john hawks weblog

paleoanthropology, genetics and evolution

metascience

  • 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.
  • 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.
  • AAA: "President Obama Supports Scientific Integrity of Anthropology"

    Tue, 2013-05-14 19:38 -- John Hawks

    The American Anthropological Association blog (on the Huffington Post) included a post last week by AAA President Leith Mullings, commenting on President Obama's address to the National Academy of Sciences: "President Obama Supports Scientific Integrity of Anthropology".

    Mullings quotes from President Obama's remarks:

    And it's not just resources. I mean, one of the things that I've tried to do over these last four years and will continue to do over the next four years is to make sure that we are promoting the integrity of our scientific process; that not just in the physical and life sciences, but also in fields like psychology and anthropology and economics and political science -- all of which are sciences because scholars develop and test hypotheses and subject them to peer review -- but in all the sciences, we've got to make sure that we are supporting the idea that they're not subject to politics, that they're not skewed by an agenda, that, as I said before, we make sure that we go where the evidence leads us. And that's why we've got to keep investing in these sciences.

    The President's comments are important, considering the last few weeks' news of Congressional antipathy toward NSF funding of work in the social sciences. Although many cultural anthropologists consider themselves to be pure humanists and non-scientists, the National Science Foundation does not fund work that is non-scientific in approach. Emphasizing the importance of hypothesis-testing and peer review in anthropology is something I think most anthropologists can rally around.

    That sounds like science has to be a part of any viable long-term plan...

  • Science and piracy

    Fri, 2013-05-03 00:21 -- John Hawks

    Paul Salopek has a story for National Geographic about the impact of Somali pirates on oceanographic science: "A Hidden Victim of Somali Pirates: Science". One of the most important scientific projects on the continental shelf off East Africa is drilling for sediment cores to examine ancient climates and volcanism. This helps us to understand the environmental context for early human evolution.

    "This problem has been going on a long time and with virtually no public awareness," says Sarah Feakins, a researcher at the University of Southern California whose work on paleoclimates has been hijacked by piracy fears. "All kinds of efforts are made to keep the commercial sea lanes around Somalia open. Nobody talks about the lost science."

    The later part of the article describes the loss of routine weather reports from ships, as they choose against broadcasting their locations to eavesdropping pirates.

  • Blogging in biological anthropology profile

    Fri, 2013-04-26 10:53 -- John Hawks

    Nature's "SpotOn" feature has interviewed University of Rhode Island biological anthropologist Holly Dunsworth about her social media mastery: "Social Media for Science Outreach – A Case Study: Blogging about Evolution".

    I also saw the blog as an opportunity to not only to find my voice, but to be comfortable doing so in public. Having been confined to a few academic papers and one reference book, I was excited to be writing about my field, and beyond, with immediate publication and full editorial control. I also hoped that blogging would open up other new opportunities. Recently I wrote a post covering many of the outcomes, direct or indirect, from my participation in social media, especially on The Mermaid’s Tale, here.

    I don't remember if I've linked Holly's post, "You gonna blog that?" but it is well worthwhile as a discussion of the use of blogging in the development of a career in biological anthropology.

  • AAPA hears about ongoing abuse of students at field sites

    Sat, 2013-04-13 08:22 -- John Hawks

    I'm sitting in a packed room this morning at the meetings of the American Association of Physical Anthropologists, in a session on ethics in the field. The most important presentation in the session was just delivered by Kate Clancy, who presented initial results from the Survey of Anthropological Field Experiences. She has made the written version of the presentation available on her blog, "'I had no power to say ‘that’s not okay:’ Reports of harassment and abuse in the field". It is essential reading for anyone involved in fieldwork in anthropology.

    The conclusion to the talk is a call to action.

    Too many of us, the authors of this study included, have told ourselves and others that we just need to “suck it up,” just endure one more day, to keep our heads down and power through. Survival in field-based academic science can’t just be about who can put up with or witness abuse the longest – that is not an appropriate metric to measure who is the best at their science. From here on out, let’s commit to opening up conversations about these issues, rather than avoiding or talking around them.

    Clancy is working together with Julienne Rutherford, Robin Nelson and Katie Hinde, and they have designed the survey as a systematic research investigation. Respondents' identities are anonymous, and the intent of their study is to quantify and describe what is going on now in the field, not to find and punish behavior. To me, the most important aspect of their research is the demonstration that the problems are systemic. Eighteen percent of female study respondents have been victims of physical assault or unwanted sexual contact in the field.

    Males have also participated in the survey, including participants who have reported serious abuse. The number of participants is, however, small. The survey is still seeking to add to the sample, so that they can quantify the ways that physical and psychological abuses are happening to all students in the field without compromising the anonymity of their respondents.

    It is important to note that the scope of the survey is not limited to sexual harassment, and that abusive situations have also been reported at field sites with female directors and senior staff. Hearing from more students and professionals about their field experiences will enable better reporting of all these problems, and I hope that many more people will participate in the survey.

    Personally I think this is the most important thing happening at these meetings. Read the presentation and if you know students or professional anthropologists who have done fieldwork, spread the word about the survey.

    Synopsis: 
    Kate Clancy reports on a survey of anthropological field experiences
  • Math for biology

    Mon, 2013-04-08 00:36 -- John Hawks

    Edward O. Wilson, in the Wall Street Journal writes: "Great Scientist ≠ Good at Math".

