Daily Archives: May 4, 2017

BOSTON -- Kelly Olynyk's head was spinning.

It was early October 2013, and the Celtics were navigating the first days of training camp under newly hired head coach Brad Stevens.

Olynyk, then a 22-year-old rookie, was trying his best to simply pick up NBA terminology and make sure he was in all the right spots as the Celtics launched a new era on the campus of Salve Regina University in Newport, Rhode Island.

"I could care less. I just want to win the next possession."

Celtics coach Brad Stevens, on Boston's pregame antics

One night, after the team's two-a-day sessions were complete, Olynyk went out to dinner with soon-to-be team captain Rajon Rondo and longtime strength coach Bryan Doo. The conversation eventually turned to two very important topics for any NBA rookie.

First, Rondo and Doo, each a father of young children, implored Olynyk to embrace the fact he was young and able to make basketball a singular focus. Second, they advised him to develop a pregame routine.

In that moment, the start of one of the NBA's most ambitious pre-tipoff routines was born.

It has been a steady evolution, but Olynyk is now a blizzard of activity in the time from lineup announcements until the game's opening jump ball, all with a goal of getting himself and his teammates pumped up for action.

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Olynyk's routine crescendos with a sequence in which he sprints from near midcourt for a flying body bump with teammate Jonas Jerebko and then spins seamlessly into a multistep handshake with Doo that ends when Olynyk brings his hands together before emphatically fanning them out skyward.

"Rondo and B-Doo were telling me, 'Bro, just live your life. Keep working, keep grinding. But right now you have no worries,'" Olynyk said. "And that's how our pregame handshake started.

"There's so much stuff in life, and then you just gotta, like," Olynyk said as he replicated a fanning motion. "You can't worry about any of that right now."

Every team in the NBA has unique pregame routines. There are plenty of well-choreographed handshakes and endless fist bumps. In Oklahoma City, Russell Westbrook and former Thunder guard Cameron Payne became a must-watch dance party last season.

Boston's pregame routines are fascinating to observe, and it's a small glimpse into the chemistry and cohesion that has positioned Boston two wins away from a trip to the Eastern Conference finals. The Celtics visit the Washington Wizards on Thursday night in Game 3 of an East semifinal series at the Verizon Center (8 p.m. ET, ESPN).

During lineup introductions, All-Star point guard Isaiah Thomas stands alone in the corner opposite the Celtics bench until his name is announced. A mosh pit ensues, with players aggressively bumping and wrestling each other until "Welcome to the Jungle" by Guns N' Roses begins and the 90-second countdown to tipoff begins.

As warm-up gear gets hurled in every direction, Stevens draws up a play for Boston's first possession. The huddle typically breaks with maybe a minute on the clock, and Boston players race to begin their routines -- some more detailed than others:

Celtics big man Amir Johnson used to peel off his warm-up shirt and simply throw it to the sky as a sideline attendant raced to catch it. The sequence evolved, and Johnson now throws his crumpled-up shirt at Doo, who crouches like a catcher on the baseline.

Teammates at first watched to see if Johnson would throw a strike. He did it frequently enough that veteran Gerald Green now stands in front of Doo, waggling an imaginary bat and then trying to make contact with his hands. Olynyk often breaks away from his own intensive routine to play the field behind Johnson.

The Celtics have been searching for a superstar like Jimmy Butler or Paul George to launch them into true title contention. But have they already found one in Isaiah Thomas?

Read about the 2017 NBA playoffs on ESPN to find out if the Cavs and Warriors are on a collision course for their third straight Finals showdown.

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"At first I was striking [Green] out," Johnson said. "But, like, [in recent] games, he's been hitting home runs now. I think my catcher [Doo] doesn't have great signals, and I have to talk to him about that. His signals are throwing me off."

Doo confirmed a recent pitcher-catcher conference, and whatever was discussed appears to have worked for Johnson. Green finds himself in a postseason slump as Johnson routinely works the corners of the plate.

Stevens and his assistants, their more subtle fist bumps concluded, sometimes sneak a glance at Johnson's opening pitch.

"I could care less [about the pregame antics]. I just want to win the next possession," Stevens said. "But sometimes I do enjoy watching Amir throw the pitch."

Told that Green had been making solid contact in his early at-bats, Stevens said he's well-aware, noting that Green hit a home run late in the regular season.

"That's probably the thing I enjoy the most," Stevens said of the pitcher-hitter sequence. "I'm not big on the mosh pit or things like Kelly jumping in the air. But everybody has to do their own thing."

Olynyk's post-huddle journey starts at the scorer's table, where he, Tyler Zeller and Jonas Jerebko dap all the starters headed to the court.

Olynyk breaks away to be part of Johnson's pitch, and then eventually makes the trek back to the bench, fist-bumping the team's media relations staffers and all the coaches along the way. There are quick handshakes and hugs with most of his teammates until he spies Jerebko.

That's when Olynyk turns, jogs a few paces in the opposite direction, touches his toes, and then speeds at Jerebko as the two leap in the air for their flying body bump. Olynyk throws some sort of midair ninja kick and then locates Doo as he spins for the grand finale.

