john hawks weblog

paleoanthropology, genetics and evolution

open science

  • "Journals seem noticeably less important than 10 years ago."

    Mon, 2012-01-16 16:56 -- John Hawks

    As ScienceOnline2012 gets underway later this week, the New York Times is running an article about open science: "Cracking open the scientific process". The article spends many paragraphs promoting a social networking startup for scientists called ResearchGate, which honestly strikes me as having a not-very-useful approach to openness. For example:

    Dr. Rajiv Gupta, a radiology instructor who supervised Dr. Madisch at Harvard and was one of ResearchGate’s first investors, called it “a great site for serious research and research collaboration,” adding that he hoped it would never be contaminated “with pop culture and chit-chat.”

    I doubt that a walled garden where scientists share their reprints is the wave of the future. The "answering questions" aspect of the site seems similar to the Faculty of 1000 and similar concepts. Such sites aim to make social sharing into a virtue for scientists by credentialing them. On the other hand, if a social network for science can succeed in filtering out politics, that might be worth paying for.

    There are many other things in the article. One thing that shocked me: The open access fee for Nature Communications is really $5000. Holy cow. For $5000 I could pay someone to sit in a coffee shop all day and hand-type the contents of my article into personalized e-mails to everyone who reads it. What the heck is that about?

  • A quick look at your Neandertal fraction

    Fri, 2011-12-16 15:13 -- John Hawks

    The 23andMe blog, the Spittoon, has a description of their new technique to use 23andMe SNPs to estimate any customer's fraction of Neandertal: "Find your inner Neanderthal".

    The result is a rough-and-ready numerical estimate of your Neandertal ancestry fraction. For me it's 2.5 percent. Gretchen is 3 percent, and she's been lording it over me all day.

    The estimate is the work of Eric Durand, who broke ground on the D-statistic method for finding introgression from archaic genomes [1]. He has made public a short white paper describing the application.

    So far, all estimates of Neandertal (or other archaic human) ancestry have come from the proportion of a genome (or genotypes from a genome) that are shared and derived with Neandertals. That includes the results I've been posting here for the 1000 Genomes Project samples this week.

    The next step is to uncover exactly which parts of a person's genome have come from Neandertal ancestors. To discover this, we have to further determine which shared alleles come from recent introgression as opposed to ancient incomplete lineage sorting. We have been working very hard on that problem here, as you'll see, and it has been an important aspect of our work in pigmentation genes in the archaic genomes.

    If you have been considering getting your genotypes from 23andMe, it has become a very good time to do this. The overall fraction of your DNA derived from Neandertals is only the beginning. Soon we'll be able to specify which parts, and in a few cases we'll have a good guess as to what difference it makes. If you want to participate in this research, I'm hoping to gather as many interested people as I can -- so keep your eyes here over the next month.

    And if you are interested in having your genotypes done, feel free to use my link to the 23andMe promotion. I've been very happy with their way of presenting the genotypes and their updates, and know many other people who have also found it interesting. As I wrote a couple of years ago, it's not something to spend your food money on, but it does have an entertainment value. And the potential to be an active research participant.


    References

  • A story behind Manis

    Tue, 2011-11-01 23:15 -- John Hawks

    A couple of weeks ago, I pointed to new research dating a mastodon kill site from Manis, Washington, to around 13,800 years ago ("Bone of the victim mastodon"). Today I ran across an interesting article in the Seattle Times that profiles the archaeologist who discovered the site, Carl Gustafson, and discusses why the Manis site became a focus of academic debate: "WSU prof was right: Mastodon weapon was older than thought, scientists say".

    What sets the story apart from the typical "maverick scientist against the establishment" theme is the candid admission that disseminating results is the standard by which we have to judge archaeology.

    Quentin Mackie, at the University of Victoria's Department of Anthropology, agreed the Clovis-first model most likely subjected Gustafson's site to unfair critiques. But over the years Gustafson, too, didn't share his results in a great number of high-profile journals.

    "I just think Carl was hiding his light under a bushel," Mackie said. "I respect what Carl did. He poured countless hours into documenting the site. But for the rest of us, we rely on publication of results in peer-reviewed journals, and I don't think his evidence was presented in a way that was persuasive enough. And I hate to say that."

    Gustafson concedes his output could have been greater.

    "I probably should have published more," Gustafson said. "But I had so much. I didn't know how to take all this information and make a story out of it."

    If you want your science to make an impact, you have to write more and write promptly. Science needs the details to get in front of more eyes.

  • Blogs, academic discourse in economics

    Wed, 2011-10-19 08:30 -- John Hawks

    Paul Krugman comments on how the growth in academic blogs in economics is a continuation of publication trends that long predate the World Wide Web: "Our blogs, ourselves".

    First of all, policy-oriented research was never as centered on refereed journals as we liked to imagine. A lot of the discussion always took place via Federal Reserve and IMF working papers, and even reports from the research departments of investment banks. The rise and fall of Fed policy via targeting of aggregates, for example, was not a debate played out in the pages of the JPE and the QJE.

