Natural selection wins again

Researchers Show How New Viruses Evolve, and in Some Cases, Become Deadly
[Via NSF News]

Researchers at Michigan State University (MSU) have demonstrated how a new virus evolves, shedding light on how easy it can be for diseases to gain dangerous mutations. The findings appear in the current issue of the journal Science.

The scientists showed for the first time how the virus called “Lambda” evolved to find a new way to attack host cells, an innovation that took four mutations to accomplish. This virus infects bacteria, in particular the common E. coli bacterium. Lambda isn’t dangerous to humans, but this research demonstrated how viruses evolve complex and potentially deadly new traits, noted Justin Meyer, MSU graduate student, who co-authored the paper with Richard Lenski, MSU Hannah Distinguished Professor of Microbiology and Molecular Genetics.

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This is a fascinating study. The lambda virus infects E. coli through a surface protein called LamB – the protein was even named because of this property. So, in the experiment, some E. coli  evolved resistant forms  dealing with  LamB to prevent infection. Then lambda developed a new form that found another way to infect the cell by using another protein, OmpF.

These new viral forms needed at least 4 separate mutations to accomplish this. And all 4 changes were needed to become fully infective.

The key aspect to get from this is not that the 4 mutations needed to occur all at once for them to appear. These changes were co-evolving with the changes in the LamB protein, so the necessary mutations became more prominent in the viral population as the E. coli also changed.

Essentially, as changes in LamB appeared – to reduce infectivity of thevirus – changes in the lambda virus were selected for – changes that brought back some of that infectivity. As LamB made further changes, lambda changed more until the fortuitous step when all 4 mutations created a virus that no longer needed LamB to enter the cell. This new form could use OmpF.

And only the ones with all four changes could use OmpF.

One of the criticisms lofted at natural selection is that intermediary forms are not useful. They say. “Lambda can only use OmpF to get into cells if all 4 mutations are present, right? So how do the 2 or 3 mutation forms even get any purchase in the population? It would seem that only viruses with all 4 mutations present simultaneously – a very rare occurrence – would be selected for.”

But this work shows how the intermediate changes appeared, were selected for and finally resulted in an entirely new activity.

Now, think if we had only two forms of bacteria – one with only LamB and one with only OmpF. The viruses that infected each would have 4 different changes between them but we would see no direct way for the virus to get from one form to the other with any intermediary stages. Each viral form only infects the one population, not the other.

But there were intermediate forms at one time.

This is the sort of scaffolding model used against the above criticism. Nothing evolves in isolation. These sorts of co-evolution events happen all the time. Then if the intermediate forms disappear, there does not appear to be any linkage, even though there once was.

This nice diagram was in the issue of Science. The co-evolving populations of E. coli and phage create a ridge – or scaffold – between changes in the gene frequencies of the two populations. Continuing selection can remove the ridge, resulting in what appears to be two different ‘species’ of E. coli and virus.

The other interesting aspect of this work was that the effect was contingent but repeatable. That is, they started the selective culture of the bacteria and virus in multiple flasks. Not every flask developed the new mutant viruses but those that did had the same sorts of mutations in the viral genome.

This demonstrates the random nature of natural selection – not every population will have the same success dealing with a changing environment – while also showing, however, the repeatability of the process.

In addition, they showed that the selective events of the bacteria also drove the evolution of the viruses. Bacterial populations with slightly different starting genomes produced different results. The chance of the viruss to develop the new ability depended on the bacterial populations in which they found themselves.

And they end their paper stating that the bacterial population in several cases had developed resistance to the OmpF mediated viral infection, thus showing that the co-evolution was not at an end and suggesting that the virus would have to find a new method to infect the cell.

This sort of evolution was accomplished in weeks with the right selective pressures. What would happen with centuries or eons?

 

Fascinating discussion of who are the experimenters and who are the experimentees

by kevin dooley

Primed by expectations – why a classic psychology experiment isn’t what it seemed
[Via Not Exactly Rocket Science]

In the early 20^th century, the world was captivated by a mathematical horse called Clever Hans. He could apparently perform basic arithmetic, keep track of a calendar and tell the time. When his owner, Wilhelm von Osten, asked him a question, Hans would answer by tapping out the correct number with his hoof.

Eventually, it was the psychologist Oskar Pfungst who debunked Hans’ extraordinary abilities. He showed that the horse was actually responding to the expectations of its human interrogators, reading subtle aspects of their posture and expressions to work out when it had tapped enough. The legend of Hans’ intellect was consigned to history. But history, as we know, has a habit of repeating itself.

For the last few decades, psychologists have been using a technique called priming. With subtle hints of words or concepts, they can trigger impressive changes in behaviour. Words of cleanliness can make people behave more morally. Words related to age can slow their bodies. Words of power sharpen our mental abilities. All of these studies have suggested that our behaviour is influenced by subtle things that lie beneath the watch of our conscious awareness.

This view could well be right, but not always in the way that psychologists believe. Stephane Doyen from the Université Libre de Bruxelles has repeated one of the classic experiments in priming and shown that, in this case at least, it’s not the words that create the effect. It’s the experimenters’ expectations.

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This is a fascinating study. The people who did the original experiment did not actually record what they thought. Instead of the words that primed behavior, it was the researcher’s expectations.

