http://deredactie.be/cm/vrtnieuws/wetenschap/1.1995171quote:Koloniale dammen sturen evolutie van vissen in Connecticut
do 12/06/2014 - 17:05 Alexander Verstraete
Nadat het fenomeen eerder al bij de elft was vastgesteld, blijkt nu ook de evolutie van de zonnebaars danig beïnvloed door de koloniale dammen die 300 jaar geleden op de rivieren en de meren van de Amerikaanse staat Connecticut zijn gebouwd. Dat blijkt uit onderzoek aan de Landbouwuniversiteit in Zweden.
quote:The game theory of life
An insight borrowed from computer science suggests that evolution values both fitness and diversity
In what appears to be the first study of its kind, computer scientists report that an algorithm discovered more than 50 years ago in game theory and now widely used in machine learning is mathematically identical to the equations used to describe the distribution of genes within a population of organisms. Researchers may be able to use the algorithm, which is surprisingly simple and powerful, to better understand how natural selection works and how populations maintain their genetic diversity.
By viewing evolution as a repeated game, in which individual players, in this case genes, try to find a strategy that creates the fittest population, researchers found that evolution values both diversity and fitness.
Some biologists say that the findings are too new and theoretical to be of use; researchers don't yet know how to test the ideas in living organisms. Others say the surprising connection, published Monday in the advance online version of the Proceedings of the National Academy of Sciences, may help scientists understand a puzzling feature of natural selection: The fittest organisms don't always wipe out their weaker competition. Indeed, as evidenced by the menagerie of life on Earth, genetic diversity reigns.
"It's a very different way to look at selection," said Stephen Stearns, an evolutionary biologist at Yale University who was not involved in the study. "I always find radically different ways of looking at a problem interesting."
The algorithm, which has been used to solve problems in linear programming, zero-sum games and a dozen other sophisticated computer science problems, is used to determine how an agent should weigh possible strategies when making a series of decisions. For example, imagine that you have 10 financial experts giving you advice on how to invest your savings. Each day you have to choose to follow one of them. At the start of the investment period, you know nothing about how well each expert performs. But every day, the multiplicative weights update algorithm, as it is called, instructs you to boost the probability of choosing the experts who have given the best advice and decrease it for those who have performed poorly.
"If you do this day after day, at the end of the year, you will do almost as well as if you had followed the best expert from the beginning," said Christos Papadimitriou, a computer scientist at the University of California, Berkeley. "It's as if you were omniscient in the beginning, singling out the best expert and following their advice day after day."
Papadimitriou and his collaborators came across the connection between game theory and evolution when they were searching for a mathematical explanation of sex, which triggers new genetic diversity by mixing up the chromosomes from each parent. They were working with equations commonly used in population genetics, first developed nearly a century ago, that describe how the frequencies of certain genetic variations change with each generation. For example, plants that flourish in the current climate might dwindle as global warming alters conditions.
When they showed the equations to Umesh Vazirani, pictured, a computer scientist at Berkeley, he noticed parallels to a repeated coordination game — a scenario in game theory in which success depends on the players choosing mutually beneficial options. As an example, consider a situation in which two prisoners are tempted to turn on each other. If one talks, both lose; if neither talks, both win. Neither prisoner knows what the other will do. (This scenario is different than the well-known prisoner's dilemma.)
Viewing the algorithm through the lens of evolution, genes are the players, and each gene has a number of different strategies in the form of genetic variations, or alleles. One variant of a gene might make a plant tolerate warmer temperatures or drier soil, for instance. The game is played over and over again; at the end of each round, the gene, or player, evaluates how well each of its alleles performed in the current genetic environment and then boosts the weight of the good performers and downsizes the weight of poor performers.
The researchers said the findings will provide a new way to examine the role of sex in evolution. For example, Papadimitriou said he believes that part of its role is to carry out the multiplicative weights update algorithm, though he hasn't yet proven this mathematically.
Traditional applications of game theory to evolution examine how evolutionary processes shape an individual's behavior. They have also been used to study the evolution of altruism and other properties. "But here, we're talking about something completely different," said Adi Livnat, a biologist at Virginia Polytechnic Institute in Blacksburg, Va., who collaborated on the study. The new study focuses on genes rather than individual organisms, and on the genetic makeup of the population instead of behavior.
The approach could illuminate a long-standing mystery in population biology. Just as in the financial world, where it's best to keep a diversified portfolio, Vazirani and his collaborators found that the algorithm values both fitness and diversity. You might be tempted to place all your money on a soaring stock. But if circumstances change and that stock starts to tank, you're better off having invested in a more balanced selection. Similarly, an organism's genes may be perfectly tailored to a particular set of environmental conditions, but if those conditions change, a genetically diverse population is more likely to survive.
