john hawks weblog

paleoanthropology, genetics and evolution

Dog domestication complexity

Tue, 2013-06-18 21:25 -- John Hawks

Ewen Callaway covers the active area of dog domestication research in a new Nature News article ("Dog genetics spur scientific spat") [1].

In recent months, three international teams have published papers comparing the genomes of dogs and wolves. On some matters — such as the types of genetic changes that make the two differ — the researchers are more or less in agreement. Yet the teams have all arrived at wildly different conclusions about the timing, location and basis for the reinvention of ferocious wolves as placid pooches. “It’s a sexy field,” says Greger Larson, an archaeogeneticist at the University of Durham, UK. He has won a £950,000 (US$1.5-million) grant to study dog domestication starting in October. “You’ve got a lot of big personalities, a lot of money, and people who want to get their Nature paper first.”

Callaway discusses the divergent genetic results, and gives details about each successive analysis. The newest contender is a preprint by John Novembre and colleagues, which is freely available on the arXiv and discussed in a Haldane's Sieve post, which has developed a good comment stream.

One reason these results have been fluctuating with the addition of more data is that the population history was complex, and a better representation of wolf and dog genomes adds the ability to reject simple models. As in human populations, there is no necessary reason to think that today's dog populations trace their ancestry predominantly from the earliest archaeological samples of dogs. A wider sample of ancient DNA from archaeological dogs should add much more information about the process and timing of domestication.


References

  1. Callaway E. Dog genetics spur scientific spat. Nature. 2013;498(7454):282 - 283.

Brain plasticity in adults and cognition

Sun, 2013-06-16 20:48 -- John Hawks

I ran across a study from a couple of years ago by Rachel Brans and colleagues, which has an interesting result showing a genetic correlation between plasticity of cortex thickness and performance on psychometric tests [1]. Plasticity is essential for brains to respond to pathological conditions like stroke; other studies have suggested that plasticity is likewise important to normal brain function. By means of conventional quantitative genetic analysis, Brans and colleagues suggest that plasticity is mechanistically related to the factors that underlie variation in cognitive performance:

Our finding that intelligence and change in cortical thickness are partly associated through shared genes is consistent with the dependence of learning and memory formation on the plasticity of neural circuits (Escobar et al., 2008). The association between intelligence and structural brain changes may also reflect an association between intelligence and plasticity in structural (Chiang et al., 2009) and functional brain networks during the resting-state (van den Heuvel et al., 2009). Moreover, because functional brain activity during cognitive tasks was recently found to be heritable (Koten et al., 2009), genes for structural brain plasticity and intellectual ability may also be relevant for brain function while performing cognitive tasks.

This is a classic twin study, examining the additive genetic variance of the change in cortical thickness measures in individuals sampled five years apart. As in almost all fMRI studies, the sample size is relatively small. But in comparison to previous studies that showed the relationship between psychometric test outcomes and the volumes of particular cortical areas, this one is much more functionally directed, looking at the change in cortical thickness across time.


References

When sequencing genomes is too boring for journals

Sun, 2013-06-16 13:33 -- John Hawks

Sequencing bacterial genomes is now the scope of project routinely undertaken by undergraduates just learning how to do research. What was once an empirical project suitable for a multinational research investment, and has until recently been the mainstay of PhD dissertations, is on the cusp of becoming too trivial to justify a journal publication. David Roy Smith points out the consequences of this shift in the new issue of Frontiers in Plant Genetics and Genomics [1].

Changes in technology always expose the differences between workaday gathering of empirical data and question-driven science. As Smith notes, a lot of genome research has been data-driven instead of hypothesis-driven:

One of the drawbacks of genome papers, however, is that they can create a mindset of sequence first, ask questions later. I once attended a Masters thesis defense where the external examiner asked the candidate why he sequenced the chloroplast genome of this particular species and what hypothesis was he trying to test. The student, looking startled, answered, “Because the genome hadn't been sequenced before and we didn't know what it looked like.” After the defense, I overheard the examiner in the hallway venting to another professor. “We've created a culture of serial genomicists,” she exclaimed. “Everyone's jumping from one genome sequence to the next, looking to score a major publication.”

We're seeing quite a bit of this now in metagenomics work, where the mere description of microbial species counts and plotting principal components against other samples of microbe communities has been a mainstay of journal articles. There has always been a large role for pure description in science, collection of empirical data as exploration without necessarily being driven by a hypothesis. Exploration, whether it involves new field sites or new examination of laboratory samples, is worthwhile in itself. But we place value on exploration that involves some risk -- where learning something new is neither predictable nor easy.