When that's done, Olynyk does some quick-stepping calisthenics, and as the pregame countdown buzzer sounds, he typically rips open the top of his warm-up shirt a la Superman.

"I'm running out of time," Olynyk playfully lamented. "Sometimes Coach takes too long to draw up the first play, and then we don't get time to do it all. I might be maxed out on what I can do."

There's plenty more to see on Boston's sideline, some of it less obvious. Marcus Smart has a personalized sequence with Green. Jae Crowder offers daps and bows to anyone he can find. Eventually, Smart locates fellow 2014 draftee James Young, and they do a more subdued version of the Westbrook-Payne dance. Second-year guard Terry Rozier and Green often do a fictional dice roll that brings back memories of Paul Pierce's huddle-breaking routine.

As silly as it can look to casual observers, do not diminish the importance of all the pre-tip chaos. NBA players crave routines and can be thrown off without them. Games in Boston's most recent Big Three era couldn't start until Kevin Garnett was done head-butting the stanchion and pounding his chest at the crowd.

Now a new generation of Celtics are trying to find their own unique ways to get ready for game action.

"It definitely gets you in game mode, gets everybody pumped up and ready to go," Olynyk said. "It kind of gets you on the same wavelength as everybody else. Everybody knows at that time what everybody else is doing.

"It kinda syncs you guys all together. It's like basketball Bluetooth."

Stevens is asked if he had any fancy handshakes as part of his pregame routine when he played collegiately at DePauw University, and the glance he offers in response confirms his pregame routine was as bland as could be. But he's fine with whatever his players need to do to get ready for game time.

"When you play 82 games, I think one of the things is, everybody has a routine and kind of a rhythm of how they get into a game," Stevens said. "I think it's really cool, and it basically adds enthusiasm through that. We're not the only team, obviously, and people have talked about other teams and their pregame stuff.

"I think it's fun. Have fun with it."

View post:

First pitches, 'basketball Bluetooth' and the evolution of Boston's pregame ritual - ESPN

Slide: 1 / of 2. Caption: Jerry W. Dragoo

Slide: 2 / of 2. Caption: Robby Heischman

After so many years in the public eye, skunks have lost their pizzazz. Its not their fault, its just that weve all forgotten how bizarre they are. Very few animals can fire sulphurous fluids out of their bums to incapacitate their foes, after all. Very few. But good on skunks, really, for keeping it weird.

One particular variety, the western spotted skunkwhich balances on its front legs before it sprays you, as if thats a charming consolationjust got even weirder. In a study published today in the journal Ecology and Evolution, researchers report that the two-pound terror has evolved into three genetically distinct groups, called clades, in an intriguing way: not with geological isolation (the classical impetus for getting populations to diverge genetically) but with climatic isolation. That is, dramatic climate change led to a genetic splintering of the species.

Its actually fairly easy to get a new species. Just run a river or a mountain range through a population, splitting it in two. In their isolation, the groups will eventually grow so genetically distinct that they can no longer mate and produce offspring. Boom, two new species. The spotted skunk is kind of up to the same thing, though it hasnt diverged enough to become new species, but instead three clades: western (California, Nevada, Baja California), Arizona, and east-central (Texas and Mexico). Though the clades existed in different geographical areas, they werent necessarily cordoned off from each other by geological boundaries.

By melding climate models and genetic work that showed when the spotted skunk began diverging, the researchers determined that the three clades likely got stuck in isolated pockets of actually habitable habitat during the Pleistocene Ice Age. The idea is that these suitable conditions would contract when glaciers were expandingit was cooler periodsand then expand during the interglacial periods, says mammalogist and study co-author Adam Ferguson of the Field Museum.

The spotted skunks divergence began about 1 million years ago, and continued as glaciers in North America expanded and contracted over millennia. Unlike the anthropogenically induced climate change we are experiencing today, the change in temperatures and rainfall patterns was more gradual, Ferguson says, occurring over thousands to tens of thousands of years. These fluctuations as the glaciers moved in and out probably created suitable wooded habitats for skunks, and destroyed others, as groups of the creatures evolved in isolation.

Really, its not hard to see how this could come about. Say a forested area started drying out, and grasslands took over for dying trees. The western spotted skunks really depend on cover and thick areas for protection from aerial predators, Ferguson says, and so crossing these open grasslands might not have been possible for them per se. Western Americas newfound plains were just as restrictive for the skunk as new rivers or mountain ranges would have been.

The beauty of it all is that scientists can use this data to get a better picture of a disorderly climatic future. By projecting into the past and understanding what happened to this species, it could give us an idea of how changing climates of the future could potentially change at least the distribution of suitable areas for this species, Ferguson says.

The spotted skunks evolutionary journey is also a reminder that climate change affects different creatures in different ways. Warming oceans are definitely bad for coral, for instance. But other species will adapt to a planet in flux, like the spotted skunk did during the Pleistocene.