"Evolution is, of course, interested in performance," Papadimitriou said.
"But it's also interested in hedging its bets, keeping around a lot of genetic diversity because who knows what will come next."
Evolutionary biologists know that in practice, a genetically diverse population is often more resilient than a homogeneous one because it is better able to respond to changing environments. But they have struggled to explain how such diversity is maintained. In the short term, one would expect diversity to drop as the fittest members of a population spread, knocking out the weaker, genetically dissimilar members. How do long-term needs surmount the short-term pressures?
The findings provide a "speculative suggestion" for how this might happen, though the authors don't propose a specific mechanism, said Nick Barton, a biologist at the Institute of Science and Technology in Austria who was not involved in the study. "I don't think it gives us the algorithm that can achieve the diversity we see on Earth in 3.5 billion years, when life first began," he said.
Stearns and others in the field say it's too soon to assess how the findings will affect our understanding of evolution. Even though the connection between different fields is interesting, "it does not actually help us understand biological evolution," said Chris Adami, a physicist and computational biologist at Michigan State University, who was not involved in the study. "Unless such a relationship allows you to say something new either in computer science or biology, it's just an observation."
Evolutionary biologists are often skeptical of mathematical insights from outsiders. Although mathematicians and computer scientists regularly publish in the field, biologists disagree over how much their contributions have done to shape it. "I think it will take some time to figure out how the paper plays out," Stearns said. "If this doesn't cause any new data to be gathered, then it won't be very important." Even if the findings don't prove relevant in the short-term, they might prove important over the long –term. Sometimes it can take decades before the right technology or approach arises to test a new theory, Stearns said.
The equations in the study are based on certain assumptions that may limit their applicability to the real world. For example, the equations don't account for mutations, which would introduce new alleles, or strategies, into the game. (Adding this factor makes the mathematics much more complex.) Some say this simplification is a serious drawback, while others maintain that it is not so important in the short term, when existing variations have the strongest impact. "What happens when you move away from the assumptions?" said Lee Altenberg, a senior fellow at the Konrad Lorenz Institute in Austria. "They have pinned a single point on the map. But to know whether that means anything, you have to start departing from that point."
One outcome of the analysis is likely to puzzle biologists. According to the standard view of evolution, the further a generation lies in the past, the less impact it has on the present — your ancestors from 1,000 years ago probably had less effect on your fitness than your grandparents. But if the Berkeley team's insights hold up, "it shows us that every past generation contributes equally to what happens in the next generation," Stearns said. "That's an intriguing and wildly implausible claim from the standpoint of regular evolution." Papadimitriou said his team was also perplexed by that outcome. "It is something that hopefully will make researchers rethink, revisit and interpret," he said.
"You can't really test these theorems in relation to real life," Barton said. "They are tools for getting intuition about how to understand evolution."
Evolution and entropy
One of the surprising discoveries of Papadimitriou's study is that natural selection values not just fitness, but also genetic diversity, which in more technical terms is referred to as entropy. This view that evolution optimizes not just mean fitness but mean fitness and entropy is not well known, "but I think it's a deep observation," Adami said.
The Berkeley team isn't the first to highlight the role entropy might play in evolution. But until now, the subject has mainly been of interest to mathematicians rather than biologists.
"Applications of entropy in evolution have had a bad name, because they were very ill-defined," Barton said. "More recently, there have been some interesting, and much sounder, ideas, which make a link between fields that are addressing a similar issue: statistical physics and evolutionary biology both try to understand the overall properties of a complicated system, independent of the microscopic details."
These more recent results are mathematically sound, but they still don't connect well with existing biological understanding, he said. "So it's not clear to biologists how [the results] might help explain their open questions."
interessant en uitgebreid artikelquote:
http://deredactie.be/cm/vrtnieuws/wetenschap/1.2046023quote:"Asteroïde kwam op slecht moment voor dino's"
ma 28/07/2014 - 17:40 Joris Truyts
Als de asteroïde die hun uitsterven veroorzaakte een paar miljoen jaar vroeger of later had ingeslagen, zou de aarde nu misschien nog steeds door dinosauriërs bevolkt worden. Die conclusie trekken onderzoekers in een nieuwe studie.
