Later On

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Archive for the ‘Evolution’ Category

A headline that made me laugh: “Monsanto Agrees to Use Gene-Editing Tool CRISPR Responsibly”

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Here’s the article.

From the article:

. . . CRISPR/Cas9 has been taking the world by storm since it was first developed in 2013by researchers at the Broad Institute. The gene-editing technology works by taking advantage of a property of DNA called clustered regularly interspaced short palindromic repeats, or small repetitions of DNA base sequences. These sequences produce an enzyme called Cas9, which essentially functions as a pair of genetic scissors which can cut the DNA sequences at certain points to add or remove small DNA segments.

Yet the ease with which researchers and companies like Monsanto could use gene-editing technology to irreversibly fuck with living things like people and plants has also raised concern that the technology might become widely deployed without understanding the consequences. This is why the “responsible use” of CRISPR/Cas9 cited by Rozen is a key stipulation in Monsanto’s latest move to corner the GMO industry (as the most recent acquisition of the chemical company Bayer, Monsanto and its affiliates now control a full 25 percent of the world’s seeds and pesticides).

Monsanto has never been a company that has been particularly lauded for doingresponsible things, and its forays into genetically modified plants have had a number of unintended consequences, such as encouraging pesticide resistant “super bugs” and weeds. In order to ensure more responsible use of this powerful gene-editing tool, the agreement prohibits Monsanto from using CRISPR/Cas9 to promote gene drives (where a genetically modified trait, such as pesticide resistance, is intentionally spread through an entire plant population), the production of sterile “terminator” seeds, or the production of tobacco to be used for smoking.

Gene drives were recently cited as a concern in a National Academy of Sciences reporton the topic since genetically modified plant traits could ravage ecosystems in ways that aren’t yet fully understood. . .

This will not end well.

Written by LeisureGuy

24 September 2016 at 1:54 pm

Observing evolution as it happens

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Emily Singer writes in Quanta:

When Rosemary and Peter Grant first set foot on Daphne Major, a tiny island in the Galápagos archipelago, in 1973, they had no idea it would become a second home. The husband and wife team, now emeritus biology professors at Princeton University, were looking for a pristine environment in which to study evolution. They hoped that the various species of finches on the island would provide the perfect means for uncovering the factors that drive the formation of new species.

The diminutive island wasn’t a particularly hospitable place for the Grants daphneisland-615x399to spend their winters. At less than one-hundredth the size of Manhattan, Daphne resembles the tip of a volcano rising from the sea. Visitors must leap off the boat onto the edge of a steep ring of land that surrounds a central crater. The island’s vegetation is sparse. Herbs, cactus bushes and low trees provide food for finches — small, medium and large ground finches, as well as cactus finches — and other birds. The Grants brought with them all the food and water they would need and cooked meals in a shallow cave sheltered by a tarp from the baking sun. They camped on Daphne’s one tiny flat spot, barely larger than a picnic table.

Though lacking in creature comforts, Daphne proved to be a fruitful choice. The Galápagos’ extreme climate — swinging between periods of severe drought and bountiful rain — furnished ample natural selection. Rainfall varied from a meter of rain in 1983 to none in 1985. A severe drought in 1977 killed off many of Daphne’s finches, setting the stage for the Grants’ first major discovery. During the dry spell, large seeds became more plentiful than small ones. Birds with bigger beaks were more successful at cracking the large seeds. As a result, large finches and their offspring triumphed during the drought, triggering a lasting increase in the birds’ average size. The Grants had observed evolution in action.

That striking finding launched a prolific career for the pair. They visited Daphne for several months each year from 1973 to 2012, sometimes bringing their daughters. Over the course of their four-decade tenure, the couple tagged roughly 20,000 birds spanning at least eight generations. (The longest-lived bird on the Grants’ watch survived a whopping 17 years.) They tracked almost every mating and its offspring, creating large, multigenerational pedigrees for different finch species. They took blood samples and recorded the finches’ songs, which allowed them to track genetics and other factors long after the birds themselves died. They have confirmed some of Darwin’s most basic predictions and have earned a variety of prestigious science awards, including the Kyoto Prize in 2009.

