Archive for the ‘Evolution’ Category
First, watch this brief (less then 3 minutes) video; then read this article by Madison Margolin in Motherboard.
Veronique Greenwood writes in Quanta:
It’s a curious fact of biology: In yeast, only one in five genes is essential. If any of the approximately 1,200 critical genes are destroyed (out of 6,000), the result is death. Remove one of the others, and the yeast soldiers on.
The same is not always true, however, if a pair of nonessential genes is removed — sometimes, death comes quickly. In these cases, it’s likely that the genes have similar roles. They might both take out the cell’s garbage, for instance, or fix damaged DNA. The loss of one might not be deadly — the other could pick up the slack. But the loss of both is catastrophic.
Can we use what happens when a pair of genes is destroyed to find out their function? This is the question that Charles Boone and Brenda Andrews, biologists at the University of Toronto, began to ask themselves about 17 years ago. If you know what one gene is doing in the cell, and destroying it kills the cell only if another, more mysterious gene goes too — can that give you clues to what the mystery gene does?
To answer the question, they began to orchestrate a precise campaign to destroy, two by two, all the genes in yeast. Using a fleet of yeast-growing robots, they created approximately 23 million strains of yeast, each effectively missing a pair of genes. By watching to see whether the yeast lived, died or grew sickly, the researchers generated data about the existence of relationships between the genes.
Now Boone, Andrews and a large team of collaborators have published inScience a sprawling report on the nearly two-decade-long set of experiments. In all, they found 550,000 pairs that, when removed, result in sickness or death. This network of genetic connections reveals a previously hidden scaffolding that underlies the operation of the cell. “The complete picture,” Boone said, “clearly shows a beautiful hierarchical structure.”
Over here are the genes involved in taking out the cell’s garbage, and over there are the genes responsible for its metabolism. Zoom out from one cluster of genes, and you’ll find the ones involved in the larger process the cluster is nested in. Zoom out from those and you’ll find all the ones that function alongside them in the same compartment of the cell. There’s something vertiginous in this view of life, a feeling that all the layers of complexity that let the organism thrive are there to look through, just as they were laid down by evolution.
As beautiful as the bird’s-eye view of the cell is, this work goes beyond biological voyeurism. This information can tell us about the evolution of the cell and, potentially, about how things go wrong in disease.
Using maps of interactions between genes or proteins is a popular approach to understanding the cell these days. Many researchers, looking at organisms from yeast to worms to humans, are building networks made up of proteins that attach to each other or genes that regulate each other. But the scale of Boone and Andrews’ effort sets it apart. In addition, their method can uncover connections that can’t be made by other tests, like those that focus on proteins that physically attach to one another. “It’s really a magisterial undertaking,” said David Botstein, the chief scientific officer of Google’s anti-aging startup Calico and a pioneer of genome mapping. When Boone and Andrews’ goal of knocking out all possible pairs of genes was floated years ago, “people thought, well, it’s just insane!” recalled Marian Walhout, a systems biologist at the University of Massachusetts Medical School. Even today, with advances in technology, it’s breathtaking, she said.
With the new information and the website where it can be navigated, researchers will be able to look up the genes they study and perhaps find that they have connections that have never been noticed before. “That utility is going to be, I predict, one of the major uses of the paper,” Botstein said. Earlier this month the yeast biochemist Yoshinori Ohsumi was awarded the Nobel Prize in physiology or medicine for his work on autophagy, the programmed destruction of pieces of the cell. “If he were doing his work now, he could go look at this data and see which genes genetically interact with the autophagy genes, and make huge progress much more quickly,” Walhout said.
For those of us who are not scientists, the research also provides an interesting reminder that . . .
The evolution of culture is another name for memetic evolution, since culture consists of memes (such as languages, methods of cooking, music, values, ideas, and so on). Joe Henrich is a professor of human evolutionary biology at Harvard University and holder of the Canada Research Chair in Culture, Cognition, and Coevolution at the University of British Columbia, where he is a professor in the departments of psychology and economics. His post at FiveBooks.com begins:
What exactly is ‘cultural evolution’?
In the last 20-30 years a lot of different disciplines—I have psychology and economics particularly in mind, but also parts of biology—have become increasingly convinced that, in order to understand humans and human behaviour, we need to take culture seriously. Economists have recently got into this, and they now have quite a bit of evidence that, in order to explain the differences among, say, the wealth of nations or innovation or growth in GDP, culture matters a lot. These sets of ideas, beliefs and values that people acquire from prior generations really have a big impact.
Then the question becomes, how do we think about this in a systematic way, because culture is notoriously fuzzy. What my colleagues and I have tried to do is to think about culture as an evolutionary system. We can think about how individuals learn from each other, right down to a child growing up: Who do they pay attention to? Who do they learn from? What kinds of ideas are they attracted to?