Leuke typo in de titel.quote:Op dinsdag 29 juli 2014 00:09 schreef zakjapannertje het volgende:
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http://deredactie.be/cm/vrtnieuws/wetenschap/1.2046023
dat was mijn computer, aan het corrigerenquote:
http://www.nationalgeogra(...)razendsnel-van-kleurquote:Onderzoekers laten vlinders van kleur verschieten
De evolutie van kleuren in de natuur is een raadselachtig proces, maar onderzoekers van Yale University hebben nu enig licht in de duisternis gebracht. Zij zijn erin geslaagd de kleur van vlindervleugels in minder dan een jaar tijd te veranderen.
Nounounou. Op basis van dit bericht vind ik de conclusie in de laatste alinea ongelooflijke onzin!quote:Op donderdag 23 oktober 2014 10:33 schreef ExperimentalFrentalMental het volgende:
21-10-2014
Is evolutie voorspelbaar? Soms wel, zo blijkt!
[ afbeelding ]
Onderzoekers vragen zich al lang af of evolutie een voorspelbaar proces is. Nieuw onderzoek onder inktvissen suggereert nu dat de evolutie van complexe organen in deze organismen – achteraf gezien – heel voorspelbaar is verlopen.
De onderzoekers bestudeerden twee soorten inktvissen: Euprymna scolopes (onder meer te vinden voor de kust van Hawaii) en Uroteuthis edulis (een Japanse inktvis die ook vaak in sushi-restaurants op het menu staat, zie de afbeelding hierboven). De twee soorten zijn heel in de verte nog aan elkaar verwant. Bovendien beschikken ze allebei over lichtgevende organen. Die organen geven licht, omdat ze bepaalde lichtgevende bacteriën bevatten. De inktvissen kunnen zelf regelen hoeveel licht hun lichtgevende organen geven.
LICHTGEVENDE ORGANEN
Waarom hebben inktvissen eigenlijk lichtgevende organen? Onderzoek suggereert dat de organen van pas komen als de inktvis behoefte heeft aan camouflage. “Als je je voorstelt dat je op je rug diep in de oceaan ligt en naar boven kijkt, zie je dat al het licht recht van boven komt,” legt onderzoeker Todd Oakley uit. “Er zijn geen muren of bomen die het licht reflecteren, dus als er iets boven je zit, werpt dat een schaduw. De inktvis kan licht produceren dat overeenkomt met het licht achter hem, zodat deze geen schaduw werpt en dat is een soort van camouflage.”
De genetische basis
De onderzoekers waren geïnteresseerd in de genen die aan deze lichtgevende organen ten grondslag lagen. Ze vroegen zich af in hoeverre de genetische basis voor deze lichtgevende organen – die de twee inktvissoorten onafhankelijk van elkaar ontwikkeld hebben – vergelijkbaar is. Om dat te achterhalen, brachten ze alle genen die tot uiting komen in deze organen, in kaart.
De resultaten
De resultaten zijn opmerkelijk. De genetische basis voor de lichtgevende organen in E. scolopes bleek opvallend sterk te lijken op de genen die in U. edulis aan de lichtgevende organen ten grondslag lagen. “Normaal gesproken zouden we, wanneer twee complexe organen zich onafhankelijk van elkaar ontwikkelen, verwachten dat ze elk heel verschillende evolutionaire paden bewandelen om terecht te komen waar ze vandaag de dag zijn,” vertelt onderzoeker Todd Oakley. “De onverwachte overeenkomsten laten zien dat deze twee inktvissen heel vergelijkbare paden bewandelden om deze eigenschappen te ontwikkelen.”
De onderzoekers demonstreren dat inktvissen gedurende hun evolutie herhaaldelijk lichtgevende organen ontwikkelden en dat de genetische bases voor die lichtgevende organen elke keer veel op elkaar leken. Het suggereert dat de evolutie van de totale genexpressie die aan convergente – door soorten onafhankelijk van elkaar ontwikkelde – complexe eigenschappen ten grondslag ligt, voorspelbaar is.
(scientias.nl)
Misschien dat de conclusie zinniger klinkt in de originele wetenschappelijke taal? Of een beetje onhandig vertaald uit het Engels?quote:Op vrijdag 24 oktober 2014 00:31 schreef Kees22 het volgende:
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Nounounou. Op basis van dit bericht vind ik de conclusie in de laatste alinea ongelooflijke onzin!
Ik bedoel de conclusie dat de evolutie van genexpressie voorspelbaar is.quote:Op zondag 26 oktober 2014 11:33 schreef Papierversnipperaar het volgende:
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Misschien dat de conclusie zinniger klinkt in de originele wetenschappelijke taal? Of een beetje onhandig vertaald uit het Engels?
