a new exhibit of fossils related to human evolution. It was reported that everyone spoke in reverential hushed tones, and a sociologist remarked Sounds like ancestor worship to me. Intense interest concerning possible human fossils continues unabated and so does the exploitation of that interest. In the middle of 2009, the 200th anniversary of Darwins birth and the 150th anniversary of the publication of The Origin of Species, a major new fossil find was announced of a lemur-like animal classified as Darwinius masillae and nicknamed Ida. It was initially billed as the earliest ancestor of humanity. Oddly, the discovery was announced by New York Mayor Michael Bloomberg, accompanied not only by a scientific paper in Science magazine, but also a book, a web site, and a documentary released within a week of the unveiling. It seemed that the announcement was choreographed in the hopes of cashing in on the year of Darwin. Unfortunately, Ida was quickly reclassified by unprejudiced scientists as an organism that could not be on the line to humans. The Ida brouhaha, and a remarkably similar one several months later over a fossil nicknamed Ardi, demonstrate Johnsons continuing point that the wish is too often the father of the ancestor in Darwinian theory.

Two decades ago Phillip Johnson also criticized reigning scientific theories of the origin of life as built upon little evidence and much interpretation. Today the advance of science has shown that there are even more severe roadblocks to chemical evolution than were recognized back then, so that the situation for materialistic origin of life theories has gotten substantially worse. Broadly speaking, for decades there have been two categories of origin-of-life theories: the metabolism-first view, where metabolic reactions in an enclosed space precede the occurrence of genetic material; and the genetics-first view, where a DNA-like polymer that is capable of carrying information precedes cells. The partisans of both camps have offered devastating criticisms of each others views, so that none are left standing. A paper published by the Proceedings of the National Academy of Sciences USA in early 2010 by the prominent Hungarian scientist Ers Szathmry and co-workers offered a mathematical model that ruled out metabolism-first, and an article in 2007 in Scientific American by New York University chemist Robert Shapiro showed the massive roadblocks facing the genetics-first scenario. Bereft of plausible theories, the only reason at present to believe in a materialistic origin of life is if one holds it as a postulate that life must have had a materialistic origin.

The early years of life on earth, when bacteria and other single-celled organisms reigned, are getting stranger and stranger from a Darwinian point of view. Although Phil Johnson didnt touch on the subject in the early 1990s, the great advance in DNA sequencing of microbes in the past twenty years have given scientists much to think about. And one conclusion that seems increasingly firm, as leading geneticists have voiced, is that Darwins idea of a tree of life where a single primordial cell gave rise to all subsequent organisms is dead. The DNA sequence data cannot be made to fit with the idea. What sort of model, if any, will emerge to take its place in scientific circles is hard to guess, but there is no reason to think that early life was dominated by Darwinian processes.

Twenty years ago Darwins theory seemed a truism, simply because rival explanations had been ruled out of bounds from the start. Then Phillip Johnsons epic Darwin on Trial cut to the heart of the debate. It wasnt about evidence; it was about assumptions. And like the proverbial drunk looking for his car keys, no one searched beyond Darwins lamppost. Two decades later, even as scientific advances accumulate, Johnsons insight remains key. We must cast off arbitrary assumptions. If we are ever to arrive at the solution the search for answers to the question of how life arose and developed has to be free to follow the evidence wherever it leads.

Photo: Tiktaalik, Field Museum, by Eduard Sol [CC BY-SA 3.0], via Wikimedia Commons.

Originally posted here:

Darwin on Trial As Fresh and Relevant as Ever - Discovery Institute

Red deer

Red deer on the Isle of Rum in Scotland are displaying one of the first evidences of wild animals evolving by altering their birthing patterns in order to adapt to global warming. And this evolution is happening in decades, not centuries!

Charles Darwin believed that evolution is a slow and gradual process. And until 1972, when Stephen Jay Gould proposed the theory of Punctuated Equilibrium, this was true for the scientific community. As per Jays theory, species stayed structurally similar for millions of years, followed by rapid bursts of change that result in a new species. However, both the models of evolution showed that it takes hundreds and thousands of years for organisms to develop different characteristics.