Problem is, its not just human-made climate change thats the issue, but human-made everything. Urban development in particular threatens mammals all over the world. If theres bigger freeways, and all these other things dividing up the land, its going to be harder for small populations to persist, says ecologist Craig Benkman.

But heres to the continued survival of the spotted skunk. I for one am glad it got its groove back.

Original post:

The Fascinating Evolution of the World's Most Charming Skunk - Wired - WIRED

Did a Christian dietary practice speed the evolution of the domestic chicken about 1100 years ago? A new report in Molecular Biology and Evolutionsuggests this may be so.

The researchers, from the UK and Germany, analyzed variants of two genes using a molecular dating technique that they developed, on ancient chicken bones.

SELECTING CHICKENS

People domesticated Gallus gallus domesticus from wild Asian jungle fowl about 6000 years ago. The chicken genome sequencewas published in 2004, but for time tracking, less information is more. Researchers compare DNA sequence variants of corresponding individual genes among pairs of species to build evolutionary tree diagrams, assigning approximate times of divergence using known mutation rates against a timepoint such as fossil evidence from a specific rock layer or an historical event. A branch from the ancestral wild fowl morphed into chickens as humans selected and bred birds displaying traits that made them easier to raise and tastier.

The selected genes encode the thyroid-stimulating hormone receptor (TSHR) and -carotene dioxygenase 2 (BCDO2). Their DNA sequences echo positive selection: mutation changing an amino acid from the ancestral to the derived species. A genetic change that doesnt alter the amino acid wouldnt change the phenotype (observable traits), so couldnt affect evolution.

The two genes confer valuable (to us) traits. Two copies of a variant of TSHRenable many domesticated animal species to reproduce continuously, rather than seasonally. In chickens, the change speeds egg-laying while tempering aggression and fear of people.

A common variant of the other gene, BCD02, cleaves carotene, removing the orange pigment from digested food and rendering the skin white or grey. A mutation new to the domestic chicken, acquired from errant mating with the grey junglefowl (Gallus sonneratii), hampers the carotene-cutting enzyme, providing the familiar yellow color to the skin of a well-fed bird. People probably came to regard yellow skin as a sign of a healthy chicken and selected for it.

The researchers obtained ancient DNA from an archaeological collection of chicken bones going back some 2200 years, from across northern Europe. The bones are abundant from the 9th to the 12th centuries AD. Computations using the degrees of difference among the gene variants in the domesticated chickens compared to their wild relatives led the investigators back to the High Middle Ages, around 920 A.D.

What was happening then?

Christian edicts began to enforce periods that forbid consumption of meat from four-legged beasts, somehow not considering chicken to be meat. The practice spread, with Christianity, across Europe and was ubiquitous by about 1000 AD.

Like a 20-piece KFC bucket today, demand for chickens a millennium ago might have put selective pressure on the genes that enable frequent egg-laying and yellow skin. At about the same time, expansion of cities might have favored stuffing chickens into tight quarters rather than grazing large quadrupeds like cows and pigs.

Ancient DNA allows us to observe how genes have changed in the past, but the problem has always been to get high enough time resolution to link genetic evolution to potential causes. But with enough data and a novel statistical framework, we now have timings that are precise enough to correlate them with ecological and cultural shifts, saidLiisa Loog, first author, from the Palaeogenomics and Bio-Archaeology Research Network at the University of Oxford.

Chicken evolution continued. Many modern characteristics come from breeding during the Victorian era between native European birds and exotic Asian chickens. Still, the researchers conclude that to our knowledge, this is the first example of pre-industrial domesticated trait selection in response to a historically attested cultural shift in food preference. The work also shows that domestication of plants and animals isnt a quick genetic switch, but a long process, continuing for thousands of years past initial attempts to control breeding, in response to a changing natural environment as well as to the dietary desires of humankind.

LAYING CLAIM TO CHICKEN SOUP

I have a slight bone to pick with the researchers. From my experience, chicken soup (a surrogate forGallus gallus domesticus) is more a Jewish staple than a Christian one, and Jewish origins certainly lie closer to the domestication of chickens 6,000 years ago than do Christian origins. Chicken soup is, of course, also known as Jewish penicillin. Archaeology tells us that potterythat could have cradled soup existed in Japan and China some 18,000 years ago, so delivery method wasnt a problem.

A little closer to the Christian claim, Greek physician Galen, in the second century AD, recommended chicken soup to treat leprosy, migraine, fever, and constipation. In the 12th century Maimonides also recommended chicken soup to treat leprosy, as well as asthma and malnutrition.

Then in the journal Chest in 2000, University of Nebraska pulmonologist Stephen Rennard MD published his landmark Chicken soup inhibits neutrophil chemotaxis in vitro,demonstrating an anti-inflammatory effect of his grandmothers chicken soup. The experiment was actually conducted in 1993 in Dr. Rennards kitchen and was quite well-controlled in terms of analyzing ingredients. Heres therecipe, but Id leave out the parsnips and turnips (theyre bitter) and the sweet potato is just weird. Up the carrots for a sweet soup.