Lekker zinloze toevoeging aan een dergelijk artikel. Dat creationisten wat cherrypicken in het fossielenbestand lijkt me niet zo relevant.quote:“VEEL CREATIONISTEN ZIEN DE ICHTHYOSAURIËR ALS HÉT BEWIJS DAT DE EVOLUTIETHEORIE NIET KLOPT”
Phys.orgquote:Game theory analysis shows how evolution favors cooperation's collapse
Last year, University of Pennsylvania researchers Alexander J. Stewart and Joshua B. Plotkin published a mathematical explanation for why cooperation and generosity have evolved in nature. Using the classical game theory match-up known as the Prisoner's Dilemma, they found that generous strategies were the only ones that could persist and succeed in a multi-player, iterated version of the game over the long term.
But now they've come out with a somewhat less rosy view of evolution. With a new analysis of the Prisoner's Dilemma played in a large, evolving population, they found that adding more flexibility to the game can allow selfish strategies to be more successful. The work paints a dimmer but likely more realistic view of how cooperation and selfishness balance one another in nature.
"It's a somewhat depressing evolutionary outcome, but it makes intuitive sense," said Plotkin, a professor in Penn's Department of Biology in the School of Arts & Sciences, who coauthored the study with Stewart, a postdoctoral researcher in his lab. "We had a nice picture of how evolution can promote cooperation even amongst self-interested agents and indeed it sometimes can, but, when we allow mutations that change the nature of the game, there is a runaway evolutionary process, and suddenly defection becomes the more robust outcome."
Their study, which will appear in the Proceedings of the National Academy of Sciences, examines the outcomes of the Prisoner's Dilemma, a scenario used in the field of game theory to understand how individuals decide whether to cooperate or not. In the dilemma, if both players cooperate, they both receive a payoff. If one cooperates and the other does not, the cooperating player receives the smallest possible payoff, and the defecting player the largest. If both players do not cooperate, they both receive a payoff, but it is less than what they would gain if both had cooperated. In other words, it pays to cooperate, but it can pay even more to be selfish.
Stewart and Plotkin's previous study examined an iterated and evolutionary version of the Prisoner's Dilemma, in which a population of players matches up against one another repeatedly. The most successful players "reproduce" more and pass along their winning strategies to the next generation. The researchers found that, in such a scenario, cooperative and even forgiving strategies won out, in part because "cheaters" couldn't win against themselves.
In the new investigation, Stewart and Plotkin added a new twist. Now, not only could players alter their strategy—whether or not they cooperate—but they could also vary the payoffs they receive for cooperating.
This, Plotkin said, may more accurately reflect the balancing of risk and reward that occurs in nature, where organisms decide not only how often they cooperate but also the extent to which they cooperate.
Initially, as in their earlier study, cooperative strategies found success.
"But when cooperative strategies predominate, payoffs will rise as well," Stewart said. "With higher and higher payoffs at stake, the temptation to defect also rises. In a sense the cooperators are paving the way for their own demise."
Indeed, Stewart and Plotkin found that the population of players reached a tipping point after which defection was the predominant strategy in the population.
In a second analysis, they allowed the payoffs to vary outside the order set by the Prisoner's Dilemma. Instead of unilateral defection winning the greatest reward, for example, it could be that mutual cooperation reaped the greatest payoff, the situation described by a game known as Stag Hunt. Or, mutual defection could generate the lowest possible reward, as described by the game theory model known as the Snowdrift or Hawk-Dove game.
What they found was that, again, there was an initial collapse in cooperative strategies. But, as the population continued to play and evolve, players also altered the payoffs so that they were playing a different game, either Snowdrift or Stag Hunt.
"So we see complicated dynamics when we allow the full range of payoffs to evolve," Plotkin said. "One of the interesting results is that the Prisoner's Dilemma game itself is unstable and is replaced by other games. It is as if evolution would like to avoid the dilemma altogether."
Stewart and Plotkin say their new conception of how strategies and payoffs co-evolve in populations is ripe for testing, with the marine bacteria Vibrionaceae as a potential model. In these bacterial populations, the researchers noted, individuals cooperate by sharing a protein they extrude that allows them to metabolize iron. But the bacteria can possess mutations that alter whether they produce the protein and how much they generate, whether and how much they cooperate, as well as mutations that affect how efficiently they can take up the protein, their payoff. The Penn researchers said a "natural experiment" using these or other microbes could put their theory to the test, to see exactly when and how selfishness can pay off.
"After this study, we end up with a less sunny view of the evolution of cooperation," Stewart said. "But it rings true that it's not the case that evolution always tends towards happily ever after."
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