References

  1. Smith DRoy. Death of the genome paper. Frontiers in Genetics. 2013;4:72.

Culture-gene coevolution and language

Sat, 2013-06-15 15:28 -- John Hawks

Simon Fisher and Matt Ridley, in a recent essay in Science, discuss the relationship between the genetic mutations that distinguish humans and other primates and the behavioral traits that those mutations may underlie [1]. They draw upon the lactase persistence example, in which the dietary "niche" of milk consumption must have been present before the causal mutations for lactase persistence were selected in human populations. The essay mistakenly lumps alcohol "tolerance" of Europeans relative to Asians in with lactase persistence as an example of adaptation after the fact (citing Guns, Germs and Steel for this fact); in reality, the Asian flushing reaction is the novel trait, apparently driven by natural selection on a new mutation within Asia.

In any event, the general point is that several Holocene examples show that humans have adapted to new cultural innovations and environmental pressures only after those ecological changes were present.

FOXP2 is not the only gene associated with the human revolution (3). However, it illustrates that when an evolutionary mutation is identified as crucial to the human capacity for cumulative culture, this might be a consequence rather than a cause of cultural change (8). The smallest, most trivial new habit adopted by a hominid species could—if advantageous—have led to selection of genomic variations that sharpened that habit, be it cultural exchange, creativity, technological virtuosity, or heightened empathy.

This seems so uncontroversial that one may wonder why it needed to be written. But there has unfortunately been a long tradition in which some archaeologists and linguists have imagined that language emerged upon a single macromutation. The entire history of analysis of FOXP2 has underlined this assumption, as it has attained outsized visibility due to its interesting pattern of evolution. People obsess about whether it is "the" language gene. The question presupposes a saltational model of language evolution.

In this respect, the well-known examples of Holocene human adaptations may not be ideal analogies for language evolution. Lactase persistence, the Duffy null blood type, and the flushing reaction are all cases where one large-effect mutation really was strongly selected in response to a novel environmental pressure. But those examples are surely the tip of the iceberg when it comes to the full picture of recent adaptation. Most human phenotypes are complex, involving many genes, and evolution of such traits in response to Holocene environmental changes almost certainly involved changes in the frequencies of standing genetic variants of much weaker effect. It is difficult for us to discover these gene networks, because of the small effect sizes and deeper history of the variants. But that pattern of multigenic adaptation must be much more likely to characterize language evolution.

Did talking come first? A true coevolution would have bootstrapped behavior, learning and genetic adaptations together.


References

Taking a blender to the skin

Sat, 2013-06-15 11:01 -- John Hawks

A new paper by Alban Mathieu and colleagues looked at the functional pathways represented by the metagenomes of microbial communities living on the skin of two humans [1]. The study of skin microbiomes among humans is quickly growing. One approach is to study the kinds of species that are present in skin microbial assemblages, and compare that species community with different people, different parts of the body, and different kinds of microbial communities ("Close contact skin microbiome smashup").

A different approach is to study the function of an ecosystem is to look more collectively across species at the parts that interact with each other. Sharp teeth mark the presence of animal flesh, lactase marks the presence of lactose as an energy source. At the microbial level, looking across an entire community at the functioning genes gives some notion of the structure of resources across the entire collection of species represented:

The role of the microbiota in regulating another critical healthy state parameter (skin acidity), which controls the permeability barrier homeostasis, is also highlighted by numerous functional subsystems associated with acid resistance detected in the databases. For instance, acidification ecosystem preservation could explain the bacterial adaptive strategy of using the butanediolic fermentation as deduced from detection of alpha acetolactate and acetoin butanediol metabolism genes for transforming pyruvate into the final product (2,3-butanediol) rather than a mixed acid fermentation. The predominance of genes involved in the arginine deiminase metabolism [17] in the metagenome datasets confirms the tolerance of bacteria to skin acidity [15]. The skin metagenome analysis also brings new clues about the extensive spread of antibiotic resistance genes among bacteria. Within the human skin Staphylococcus populations of the two individuals, various Staphylococci seem to be intrinsically resistant to methicillin (fig. 3), although neither of the two individuals had recent contact with a methicillin-rich environment (hospitalization and/or methicillin treatment). Moreover, the level of teicoplanin and bacitracin resistance genes was particularly high in the sequence datasets.

The analysis is very coarse-grained, without the ability to show the relationships between distinct components of this skin microbial community and other microbiota. It's a little like sticking a forest into a gigantic blender and studying the resulting mush. One advantage of this approach is that it is less easily distracted by very rare components of the biota. The results show the important energy and nutrient flows. In particular, turning from this approach (pooled sequencing over a long time) to transcriptome sequencing (sequencing of RNA expressed in cells) can give a picture of what is metabolizing at a particular time slice in a microbial community. Mapping the overall metabolic breakdowns of more and more communities will help to clarify what resources are structuring the microbial colonization of humans and their evolution over time.