While Im not an expert in Christianity or math, or even Judaism, I do know how to make Jewish chicken soup. (One of my best friends surreptitiously slips in a cube with a chicken cartoon on it.) Its easier than Dr. Rennards grandma suggested. So here it is:

1. At night, before bedtime, stick a small whole chicken, 2 or 3 handfuls of baby carrots, a small onion, and astalk of celery, plus salt, pepper, and a bit of cilantro, into a crockpot and fill it with water. Turn the crockpot on low, remembering to check that it is plugged in. 2. Sometime the next day, remove the collapsed chicken, onion, celery, cilantro, and some carrots. Either strain into a pot and pour it back into the crockpot, or fish out the chicken from the crockpot, but this can leave behind bone slivers or gross stuff. (Note: Cats will not eat chicken cooked this long. Dont even try. Just discard.) 3. About 2 hours before consumption, throw in, uncooked, (a) noodles, (b) rice, (c) matzo balls (aka kneidlach, (d) dumplings (akakreplach), or (e) any combo of the above.

Because the yellow skin and the fat blobs that cling to it are essential to a good soup, its pretty clear to me that the attribution of the invention of chickens or their soup to Christianity is crying fowl.

Read the rest here:

Did Christianity Speed Chicken Evolution? - PLoS Blogs (blog)

Peter S. Ungar Princeton University Press: 2017. ISBN: 9780691160535

Buy this book: US UK Japan

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Cast of a reconstructed Neanderthal skull. The teeth of fossil hominins can reveal what our extinct relations were able to eat.

Teeth are a unique, enduring archive of a lifetime's experiences, stretching back to before birth. They can reveal childhood hardship, seasonal migration, exposure to pollution, radiation or congenital syphilis, cultural modification, and age at death as well as a wealth of information about diet. Thus, the teeth of our hominin predecessors in the archaeological and fossil record are a prodigious store of evidence. It's hardly surprising that many scientists dedicate their careers to unlocking the evidence from modern and fossil teeth.

In Evolution's Bite, palaeoanthropologist Peter Ungar offers a compelling account of how the interaction of teeth, diet and environment has shaped human evolution. This tale ranges from the formidable dentition of early hominin Paranthropus boisei, which roamed eastern Africa between 2.3 million and 1.3 million years ago, to the mismatched jaws and teeth of many living humans. The book also takes us on a fascinating tour of the fossil and archaeological record, climate history, field observations and lab-based analysis.

To kick off his exploration of human evolution, Ungar analyses the interplay of food and tooth form. Hard, brittle foods such as seeds can be crushed between teeth with rounded cusps and shallow basins. Tough foods, such as raw meat or leaves, need to be sliced or sheared by teeth with thinner, blade-like crests. But when researchers set out to learn whether living primates' diets could be predicted from the shape of their teeth, study after study revealed a mismatch between observed and expected diet. Tooth form reveals what primates are capable of eating but that is not necessarily what they choose to eat when times are good.

Fortunately, there are more direct ways of inferring diet from fossil teeth. Foods leave distinctive traces on enamel, and these microscopic marks reveal what was eaten in the days or weeks before death. A P. boisei specimen found in 1.8-million-year-old deposits at Olduvai Gorge in Tanzania is particularly striking. Once known as Nutcracker Man, it has enormous back teeth and flared cheek bones to accommodate massive chewing muscles, anchored by a skull-top crest. Scientists assumed that these were adaptations for crushing nuts and roots, which would leave pits and craters on the teeth. But microwear analysis revealed just a few wispy scratches, confirming a mismatch between capability and choice. Ungar concludes that teeth and jaws have evolved to contend with less-accessible foods that animals resort to when their preferred diet is unavailable.

Palaeoanthropologists and archaeologists continue to debate what it means to be human (S. C. Antn et al. Science 345, 1236828; 2014); Ungar demonstrates how changes in food choice, acquisition and processing intersect with many perspectives on this issue. Humans' large brains five times the mass expected in a similarly sized mammal demand a reliable source of high-quality food. Our linear body allows us to access diverse sources of nourishment by hunting down prey through endurance running. Sharing food within the immediate family or broader community underpins our social interactions and helps to ensure that our children survive. Technological advances such as tool use and cooking enable us to extract otherwise inaccessible nutrients and energy.

Ungar suggests that the concentrations of stone artefacts and butchered animal remains found at sites such as Koobi Fora in Kenya, and dated to around 2 million years ago, mark the point at which meat and bone marrow became a regular part of the human diet. He shows how teeth from early specimens of the genus Homo are better adapted for slicing than those of their australopith predecessors, and varied microwear suggests that Homo had more flexible diets. Tool use and, later, cooking may have relieved selective pressure for large teeth and jaws, but the reduction in tooth size seems to have been gradual.