So, in my book, what I try to do is approach that from an evolutionary perspective. Humans are a kind of animal, and we seem to be very dependent on culture and cultural learning for very basic things — like how to find food, how to organise our societies, how to make the basic tools which allow us to survive. We can think about culture as a genetically evolved cognitive adaptation for learning from other people. Natural selection is operating over generations to make people better at learning from the other members of their social milieu — figuring out who in their environment they should tune in to, what kinds of ideas they should pay attention to, and how they should integrate information across diverse people.
This turns culture into an evolutionary process that can change over long periods of time; that can reach stable states — the way genetic evolution will produce stable species for long periods. It creates clumpings or groups — where some people tend to do things one way, and other groups tend to do things in other ways. It creates something called ‘social norms.’ Once people can culturally learn the standards by which they judge others, you get social norms out of this process.
Genetic evolution is shaping us to be cultural learners, but then the interesting part is that that turns around, and cultural evolution begins to shape our genetic evolution.
Say something simple like the evolution of technology: you begin to produce fire and cooking and knowledge about how to process plants and animals, how to cook meat. This then shapes our digestive system: we have small stomachs and small teeth and short colons because we’re the cooking animal, or the food-processing animal more generally. A lot of our digestion is actually done externally — so we have to put much less energy into our digestive system. This is because we have all this culturally learned know-how about how to process foods.
Why does the term ‘cultural evolution’ seem to be somewhat controversial, then? Is it that some scientists, focusing primarily on genetics, feel that culture doesn’t have a role to play in evolution — just as, I suppose, some economists also would argue that straight economics doesn’t need any inter-disciplinary input either?
One interesting thing about the sociology of the field is that in the 1970s, when socio-biology first began to emerge and try to apply evolution to explain human behaviour, the culture wars emerged. One side would insist that human behaviour is determined by culture — so there were anthropologists like Marshall Sahlins who wrote a book called The Use and Abuse of Biology. On the other side, people like Richard Dawkins argued that genetic evolution played an important role in explaining behaviour and human behavioural variation.
What’s interesting about the approach that my colleagues and I have been working on is that it actually dissolves that unhelpful and—I think—scientifically destructive dichotomy. We say, ‘Yes, culture is important. But to understand the foundations of human learning, we need to think of ourselves as an animal with adaptations for learning from others.’ Then we can say a lot about cultural evolution and about how societies evolve and what kinds of things we should expect of the world by understanding how natural selection has shaped our minds to make us better learners. That single move diffuses the difference between culture on one side and genes on the other.
The interesting thing that comes out of this is the idea that culture can actually be the driving force in human genetic evolution. I argue in my book that the central driving force in human genetic evolution—that gave us big brains, shaped our hands and dexterity as well as our feet and other parts of our anatomy—was actually created by cultural evolution. Tools and social institutions and languages shaped our genes. That idea—that genetic evolution was driven by cultural evolution—is relatively new and certainly hasn’t been widespread until recently.
And some people might disagree. Are you finding a lot of resistance to the idea?
Of course there is disagreement, there is always going to be disagreement. One of the central lines of this disagreement is how important this learning process is versus what some evolutionary psychologists call ‘evoked culture.’ This is the idea that our minds are like jukeboxes and respond to environmental cues. When you have certain environmental cues, you get different behaviours and different psychology. It’s not because people learn different things from previous generations: instead, it is just their minds responding, in a pre-programmed way, to different input cues.
For example, some people have argued that personality types—introversion/extroversion—are a product of the pathogen environment. In environments high in pathogens, people are nervous about strangers who might carry pathogens, so they become more introverted, more xenophobic, less willing to engage with others. But once the pathogens are removed from the environment, then it is much more beneficial and adaptive to interact more broadly with large social networks because you are less likely to get pathogens.
The case that I’ve made is that both of these are important. A lot of times the environment, the things that cue up these different psychological processes, are themselves influenced by cultural evolution. In the case of the pathogens—if you buy that account and there is at least some evidence for it—you have to take into account that there’s been massive cultural evolution to reduce the pathogens in our environment. There used to be malaria in southern England. But because of institutions, now there’s not. So that changes the pathogen environment in ways that then shift this evoked psychology. That’s one of the points of debate: where is this evoked psychology, what role does it play, and how important is it?
So you’re working with academics from all sorts of different fields: anthropology, archaeology? . . .
Later in the interview:
With growing inequality around the world today, does reading this book help shed any light onto current problems?
It points to something that is recurrent in the work of many researchers — also like Peter Turchin, the ecologist-turned-historian. When societies are competing, this high competition tends to keep inequality down. Then, over time, the elite of a society—consciously or unconsciously—gradually twist the institutions and change the social norms so they get a disproportionate share of the pie.
What we are seeing is a process that’s repeated itself many, many times over, where gradually, over a long period of time, the elites change the rules of the game so they are increasingly favoured. There are various ways to get out of the trap. The usual one is revolution, collapse and discord, but hopefully there are other ways out too.
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.
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 to 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? . . .
Fascinating article in Motherboard by Kate Lunau.
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. . .