References

New Gibraltar blog by Clive Finlayson

Mon, 2013-06-10 21:29 -- John Hawks

Clive Finlayson has started a new blog featuring some of the day-to-day story of ongoing fieldwork at Gorham's and Vanguard Caves, Gibraltar: "Clive Finlayson's Human Evolution Blog".

The first installment has a rich array of photos showing the logistics of getting material in and out of the sites. The caves are just above sea level, but only accessible by land via a very high climb, so some materials are brought to the site by boat. Also Geraldine Finlayson and Darren Fa are involved in some underwater exploration off the coast. These are incredible archaeological sites and I hope to visit there again soon!

Speak up and matter

Fri, 2013-06-07 14:55 -- John Hawks

Current Biology is running a short editorial by Geoffrey North, wishy-washing its way through a non-opinion about the value of blogging in science ("Social Media Likes and Dislikes") [1]. North gives a brief synopsis of the arsenic-eating bacteria fiasco ("An arsenical profile", "Alien biology hype"), which he admits was a victory for the importance of blogging and the open science approach.

But he can't help worrying about all those people exercising their free speech in science:

But there is also, I think, a danger here, which lies in the very speed of response, and the way that blogs are essentially “vanity publications” which lack the constraints of more conventional publishing — they are not reviewed, and do not even have to pass the critical eye of any editor. In principle, anyone can write a blog and criticize anything — they do not have to have any specific expertise. And the criticism can be picked up, advertised and amplified, for example by Twitter, by those who feel a post supports their agenda.

Such criticism can of course be harmful — at the least there tends to be a “no smoke without fire” effect. And once a scientific reputation has been tainted, it can be hard to restore confidence.

I have little patience for the risk-averse culture of academics.

The bottom line is: People need to decide if they want to be heard, or if they want to be validated. I have long been an associate editor at PLoS ONE, and once I edited a paper that received a lot of critical commentary. That journal has a policy of open comment threads on papers, so I told disgruntled scientists to please write comments. The comments appear right with the article when anybody reads it, they appear immediately without any delay, and they can form a coherent exchange of views with authors of the article and other skeptical readers.

Some of the scientists didn't want to submit comments, they wanted to have formal letters brought through the editorial review process. "Why?" I wrote, when you could have your comments up immediately and read by anyone who is reading the research in the first place? If you want to make an impact, I wrote, you should put your ideas up there right now.

They replied, "How would you feel if someone published something wrong about Neandertals? Wouldn't you want to publish a formal reply?"

I wrote: "In that case, I would probably get a blog."

What is the difference between being heard and being validated? It's whether you are contributing to the solution or to the hindsight.


References

  1. North G. Social Media Likes and Dislikes. Current Biology. 2013;23(11):R461.

Quote: Donald Kagan on liberal arts education

Tue, 2013-06-04 23:34 -- John Hawks

Yale University classicist and historian Donald Kagan has just retired from a long and distinguished career. He has an essay in the current New Criterion, reflecting on the history of the liberal arts education and its value to students today: Ave atque vale.

Earlier generations who came to college with traditional beliefs rooted in the past had them challenged by hard questioning and the requirement to consider alternatives and were thereby unnerved, and thereby liberated, by the need to make reasoned choices. The students of today and tomorrow deserve the same opportunity. They, too, must be freed from the tyranny that comes from the accident of being born at a particular time in a particular place, but that liberation can only come from a return to the belief that we may have something to learn from the past.

Crazy evolution movies

Tue, 2013-06-04 21:32 -- John Hawks

io9 has a fun list of "The most ludicrous depictions of evolution in science fiction history". Star Trek and Doctor Who come in for the treatment, but how can I not quote the most famous movie evolution of all?

In the original Charlton Heston movie, three astronauts from 1971 crash land on an unknown planet in what is now the year 3978. The world is ruled by intelligent apes, who have enslaved the mute, primitive humans. At the risk of spoiling one of the most famous forty-year-old twists in movie history, Heston eventually discovers this strange planet is actually Earth. You can probably spot the problem with this story, evolutionarily speaking. There's absolutely no way apes could evolve into intelligent beings in 2006 years.

To be fair, this scenario is quite consistent with some people's models of human evolution, in which human language and symbolic thinking arise suddenly in a single evolutionary spasm. Of course, those people are just wrong.

This is going to be very convenient for my students, as I regularly assign this as a paper topic -- pick a famous movie or book depiction of evolution and explain how it is inconsistent with what we know about the evolutionary process.

Quote: Stephen Downes on the value of open courses

Sun, 2013-06-02 18:43 -- John Hawks

Stephen Downes, widely recognized as one of the original inventors of the "MOOC" concept, on why courses should be open: "MOOC - The Resurgence of Community in Online Learning".

Why make our courses open? Think of a course as like a language. If a language is closed, it dies. If people are not allowed to speak it, it dies. To enable people to genuinely participate in the culture of a discipline, whether it be physics or chemistry or political science, the content and the materials of the discipline must be open.

