Big-data analysis consists of searching for buried patterns that have some kind of predictive power. But choosing which "features" of the data to analyze usually requires some human intuition. In a database containing, say, the beginning and end dates of various sales promotions and weekly profits, the crucial data may not be the dates themselves but the spans between them, or not the total profits but the averages across those spans.
Researchers from the Structural Biology Computational Group of the Spanish National Cancer Research Centre, led by Alfonso Valencia, in collaboration with a group headed by Francesco Gervasio at the University College London (UK), have developed the first computational method based on evolutionary principles to predict protein dynamics, which explains the changes in the shape or dimensional structure that they experience in order to interact with other compounds or speed up chemical reactions.
Another very nice piece of work by Andreas Wagner. Subject is related to his theory (I refuse to use hypothesis here) on reconciliation of drift and shift, but it goes way beyond that and it might have tremendous if picked up. They perform in vitro evolution experiments on a ribozyme including a valid determination of fitness. The idea is good, then they searched for a nice system to test their idea and they develop the complete thing in the wetlab. This is top science! Impact will be on how we understand early evolution, as such that this is yet another findings that explains why evolution happens so fast. It is also a very good instance of real evolution. I wonder if the Discovery Institute picked this up, they will hate it!
Life is quirky. Although the molecules that make up all living things obey physical and chemical laws, they do so with a puzzling twist. How did the distinctive molecular features of life emerge, and what can they tell us about life on Earth and elsewhere in the universe?
Arjen ten Have's insight:
Maybe God doesn't throw dice, Nature does: New model derives homochirality from basic life requirements
Scientists have halved the amount of time it takes to perform genome sequence diagnoses in cases involving critically ill newborns. A new study published this week shows how physicians can diagnose genetic illnesses affecting babies in just 26...
Why is it that people that work in evolution make such terrible mistakes? Evolution predictable? You can only predict evolution if you actually know the functional constraints that obviously depend on the novel, hence unknown function. Just because there are X instances of convergent evolution does not allow for even suggesting predictable molecular evolution. Come on, this is Science.
Evolution on a time scale similar to ecological dynamics has been increasingly recognized for the last three decades. Selection mediated by ecological interactions can change heritable phenotypic variation (i.e., evolution), and evolution of traits, in turn, can affect ecological interactions. Hence, ecological and evolutionary dynamics can be tightly linked and important to predict future dynamics, but our understanding of eco-evolutionary dynamics is still in its infancy and there is a significant gap between theoretical predictions and empirical tests. Empirical studies have demonstrated that the presence of genetic variation can dramatically change ecological dynamics, whereas theoretical studies predict that eco-evolutionary dynamics depend on the details of the genetic variation, such as the form of a tradeoff among genotypes, which can be more important than the presence or absence of the genetic variation. Using a predator–prey (rotifer–algal) experimental system in laboratory microcosms, we studied how different forms of a tradeoff between prey defense and growth affect eco-evolutionary dynamics. Our experimental results show for the first time to our knowledge that different forms of the tradeoff produce remarkably divergent eco-evolutionary dynamics, including near fixation, near extinction, and coexistence of algal genotypes, with quantitatively different population dynamics. A mathematical model, parameterized from completely independent experiments, explains the observed dynamics. The results suggest that knowing the details of heritable trait variation and covariation within a population is essential for understanding how evolution and ecology will interact and what form of eco-evolutionary dynamics will result.
Author Summary The brain is never quiet. Even in the absence of environmental cues, neurons receive and produce an ongoing barrage of fluctuating signals. These fluctuations are well studied in the sensory periphery but their potential influence on central circuits and behavior are unknown. In particular, activity fluctuations in action selection circuits—neural populations that drive an animal’s actions from moment to moment—may strongly influence behavior. To shed light on the influence of
Arjen ten Have's insight:
This is not only a research that has direct biological impact. More importantly it shows how complexity can arise and it is yet another step in explaining how evolution of complex organisms, doing even more complex things as driving a car through a busy city center, can actually have taken place!
The FDA has started testing the precisionFDA platform it developed with DNAnexus. The closed beta test phase is the precursor to a more widespread rollout of the system, which the CEO of DNAnexus has described as being "the most advanced bioinformatics platform in the world."
Arjen ten Have's insight:
This sounds about right but I think we need to see what it actually is. Typically these platforms are more genomics than bioinformatics/biocomputation...
Luckily we are not worms. Or are we? The message is that males prefer sex over a meal and that women prefer sustenance. In terms of evolution this does make sense. Does that explain why men are better cooks? A Dutch proverb goes "The love of a man comes through the stomach" Well, that is apparently not the best way of putting it.
In a similar vein to the Human Genome Project, researchers working on the Human BioPlex Project aim to complete a map of the colossal complex web of protein-protein interactions within human cells. The first results of this...
Bacterial infections comprise a global health challenge as the incidences of antibiotic resistance increase. Pathogenic potential of bacteria has been shown to be context dependent, varying in response to environment and even within the strains of the same genus.
Arjen ten Have's insight:
Potentially interesting this might be an oversimplification.
This might seem as too obvious but this is more about how the dynamics of negative, neutral and positive selection. An on the average negative mutation will behave differfently than that that is on the average positive.
Excellent work again of Andreas Wagner, builiding upon his hypothesis (which IMO should be theory) of neutral evolution paving the way for positive selection. Basically, the hypothesis says that many neutral substitutions are connected in protein solution space, thereby gaining access to more mutations that might give advantage. Not only does this explain why evolution is so fast, it also explains why so many susbstitutions are detected as positive, neutral steps become positive when the last positive mutation kicks in. Simple and elegant!
Biologists at ETH Zurich have developed a method that, for the first time, makes it possible to measure concentration changes of several hundred metabolic products simultaneously and almost in real time. The technique could inspire basic biological research and the search for new pharmaceutical agents.
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