A more varied diet, aided by increasingly sophisticated technologies, enabled hunter-gatherers to colonize most of the world's ice-free land masses by the end of the last ice age, around 12,000 years ago. The transition from foraging to agriculture the Neolithic Revolution had profound implications, which Ungar describes as the point at which we change the rules of the game and begin to stock the buffet ourselves. Permanent settlement and a predictable larder allowed larger communities to form complex societies. In some places, environmental change almost certainly forced the transition: at Abu Hureyra in Syria, the first tentative signs of plant cultivation around 13,000 years ago coincide with the start of the cold, arid Younger Dryas, when wild foods became scarcer.

For enthusiasts of the 'palaeo' diet, this is when it all went wrong. But as Ungar shows, versatility is key to the human dietary niche. It would be pointless to try to emulate a single ancestral diet: there wasn't one. Humans have continued to evolve since the Neolithic Revolution, and many of us have enzymes that our ancestors did not have, enabling us to digest starchy foods effectively and digest milk as adults. It can be argued, however, that our teeth and jaws are out of sync with modern menus. Many people today have crowded, crooked or impacted teeth because our jaws are underdeveloped a soft, processed diet just doesn't stimulate sufficient growth (see Daniel Lieberman's The Evolution of the Human Head; Harvard Univ. Press, 2011). The human love affair with sugary foods also leads to tooth decay and gum disease caused by bacteria that feast on residues on our teeth.

Homo sapiens is the last of the hominin lineage. But as evidence accumulates that diverse hominin species coexisted from at least 3.5 million years ago until around 40,000 years ago, a future challenge will be to understand how different foraging strategies enabled them to share the landscape.

Continue reading here:

Palaeontology: Evolution with teeth - Nature.com

Editors note: Nylon is a modern syntheticproduct used in the manufacturing, most familiarly, of ladies stockings but also a range of other goods, from rope toparachutesto auto tires.Nylonase is a popular evolutionary icon, brandished by theistic evolutionist Dennis Venema among others. In a series of three posts, Discovery Institute biologist Ann Gauger takes a closer look.

A significant problem for the neo-Darwinian story is the origin of new biological information. Clearly, information has increased over the course of lifes history new life forms appeared, requiring new genes, proteins, and other functional information. The question is how did it happen? This is the central question concerning the origin of living things.

Stephen Meyer and Douglas Axe have made this strong claim:

[T]he neo-Darwinian mechanism with its reliance on a random mutational search to generate novel gene sequences is not an adequate mechanism to produce the information necessary for even a single new protein fold, let alone a novel animal form, in available evolutionary deep time.

Their claim is based on the experimental finding by Doug Axe that functional protein folds are exceedingly rare, on the order on 1 in 10 to the 77th power, meaning that all the creatures of the Earth searching for the age of the Earth by random mutation could not find even one medium-size protein fold.

In contrast, Dennis Venema, professor of biology at Trinity Western University, claims in his book Adam and the Genome and in posts at the BioLogos website that getting new information is not hard. In his book, he presents several examples he thinks demonstrate the appearance of new information the apparent evolution of new protein binding sites, for example. But the best way to reveal Axe and Meyers folly, he thinks, (and says so in his book and a post at BioLogos) would be to show that a genuinely new protein can evolve.

[E]ven more convincing would be an actual example of a functional protein coming into existence from scratch catching a novel protein forming in the act as it were. We know of such an example the formation of an enzyme that breaks down a man-made chemical.

In the 1970s, scientists made a surprising discovery: a bacterium that can digest nylon, a synthetic chemical not found in nature. These bacteria were living in the wastewater ponds of chemical factories, and they were able to use nylon as their only source of food. Nylon, however, was only about 40 years old at the time how had these bacteria adapted to this novel chemical in their environment so quickly? Intrigued, the scientists investigated. What they discovered was that the bacteria had an enzyme (which they called nylonase) that effectively digested the chemical. This enzyme, interestingly, arose from scratch as an insertion mutation into the coding sequence of another gene. This insertion simultaneously formed a stop codon early in the original gene (a codon that tells the ribosome to stop adding amino acids to a protein) and formed a brand new start codon in a different reading frame. The new reading frame ran for 392 amino acids before the first stop codon, producing a large, novel protein. As in our example above, this new protein was based on different codons due to the frameshift. It was truly de novo a new sequence.

Venema is right. If the nylonase enzyme did evolve from a frameshifted protein, it would genuinely be a demonstration that new proteins are easy to evolve. It would be proof positive that intelligent design advocates are wrong, that its not hard to get a new protein from random sequence. But the story bears reexamining. Is the new protein really the product of a frameshift, or did it pre-exist the introduction of nylon into the environment? What exactly do we know about this enzyme? Does the evidence substantiate the claims of Venema and others, or does it lead to other conclusions?

First, some history. In the 1970s Japanese scientists discovered that certain bacteria had developed the ability to degrade the synthetic polymer nylon. Okada et al. identified three enzymes responsible for nylon degradation, and named them EI, EII, and EIII. The genes that encoded them were named nylA, nylB, and nylC. They sequenced the plasmid on which the genes were found, and discovered that there was another gene on the same plasmid that was very similar to nylB; they named it nylB. (We will focus on the story of nylB and nylB because they are the ones relevant to Venemas story.)