When the subjects took the test from researchers who expected the subject to walk slower afterward, lo and behold, the subjects did walk slower. But when a double-blind was done, with the researcher not knowing who was supposed to walk slower – and the inclusion of independent time keepers – all the priming disappeared.

Really cool. It shows that the test was not very important at all as to the results – it was mostly the researcher’s expectations. The subject would walk faster if the researcher expected that, even if the test should have made them walk slower.

Expectations matter, whether it is a researcher or a teacher. Humans tend to do what others expect them to.

Maybe Humans could use some more self-domestication

Bonobos: the self-domesticated ape?
[Via Not Exactly Rocket Science]

The two apes above might look very similar to the untrained eye, but they belong to two very different species. The one on the right is a bonobo; the one on the left is a chimpanzee. They are very closely related but the bonobo is slimmer, with a smaller skull, shorter canines and tufts of lighter fur. There are psychological differences too. Bonobos spend more time having sex, and playing with one another. They’re less sensitive to stress. They’re more sensitive to social cues. And they are far less aggressive than chimps.

Many years back, a young researcher called Brian Hare was listening to the Harvard anthropologist Richard Wrangham expound on this bizarre constellation of traits. “He was talking about how bonobos are an evolutionary puzzle,” recalls Hare. “They have all these weird traits relative to chimps and we have no idea how to explain them.”

But Hare had an idea. “I said, ‘Oh that’s like the silver foxes!’ Richard turned around and said, ‘What silver foxes?’”

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It turns out that selecting for “niceness” produces a host of physical changes also. In a social group, perhaps those that were more nice had more offspring.

And we sure have small canines, not much hair and love sex.

I wonder if something similar happened with Homo. Nature just published an article looking at the social networks of hunter-gatherers to see how they compared with modern social networks.

One thing they found was that people who were more cooperative connected strongly to others who were cooperative. And those who did not want to play nice with others tended to socialize with people who felt the same.

Perhaps many of our physical traits stem from a selection for nicer people to socialize with? It would certainly be an interesting rebuttal to the killer ape theory.

In many ways chimps fit the killer ape model – patriarchal hierarchies, violent displays to control behavior, very wary of outsiders, stress-filled lives – and bonobos fit the nice model – much more cooperative behavior, sex to control behavior, lower stress levels. When two chimpanzees are placed in a situation where there is no ability to share food, we see increases in hormones priming them for competition, and increase in stress and a resistance to physical contact.

In contrast, hormone levels in bonobos indicate a lowering of stress and an inclination towards soothing physical contact.

Like a bad Star Trek episode, the opposing natures of these apes split into two different forms, each taking a different path, about a million years ago.

In particular, many of the traits of the bonobos results from continuing juvenile traits to adulthood.

Both chimp and bonobo infants show very similar patterns of cooperation when young. As they age, chimps change their behavior towards more competitive urges while bonobos continue the juvenile approaches. Perhaps, one species might have used self-domoestication to become the bonobo.

The fact that known examples of domestication follow similar pathways as seen between chimps and bonobos certainly suggests as much.

Humans separated from the chimp-bonobo line about 6 million years ago. Chimps and bonobos separated only 1 million years ago. So, it is likely that we started with both tendencies – both killer and cooperative ape. Instead of separating into two species, we maintained both traits and have used both to our advantages, depending on the circumstance. Violence and fear have been just as important aspect of civilization as cooperation.

It is like the dirty hippies versus the Man. Chill-out vs. taste my knuckles.

We see this in so many of our social interactions – groups whose first impulse is violence and those whose first impulse is cooperation. But the former might be at a disadvantage today since our violent impulses now have the power to do large amounts of harm to the entire species. They have to be a little more restrained – a little more repressed –i n their first impulse   or find ways to divert that need into other actions.

I wonder if cooperative individuals would then have a selective advantage for the future?

Of course, this is spinning as “just-so” story from a few articles and facts. But it does make for an interesting point of discussion. Do people who cooperate have smaller canines and less body hair than those who are violent? Do they use cooperative sex more to control behavior? Do humans have less body hair and other physical changes that would match self-domestication?

Are we becoming a world where people stay ;ids; longer, both socially and physically?

Indiana on the path to ludicrous teducation plan.

Indiana creationist bill passes committee
[Via NCSE - National Center for Science Education - Defending the Teaching of Evolution in Public Schools.]

Indiana’s Senate Bill 89, which if enacted would allow local school districts to “require the teaching of various theories concerning the origin of life, including creation science,” was passed by the Senate Committee on Education and Career Development on January 25, 2012. The vote was 8-2, with the bill’s sponsor and committee chair Dennis Kruse (R-District 14), Carlin Yoder (R-District 12), Jim Banks (R-District 17), Jim Buck (R-District 17), Luke Kenley (R-District 20), Jean Leising (R-District 42), Scott Schneider (R-District 30), and Frank Mrvan Jr. (D-District 1) voting for and Earline S. Rogers (D-District 3) and Tim Skinner (D-District 38) voting against the bill.

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It simply does not matter how many times it has been shown that creation science is actually not science and is a religious philosophy, some people feel it should be required teaching. Who thinks it is okay to require specific religious teachings in school?

I feel sorry for the students in Indiana.