There is the danger that a cultural or linguistic group will retreat into itself in the face of this risk. I look, for example, at the state of publishing in communities like Finland or Sweden, and find that open access is very limited, as the publishers imagine that there is no other place for Finnish or Swedish speakers to turn. But they do turn, as we know, to open online content in English.

MOOCs and disabilities

Sun, 2013-06-02 17:23 -- John Hawks

The Coursera blog today relates a remarkable story: "Not Impossible: The Story of Daniel, a 17 Year Old with Severe Autism & His 6 Completed Coursera Courses".

He even had a moment of stardom. We took him to the ModPo final webcast at Penn, and at one point one of the TAs asked members of the audience to pick two words that encapsulated their ModPo experience. Dan’s were “not impossible” and under Al Filreis’ gentle urging he managed to say those words aloud to however many hundreds of people were watching around the world. Someone made a forum topic out if it and for 72 hours “Not impossible” was the top thread on the ModPo forum as people wrote in from all over saying that Dan had inspired them and that “not impossible” was going to be their new watchword. Can you imagine what it does for a person like Daniel to feel useful?

The story, written by Daniel's father, goes through the accommodations that the parents devised to enable Daniel to be a full participant in the college-level humanities courses.

This story reinforces one of the key values of open education resources: accessibility. Being usable on multiple platforms, accessible to screen readers and other accessibility tools, is an essential part of planning online courses. For paleoanthropology, one of the most important aspects of accessibility is how we make use of images, since the materials are so often visual. During this month, I am spending enormous time working on the visual resources for my MOOC, ensuring that we are using images with a standardized format, with descriptive metadata, and with links to data sources.

"Can you help me with my report?"

Sun, 2013-06-02 13:22 -- John Hawks

Lately, I've been getting an increasing number of e-mail requests from middle school and high school students, whose teachers have assigned them projects that require them to find experts and ask questions about their chosen research topics. At a certain time of year, I actually get more of these kinds of questions in my e-mail than I get from my actual undergraduate students, the ones who are paying me to answer questions. So it's a lot.

It turns out I'm far from alone in this trend. Carl Zimmer has also been getting a lot of similar requests from students, and he doesn't have time to answer them, either: "An open letter to science students and science teachers".

It’s great that you are looking for new ways for your students to do research and learn about science. But having them send emails to scientists and writers has failure stitched into its very concept. Writers are perpetually scrambling to meet deadlines and pitch new stories. Scientists have full plates as well, between their research, their eternal quest for the next grant, and their teaching. To answer a single email from a student–either in the form of a long list of questions or just an open-ended plea for help–takes a lot of time. We may respond to the first few emails we get, but as they keep pouring in, we tend to burn out. And the more popular this becomes as a pedagogical tool, the more emails students will be sending to scientists and writers. And that makes people burn out even faster. It doesn’t seem fair to the students for their grade to depend on whether they get a reply from their email. Even the most polite email may land in the inbox of someone who decided long ago never to respond to such requests.

I want to reinforce what Carl has written. I really like to answer student questions, and some of my most delightful exchanges have been with talented high school students who genuinely have developed an interest in paleoanthropology. I was one of those high school students once. In the days long before e-mail, I wrote letters to NASA requesting information about their programs and technologies, and used the agency's informative materials in my reports and public speaking. But NASA has paid public outreach specialists. I don't. I give students a lot of credit for having the courage to write and ask original questions, but when I get form letters by e-mail, they have to go unanswered.

The great thing is that there are better ways for teachers to get experts involved in classrooms. As Carl suggests, many scientists make time for outreach, and anthropologists are more accessible than most. It is usually the best idea to make a relationship with a nearby university or college, where experts might not be exactly on topic but will often be eager to establish a longer-term relationship with your school -- and may even have research opportunities for your students. Many experts, like me, will make themselves available by Skype for remote classroom interactions where many students can benefit.

And with the upcoming MOOC, we'll have a lot of open access materials for teachers to use in classrooms, including interviews with dozens of experts that focus on just the kinds of questions students are most likely to ask. It's a great time for getting more expert insight into high school and middle school classrooms, both in terms of personal relationships with local experts and in terms of public content!

Quote: Hockett and Ascher on signs and symbols

Fri, 2013-05-31 17:28 -- John Hawks

From "The human revolution", by Charles Hockett and Robert Ascher, footnote 2 [1]:

Some recent discussions (e.g., Critchley 1960) try to deal with the emergence of language merely in terms of the contrast between "sign" and "symbol"; intentionally or not, these treatments give the impression that our ancestors acquired language in a single enormous leap. Anyone aware of the intricacy of design of every human language knows that such a leap was impossible; there had to be steps and stages. The contrast between "sign" and "symbol", first carefully discussed by Langer (1942), then adopted and developed by White (e.g., 1949, 1959), is too gross to serve.


