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Data from: Parasitic plants have increased rates of molecular evolution across all three genomes - Dryad

Data from: Parasitic plants have increased rates of molecular evolution across all three genomes - Dryad | Darwinian Ascension | Scoop.it
Arjen ten Have's insight:

This is like dream scenario for a Molecular Evolutionist. Increased mutation rates!

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PLOS Computational Biology: The Emergence of Environmental Homeostasis in Complex Ecosystems

PLOS Computational Biology: The Emergence of Environmental Homeostasis in Complex Ecosystems | Darwinian Ascension | Scoop.it
PLOS Computational Biology is an open-access
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Cartels Are an Emergent Phenomenon, Say Complexity Theorists

Under certain market conditions, cartels arise naturally without collusion. This raises important questions over how the behavior should be controlled.

 

The price of gas is a puzzle. Monitor the average price in gas stations in a particular city and it will vary dramatically, sometimes in a matter of hours and often in ways that appear cyclical. 

 

Economist have long scratched their heads over this kind of pattern. One explanation is that this behaviour emerges when two competing companies change their pricing strategy at each stage by reacting to the other. The resulting behaviours are known as Edgeworth Price Cycles.

 

The problem is that gas station prices are not controlled by two competing players but many competing retailers. It’s easy to assume that the many-body problem produces similar patterns but nobody has been able to show this. 

 

Until now. Today Tiago Peixoto and Stefan Bornholdt, physicists at the University of Bremen in Germany, show how a more complicated model with many buyers and sellers reproduces this kind of behaviour. 

 

But it also goes further. Peixoto and Bornholdt say that when condition are right, cartel-like behaviour emerges naturally without collusion between sellers.


Via Ashish Umre
Arjen ten Have's insight:

Complex or Complicated?. The latter. This phenomenon is easily explained by what is called group selection. This is an erroneous theory that tries to explain behaviour of certain biological units. The idea is that natural selection can act on groups, which is utter nonsense. Cartel formation would be an example and .......... tyipically does not make a generation, not to mention offspring because there is always a selfish unit in the group that breaks the pact.

 

Obviously you can MAKE complex models in order to study this and you will find indeed that the distances between buyers and sellers do affect when the act is broken, but that is making things actually more complicated than they actually are.

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Constraint and Contingency in Multifunctional Gene Regulatory Circuits

Constraint and Contingency in Multifunctional Gene Regulatory Circuits | Darwinian Ascension | Scoop.it

Many essential biological processes, ranging from embryonic patterning to circadian rhythms, are driven by gene regulatory circuits, which comprise small sets of genes that turn each other on or off to form a distinct pattern of gene expression. Gene regulatory circuits often have multiple functions. This means that they can form different gene expression patterns at different times or in different tissues. We know little about multifunctional gene regulatory circuits. For example, we do not know how multifunctionality constrains the evolution of such circuits, how many circuits exist that have a given number of functions, and whether tradeoffs exist between multifunctionality and the robustness of a circuit to mutation. Because it is not currently possible to answer these questions experimentally, we use a computational model to exhaustively enumerate millions of regulatory circuits and all their possible functions, thereby providing the first comprehensive study of multifunctionality in model regulatory circuits. Our results highlight limits of circuit designability that are relevant to both systems biologists and synthetic biologists.

 

Payne JL, Wagner A (2013) Constraint and Contingency in Multifunctional Gene Regulatory Circuits. PLoS Comput Biol 9(6): e1003071. http://dx.doi.org/10.1371/journal.pcbi.1003071

 


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The fight against genome parasites

The fight against genome parasites | Darwinian Ascension | Scoop.it
In the gonads of animals, genome parasites such as transposons pose a serious threat to evolutionary fitness. With their ability to bounce around in the genome, they often cause dangerous mutations.
Arjen ten Have's insight:

I am sure that genomic parasites are a danger BUT, there is always a BUT.

If there are no mutations, and all types of mutations are important. point mutations, recombinational shuffling but also those induced by transposons, the genome becomes static. In other words: Transposons do help as well. It is the same as with the symbiosis of all that bacteria inside your body: some help, some don't and some.... well for some it depends. A usual it is not so simple and I would say that transposons and the alike are genomic symbionts , with symbionts in its broad meaning.