So far all I have given you are the facts. Now heres the interpretation of these facts. Some claimed that the nylonase enzyme, as it was called, had originated some time after people began making nylon (in the 1930s). That seemed plausible because nylonase was unable to degrade naturally occurring amide bonds it could degrade only the amide bonds in nylon and so had not existed previously, it was thought. The popular conclusion was that the nylonase activity evolved in response to the presence of nylon in the environment, and thus was only forty years old. And heres the big interpretive leap: it must not be hard to get new enzymes if a new one can evolve within a period of forty years.

Okada et al. had sequenced the genes encoding nylB and nylB. They concluded that the nylonase activity was the result of a gene duplication followed by several mutations to the nylB gene. But at this point Susumu Ohno, an eminent molecular geneticist and evolutionary biologist, noticed something unusual about the nylB gene sequence (Ohno, 1984). Ohno had a theory that DNA with repeats of the right kind had the potential to code for protein in multiple frames, with no interrupting stop codons, and might thus be a source for new proteins. (If you are unfamiliar with the terms I just used, I invite you to take a look at my post tomorrow, where I will explain the necessary concepts. For those already familiar, I present some relevant data concerning the rarity of sequences that can be frameshifted.)

Ohno noticed that nylB, the gene for nylonase, might originally have encoded something else if a certain T was removed. The nylonase gene as it exists now has 1179 bases, which encode a 392 amino acid protein. Without a particular T embedded in the ATG start codon, though, the sequence would have specified a hypothetical original gene with a longer open reading frame (ORF) of 427 amino acids, in a different frame. Thus, Ohno proposed a new protein with a new function acting on a new substrate was born when a T inserted in between a particular A and G in the DNA, making a new ATG start codon and shifting the frame to code for a new protein, the protein we now call nylonase.

Ingenious. According to Ohno, nylonase could be a new enzyme, appearing suddenly with no known precursors via a sudden frameshift. (Note that all of this assumes that new protein folds are easy to get.) Ohno published this hypothesis in the Proceedings of the National Academy of Sciences. It was a hypothesis only, however, as a careful reading of his paper shows. One heading, for example:

R-IIA Coding Sequence [nylB] for 6-AHA LOH [nylonase] Embodies an Alternative, Longer Open Reading Frame That Might Have Been the Original Coding Sequence [Emphasis added.]

and the text says:

I suggest that the RS-IIA base sequence [nylB] was originally a coding sequence for an arginine-rich polypeptide chain 427 or so residues long in its length and that the coding sequence for one of the two isozymic forms of 6-ALA LOH [nylonase] arose from its alternative open reading frame. [Emphasis added.]

Ohno presented arguments for why his suggestion was plausible, but did not provide evidence that the original gene ever existed or was used (in fact he says it was unlikely to be useful based on its amino acid composition), or that the insertion ever happened. Nonetheless, the frame-shift hypothesis for the origin of nylonase has been widely proclaimed as fact (though, notably, not by Okada et al. who have done most of the work).

If the nylonase story as told above were true, namely that a frameshift mutation resulted in the de novo generation of a new protein fold with a new function, it would indeed constitute a substantial refutation to Meyer and Axes claim. If a frame-shift mutation can produce a random new open reading frame in real, observable time, and give rise to a new functional enzyme, then it must not be that hard to make new functional protein folds. In other words, functional protein folds must not be rare in sequence space. And therefore Stephen Meyers arguments about the difficulty of getting enough new biological information to generate a new fold must be wrong as well. Venema flatly asserts:

If de novo protein-coding genes such as nylonase can come into being from scratch, as it were, then it is demonstrably the case that new protein folds can be formed by evolutionary mechanisms without difficulty.[I]f Meyer had understood de novo gene formation as we have seen, he mistakenly thought it was an unexplained process he would have known that new protein folds could indeed be easily developed by evolutionary processes.

Slam dunk, right?

A little caution in accepting this story without hard evidence would be wise. In genetics we are taught that frame-shift mutations are extremely disruptive, completely changing the coding sequence and resulting in truncated nonsense. In fact, one term for a frameshift mutation is nonsense mutation. A biologists basic intuition should be that frameshifts are highly unlikely to produce something useful. The only reasons for the widespread acceptance of Ohnos hypothesis that I can come up with are the unusual character of the sequence itself, Ohno reputation as a brilliant scientist (which he was), and wish-fulfillment on the part of some evolutionary biologists.

Fortunately, science marches on, and evidence continues to accumulate. The same group of Japanese scientists continued their study of the nylonase genes. nylB appeared to be the result of a gene duplication of nylB that occurred some time ago. EII (the enzyme encoded by nylB) had very little nylonase activity, while EII (the enzyme encoded by nylB) was about 1000 fold higher in activity. The two enzymes differed in amino acid sequence at 47 positions out of 392. With some painstaking work, the Japanese determined that just two mutations were sufficient to convert EII to the EII level of activity.

They then obtained the three-dimensional structure of an EII-EII hybrid protein. And with those results everything changed or should have.