Now nearly 80, the couple have slowed their visits to the Galápagos. These days, they are most excited about applying genomic tools to the data they collected. They are collaborating with other scientists to find the genetic variants that drove the changes in beak size and shape that they tracked over the past 40 years.Quanta Magazine spoke with the Grants about their time on Daphne; an edited and condensed version of the conversation follows.

QUANTA MAGAZINE: Why did you decide to go to the Galápagos? What drew you to study finches specifically?

ROSEMARY GRANT: I had more of a genetics background and Peter more of an ecological background. But we were both interested in the same process — how and why species form. We both wanted to choose a population that was variable in a natural environment.

The Galápagos had several things that were very important. The islands are young, and there are lots of populations of finches that occur together and separately on the different islands. The islands were in close to pristine condition, having never been inhabited by humans. We knew that any changes would be natural changes and not the result of human interference.

The climate is extremely dynamic. The archipelago lies astride the equator and is subject to the El Niño–Southern Oscillation phenomenon. There are years with a terrific amount of rainfall, which is very good for finches. But it can also get years of drought, when many birds die. We now know that up to 80 to 90 percent of birds on the small islands die in times of drought. Those extremes would give us the opportunity to measure the climate variations that occurred and the evolutionary responses to those changes.

PETER GRANT: We had three main questions in mind. First, how are new species formed? That’s the Darwinian question of the origin of species. Second, do species compete for food? If they do, what effect does that have on the structure of animal communities? That was a hot topic in the early 1980s. There was very little experimental evidence at the time, so there was plenty of scope for taking a position one way or another. Third, why do some populations exhibit large variation in morphological traits like body size and beak size?

What was it like stepping on the island for the first time? . . .

Continue reading.

Written by LeisureGuy

22 September 2016 at 6:22 pm

Posted in Evolution, Science

This Chewing Stingray Sheds Light on the Evolution of How Animals Eat

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Fascinating article in Motherboard by Kate Lunau.

Written by LeisureGuy

15 September 2016 at 12:59 pm

Posted in Evolution, Science

“A hundred walked out of my lecture”

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Dr. Susan Blackmore describes the academic spirit nowadays, which lacks the spirit of inquiry:

I’m still shaken by yesterday’s lecture and its aftermath. Oxford in the 21st century was, I’d fondly assumed, the epitome of somewhere I could speak freely and fully, and expect people to listen and then argue and disagree if they wished to. Apparently not.

I was invited to give a lecture on memes by the “Oxford Royale Academy”, an institution that has nothing to do with the University of Oxford but hosts groups of several hundred 17-18 year-olds for two weeks of classes and, I guess, some kind of simulation of an ‘Oxford experience’. I was told they were of 45 nationalities and I assumed many different religions. So I prepared my lecture carefully. I tried it out the day before on my husband’s grandson, a bright mixed-race 16 year-old from Paris, and added pictures of the latest craze for ‘Fatkini posts’ and more videos, including my favourite Gangnam Style parody (Python style), but I wasn’t going to avoid the topic of religious memes – religions are an example, par excellence, of memeplexes that use wicked tricks to ensure their own survival. I simply made sure that my slides included many religions and didn’t single one out.

Looking back I should have seen trouble coming early on. I began with a pile of stuffed animals on the desk that I use to illustrate natural selection. Many laughed at my ‘dangerous predator’ eating them but at the word ‘evolution’ a young man in the second row began swaying side to side and vigorously shaking his head. I persevered, trying to put over the idea that evolution is inevitable – if you have information that is copied with variation and selection then you must get (as Dan Dennett p50 puts it) ‘Design out of chaos without the aid of mind’. It is this inevitability that I find so delightful – the evolutionary algorithm just must produce design, and once you understand that you have no need to believe or not believe in evolution. You see how it works. So I persevered.