    For many young people who aspire to be scientists, the great bugbear is mathematics. Without advanced math, how can you do serious work in the sciences? Well, I have a professional secret to share: Many of the most successful scientists in the world today are mathematically no more than semiliterate.

    Wilson takes himself as the canonical model. Razib Khan comments somewhat critically ("Does one need math for a career in science?"). I think that field biology requires working diligently and independently in the field in a way that some kinds of science do not, and personal qualities that set successful fieldworkers apart are pretty much orthogonal to math skill.

  • Notes on a broken science funding system

    Sun, 2013-04-07 13:14 -- John Hawks

    A jeremiad from Henry Bourne: "Writing on the wall" [1].

    Competition drives scientific discovery, but too much competition for scarce resources can block progress, and has done so. Thus, the growing flood of grant applications surpasses growth in NIH dollars, reduces the proportion of grants that are funded, and renders peer review increasingly arbitrary because a project ranked in the 20th percentile is often no less meritorious than one ranked in the 10th percentile (Berg, 2013).

    Another problem is that we now have a ‘holding tank' of postdoctoral scholars that is overflowing with bright young scientists who are indentured to greying lab chiefs and are thus unable to break new ground as independent researchers (Bourne, 2012). The worst consequence, but harder to quantify, is that scientists avoid risky, creative projects in favour of ‘sure things’ more likely to be funded by conservative reviewers (Nicholson and Ioannidis, 2012).

    Probably most people who have thought about these problems recognize the fundamental catch-22 represented by centralized funding of science. It would be more efficient of time, training, and human capital of all kinds to simply pick a limited number of "winners" early in their careers, provide adequate funding to a relatively small number of institutes, and turn excess talent away at the door. But large institutes often breed groupthink and complacency. There is no accurate indicator of "talent" that would allow selection of those who will achieve great scientific findings from the vast pool of undergraduates. And forcing people to compete every so often does provide a mechanism for cutting out deadwood. That is to say, the likeliest alternative to the current system has lots of obvious problems.

    Yet as Bourne and many others say, granting agencies have become the main drivers of groupthink and complacency, we have set up a system where talented creative people are actively turned away from science careers, and no "deadwood" is ever actually cut out of the system because networks of greyhairs protect each other zealously.

    I want to draw attention to the comment section of the essay, which has a series of thoughtful exchanges. This passage from Bourne deserves to be front-paged:

    A more vexing and crucial problem is that even the faculty who agree with me remain silent and virtually inert. They worry constantly about difficulties getting grants funded, and (correctly) feel pressured to spend most of their time writing grant applications, scrambling to support students and postdocs, and wrangling with prestigious journals. These pressures combine with habituation (in earlier years) to a friendlier funding climate to impose a devastating inertia.

    My instinct is that we need to democratize the process of science. A wider group of researchers should have power, not just a stake in the results.


    References

    1. Bourne HR. The writing on the wall. eLife. 2013;2:e00642 - e00642.
  • Anthropology's online ecology

    Fri, 2013-04-05 10:19 -- John Hawks

    Jason Antrosio has composed a short report on the "Anthropology Blogosphere 2013 – Ecology of Online Anthropology". I appreciate his kind words about my work here, and love how he has connected the new media activity of many prominent anthropologists, the move to open access by Cultural Anthropology, and the increased activity of social media networks dedicated to connecting anthropologists. It really is an ecology with many niches for people to increase their engagement and connections across fields.

  • What should be the shape of the science journal landscape?

    Tue, 2013-04-02 23:12 -- John Hawks

    Michael Eisen, one of the founders of the Public Library of Science, has thought a lot about how to make the system of scientific publishing better. He has posted the text of a presentation he recently gave, which explains many of the current problems with access and curation: "The Past, Present and Future of Scholarly Publishing". In this passage, he suggests a different system that would obviate the problems finding appropriate research among the 10,000 different journals of the current publishing environment:

    So what would be better? The outlines of an ideal system are simple to spell out. There should be no journal hierarchy, only broad journals like PLOS ONE. When papers are submitted to these journals, they should be immediately made available for free online – clearly marked to indicate that they have not yet been reviewed, but there to be used by people in the field capable of deciding on their own if the work is sound and important.

    The journal would then organize a different type of peer review, in which experts in the field were asked if the paper is technically sound – as we currently do at PLOS ONE – but also what kinds of scientists would find this paper interesting, and how important should it be to them. This assessment would then be attached to the paper – there for everyone to see and use as they saw fit, whether it be to find papers, assess the contributions of the authors, or whatever.

    This simple process would capture all of the value in the current peer review system while shedding most of its flaws. It would get papers out fast to people most able to build on them, but would provide everyone else with a way to know which papers are relevant to them and a guide to their quality and import.

    So far, this kind of value-added curation is not happening very much with PLoS ONE. I'm an associate editor and I still can't keep track of all the research in the journal relevant to me. But even though I have access to many paywall journals through my university library, I still love the ease of just clicking on a link to a PLoS article. It just works, no library proxy, no password, just text. Creative Commons text and graphics, that I can freely comment and reuse. The way science should be.

Pages

Subscribe to metascience

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.