Heres what Venema takes from the paper and interprets the evidence:

the three-dimensional structure of the protein has been solved using X-ray crystallography, a method that gives us the precise shape of the protein at high resolution. Nylonase is chock full of protein folds exactly the sort of folds Meyer claims must be the result of design because evolution could not have produced them even with all the time since the origin of life. [Emphasis added.]

Unfortunately, Venema doesnt have the story straight. Nylonase has a particular fold, a particular three-dimensional, stable shape. Most proteins have a distinct fold there are several thousand kinds of folds known so far, each with a distinct topology and structure. Folds are typically made up of small secondary structures called alpha helices and beta strands, which help to assemble the tertiary structure the fold as a whole. Venema seems unclear about what a protein fold is, and the distinction between secondary and tertiary structures. Nylonase is not chock full of folds. No structural biologist would describe nylonase as chock full of protein folds. Indeed, no protein is chock full of folds. Perhaps Venema was referring to the smaller units of secondary structure I mentioned above, the alpha helices or beta strands. But it would appear he doesnt know what a protein fold is.

Maybe that explains why Venema missed the essential point of the paper describing nylonases structure. The crystal structure of EII-EII (a nylonase hybrid necessary to be able to crystalize the protein) revealed that it is not a new kind of fold, but a member of the beta-lactamase fold family. More specifically, it resembles carboxylesterases, a subgrouping of that family. In addition, when the scientists checked EII and EII, they found that both enzymes had previously undetected carboxylesterase activity. In other words, the EII and EII enzymes were carboxylesterases. If it looks like a duck and quacks like a duck, it is a duck.

Thus, EII and EII did not have frameshifted new folds. They had pre-existing folds with activity characteristic of their fold type. There was no brand-new protein. No novel protein fold had emerged. And no frameshift mutation was required to produce nylonase.

Where did the nylon-eating ability come from? Carboxylesterases are enzymes with broad substrate specificities; they can carry out a variety of reactions. Their binding pocket is large and can accommodate a lot of different substrates. They are promiscuous enzymes, in other words. Furthermore, the carboxylesterase reaction hydrolyzes a chemical bond similar to the one hydrolyzed by nylonase. Tests revealed that both the EII and EII enzymes have carboxylesterase and nylonase activity. They can hydrolyze both substrates. In fact it is possible both had carboxylesterase activity and a low level of nylonase activity from the beginning, even before the appearance of nylon.

nylB may be the original gene from which nylB came. Apparently there was a gene duplication at some point in the past. The two genes appear to have acquired mutations since then they differ by 47 amino acids out of 392. The time of that duplication is unknown, but not recent, because it takes time to accumulate that many mutations. However, at least some of those mutations must confer a high level of nylonase activity on EII, the enzyme made by nylB. The enzyme EII made by nylB has only a low ability to degrade nylon, while EII degrades nylon 1000 fold better. So one or more of those 47 amino acid differences must be the cause of the high level of nylonase activity in EII. Through careful work, the Japanese workers Kato et al. identified which amino acid changes were responsible for the increased nylonase activity. Just two step-wise mutations present in EII, when introduced into EII, could convert the weak enzyme EII to full nylonase activity.

From Kato et al. (1991):

Our studies demonstrated that among the 47 amino acids altered between the EII and EII proteins, a single amino acid substitution at position 181 was essential for the activity of 6-aminohexanoate-dimer hydrolase [nylonase] and substitution at position 266 enhanced the effect.

So. This is not the story of a highly improbable frame-shift producing a new functional enzyme. This is the story of a pre-existing enzyme with a low level of promiscuous nylonase activity, which improved its activity toward nylon by first one, then another selectable mutation. In other words this is a completely plausible case of gene duplication, mutation, and selection operating on a pre-existing enzyme to improve a pre-existing low-level activity, exactly the kind of event that Meyer and Axe specifically acknowledge as a possibility, given the time and probabilistic resources available. Indeed, the origin of nylonase actually provides a nice example of the optimization of a pre-existing folds function, not the innovation or creation of a novel fold.

As the scientists who carried out the structural determination for nylonase themselves note:

Here, we propose that amino acid replacements in the catalytic cleft of a preexisting esterase with the beta-lactamase fold resulted in the evolution of the nylon oligomer hydrolase. [Emphasis added.]

Lets put to bed the fable that the nylon oligomer hydrolase EII, colloquially known as nylonase, arose by a frame-shift mutation, leading to the creation of a new functional protein fold. There is absolutely no need to postulate such a highly improbable event, and no justification for making this extravagant claim. Instead, there is a much more parsimonious explanation that nylonase arose by a gene duplication event some time in the past, followed by a series of two mutations occurring after the introduction of nylon into the environment, which increased the nylon oligomer hydrolase activity of the nylB gene product to current levels. Could this series of events happen in forty years? Most certainly. Probably in much less time. In fact, it has been reported to happen in the lab under the right selective conditions. And most definitely, the evolution of nylonase does not call for the creation of a novel protein fold, nor did one arise. EIIs fold is part of the carboxylesterase fold family. Carboxylesterases serve many functions and have been around much longer than forty years.