Introducing memes, I asked for volunteers to come up on the stage and invent a new meme. This same young man, called Moritz, was up in a flash, followed by four others. I asked him, at the word ‘go’, to make some simple movements and sounds. ‘One, two, three, Go,’ I said, and he waved one hand around in a circle, chanting ‘In the beginning was the word, and the word ….’. The others then imitated him and that was fun. Three obediently began reciting from the Bible but the fourth threw both arms in the air and declared ‘There’s a big old man in the sky’ and raised a huge laugh and cheer from (some of) the audience. This seemed an opportunity not to be missed so I asked the whole audience, at the word ‘go’, to imitate either of these two new memes, whereupon a great cry burst out of, ‘In the beg…’, ‘There’s an old man …’. Great, I said, we’ve now got two memes, you have just seen meme creation and selection at work.

Then I arrived at religion. I pointed out that religions demand lots of resources (I showed them pictures of a church, a Hindu temple, a Jewish menorah and Muslim pilgrims on Hajj); they pose threats to health (I showed people ‘purifying their souls’ by wading in the stinking germ-laden Ganges) and make people do strange things (I showed rows of Muslims bent over with their heads on the floor). I hadn’t gone far with this before five or six young men got up and began to walk out. They had a good distance to go across the large hall, so I said ‘Excuse me, would you mind telling me why you are leaving?’ There was a long silence until one said, ‘You are offending us. We will not listen,’ and they left. Soon after that another bunch left, and then another.

I explained the idea of religions as memeplexes: they package up a set of doctrines, tell believers to learn them, to pass them on, to have faith and not doubt, and they ensure obedience with fearsome threats and ridiculous promises. This I illustrated with images of Christian heaven and hell. Then I read from the Koran “those that have faith and do good works, Allah will admit them to gardens watered by running streams … pearls and bracelets of gold.” “Garments of fire have been prepared for the unbelievers. They shall be lashed with rods of iron.” More walked out. By the time I arrived at a slide calling religions (Richard’s fault!) ‘Viruses of the mind’, the lecture hall was looking rather empty.

The cartoon was worse. . .

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Written by LeisureGuy

14 September 2016 at 6:47 pm

Mutant cattle show exactly what’s wrong with the meat industry

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Wow. Just read and view.

Written by LeisureGuy

12 September 2016 at 6:35 pm

Cellphones vs. Education

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Joelle Renstrom writes in Aeon:

ave a rule about cellphones in class: if one disrupts us by ringing, vibrating or sounding an alarm, the owner has to sing a song or bust some dance moves in front of the class. At first, this provision in the syllabus elicits snickers, but it’s no laughing matter. You need to be able to turn off your phones and pay attention, I say. On the first day of class, they shut off their phones. But it doesn’t stay that way.

While my students – undergraduates at Boston University who are taking classes on writing and research – agree that there’s a problem if they can’t go 50 minutes without checking their phones, few of them can resist, despite knowing that this is my biggest pet peeve. A University of Nebraska-Lincolnstudy indicates that 80 per cent of college students send text messages during class. Nearly 100 per cent of them text before and after class. In the minutes before class – the ones I used to spend shooting the breeze with students about TV shows, sports or what they did over the weekend – we now sit in technologically-induced silence. Students rarely even talk to each other anymore. Gone are the days when they gabbed about the impossible chemistry midterm they just took or the quality of the food at the dining halls. Around the 30-minute mark in class, their hands inch toward their backpacks or into their pockets, fingers feeling around for the buttons as though their mere shape offers comfort. When I end class, they whip out their phones with a collective sigh of relief, as though they’ve all just been allowed to go to the bathroom after having to hold it all day.

Even when my students stash their cellphones, my classes look like an Apple commercial – faces hide behind screens embossed with the same famous fruit. I have no delusions that they’re taking notes for class or referencing that day’s reading. A University of Waterloo professor who put a postgraduate at the back of his lecture hall to observe his students learned that 85 per cent of them did something unrelated to class on their laptops; a Cornell University study confirms that most students engage in ‘high-tech “doodling”’ and communication during class. One might think that the whopping $65,000 cost of attending Boston University for a year would provide ample reason to maintain focus during class, but one would be wrong.

Even students who take notes on their laptops miss out. A study from Princeton University shows that we process information better when taking notes by hand because writing is slower than typing (an argument often spun in favour of laptops), which helps students learn and retain the material. Similarly, people better comprehend what they’re reading if it’s on paper rather than on the screen. In a study from the University of Stavanger in Norway, readers on Kindle struggled to remember plot details in comparison with those who read printed books, perhaps because the physical act of turning the pages helps our memories encode the words.Another study revealed comprehension loss for subjects reading PDF versions of texts. Such findings have caused professors to ban computers in the classroom, which is something I used to do but can’t any more.