    Second, even for more academic research, the journals ceased being a means of communication a long time ago – more than 20 years ago for sure. New research would be unveiled in seminars, circulated as NBER Working Papers, long before anything showed up in a journal. Whole literatures could flourish, mature, and grow decadent before the first article got properly published

    It's a model worth examining, as Krugman notes the effect of blogs is to broaden the conversation to people who once were locked out of these conversations, but who are nevertheless affected by them.

  • Can Watson navigate the medical literature?

    Wed, 2011-09-21 08:30 -- John Hawks

    Last week, Computerworld reported that IBM's famous "Watson" supercomputer is moving to its next challenge: prescribing cancer treatments for the WellPoint health plan.

    For example, Watson's analytics technology, used with Nuance's voice and clinical language understanding software, could help a physician consider all related texts, reference materials, prior cases, and latest knowledge in journals and medical literature when treating an illness. The analysis could quickly help physicians determine the best options for diagnosis and treatment.

    "There are breathtaking advances in medical science and clinical knowledge [but] this clinical information is not always used in the care of patients," said Dr. Sam Nussbaum, WellPoint's Chief Medical Officer, in a statement.

    Looks to me like a first step to removing humans from the decision-making chain. A.I., the ultimate bureaucrat. Plus, it can beat Ken Jennings on Jeopardy!

    It occurs to me that the current medical literature is really poorly suited for AI trawling, in many ways. The data and results are obfuscated in many ways, and there's a strong publication bias toward positive results. Someone asked me just today about why open science is interesting to many of us, and the positive results bias struck me as a really important aspect. When you are keeping an open notebook, the negative results are right there along with the positives. Open notebook science might be better for AI-enhanced treatment plans. In any event, a more standard form of result reporting would be helpful. Why can't anyone run their own meta-analysis anytime she chooses?

  • Agitating for open science

    Wed, 2011-09-07 20:13 -- John Hawks

    Cameron Neylon in New Scientist: "Time for total scientific openness".

    Above all, you should care because science thrives on new ideas and critical analysis, wherever they come from. Open science is better science. There will be growing pains as we figure out how best to enable that. But if we believe that science enriches society then we must accept that society can, and perhaps should, enrich our research. And that can only happen if it is open.

    Open science will not work unless it is better science. I think it will be better. I think the history in paleoanthropology shows very clearly that keeping results behind closed doors for years is not good enough. The results speak for themselves.

    We're already getting some incredible feedback on the Malapa Soft Tissue Project, and it has just gotten started. If you've got a lead and haven't written yet, why not?

  • Announcing the Malapa Soft Tissue Project

    Sat, 2011-09-03 17:34 -- John Hawks

    I am pleased to announce a new open science initiative, focused on a discovery that is unique in paleoanthropology. Together we are going to find out if the Malapa site has preserved evidence of soft tissue from an ancient hominin species.

    If you've arrived at this page from outside the site, here's a link to the main project headquarters.

    In the August, 2011 issue, National Geographic reported on the Malapa fossils, including a teaser that the site may preserve skin from two hominin individuals. (I pointed to the article last month.)

    The suggestion is obviously surprising. Many readers will remember how much controversy surrounded claims about soft tissue preservation from dinosaurs several years ago. Yet extraordinary preservation contexts do exist in the fossil record. Indeed, a few years ago Lee Berger's team, including several of the people now working on the Malapa hominins, identified hair preserved inside hyena coprolites from Gladysvale cave, more than 200,000 years old and only a short distance from Malapa [1].

    Could Malapa present the first evidence of soft tissue from a fossil hominin? If so, what can it tell us about human evolution?

    The day the National Geographic article was published online, I was standing with Lee in his lab looking at what might be australopithecine skin. I'm not talking about an imprint of skin, like a skin cast. These appear to be thinly layered, possibly mineralized tissue.

    Suppose it's really skin, or some other soft tissue, I thought. How would you go about testing the hypothesis? Extraordinary claims require extraordinary evidence. Even if you could demonstrate it to your own satisfaction, what would it take to convince the doubters? How many distinct observations would be possible from these objects? What instruments would you use, and what comparative samples would you need?

    Lee said this was his problem as well. He has access to some of the most sophisticated technology in the world. Some kinds of observations are obvious. He can micro-CT the apparent soft tissue evidence, look within the rock at its structure. He can sample the chemical content, and use scanning and confocal microscopes to examine it. He could sacrifice a small sample to be microscopically dissected. At the end, he would have an answer involving all these comparisons. But would it be convincing?

    Lee then made an inspired proposal: What if the process itself were an experiment?

