More evolutionary monkeyshines

Is it ignorance? Early-onset senility? A misinformation campaign secretly funded by fundamentalist religious organizations? Or are most science journalists actually monkeys who have been chained to desks and trained to write blogs, in exchange for food?

You’d think that after 150 years of research and education, people who write about evolution would have acquired a dim understanding of it. On the other hand, you don’t need any qualifications at all to write about anything under the sun these days. I refer to a press tizzy triggered by a recent publication in Nature Communications. The subject was the fascinating field of monkey faces. You can find the paper here.

The paper demonstrates three things, which can be recovered from the abstract, if you take the time to read it:

• Scientists can model the faces of closely related species of primates on the computer.
• An analysis of markings on their faces show that over time, the faces of closely related species of monkeys have become more and more different.
• This could have had an evolutionary function by helping a member of one species identify members of its own species to mate with, which was more liable to produce fertile offspring than mating with members of another species.

What the popular press made of this was quite different. Here are some outtakes:

“The reason we all look different has been revealed by scientists – it is to avoid inter-breeding. Primates were found to have developed different facial appearances so that their group was easily recognizable as being different from closely related and local species.”

And:

“Have you ever wondered why humans don’t all look the same? After all, we share a number of similarities on the inside, but on the outside we all have unique features. The answer, according to scientists at the University of Exeter and New York University, is that some animals developed this was (sic) to deliberately avoid interbreeding.”

Oh my, where to start? First of all, we have a confusion of inbreeding with interbreeding. Both are things you probably want to avoid, but it doesn’t hurt to keep them straight.

Inbreeding refers to mating between very closely related members of the same species – humans have laws against that; it falls under the category incest. The citations above focus on differences between the faces of humans – ergo inbreeding – which this paper tells us nothing at all about. If it did, the findings would imply that your brother or sister ought to look a lot different than you, presumably so that you wouldn’t be attracted to them and choose them as a mate.

The paper’s authors are actually talking about interbreeding between different species. It’s more like an explanation for why we look different from Neanderthals, or gorillas. If at some point humans, gorillas, and Neanderthals ran into each other all the time, maybe they visited the same pubs, you’d need to keep them straight. Otherwise at closing go home with a member of another species.

That might make for an interesting one-night stand, but any offspring produced by these encounters probably wouldn’t be fertile. Hybrids might go on to live long and happy lives, but since they couldn’t reproduce, they wouldn’t pass along their genes. So you’d never know – unless they wrote blogs about their experiences. Maybe they have. I haven’t checked.

Now an even worse mistake, from the point of evolution, is to assume that people, or monkeys, or anything else evolved some feature in order to achieve something. In fact, the opposite is true. A feature already has to be around for natural selection to work on it. If monkey faces look different, and natural selection gets its hands on them, then they might end up looking more different. You can’t actually prove that this is why their faces evolved this way, but at least it’s a plausible story.

The best way to understand this might be by looking at another paper published in Nature, concerning the discovery of variant of a gene called EPAS1 that helps Tibetans live at extremely high altitudes. What didn’t happen was some sort of committee meeting among early inhabitants of Tibet, where they sat around and said, “Hey, we ought to evolve in order to live up there in the high mountains.” Instead, a gene variant evolved that allowed some people to live much more comfortably at high altitudes. So they moved up the hill, got jobs as Sherpas and Yeti-hunters, and left everybody else down at the base camp.

And actually the new paper shows that Tibetans probably acquired this form of EPAS1 by mating with an earlier population of modern humans called Denisovans, who apparently belonged to a different sub-species. I guess they didn’t look different enough; after enough beer, or in the dim lighting of a bar, some interspecies mating took place. In this case the kids were fertile, at least some of them, and they did well at high altitudes. So the best place to find their descendants is a high mountain somewhere. They don’t have to live there, but they can. It would cut down on unwanted visitors and cell phone calls.

But this sort of “secret intentionality” is found all over the place in discussions of evolution – even in articles which are otherwise relatively good. In this one, for example, a writer summarized a new findings about feathers on Archaeopteryx, a dinosaur from the Jurassic period:

“The function of the Archaeopteryx’s feathers, the Jurassic specimen, on their hind limbs has left researchers scratching their heads. Scientists constantly debate about the use of the Archaeopteryx’s feathers, but it seems that finally they are yielding some possible answers.

“Paleontologists from the Ludwig-Maximilians-Universität (LMU) aim to put an end to the dispute with regard to a well preserved specimen. The findings reveal that the first Archaeopteryx feathers were not evolved for flight, but for display.”