Douglas Axe and Stephen Meyer readily admit that this kind of evolutionary adaptation happens easily. A protein that already has a low level of activity for a particular substrate can be mutated to favor that side reaction over its original one, often in just a few steps. There are many cases of this in the literature. What Axe and Meyer do claim is that generating an entirely new protein fold via mutation and selection is implausible in the extreme. Nothing in the nylonase story that Dennis Venema tells shows otherwise.

Tomorrow: The Nylonase Story: How Unusual Is That?

Photo: Nylon parachute, by Lance Corporal Brian D. Jones, U.S. Marine Corps [Public domain], via Wikimedia Commons.

See more here:

The Nylonase Story: When Imagination and Facts Collide - Discovery Institute

Cristiano Ronaldo recorded his 42nd career hat trick in style as Madrid took a commanding first-leg lead over Atletico. Cristiano Ronaldo recorded his 42nd career hat trick in style as Madrid took a commanding first-leg lead over Atletico. Cristiano Ronaldo recorded his 42nd career hat trick in style as Madrid took a commanding first-leg lead over Atletico. Cristiano Ronaldo recorded his 42nd career hat trick in style as Madrid took a commanding first-leg lead over Atletico. Cristiano Ronaldo recorded his 42nd career hat trick in style as Madrid took a commanding first-leg lead over Atletico. Cristiano Ronaldo recorded his 42nd career hat trick in style as Madrid took a commanding first-leg lead over Atletico. Cristiano Ronaldo recorded his 42nd career hat trick in style as Madrid took a commanding first-leg lead over Atletico. Cristiano Ronaldo recorded his 42nd career hat trick in style as Madrid took a commanding first-leg lead over Atletico.

Back in August 2016, expectations were high among Real Madrid fans. They had good reasons.

Before the summer, Zinedine Zidane's team had added another Champions League title to their trophy cabinet. Their impressive comeback in La Liga, although unsuccessful, was indeed a good omen, a sign that they would compete for the most important domestic tournament in the upcoming season.

The squad looked deep, and the promise of an excellent and complete term from Gareth Bale, coupled with a centre-forward version of Cristiano Ronaldo, made most supporters hope for a year full of great performances and plenty of silverware.

Had they known that this would become Bale's least-productive term in a Real Madrid shirt, their hopes would have sunk. The Wales international was key in the final push in La Liga last year, and his participation seemed essential for another fruitful season. However, at this point, with nine goals in 26 matches played, the disappointment has been remarkable.

To a bigger extent than in previous years, injuries have derailed Bale's ability to perform. And it's remarkable how the side have survived the recurring physical issues of one of their best players.

Bale's absences have not been helped by an also frustrating Karim Benzema. Sometimes inspired, sometimes inaccurate, the France striker's most defining characteristic is his inconsistency, and not even Zidane's noteworthy confidence in him has transformed the player into a dependable attacking weapon.

Of course, other players have chipped in at specific moments of the season to cover for Bale's attacking production or lack thereof. Alvaro Morata has had his moments but can't get a single start in any important match. James Rodriguez in midseason, Isco in the past couple of months, Marco Asensio and Lucas Vazquez have all participated well to keep the team's challenge for the Champions League and La Liga titles alive. The instrumental goals of Sergio Ramos, of course, can't be forgotten.

But in recent weeks, as the stakes have become higher and higher, there's only one name on the scoresheet. Indeed, the "B" team has given starters the chance to rest while they get the results against lower opposition, but Ronaldo's output since the knockout stages of the Champions League started is overwhelming.

His agreement with Zidane to reduce his minutes is well known, and the numbers show the difference. This might be the first season since 2009-10 in which the Portugal forward ends up playing fewer than 30 matches and 2,500 minutes in La Liga. Compared to last season, that would represent seven fewer matches and over 600 fewer minutes played.

Long gone are the times in which Ronaldo wanted to play every minute in La Liga. The difference between his exhausted version in the past few matches of last season and the plethoric, clinical striker of the past month is telling. Listening to Zidane, accepting his new role and understanding the team's need for him to dose his playing time are signs of Ronaldo's evolution as a player and of his maturity as a leader.

If his records and titles during his tenure so far with Real Madrid had already made him an idol, a legend of the club, this end of the season is taking him to another level in qualitative terms. His heroics against top opposition in do-or-die matches has added a new dimension to his perception among the fans: a closer one, in which numbers are less important than feats.

The obsession to reduce everything to facts and figures can't justly summarise the greatness of Ronaldo this season. He'll probably end up with his lowest number of goals scored in his past eight years with Madrid. However, after having stolen a show that seemed prepared for Bale, this season may well be the one that most Madridistas will remember more fondly when discussing the great Ronaldo.

Eduardo is one of ESPN FC's Real Madrid bloggers and has been a socio since 1995. Follow him on Twitter @alvarez.

Read more from the original source:

Ronaldo's evolution as a player is lifting him to unprecedented heroics - ESPN FC (blog)