An increasing number of students present me with documentation from the student disabilities office that entitles them to use a laptop to take notes. If students see a few classmates with laptops, they inevitably start using theirs too. I can’t tell them that only a couple people are sanctioned to use the computers because of learning or cognitive difficulties without infringing on the students’ privacy, so I try instead to encourage students to take notes by hand and I ask to see their faces, not their Apples.

In an effort to save my students exorbitant coursepack fees, I used to photocopy course readings. But when my department clamped down on copier use, I scanned the articles and put them online, which meant I had to allow students to open their laptops during discussions. On the one hand, they’re adults – if they want to go to shop for shoes on the Zappos website or look at celebrities’ Instagram accounts during class, they’ll have to deal with the consequences. But our discussions suffer, which makes my job harder. When reading on screens, students don’t annotate or reread. They get glassy-eyed, zone out, and then struggle to find quotes they only vaguely remember when it comes time to write the paper. The endless opportunities for distraction also mean that they miss other aspects of class, including important instructions.

That’s when they come to me and we have some version of the following conversation:

Student: ‘I have no idea what’s going on.’

Me: ‘What do you mean “no idea”? The assignment sheet details all the requirements, we’ve reviewed them in class, and we’ve read example essays. What exactly are you having trouble understanding?’

Student: ‘I don’t know… everything?’

I used to jump to the conclusion that students with whom I had such interactions were inherently flawed, academic lost causes. But that’s a reductive explanation, and doesn’t get at the heart of the problem; it’s not just that they have trouble paying attention or are distracted by their phones or laptops in the classroom. The problem is their use of technology in general. Technology demands a significant amount of time and attention and has conditioned them to not question it. It takes up more and more of their bandwidth, and the net effect is lobotomising.

onsumed by technology that they cannot bear to disable or ignore, my students lose awareness of what’s going on around them. They don’t know what they’ve missed – often, they don’t know that they’ve missed anything. They’re still accountable for it, but such mindlessness has become an epidemic: a study from the Ohio State University found that walking while texting has caused a significant rise in injuries. In Chongqing in China, sidewalks contain a special lane for people who can’t be bothered to look up from their phones. And in the German city of Augsburg, there are traffic signals on the ground for people who would otherwise endanger themselves by failing to notice red lights.

Part of the reason people can’t seem to look up from their phones is that we’ve convinced ourselves we’re multitasking, rather than failing to focus (like the way I toggle between various browser tabs and apps even as I write this). A California State University study monitored middle-, high-school and college students who had been instructed to research something important for 15 minutes. Two minutes in, students’ focus started to wane as they checked messages, texts and various websites. The average student lasted six minutes before caving to the temptation to engage in social media. Despite being watched, students spent only approximately 65 per cent of the allotted time studying. Given that most students spend far longer than 15 minutes trying to do coursework, it’s easy to see how little gets done, and how checking messages or opening up another browser tab would be increasingly difficult to resist, especially if we tell ourselves it’s related to work or study. . .

Continue reading.

I actually have been pondering this general phenomenon—how cellphone messaging, laptop computers, and the like are changing human culture. I was thinking that people in general no longer seem able to immerse themselves in a long novel, losing track of time because they are so involved with the story. I imagine that few today read (say) War and Peace and the reason is simply its length and the amount of time it takes.

Stephen Covey in his book The 7 Habits of Highly Effective People talks about the difference between “urgent” and “important.” Some important things are indeed urgent, but many urgent things are not. If your phone is ringing, then there is a sense or urgency—you must take the call—but often the call is not important. But those urgent unimportant can crwod out the non-urgent important: the very things that pay off over time.

The situation seems easier to understand if you look at it as the evolution of memes in response to natural selection. Success for a meme means that it propagates widely and exploits its environment (our attention) better than competing memes. The Internet is a rich environment for memes—they can easily and quickly be passed from person to person and they can evolve quickly. Moreover, by demanding our time and attention they crowd out memes that do not capture out time and attention so well: a dozen text messages every hour or two pretty much triumphs over War and Peace in terms of one’s attention.