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Synthetic circuits integrating logic and memory in living cells

Synthetic circuits integrating logic and memory in living cells | Darwinian Ascension | Scoop.it

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Socrates Logos's curator insight, February 10, 2013 5:40 PM

by
Piro Siuti,John Yazbek& Timothy K Lu

"Logic and memory are essential functions of circuits that generate complex, state-dependent responses. Here we describe a strategy for efficiently assembling synthetic genetic circuits that use recombinases to implement Boolean logic functions with stable DNA-encoded memory of events. Application of this strategy allowed us to create all 16 two-input Boolean logic functions in living Escherichia coli cells without requiring cascades comprising multiple logic gates. We demonstrate long-term maintenance of memory for at least 90 cell generations and the ability to interrogate the states of these synthetic devices with fluorescent reporters and PCR. Using this approach we created two-bit digital-to-analog converters, which should be useful in biotechnology applications for encoding multiple stable gene expression outputs using transient inputs of inducers. We envision that this integrated logic and memory system will enable the implementation of complex cellular state machines, behaviors and pathways for therapeutic, diagnostic and basic science applications."

http://bit.ly/123ToU3

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What is chemical intuition? - Scientific American (blog)

What is chemical intuition? - Scientific American (blog) | Darwinian Ascension | Scoop.it
What is chemical intuition? Scientific American (blog) While armchair speculation and order-of-magnitude calculations can certainly be very valuable, no chemist can design a zeolite, predict the ultimate product of a complex polymer synthesis or...
Arjen ten Have's insight:

Now this is interesting. Chemist should have more intuition than phycisists. I would have to agree and being an evolutionary biologist myself I can put Biologists as much more intuitive. Intuition is as the blogger refers to described in Dan Dennetts recent Intuition Pumps. It is basically (my opinion, did not read the book yet) a matter of heursistics and complexity. Biology is more complex than chemistry more comples than physics. Hence, you need heuristic algorithms to shortcut through the complex matter. Experience contributes to intuition. Cool, love it!

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Cosmological natural selection and the purpose of the universe

The cosmological natural selection (CNS) hypothesis holds that the fundamental constants of nature have been fine-tuned by an evolutionary process in which universes produce daughter universes via the formation of black holes. Here, we formulate the CNS hypothesis using standard mathematical tools of evolutionary biology. Specifically, we capture the dynamics of CNS using Price's equation, and we capture the adaptive purpose of the universe using an optimization program. We establish mathematical correspondences between the dynamics and optimization formalisms, confirming that CNS acts according to a formal design objective, with successive generations of universes appearing designed to produce black holes.

 

Cosmological natural selection and the purpose of the universe

Andy Gardner, Joseph P. Conlon

Complexity, Early View

http://dx.doi.org/10.1002/cplx.21446


Via Complexity Digest
Arjen ten Have's insight:

This ought to be interesting, but look at that. It is the other way around. It is not a law of physics that rules biology. It is a biological theory that governs physics?? Or is it?

The principle of evolution by selection is that strong (and clear, except for when you are an IDiot) that it applies to everything. Natural selection is like the rule that rules it all. It is      GOD!

I have to read this but for sure can say that the Universe has no purpose.

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Origins of life? Discovery could help explain how first organisms emerged on Earth

Origins of life? Discovery could help explain how first organisms emerged on Earth | Darwinian Ascension | Scoop.it
(Phys.org) —A structural biologist at the Florida State University College of Medicine has made discoveries that could lead scientists a step closer to understanding how life first emerged on Earth billions of years ago.
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UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

Arjen ten Have's insight:

More evidence for the optimization of the genetic code. Microbiome sequencing comes of age!

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Cyclic Game Dynamics Driven by Iterated Reasoning

Cyclic Game Dynamics Driven by Iterated Reasoning | Darwinian Ascension | Scoop.it

Recent theories from complexity science argue that complex dynamics are ubiquitous in social and economic systems. These claims emerge from the analysis of individually simple agents whose collective behavior is surprisingly complicated. However, economists have argued that iterated reasoning–what you think I think you think–will suppress complex dynamics by stabilizing or accelerating convergence to Nash equilibrium. We report stable and efficient periodic behavior in human groups playing the Mod Game, a multi-player game similar to Rock-Paper-Scissors. The game rewards subjects for thinking exactly one step ahead of others in their group. Groups that play this game exhibit cycles that are inconsistent with any fixed-point solution concept. These cycles are driven by a “hopping” behavior that is consistent with other accounts of iterated reasoning: agents are constrained to about two steps of iterated reasoning and learn an additional one-half step with each session. If higher-order reasoning can be complicit in complex emergent dynamics, then cyclic and chaotic patterns may be endogenous features of real-world social and economic systems.

 

Frey S, Goldstone RL (2013) Cyclic Game Dynamics Driven by Iterated Reasoning. PLoS ONE 8(2): e56416. http://dx.doi.org/10.1371/journal.pone.0056416


Via Complexity Digest
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Barry Schachter's curator insight, February 22, 2013 7:43 AM

This paper provides additional evidence that financial risk management can benefit by incorporating more insights from the area of complex systems into various aspects of risk modeling and control.