However, the shift in the red deers birthing pattern is one of the very rare instances of evolution occurring in nature over such a short period of timethat too because of anthropocentric warming acting as the environmental trigger.

The shift in birth timings is down to the effects of warmer temperatures on the deers behaviour and physiology. Now, researchers hope that this new adaptation may very well help the red deer population thrive as the climate continues to warm.

A red deer bellows

Previous studies have shown that since the 1980s, red deer repeatedly began giving birth to their young ones earlier than normal. Data shows this date has been shifting backwards at a rate of about three days per decade.

In the new research published this week, a team of scientists, led by Dr Timothe Bonnet of the Australian National University, has documented evolution in action using field records and collecting genetic data on rum deer over a 45-year period, dating back to 1972.

In this study, the researchers observed that the deer that give birth earlier in the year experience more reproductive success. Female red deer, called hinds, are known to give birth to a single calf each year. However, those that give birth earlier in the year produce more calves over their lifetime compared to the hinds that give birth during the latter stages of the year.

Subsequently, as the deer that give birth early have multiplied faster, the gene that causes birth earlier has become much more common among the rum deer population over the past few decadesin line with the natural selection process from Charles Darwins Theory of Evolution.

The study is published in the journal PLOS Biology.

The Weather Companys primary journalistic mission is to report on breaking weather news, the environment and the importance of science to our lives. This story does not necessarily represent the position of our parent company, IBM.

Read more:

Evolution Fast Forward: Study Shows Red Deer are Evolving Within Decades to Adapt to Global Warming - The Weather Channel

On Oct. 24, Bo Winegard, an assistant professor of psychology at Marietta College, led a seminar entitled The Evolution of Human Diversity, during the ALLELE seminar series hosted by the Evolution Working Group (EVOWOG) at The University of Alabama.

During his seminar, Winegard discussed topics of human diversity that did not align with the Evolution Working Groups views.

Winegards research, which discusses psychological differences across human populations, has been criticized for resembling the pseudoscience employed by eugenicists. Eugenics is the belief of improving the human species by selectively mating people with specific desirable hereditary traits. Early supporters of eugenics believed people inherited mental illness, criminal tendencies and even poverty, and that these conditions could be bred out of the gene pool.

In the peer-reviewed article from 2017 titled Human Biological and Psychological Diversity, Winegard and two of his colleagues discussed the theory that specific population groups differ psychologically and that biological diversity is the rule of life. In the article, they argue that the benefits of discussing population difference outweigh the risks of that research inciting racist social policies.

Winegard has also written several times for Quillette, a magazine that claims to respect ideas, even dangerous ones, on topics such as progressive bias and the decline of the West.

On Oct. 28, Thomas Tobin, co-chair of EVOWOG, released a statement to The Crimson White apologizing for the event.

In their statement, EVOWOG said once they learned of the direction of his planned talk, they withdrew promotion and advertisement of the event, canceled several meetings, and alternative assignments were created for students who had been offered credit for attending. Ultimately, they decided that canceling the seminar would be counterproductive.

We realized from this process that over the past almost 15 years, we have basically allowed one person to suggest someone, and we kind of relied on them to do a bunch of background research, Tobin said. Normally we spend a little bit of time in our committee kind of discussing and looking at these people, and because this person was someone who was invited to fill in a gap, we didnt go through that.

Winegard gave his talk at 7 p.m. that night, where about 40 students and faculty showed up. Several in the audience, however, were there to address the racist implications of his research.

While The Crimson White was not able to attend the first part of the lecture, we were able to obtain Winegards slides, which present how to conceptualize diversity, physical diversity, psychological diversity, human migrations to different environments and moral cautions as topics of discussion.