Once again, “were not evolved for flight, but for display…” Saying that feathers evolved for something is getting things backwards again. It would be better to write something like: “Feathers evolved in Archaeopteryx before it could fly. Once they appeared, they may first have influenced choices of mates, leading to adaptations in response to sexual selection. Whatever selective pressures acted on feathers, the result was structures that permitted flight. Once Archaeopteryx had that capacity, feathers surely underwent further changes as a result of new selective events.”

Reference:
William L. Allen, Martin Stevens & James P. Higham. Character displacement of Cercopithecini primate visual signals. Nature Communications 5, Article number: 4266 doi:10.1038/ncomms5266.

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My work in early music

For those of you who don’t know about my other professional career, the “Anglistenchor” of the University of Heidelberg and my instrumental ensemble “Syntagma” are performing the second of two concerts under the title “Strike the viol” in Heidelberg this Sunday, July 27, 7pm at the Peterskirche. If you want to hear Baroque music like you’ve never heard it before, come by! Tickets can be purchased on-line or directly at the concert. You can see a short interview with me and the conductor and a member of the choir here. This time the composers are JS Bach, Purcell, and their contemporaries.

…and now back to science…

Another “before and after” text from a new science writer

Jon Paul Hildahl, a postdoctoral researcher at the University of Oslo, wanted to try some popular science writing and produced this text. We worked on it a bit together and then he revised it. Here are the “before” and “after” versions. I’ll provide some commentary in the next post. The main issues were editing – removing redundant or unnecessary language, unraveling a bit of the science, and providing illuminating explanations for a more general audience. Thanks for providing this, Jon – you truly have a future as a science writer (alongside your own excellent research, of course). Jon currently works in the group of Gareth Griffiths at the University of Oslo, where I conduct a week-long course every December for Masters’ students. It’s always one of the highlights of my year. Thanks to Jon for letting me post this, with his name.

BEFORE:

Regulation of immunity and disease resistance by commensal microbes and chromatin modifications during zebrafish development
Jorge Galindo-Villegas et al 2012 PNAS

It is obvious that we are not alone in this world, but it is becoming increasingly clear that we are not even alone in our own bodies. We are covered inside and out by small critters called microbes that include many helpful bacteria, archaea and fungi, collectively called commensals. The resident population that we carry throughout much of our life is called our microbiome. It is very abundant; our body contains 10 times as many microbial cells as human cells. It is not surprising then that these cohabitants play an important role in human health. Indeed their effect on animal health is an area of active research. In particular, it is becoming clear that a little dirt is good for you, especially in your early formative years. It has been shown in multiple animal models that microbes in the environment during early development can help establish the immune system and protect the host from attack by disease causing bacteria. This study helps to clarify the mechanisms by which this initial microbial exposure is controlled at the cellular and genetic level using a powerful fish model.

These researchers have used two powerful models to delineate the role of commensal bacteria during development of the immune system: 1.) germ free condition in 2.) the zebrafish model. Many studies of the role of environmental bacteria use germ free models. This provides a reference to what would happen in the absence of resident microbes. This can then be compared to the natural situation of exposure and colonization by commensals. Fish are exposed to a rich microbial ecosystem in their aquatic environment, which suggests that they have evolved ways to deal with environmental microbes both good and bad. You might ask, however, what a fish can tell us about human biology? Luckily, many if not most developmental processes are conserved among distantly related animal groups. Additionally, the zebrafish have many advantages as a research animal since they develop quickly in transparent eggs that can be easily followed and manipulated. They also have a well-characterized genome and sophisticated genetic tools that allow researchers to add or subtract gene products and measure the level of gene expression. It is known that the initial and fast acting (also called innate) immune system develops within days and before hatching for zebrafish.

In this study, the authors were able to follow the immune response of zebrafish from the time they hatch, at around two days after fertilization, and for the first days of exposure to the external environment when commensal colonization is believed to occur. They showed that zebrafish have a rapid and punctuated innate immune response after hatching, peaking after one day and then decreasing. This initial activity improves the response of early immune cells, providing a better protection against pathogenic bacterial infection and tissue damage compared to fish reared in germ free conditions. The researchers were also able to show that innate immune cells respond by a conserved mechanism, involving a intracellular response pathway by the myeloid differentiation primary response protein 88, MyD88. Another important finding from this study is that epigenetic regulation, which modifies the ability of genes to be expressed, modifies the immune response such that a robust emergency response is in place in case of infection or injury, while reducing the risk of adverse immune effects due to excessive inflammation by providing initial responders (antimicrobial effector proteins) that are not limited by epigenetic regulation.