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A Cross-National Test of the Uncertainty Hypothesis of Religious Belief

Arjen ten Have's insight:

Rather poor I would say: " The author predicts that religious belief would decline in economically developed countries where there is greater existential security, including income security (income equality and redistribution via welfare states) and improved health."

 

How about cause and relation? Important since although this might seem obviuous, I believe there is an important role for eduction. Where existential security is lacking (US) also proper education is lacking, specifically regarding evolution which is the other explanation for existence in the first place. Quite likeley all contributes but the way at least it is put in the abstract puts too much weigth on well being and thus on ego.

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Researchers say ability to throw played a key role in human evolution

Researchers say ability to throw played a key role in human evolution | Darwinian Ascension | Scoop.it
It's easy to marvel at the athleticism required to throw a 90-mile-per-hour fastball, but when Neil Roach watches baseball, he sees something else at work – evolution.
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Two Mutations Triggered An Evolutionary Leap 500 Million Years Ago

Two Mutations Triggered An Evolutionary Leap 500 Million Years Ago | Darwinian Ascension | Scoop.it
Research by Joe Thornton shows that two key mutations 500 million years ago set the stage for how our hormonal and reproductive systems function today.
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Cities are a new kind of complex system: part social reactor, part network

Cities are a new kind of complex system: part social reactor, part network | Darwinian Ascension | Scoop.it

Cities have long been likened to organisms, ant colonies, and river networks. But these and other analogies fail to capture the essence of how cities really function.

 

New research by Santa Fe Institute Professor Luis Bettencourt suggests a city is something new in nature – a sort of social reactor that is part star and part network, he says.

 

"It’s an entirely new kind of complex system that we humans have created," he says. "We have intuitively invented the best way to create vast social networks embedded in space and time, and keep them growing and evolving without having to stop. When that is possible, a social species can sustain ways of being incredibly inventive and productive."

 

In a cover paper appearing this week in the journal Science, Bettencourt derives a series of mathematical formulas that describe how cities' properties vary in relation to their population sizes, and then posits a novel unified, quantitative framework for understanding how cities function and grow.

 

Read the paper in Science (June 20, 2013)


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Pan genome of the phytoplankton Emiliania underpins its global distribution : Nature : Nature Publishing Group

Pan genome of the phytoplankton Emiliania underpins its global distribution : Nature : Nature Publishing Group | Darwinian Ascension | Scoop.it
Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20[thinsp]per cent of total carbon fixation in some systems.
Arjen ten Have's insight:

Yet another interesting paper with respect to evolution. 10% genome variabilty among strains a E. huxleyi,. Imagine that is 3 times more than the difference between Human and Chimpanzee. Obviously this explians the broad niche of the bug. Or are we looking at something more complex? My guess would be yes. This fits very nicely into the "community" type evolution that is used to explain early prokaryotic evolution and the optimization of the genetic code. In early evolution there were no real specias, but more more communities that shared the genetic code and their genes. This explains the fact that the genetic code is nearly optimal. So why then would E huxley still be in this community mode? Well because it works obviously. it allows the "species" to replicate. In the end it is all about genes of course. In addition, this is not so uncommon among algea. The taxonomy of algea is a mess. Why? Because there appears to be a lot of lateral gene transfer.

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PLOS Computational Biology: Mate Choice and the Origin of Menopause

PLOS Computational Biology: Mate Choice and the Origin of Menopause | Darwinian Ascension | Scoop.it
PLOS Computational Biology is an open-access
Arjen ten Have's insight:

This might seem hilarious, well actually I had a good laugh, but again, as always with evolution this makes perfect sense. The granny theory always felt a bit awkward to me. Basically the authors claim that because men go for younger women, older women simply no longer bother producing eggs. One small problem? The chicken and the egg? NO, not at all. The constraint is not that older women are less fertile, that would be NO egg and the man a chicken, no, the older woman is just less mother, the chance she dies and does not take care of the manś offspring is too high. Better a young woman. So in the end, man are just doing the right thing when they exchange their 35 year old woman for a girl of 22! Evolution FORCES men to do that. They can help themselve.

 

It makes perfect sense ........ and is hilarious at the same time, I just love evolution!!

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Forgetting Is Harder for Older Brains: Scientific American

Forgetting Is Harder for Older Brains: Scientific American | Darwinian Ascension | Scoop.it
Adults hang on to useless information, which impedes learning

Via FastTFriend
Arjen ten Have's insight:

There is two interesting aspect to this. The fact that learning can be hampered by ehm yeah well, learning and of course that this is a clue about the heuristics of memory storage in human brains.

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FastTFriend's curator insight, June 8, 2013 10:32 AM

More dramatically, their brains could barely weaken their synapses, a process that allows the loss of useless information in favor of more recent data.