In his final slides on the future of human diversity, Winegard notes that groups may vary on socially significant traits (on average) such as intelligence, agreeableness, athleticism, cooperativeness [and] criminality, and attributes a lack of research on these differences to sacred values about group sameness.

Human decency and toleration dont require silencing the truth they require discussing it openly, honestly and judiciously, he wrote on the last slide.

Jack Kappelman, a sophomore majoring in political science, live-tweeted the lecture, likening Winegards research to the phrenology of Josiah Nott, a eugenicist for whom Nott Hall on campus is named.

Charity McCalpin, a junior majoring in anthropology, is the secretary of Young Democratic Socialists. McCalpin said she heard about the event through the anthropology department but also heard about it through several group chats in more of a negative way.

McCalpin referenced Winegards slide where he talked about gene-culture coevolution, the idea that cultures and genes co-evolve based on different niches and the various selective pressures of those environmental niches.

Where I disagree with him, is applying these specialization of niches to psychology, she said. He said that people in colder climates, because the differences in brain size, have more propensity for cooperation. He used some very sketchy evidence about Asian people being more independent on cultural collectivism Its been postulated many times before for the last probably 50 years of anthropological evidence that race is simply a social construct.

Bos hypothesis about how culture and environment impacted evolution of the human race made many attendees outraged.

We might disagree on whats racist, Winegard said after addressing McAlpins comment about his work, to which a student responded, Thats because youre racist.

OK, thats fine, Winegard said in response.

Anthony Earl, a junior majoring in political science, questioned Winegards claims of objectivity.

My concerns are more social/political, the idea that science help us find the objective truth, he said. Objectivity is a little more elusive than that. My concern is when you explore science without keen eye to ethics or history, or how even that science that youre trying to do may be informed by your social or economic position, your ideology, then you lose control of it in a way, and it can become dangerous. I think thats why that one guy made the allusion to Hitler.

Earl was referring to a student in the crowd who compared Winegards research with Hitlers racist ideology, to which Winegarded responded: Hitlers regime was not informed by science.

Thats definitely not true, Earl said. Hitler was certainly informed by science, and a lot of the race scientists were Americans. The Germans admired the American caste system, the racial system that we had.

After falsely noting that the ideas of ethnic cleansing were not influenced by sophisticated science of the time, Winegard expressed a need to return to conversations about racial genetic difference, which has also proven to be false.

I think what Im trying to do here is have reasonable conversation about it, precisely so that those more extreme voices get drowned out by more moderate voices, Winegard said in response to the question. Thats what I think. I could be wrong about that and we could have that discussion. But I honestly think thats true. That it would be better, not worse for society that more people talked about this in a moderate, judicious way.

Tobin said Winegards talk demonstrated the failure of the groups informal system of inviting speakers, and the group is now planning on implementing a more rigorous vetting process.

Were still figuring out what that will exactly look like, but it will certainly involve multiple people evaluating a speaker, and it may involve having individual departments that have subject matter correspondence with the speaker to sort of give a stamp of approval basically, he said. This was definitely a mistake on our part that we are going to make sure doesnt happen again.

Tobin said EVOWOG plans to talk to other departments and on-campus groups about what happened, but so far have only issued a statement of apology to The Crimson White and not through any other platform. You can read the statement in full below.

On Thursday, October 24, the ALLELE Seminar Series hosted Dr. Bo Winegard, a professor from Marietta College. We, the members of the Evolutionary Working Group (EVOWOG), want to make clear that we do not endorse the views expressed by Dr. Winegard, which are non-scientific. We want to apologize to anyone who attended the talk, as well as anyone in the campus and local community who felt unwelcome because of the subject of the seminar.

It was our mistake to invite this speaker. To date, the EVOWOG committee has operated with no formal structure or by-laws, and no formal vetting process for inviting speakers. While this system has largely worked in the past 14 years, it clearly failed here. When we learned of the direction of his planned talk on Thursday morning, our immediate options were limited. We withdrew our promotion and advertisement of the event, cancelled several meetings, and alternative assignments were created for students who had been offered credit for attending. Ultimately, we decided that cancelling the seminar would be counterproductive.