AFTER:

The ying and yang of germ warfare

None of us go through life alone – not even within our own bodies. We are covered inside and out by microbes that include many helpful bacteria, archaea and fungi, collectively called commensals. The resident population that we carry throughout much of our life is called our microbiome. It is very abundant; each body contains 10 times as many microbial cells as human cells. It is not surprising then that these cohabitants play an important role in human health, an area of active research. One of the results is to show that a little “dirt” is good for you, especially in your early formative years. Studies using several animal models show that during early development, environmental microbes help establish the immune system and protect the host from disease-causing bacteria. A recent paper entitled, “Regulation of immunity and disease resistance by commensal microbes and chromatin modifications during zebrafish development” uses a powerful fish model to provide new insights into the mechanisms by which this early microbial exposure mediates cellular and genetic responses.

Jorge Galindo-Villegas and colleagues at the University of Murcia in Spain have compared zebrafish in two settings to clarify the role of commensal bacteria during immune system development: fish raised in a normal environment, and those raised in germ-free conditions. Germ-free models are commonly used to simulate what might happen in the absence of resident microbes, compared to the natural situation of exposure and colonization by commensals. Fish are normally exposed to a rich microbial ecosystem in their aquatic environment, which suggests that they have evolved ways to deal with environmental microbes that have both good and bad effects.

What, you may ask, can a fish tell us about human biology? Luckily, most significant developmental processes are conserved among distantly related animal groups. And zebrafish have many advantages as a research animal: They develop quickly in transparent eggs that can be easily observed and manipulated. Their well-characterized genome and sophisticated genetic tools allow researchers to add or subtract molecules and measure how genes – including the components of the immune system – respond. Another advantage is that the initial, fast-acting (“innate”) part of the immune system develops within days – even before zebrafish hatch.

The authors of this study followed the immune response of zebrafish from the time they hatch (at around two days after fertilization) through the first days of exposure to the external environment, when most commensal colonization is believed to occur. They showed that zebrafish have a rapid and punctuated innate immune response after hatching, which peaks after one day and then decreases. This initial activity improves the response of early immune cells, providing better protection against later pathogenic bacterial infections and tissue damage than is observed in fish reared in germ-free conditions. The researchers also showed that innate immune cells respond to these early infections using a mechanism that is found in many other animals, including humans. The response activates a biochemical signaling pathway in cells involving the myeloid differentiation primary response protein 88, or MyD88, which helps recognize microbes and initiate a immune response.

Another important finding from the study is that during early development, factors that influence the way DNA is packaged alter the patterns by which genes typically respond to stimuli. While fish that are exposed possess the same genes as fish that are not, early infections and environmental conditions cause their cells to establish patterns in which certain genes become active and others remain silent. The effect of this type of “epigenetic” regulation is to provide an extra level of control, giving cells the ability to mount a robust emergency response in case of infection or injury, but without the adverse immune effects – which can happen when inflammation reaches a serious level. Even fish raised under germ-free conditions mounted a slight immune response by this means. In contrast, antimicrobial effector proteins, which provide the fish with a fast-acting initial response system, have sustained high expression that is not limited by epigenetic regulation. Altogether, this study nicely demonstrates how commensal bacteria are closely intertwined with the development of the their host’s immune system.

Author: Jon Paul Hildahl
Link to the free full text of the original article

Searching for Oslo: a non-hypothesis-driven approach

Note: I will be speaking at a conference on science communication in Oslo in September. This is not the talk I will give there; however, it was inspired by the invitation.

First let me thank the conference organizers for this wonderful event and inviting me to this lovely city. I’ve been to Oslo many times and have always enjoyed it, but I’m not the type of tourist who studies up on a place before he goes. In fact, and this is embarrassing to admit, I’m not even sure exactly where I am. I told one of my kids I was coming to Oslo and she said, “Where exactly is Oslo, anyway?”

“It’s up, and to the left,” I told her.

Actually I didn’t have the slightest idea. I’d never looked it up on a map. I realized that I hardly ever use maps anymore. Almost nobody does. You don’t need to. You just go to the airport on time, go to the right gate, and the airlines and trains take care of the rest. Or you have an iPhone. You tell it where you want to go and it calculates your route, starting with your exact current position. Your iPhone says: “Go out the door. Turn left. Walk 1,213 kilometers. Turn right.”

If you’re going to go looking for something, it’s a good idea to start out with a general idea of its location. In the case of Oslo, it’s helpful to know that it is located in the Milky Way galaxy. It helps more to know it’s in our own solar system, even right here on our planet. It’s hard to calculate the odds of that happening; we’d need to know more about the state of the early universe at 0.00001 seconds after the Big Bang. However Oslo got here on Earth, its location is convenient. If it were anywhere else in the solar system, for example on Mars, we probably wouldn’t know it existed.

Once you have narrowed the search area to Earth, you’re getting close. At that point my knowledge of geography starts to get fuzzy, so you should just stop somebody and ask for directions.