References

  1. Hockett CF, Ascher R. The human revolution. Current Anthropology. 1964;5:135–168.

The DNA portrait artist

Fri, 2013-05-31 13:44 -- John Hawks

Twitter gets results! A group of geneticists (honestly, including me) were kvetching on Twitter about this NPR story: "Litterbugs Beware: Turning Found DNA Into Portraits". The story profiles an artist, Heather Dewey-Hagborg, whose chosen project blends the idea of genetics with identity:

Yet it might seem Dewey-Hagborg would be more comfortable in a studio than a laboratory. She's an artist; a doctoral student in Information Art at Rensselaer Polytechnic Institute in Troy, N.Y. For her most recent project, though, much of the creative process takes place in front of a centrifuge, wearing latex gloves, deep in the map of the human genome.

In short, Dewey-Hagborg extracts DNA from these samples of trash and turns that information from code into life-sized 3-D facial portraits resembling the person who left the sample behind. She can code for eye color, eye and nose width, skin tone, hair color and more.

Now, for those of us who are actually working in human genetics, the premise of this story is obviously science fiction. There is no way to create accurate "life-sized 3-D facial portraits" of people based on their DNA. There is some information about skin, hair and eye pigmentation, but even that is not sufficient to generate a portrait of these traits for an individual with forensic accuracy.

Forbes reporter Matthew Herper caught wind of the Twitter convo and began investigating the story. He interviewed Dewey-Hagborg by e-mail and got her response to the criticism that her portraits are not rooted in scientific accuracy. I think her responses stand for themselves: "Artist Creates Portraits From People's DNA. Scientists Say 'That's Impossible'". It's a conceptual art project, as she writes, "The point of the work is to create a provocation".

Well, it is provocative. My concern is that it plays on people's fears of genetics in ways that reinforce widespread misconceptions about the power and process of science.

Herper concludes:

But though our genetic privacy may not be safe, our faces probably are. Dewey-Hagborg’s portraits may rarely resemble the people whose DNA she’s using to generate them. The whole thing — most disturbingly the fact that she’s been contacted by law enforcement officials — shows how ill-prepared we are for dealing not only with what biotech may do in the future, but for what biotech can do now. She needs to work at making her message clearer.

It would be more illustrative to use a series of photographs of people who have the same genotypes as the person who left a cigarette butt, to show the range of different facial shapes and features instead of pretending we can focus on a single one. After all, we already know the effects of stereotyping upon witness reports from crime scenes. Adding a new category of genetic stereotyping based on a very limited degree of gene-phenotype associations can only push things further into the realm of misinformation.

Moving beyond science communication toward engagement

Tue, 2013-05-28 00:08 -- John Hawks

PLoS Biology recently published an essay by Brooke Smith and colleagues, focused on "Navigating the rules of scientific engagement" [1]. The authors represent COMPASS, a nonprofit organization dedicated to bringing the knowledge of ocean scientists to greater public awareness and influence in public policy decisions. The essay includes some insightful themes on bringing more effective modes of public engagement into scientific research. The essay is open access and under a Creative Commons license, so I'll excerpt a few passages I think are especially worthwhile.

To begin with, the essay explains why engagement is a key concept in science communication:

Science communication was once considered primarily a unidirectional conveyance of information, based on the assumption that if scientists and other experts could convey their knowledge to the public, typically through “data dumps," society's problems could be solved (i.e., if you knew what I know, you would believe what I believe). This perspective, “the science deficit model of the public", is explored in a body of communications literature [6]–[8]. We know it does not work [9].

Communications is not only about speaking in a clear, compelling, and relevant manner, nor simply about promoting findings. Effective communications is an integrated process of understanding your audience and connecting with that audience on their terms. It requires listening as well as talking.

As practitioners within the evolving field of science communication, we've also adapted our approach to one that facilitates dialogue and encourages engagement. We've learned that if scientists want to have impact beyond their disciplines and in the world, communications must be central to their enterprise [10]. This is why academia should reconsider its measures of success and make communication training an integral part of graduate-level education.

The "deficit model" is the naive assumption made by many scientists, who may believe that the reason why the public misunderstands scientific concepts is that people just haven't spent time learning the correct explanations. Of course, the public is heterogeneous and some people will be receptive to a simple explication of a scientific finding or principle. But in well-entrenched areas of misunderstanding of science, the deficit model is rarely an accurate picture. Talking "at" people is very likely to increase their resistance to scientific reasoning, precisely because it shows the scientists themselves to be unreasonable. As the essay discusses, listening and responding sincerely to an audience's concerns and questions are fundamental parts of engagement.

The essay approaches the issue of "science by press release" with a heterodox viewpoint: Getting broad public attention for a controversial finding may in some cases help scientific progress, if the researchers are prepared to make productive use of critical commentary.