I have fairly often recommended Susan Blackmore’s book The Meme Machine (and it is available as a Kindle edition, though some of the secondhand copies at the title link cost less).

Read that and think about what you see our current cultural life in terms of the struggle of memes to survive and you’ll see how quickly memes evolve. And memes evolve to ensure their own survival: what happens to their (human) hosts is not so important—cf. Richard Dawkins’s book The Selfish Gene.

Written by LeisureGuy

12 September 2016 at 5:13 pm

A pipeline fight and America’s dark past when immigrants committed genocide against Americans

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The crimes that Donald Trump claims that Mexican immigrants commit are absolutely nothing compared to what earlier immigrants did to Americans: the great genocide of Native Americans is a national crime on a level with institutionalized slavery.

Bill McKibbben comments in the New Yorker:

This week, thousands of Native Americans, from more than a hundred tribes, have camped out on the Standing Rock Sioux reservation, which straddles the border between the Dakotas, along the Missouri River. What began as a slow trickle of people a month ago is now an increasingly angry flood. They’re there to protest plans for a proposed oil pipeline that they say would contaminate the reservation’s water; in fact, they’re calling themselves protectors, not protesters.

Their foe, most directly, is the federal government, in particular the U.S. Army Corps of Engineers, which has approved a path for the pipeline across the Missouri under a “fast track” option called Permit 12. That’s one reason the Dakota Access Pipeline, as it’s known, hasn’t received the attention that, say, the Keystone XL Pipeline did, even though the pipe is about the same length. Originally, the pipeline was supposed to cross the Missouri near Bismarck, but authorities worried that an oil spill there would have wrecked the state capital’s drinking water. So they moved the crossing to half a mile from the reservation, across land that was taken from the tribe in 1958, without their consent. The tribe says the government hasn’t done the required consultation with them—if it had, it would have learned that building the pipeline there would require digging up sacred spots and old burial grounds.
In fact, the blade of a bulldozer cut through some of those burial grounds on Saturday—during a holiday weekend, days before a federal judge is supposed to rule on an emergency petition filed by the tribe which would slow the project down, and immediately after the tribe identified the burial grounds’ locations in a filing to the court. The company building the pipe—Energy Transfer Partners—has already constructed more than half the pipeline, which, when completed, would stretch from Stanley, North Dakota, near the Canadian border, to Patoka, in southern Illinois. It apparently wanted to create facts on the ground in North Dakota—wanted to do so badly enough, it seems, that it was willing to employ a private security force, which used dogs to confront the Native Americans who tried to prevent the desecration of old graves. Tribal officials said that the dogs bit six protesters, including a small child. (The company did not respond to requests for comment, but had previously stated that demonstrators “attacked” their workers and the guard dogs. It has stressed in the past that it has been “constructing this pipeline in accordance with applicable laws, and the local, state and federal permits and approvals we have received.”)
Pictures from that confrontation recall pictures from Birmingham circa 1963. But the historical parallels here run much deeper—they run to the original sins of this nation. The reservation, of course, is where the Native Americans were told to live when the vast lands they ranged were taken by others. The Great Sioux Reservation, formed in the eighteen-sixties, shrunk again and again—in 1980, a federal court said, of the whole sad story, “a more ripe and rank case of dishonorable dealings will never, in all probability, be found in our history.” In the nineteen-fifties and early sixties, the Army Corps of Engineers—the same Army Corps now approving the pipeline—built five large dams along the Missouri, forcing Indian villages to relocate. More than two hundred thousand acres disappeared beneath the water.
Sioux history, and Native American history, is filled with one massacre and battle after another. Most of us have never heard of some of those encounters—the Whitestone, or Inyan Ska, massacre, for instance, not far from the present encampment, where at least three hundred Sioux lost their lives when Brigadier General Alfred Sully attacked men, women, and children feasting after a buffalo hunt. Some we do remember, albeit differently: . . .

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Written by LeisureGuy

8 September 2016 at 11:51 am

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