But a little more information can help. I knew Oslo was in Scandinavia, which means you won’t waste a lot of time looking for it in the Pacific Ocean, or South America. I would like to note, here, that Scandinavia is a concept I don’t fully understand. We usually give names to continents, or countries, or hurricanes, or new species. As far as I can tell Scandinavia doesn’t fit into one of those categories, so I’m not sure why it needs a special name. On the other hand, if people want to call themselves Scandinavians, I guess there’s no law against it. At least they picked a nice name. Usually these things are decided in a committee, and you know how committees are. If you let a committee pick the name, Scandinavia would probably be called “Roger”.

I don’t know if you’ve ever seen a map of Scandinavia, but it’s huge. And there are a lot of blank areas. Many of these appear to be isolated regions that have never been explored. Scandinavia is so large that there could be 10 Oslos hiding out there, and you could spend your whole life looking for them, especially if they didn’t want to be found. Plus, we’re lacking a lot of information that would have been helpful. It is unclear how many groups have gone off searching for Oslo and failed to find it. These were negative results, so they couldn’t get their papers published. In other cases, groups found one Oslo and then broke off the search, never considering that there might be 9 more Oslos out there. So the data may be skewed toward one Oslo that happens to be easiest to find.

Today you should never start any scientific project without an exhaustive search of the literature, for example, by typing “Oslo” into Google. Here you find one fact that can significantly narrow the search area: Oslo is located in Norway. With that piece of information alone you can eliminate 2/3rds of Scandinavia from the search area. So it would only take 0.33333… lifetimes to search the remaining area and find 10 Oslos. The probability of finding only 1 Oslo would be a tenth of that, so you ought to calculate 3.3333… lifetimes. In a grant application, that comes to three full-time positions and one third-time position, probably a technician.

Now I think it’s reasonable to invest that much effort in searching for Oslo, especially since you might find other things while you were at it. Who knows what remains to be discovered in these large, unexplored areas of the country? You might find a species of Archaea that evolved 3 billion years ago in a thermal vent on the ocean floor. It’s a long ways from that deep ocean vent to a valley in Norway, but you can crawl a long way in 3 billion years. Especially if the colony is being driven by a male Archaea, who doesn’t waste time seeing the sights along the way, and keeps the pit stops as short as possible. You might also find the last surviving tribe of Yeti. Or secret UFO landing sites. You should keep your eye out for these things. If you find one of them, you should mention it in your supplemental data.

It’s quite common in science to start looking for one thing and end up finding something else. In fact, sometimes you find things when you aren’t looking for anything particular at all. You know how it is: you come into the lab on a Sunday, just to putter around a bit, and suddenly, lying there in your Petri dish, is the ribosome.

This is the type of science we call non-hypothesis driven research. You grope around in the dark and suddenly your hands grasp onto something. Please don’t think of this as a reference to some sort of sexual activity because it is not. In any case, in non-hypothesis-driven research, you should always be prepared for surprises. You’re out in the field looking for Oslo, or maybe a new species of Archaea, and suddenly you find a Yeti. You’ll never get a Yeti back to the lab in a Petri dish. So when you’re doing non-hypothesis driven research, you should always take along a big net. And some tranquilizer darts.

It’s hard to get funding for this kind of research. When you apply for a grant they always ask what you’re expecting to find. This is kind of silly, because if you already knew, you wouldn’t need their money to find it. So when you’re applying for a grant you just sort of pretend that you don’t know what you’re going to find.

That’s harder to do when you’re trying to get funding for non-hypothesis-driven research. Under the section on “Expected results and impact,” you can’t just write, “I have absolutely no idea.” Instead you should say something like, “We expect to find either a new species of Archaea, the city of Oslo, or a Yeti.” It’s wise not to mention secret UFO landing sites in grant applications.

You work hard to finish the application, send it off, and then you start waiting. You wait for years and years, and you never hear back from the grant commission. The entire system is biased against non-hypothesis-driven research.

But think where we’d be without it. I don’t know who the first person was who discovered Oslo, but he certainly didn’t find it by using a map. Without that bold pioneer, we wouldn’t be here. We’d be somewhere else. Probably in Stockholm.

A novel, non-hypothesis-driven method to determine the location of Oslo

Abstract. Traditional methods of locating large foreign cities involve a time-consuming, manual inspection of maps, sometimes with the aid of a magnifying glass. Recent years have seen the development of automated, high-throughput technologies such as Google Maps. These methods, however, are of limited applicability in cases where you don’t have the right map, or when you are at Starbucks and the Internet server crashes. Here we use Oslo as a model system to develop a novel, non-hypothesis-driven approach for determining the location of any large object on Earth. The method can easily be adapted to find other cities as well as smaller entities, such as new species of Archaea, or Yeti.