We remind the authors that making a splash in the mainstream press tends to incite controversy, whether over the science itself, the communication of it, or both. Backlash is never pleasant, but it is not necessarily negative [5]. In our experience, when the science is robust, and authors are committed to the questions instead of the results, criticism can catalyze productive collaborations and push the field forward.

The authors include an example along these lines, in which a controversial research result led to the creation of a collaborative group that broadened the scope and public application of the line of research.

This is a valuable insight:

Scientists who can clearly explain a research finding and why it matters are poised to succeed not just in outreach, but also in grant writing, interdisciplinary collaborations, teaching, and other essential roles. Being a good communicator is not a tradeoff; it is a key component of scientific success. Like most other elements of a strong academic career, it's a skill that may be rooted in natural talent and personal interest, but can always be further developed by training, preparation, and practice.

We work on making our students good communicators in many ways -- from encouraging them to present their research to the public, school groups, at professional meetings, and in the university. Part of this strategy of multilevel communication is to enable students to discuss their work effectively at different lengths -- from the "elevator talk" to a full research presentation.

But the COMPASS essay suggests to me that "listening" skills also need to be part of our training. I have learned over time the value of having many different ways to describe my research, so that I can deploy the most relevant and topical information to the person I'm meeting. Being able to do quickly switch contexts requires an ability to ask questions of other people, out of genuine interest in what they bring to the conversation. That is engagement.


References

Hunting for Dyson spheres

Mon, 2013-05-27 14:19 -- John Hawks

From Markus Hammonds at io9: "The Hunt for Alien Megastructures". Turns out that people are already using observational data to try to identify planet-scale structures that may exist in other solar systems:

To find a Dyson sphere, you need to look for a specific signature of infrared light, emitted at just the right set of wavelengths.

And that’s just what an ongoing project, headed by Dick Carrigan at Fermilab, has been doing. Astronomers regularly survey the sky to see what they might find, and Carrigan has been hunting through infrared data to search for Dyson spheres. To date, the project has a handful of candidates, but nothing definitive. Not yet.

It's interesting that there's a certain foundation of science fiction concepts that were established in the early days of the Space Age, when mainstream scientists and writers shared much more: Dyson's paper describing the infrared discovery of artificial megastructures was published in Science, after all [1]. It would be worthwhile to devise a new fusion of these concepts of future technologies with what we are learning about genetic engineering.


References

Domestication, plant breeding, and micronutrients

Sun, 2013-05-26 14:17 -- John Hawks

An interesting essay in the New York Times today by Jo Robinson: "Breeding the Nutrition Out of Our Food". The theme is that plant domestication selected for certain traits that made our grains and vegetables more amenable to rapid calorie production, but these have often decreased the amounts of micronutrients in the resulting food products:

Studies published within the past 15 years show that much of our produce is relatively low in phytonutrients, which are the compounds with the potential to reduce the risk of four of our modern scourges: cancer, cardiovascular disease, diabetes and dementia. The loss of these beneficial nutrients did not begin 50 or 100 years ago, as many assume. Unwittingly, we have been stripping phytonutrients from our diet since we stopped foraging for wild plants some 10,000 years ago and became farmers.

These insights have been made possible by new technology that has allowed researchers to compare the phytonutrient content of wild plants with the produce in our supermarkets. The results are startling.

I think it's useful to keep in mind that the qualities of food that loom important for us now, in an age of rapid transcontinental refrigerated food transportation, are not the same qualities that mattered to the first agriculturalists. Five thousand years ago, people needed food products that could be stored through the lean season, that made harvesting the plants easier, and that resisted the insults of bad weather and pathogens. Robinson focuses attention on the developments of the last hundred years, in which some crop varieties have been selected for much higher sugar content, but the long history of domestication before these recent events has also shaped the taste and nutrient content of foods.

I also demur from the conclusion about the health of ancient people:

Were the people who foraged for these wild foods healthier than we are today? They did not live nearly as long as we do, but growing evidence suggests that they were much less likely to die from degenerative diseases, even the minority who lived 70 years and more. The primary cause of death for most adults, according to anthropologists, was injury and infections.

I wouldn't generalize on this point, which would be tricky to demonstrate given the evidence we have. My inclination is exactly the opposite of Robinson's implication here: the minority of hunter-gatherers who live to advanced ages are relatively healthy because the slightly less healthy ones at all life stages are more likely to be felled by infections and injury. This is the concept of "frailty" in life history theory, and is well demonstrated in some historical famines and epidemics. The people who are least healthy are least likely to survive. What we have today is an advanced ability to allow relatively unhealthy people to survive to advanced ages despite their health problems.

Still, I think the essay's bottom line is basically correct. More diversity of foods is better. Selecting foods as part of your diet that have come from a broader array of heirloom and wild varieties is one way to add to that diversity.