One of the first actions we plan on taking is to formalize this committee, and adopt a clear vetting process for speakers. Anyone within the University community who would like to participate in this committee has always been, and will continue to be, welcome to join. The mission of the ALLELE lecture series is to provide accurate, informative, research-based evolutionary science and outreach to the UA community and the general public. We would love for people to see this mission in action at our next seminar by Dr. Gunter Wagner, a world-renowned evolutionary biologist (November 7, 7:30 pm in 2008 North Lawn Hall).

Sincerely,

The Evolutionary Working Group (EVOWOG)

Go here to see the original:

Evolution Working Group on hosting Bo Winegard: 'It was our mistake' - The University of Alabama Crimson White

Editors note: Phillip E. Johnson, Berkeley law professor and author ofDarwin on Trialand other books, died on November 2. Evolution Newsis sharing remembrances from Fellows of Discovery Institute. Dr. Meyers forthcoming book isThe Return of the God Hypothesis. Thefollowing essay is drawn from the FestschriftDarwins Nemesis: Phillip Johnson and the Intelligent Design Movement.

I first met Phillip Johnson at a small Greek restaurant on Free School Lane next to the old Cavendish Laboratory in Cambridge in the fall of 1987. The meeting had been arranged by a fellow graduate student who knew Phil from Berkeley. My friend had told me only that his friend was a quirky but brilliant law professor who was on sabbatical studying torts, and that he had become obsessed with evolution. Would you talk to him? he asked.

His description and the tone of his request led me to anticipate a very different figure than I encountered. Though my own skepticism about Darwinism had been well cemented by this time, I knew enough of the stereotypical evolution-basher to be skeptical that a late-in-career non-scientist could have stumbled onto an original critique of Darwins theory.

I should have known better, but only later did I learn of Johnsons intellectual pedigree: Harvard B.A.; top of class University of Chicago law grad; law clerk for Chief Justice Earl Warren; leading constitutional scholar; occupant of a distinguished chair at the University of California, Berkeley. In Johnson, I encountered a man of supple and prodigious intellect who seemed in short order to have found the pulse of the origins issue.

Johnson told me that his doubts about Darwinism had started with a visit to the British Natural History Museum where he learned about the controversy that had raged there earlier in the 1980s. At that time, the museum paleontologists presented a display describing Darwins theory as one possible explanation of origins. A furor ensued resulting in the removal of the display when the editors of the prestigiousNaturemagazine and others in the scientific establishment denounced the museum for its ambivalence about accepted fact.

Intrigued by the response to such an (apparently) innocuous exhibit, Johnson decided to investigate further. He began to read whatever he could find on the issue: Gould, Ruse, Ridley, Dawkins, and Michael DentonsEvolution: A Theory in Crisis. What he read made him more suspicious of evolutionary orthodoxy. Something about the Darwinists rhetorical style, he told me later, made me think they had something to hide.

An extensive examination of evolutionary literature confirmed this suspicion. Darwinist polemic revealed a surprising reliance upon arguments that seemed to assume rather than demonstrate that life had evolved via natural processes. Johnson also observed an interesting contrast between biologists technical papers and their popular defenses of evolutionary theory. When writing in scientific journals, he discovered, biologists acknowledged many significant difficulties with both standard and newer evolutionary models. Yet, when defending basic Darwinist commitments (such as the common ancestry of all life and the creative power of the natural selection/mutation mechanism) in popular books or textbooks, Darwinists employed an evasive and moralizing rhetorical style to minimize problems and belittle critics. Johnson began to wonder why, given mounting difficulties, Darwinists remained so confident that all organisms had evolved naturally from simpler forms.