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What the smallest infectious agents reveal about evolution

What the smallest infectious agents reveal about evolution | Darwinian Ascension | Scoop.it
Radically different viruses share genes and are likely to share ancestry, according to research published in BioMed Central's open access journal Virology Journal this week.
Arjen ten Have's insight:

"Viral evolution is more complex than we thought" As usual it is more complex. That is what evolution does: it makes things complex. Why? For no reason whatsoever, it just does so. Never ever be surprised by what biology (or evolution) puts forward. Thatś what makes it so interesting.

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Culture, Genes, and the Human Revolution

State-of-the-art DNA sequencing is providing ever more detailed insights into the genomes of humans, extant apes, and even extinct hominins, offering unprecedented opportunities to uncover the molecular variants that make us human. A common assumption is that the emergence of behaviorally modern humans after 200,000 years ago required—and followed—a specific biological change triggered by one or more genetic mutations. For example, Klein has argued that the dawn of human culture stemmed from a single genetic change that “fostered the uniquely modern ability to adapt to a remarkable range of natural and social circumstance”. But are evolutionary changes in our genome a cause or a consequence of cultural innovation?

 

Culture, Genes, and the Human Revolution
Simon E. Fisher, Matt Ridley

Science 24 May 2013:
Vol. 340 no. 6135 pp. 929-930
http://dx.doi.org/10.1126/science.1236171


Via Complexity Digest
Arjen ten Have's insight:

The main question the authors hopefully address is whether evolutionary changes in our genome are cause or consequence of cultural innovation. Rather a philosophical question, most likely a question without an answer. Evolutionary biologists are indeed at a crosspoint, where they have to get philosophical and they are at the point where they discuss how plasticity is related to the adaptability. In the end it all comes down to the fact that evolution has no goal, is blind but it has to follow the challenges its environment puts and it has to do that with the mutations provided. WTF? Cultural innovation will obviously direct evolution and evolution will direct cultural innovation.

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Cambridge Journals Online - Behavioral and Brain Sciences - Abstract - Whatever next? Predictive brains, situated agents, and the future of cognitive science

Cambridge Journals Online - Behavioral and Brain Sciences - Abstract - Whatever next? Predictive brains, situated agents, and the future of cognitive science | Darwinian Ascension | Scoop.it
Brains, it has recently been argued, are essentially prediction machines. They are bundles of cells that support perception and action by constantly attempting to match incoming sensory inputs with top-down expectations or predictions.
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Retooling spare parts: gene duplication and cognition : Nature Neuroscience : Nature Publishing Group

Retooling spare parts: gene duplication and cognition : Nature Neuroscience : Nature Publishing Group | Darwinian Ascension | Scoop.it
Two new studies provide experimental evidence of how ancient genomic duplications of synaptic genes provided the substrate for diversification that ultimately expanded vertebrate cognitive complexity.
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Gene transfer from bacteria and archaea facilitated ... [Science. 2013] - PubMed - NCBI

PubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Arjen ten Have's insight:

This  is fascinating ....... but also should be considered old news in the great scheme of scientific development. From the current theories regarding the evolution of the genetic code we KNOW that (microbial) communities in early evolution completely depended on HGT. When compared to higher eukariotes (the ones that have sex), HGT is simply sex: Evolution is INNOVATE or extinguish.... So put a bug in an extreme environment and it will develop thanks to HGT. Still a neat study of course!

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Plants do communicate—and kin relationship has a bearing

Plants do communicate—and kin relationship has a bearing | Darwinian Ascension | Scoop.it
If you're a sagebrush and your nearby kin is being eaten by a grasshopper, deer, jackrabbit, caterpillar or other predator, it's good to be closely related.
Arjen ten Have's insight:

Fascinating of course..... BUT I would need to read the original paper but at least have some problems with the way this comment puts it, rather anthropomorphic I am afraid. First of all they state that plants communicate. Here we need to put attention to what is meant. It is meant primarily unidirectional as such that I communicate this to you who reads it but likely you do not reply (although you are welcome to correct me). You might act and decide to become interested in Evolution but that is about it. In the same way a plant can recognize certain volatiles, even might perceive those produced by his kin more efficiently (Selfish gene explains kin selection here) but likely it does not signal back such as: "Careful, he is behind you!". In the same way I would not state plants recognize kin since this would imply a certain level of consciousness. We put that label whereas, in terms of selection, this kind of kin selection is simple Darwinian selection. It favors you to know your kin (which is close by since plants are typically sessile) is in danger since it means you are in danger. You better warn your kin than other plants of the same species since that has a larges positive effectr on the reproduction of your genes! I will not explain that warning and receiving specific messages co-evolve, I hpoe you trust me on that.

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