Tracking the potato pathogen

Sun, 2013-05-26 13:04 -- John Hawks

An increasing number of authors of scientific papers are writing good blog summaries of their work. The really great part is that the authors tend to give background details that help explain not only what the work means but also how it was done.

This week, one of the coolest new papers was the genetic characterization of the fungus that caused the Irish potato famine. Detlef Weigel describes the paper in a post at Haldane's Sieve, a group blog devoted to describing open preprints in genetics and biology: "Our paper: The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine". The post goes over the multidisciplinary team of researchers whose specialties were needed for the paper -- from ancient DNA to pathogen genomics and systematics -- and gives some neat details about the samples themselves:

Our conclusions are based on Illumina sequencing of 11 herbarium samples of infected potato and tomato leaves collected in Ireland, the UK, Continental Europe and North America and preserved in the herbaria of the Botanical State Collection Munich and the Kew Gardens in London. Both herbaria placed a great deal of confidence in our abilities and were very generous in providing the dried plants. The degree of DNA preservation in the herbarium samples was impressive, much higher than in other examples of ancient DNA, and the majority of recovered DNA was from the host plant, with some samples having in addition over 20% pathogen DNA. In contrast to recent studies of historic human pathogens, no target DNA enrichment was required. We compared the historic samples with modern strains from Europe, Africa and North and South America as well as two closely related Phytophthora species. Due to the 150-year long period over which the individual samples had been collected, we were able to estimate with great confidence when the various P. infestans strains had emerged during evolutionary time. Here, too, we found connections with historic events: the first contact between Europeans and Americans in Mexico falls exactly into the time window in which the genetic diversity of P. infestans experienced a remarkable increase. Presumably, the social upheaval following the arrival of the Europeans somehow led to a spread of the pathogen at the beginning of the sixteenth century, which in turn accelerated its evolution.

What a unique historical record of samples taken from potato plants across one hundred and fifty years. Now it has become possible for DNA investigation to trace down the evolutionary dynamics that led to one of the most famous epidemics in history. This kind of ancient DNA analysis, across multiple time layers to work out the diachronic record of changes in frequencies, has really developed during the last year or two.

Weaning a Neandertal

Sat, 2013-05-25 13:02 -- John Hawks

Last week, Nature published a paper by Christine Austin and colleagues, in which they developed a new approach to understand how breastfeeding affects the elemental content of tooth enamel [1]. Barium and strontium are chemically similar to calcium (all three are in the same column of the periodic table of elements), and a small fraction of both elements are incorporated into enamel and dentine in place of calcium. The fractions of barium and strontium incorporated in teeth depend on an individual's diet; different food sources have different concentrations of these elements. So the concentrations of these elements in tooth enamel give some indication of the diet sources that an individual relied upon when her teeth were developing.

Two of the most significant diet changes occur early in life -- the change at birth when an infant begins relying upon mother's milk, and the change at weaning from milk to other kinds of foods. Austin and colleagues set out to examine whether they could reliably determine the timing of these two transitions, based upon knowledge of the enamel deposition process:

We propose that micro-spatial analysis of barium/calcium ratios (Ba/Ca) in dental tissues represents a powerful approach to assess dietary transitions. Whereas prenatal Ba transfer is restricted by the placenta, marked enrichment occurs immediately after birth from mother’s milk or infant formulas, which contain higher Ba levels than umbilical cord sera. In response to these variations in dietary Ba exposure, Ba/Ca in enamel and dentine should increase at birth, remain elevated for the duration of exclusive breastfeeding and rise further with introduction of infant formula. Circulating Ba levels are expected to change at weaning as Ba (and Ca) content and bioavailability is markedly different across plant and animal food sources. To test this hypothesis, we investigated Ba/Ca patterns in teeth from human children for whom early life diets were recorded prospectively, and in teeth from captive macaques in which maternal milk was collected and suckling behaviour observed.

They applied their method to deciduous teeth that came from children whose mothers had participated in the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS) study in Monterey County, California. This allowed Austin and colleagues to examine the fraction of barium in enamel and dentin, layer by layer, within children whose diets had been recorded including the dates of exclusive breastfeeding, supplemented breastfeeding, transition to infant formula and full weaning. The sample of teeth is not very large (only 25 individuals) but the barium signals within the teeth tracked very well with the dates reported for birth, breastfeeding and transition off milk. Additionally, Austin and colleagues considered the teeth of four macaques whose record of suckling and weaning had been recorded. The macaques did not have the confounding influence of formula supplementation, and their barium/calcium signatures gave quite clear records of natural, gradual weaning versus abrupt weaning upon the separation of mother and juvenile.