InDarwin on Trial (Regnery, 1991, 188 pages)Johnson argued that evolutionary biologists remain confident about neo-Darwinism, not because empirical evidence generally supports the theory, but instead, because their perception of the rules of scientific procedure virtually prevent them from considering any alternative view. Johnson cited, among other things, a communiqu from the National Academy of Sciences (NAS) issued to the Supreme Court during the Louisiana creation science trial. The NAS insisted that the most basic characteristic of science is a reliance upon naturalistic explanations.

While Johnson accepted methodological naturalism as an accurate description of method in much of science, he argued that treating it as a normative rule when seeking to establish that natural processes alone produced life, assumes the very point that Darwinists (and neo-Darwinists) are trying to establish. Johnson reminded readers that Darwinism does not just claim that evolution (in the sense of change) has occurred. Instead, it purports to establish that the major innovations in the history of life arose by purelynaturalmechanism that is, without intelligent direction or design. He thus distinguished the various meanings of the term evolution from the central claim of Darwinism, which he identifies as the Blind Watchmaker thesis, following Richards Dawkins the staunch modern defender of Darwinism.

Yet if the design hypothesis must be denied consideration from the outset, and if, as the NAS also asserted, exclusively negative argumentation against evolutionary theory is unscientific, then Johnson argued that the rules of argument. . . . make it impossible to question whether what we are being told about evolution is really true. Defining opposing positions out of existence may be one way to win an argument, but, says Johnson, it scarcely suffices to demonstrate the superiority of a protected theory.

To establish that such philosophical gerrymandering lies behind the success of the evolutionary program,Darwin on Trialevaluated the scientific arguments that ostensibly establish the fact of evolution. Johnson trained his considerable facility for analysis upon the whole edifice of Darwinist argumentation. He found a panoply of euphemism and wishful thinking masquerading as evidence: the pattern of gaps and sudden appearance in the fossil record described as rapid evolutionary branching, superficial variations in moths or fruit flies cited to substantiate the possibility of grand macroevolutionary changes, elaborate depictions of human ancestors based on scanty bone fragments, and biochemical observations laden with evolutionary assumptions used to justify evolutionary claims.

Along the way,Darwin on Trialasks a good many questions rarely asked in polite biological society. Given the fossil evidence, how do we know that hypothetical transitional organisms ever existed? How do we know that natural selection can create complex organs and organisms when genetics suggests the vast improbability of random mutations producing advantageous and novel structures? How do we know that the first cells did arrange themselves from simple chemicals if we havent yet established that they could? In each case, Johnson argued that we know because we have equated scientific method with a philosophy of strict naturalism and materialism. We know because the rules of science imply that some form of naturalistic evolutionmustbe true.

Johnsons attempt to re-open such questions has angered many members of the biological establishment who had grown accustomed to offering the public what Johnson called proof through confident assertion. His criticism of Darwinist orthodoxy initially earned him dismissive reviews inScience,Nature, andScientific American, the latter written by Stephen Jay Gould. Yet these reviews also helped publicize Johnsons thesis which has since struck a responsive cord with many scientists. For example, biochemist Michael Behe, who later authoredDarwins Black Box, the seminal case for intelligent design, first came to Johnsons attention after Behe wrote a letter defendingDarwin on Trialin response to theNaturereview.

Moreover, by the early 1990s some prominent neo-Darwinists such as Arthur Shapiro of the University of California, Davis, and Michael Ruse of the University of Guelph had welcomed the spirited challenge that Johnson provided to their views. Shapiro, Ruse, and eight other scientists and philosophers (including both defenders and critics of modern Darwinism) joined Johnson at Southern Methodist University in the Spring of 1992 to debate the central thesis of his book. The success of that event led to many others like it and a growing movement of scientists and scholars willing to examine the issues thatDarwin on Trialfirst raised.

Darwin on Trialre-opened long-dormant questions by challenging the evolutionary establishments reliance upon philosophically tendentious rules of method. In the process, it helped inspire an intellectual movement and a scientific research program that has begun to redefine our understanding of science and the origin of life.

Read more from the original source:

Your Witness, Mr. Johnson: A Retrospective Review of Darwin on Trial - Discovery Institute