Although both barium and strontium may provide a signal of these diet changes, Austin and colleagues focused on barium because strontium is more likely to be shifted within ancient tooth enamel after it has been buried in the ground. The goal of the paper was not only to show that the signature of breast feeding is consistent within living populations (in this case, macaques and humans) but also to provide a way to infer these dietary transitions in ancient primates. To that end, they examined the pattern within a Neandertal tooth from Scladina, Belgium:

Chemical and temporal mapping of Neanderthal first molar enamel (Fig. 3) revealed a transition pattern similar to the macaque that weaned abruptly. After approximately 13 days of prenatal enamel formation, Ba/Ca near the enamel–dentine junction increased and remained elevated until approximately 227 days of age (~7.5 months), followed by intermediate values until 435 days of age (1.2 years). After this age Ba/Ca rapidly returned to prenatal levels for the final 1.15 years of crown formation.

They infer that the Neandertal child was moved off exclusive breastfeeding to partial supplemented breastfeeding at around 7.5 months of age, which the authors suggest is consistent with the pattern in other primates. Then, they suggest that the extended period of breastfeeding in conjunction with solid food supplementation was "abruptly" cut off at the unusually low 1.2 years. After that time, the child continued to grow, apparently without mother's milk.

Katie Hinde, one of the authors of the research paper, has written a blog post giving a lucid explanation of the research and its background: "Teeth and Weaning and Neanderthal… OH MY!" She discusses whether the Scladina tooth is sufficient to make inferences about Neandertal life history more generally:

So do we think we know the species typical pattern of Neanderthal weaning? Not at all. The precipitous decrease of barium at 1.2 years of age pretty clearly suggests that the Scladina Neanderthal was abruptly weaned in a non-typical fashion.

...

We have a really powerful way to investigate the period of exclusive milk feeding and the weaning process with high precision and resolution. For the first time we have a method to look at individual differences in these parameters in primates “collected” by old school naturalists gathering dust in natural history museums or skeletal material recovered at primate field sites. And we can do this in well-preserved fossil hominins... if colleagues are willing to share.

I think this research is really great, and I was talking about it the other day as an example of how we are uncovering evidence about ancient people that was previously invisible to us. Obviously, I'd like to see the same kind of analysis extended to much larger samples of teeth. This paper is a very promising start to the research, but we need to understand what variation there may be within living humans who are eating a broader range of diets, and who may have somewhat different patterns of tooth development.

What I think is most encouraging about this line of research is that breastfeeding may give a natural chemical tracer that will allow researchers to confirm the periodicity of enamel formation in people of known breastfeeding history. A problem in earlier research on tooth development has been the lurking possibility that the deposition process varies among people in ways that make inferences about life history and diet transitions in prehistoric humans somewhat doubtful. A more extensive record of comparative work on breastfeeding and tooth development, with large human and primate samples, has the potential to test whether between-population and within-population variation in developmental processes is important here.

As the research develops, I keep reflecting on the plasticity of childhood development. Here we see breastfeeding as an influence upon the stable isotopes represented in teeth, but the teeth grow with or without that food source. One of the macaques showed a pulse of increased barium after being weaned entirely, which the authors suggest may have been caused by the release of barium and calcium from the skeleton and incorporation in the teeth. Our bodies use stored minerals within the skeleton as a reservoir for later biochemical needs, and acquisition of nutrients from the mother's bodily stores is an important part of that process. Human development relies upon buffers against environmental variability, and in certain physiological processes -- such as enamel formation -- we see a complex trace of those buffers interacting with extreme shifts in environmental resource availability.

This is a really complicated way of saying that our bodies have to cope with losing people, because our ancestors lost their parents much more often than we do today. The Scladina child was part of this heritage of survival.


References

White House to recognize open science

Wed, 2013-05-22 13:53 -- John Hawks

The White House is looking to recognize people who are leading in open science efforts, either by providing free access to data or by using data that is already publicly available. I imagine that public education efforts using open data would also qualify for this recognition: "Seeking Outstanding 'Open Science' Champions of Change". The reward is a trip to a White House event June 20.

We are asking for your help to identify “Open Science” Champions of Change—outstanding individuals, organizations, or research projects promoting and using open scientific data for the benefit of society. For example, a Champion’s work may involve:

Providing free access to data or publications generated from scientific research; or

Leading research that uses publically available scientific data.

Anyone can nominate an “Open Science” candidate for consideration by May 23, 2013 (under “Theme of Service,” choose “Open Science”). In the “Reason for Nominating” section of the nomination form, please also include information about any upcoming open-science-related announcements or new steps that the individual or organization you are nominating has planned, which could potentially be launched at the Champions of Change event.

I just found out about this process this morning, but it looks like a constructive step in recognizing people who are moving science in a more open direction. Earlier this year, the White House recommended a new policy on data access, which I found to be very helpful in comparison to the concurrent policy on publication access "White House policy on data access".

Nominations for this honor are due tomorrow (Thursday), using the short online nomination form. I hope many worthy people can be recognized in this way!

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Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.