    Much of the criticism of other surprising fossil discoveries has been fueled by their secrecy. Science done by a closed process means fewer eyes looking at data, and too many chances for errors to pass unnoticed. Unnoticed, that is, until publication. Then, a firestorm of controversy may erupt as the scientific community at last examines the methods and results closely. In anthropology, the most critical errors are often missed comparisons -- sometimes simple things that a research team could have looked at, if they had only thought of it.

    An open process has the chance of improving research by broadening it. We want stronger, clearer results, and we want to anticipate every important criticism. If a significant comparison can be added by people who have the right tools, why not get those people involved? If we stand a chance of finding those people by making the process more open, why not do it?

    Lee suggested that this soft tissue evidence could be the basis of a true experiment in whether paleoanthropology could be done as open science. I've been agitating about open science for years, and I volunteered right away to host the experiment and work to make it a success. We went immediately to Rachelle Keeling, the graduate student who will be coordinating the project, and described how we thought it could work. She was enthusiastic about the idea of a truly new kind of scientific project, one that had the potential to involve so many people in the process of discovery.

    And so, after a month of putting things into order, here we are. How can you participate in the project, or at least follow its progress?

    I have set up a home page for the project, here as a special category page on the blog. This page is the online headquarters of the work, and includes a feed that will have all project updates. As the project proceeds, it will generate suggestions, results, and press. I'll be tracking all of these and updating as we learn more.

    The project has an official e-mail address hosted here: skin@johnhawks.net. We want to hear from anyone with the expertise or ideas to solve this problem. Rachelle and I will be reading through the e-mails, discussing them with other project members, and following up on them.

    We don't know what to expect but I hope we get hundreds of responses. We can't promise replies to anyone, but everyone will receive an automatic acknowledgement that we've received their messages, and we will follow up personally with those that have suggestions or proposals we can take action on. We're going to ask people to participate in the project, perform research, and coauthor the scientific work: this is real open science.

    Members of the Malapa team are biologists who know comparative skin and hair biology. I'll be posting quite a lot about these biological topics for people following the project.

    We know that there are many researchers who have been working with methods that would be useful on these unique samples of possible soft tissue. People working with the trace chemistry of organic compounds in mineral samples, people working with the microscopic structure of other ancient soft tissue samples, people who study preservation of organic materials in forensic contexts. There are many others that I don't even know I should be listing.

    If you know a person with the right expertise to help, please share this information and encourage her to write.

    Most important to the success of the project is showing that we can produce top quality science by this open process. That means we need journals to acknowledge the value of open science instead of penalizing it for not being secret and embargoed. If you're a journal editor reading this, I'm calling you out. And if you're a reviewer or editorial board member, you can support this project and encourage more like it by encouraging the submission of open manuscripts.

    And if you don't have a suggestion right now, keep watching. This project will develop and I expect it to become more interesting as it becomes broader. I can't predict how it will end, and that's pretty exciting!


    References

    Synopsis: 
    I announce and describe a project to study possible soft tissue evidence from a 2-million-year-old fossil hominin site.
  • The Malapa Soft Tissue Project FAQ

    Sat, 2011-09-03 17:07 -- John Hawks

    These are a few of the questions that I think are essential to understand our aims with the project and how we expect it will unfold. The future depends on what we hear from people with their ideas about how to analyze this unique evidence. I'll be updating this FAQ as we learn more about the samples. This is an open science project, and we'll be reporting on some results as they occur. But it all depends on people's participation.

    If you've arrived at this page from outside the site, here's a link to the main project headquarters.

    How did the project come about?

    When I was in South Africa in July, Lee Berger gave me an extraordinary overview of the discoveries from the new Malapa site. Embedded in the breccia that surrounded the cranial remains of MH1 and MH 2 are some relatively small, thin layers that visually appear to be organic (relative to the surrounding matrix). Under a light microscope look like they could be mineralized or preserved soft tissue. They do not appear to be skin impressions within the matrix, they appear to be thin layers that are a different substance from the surrounding matrix.

    Naturally these are incredibly interesting. But it is not obvious what will be the best way to establish what they are, and what we can learn from them.

    Lee suggested that this would be an ideal test case to see if open science can help solve a problem in paleoanthropology. We want to reach the people with the best ideas and ability to test hypotheses about these objects, and we don't know in advance where the answers will come from. That's the nature of the project: finding the right people and making the science happen.

    What do we want people to do?

    We want the best suggestions about how to evaluate this unique evidence and how it can test hypotheses about human evolution. We're reading all the suggestions sent to skin@johnhawks.net.

    We're especially keen to make contact with people who have the ability to make their suggestions happen. Some people out there have the knowledge to apply highly specialized analytical methods to samples like this. We want people like that to get involved with this project.

    Some people out there may have comparative samples that will be key to interpreting this evidence. How can tissue be preserved in a context where breccia is forming? Was there natural mummification or some kind of anoxic environment? To answer those questions, we need people who study the response of tissue to those contexts and who know the right samples to examine.

    Berger's team working on the Malapa hominins have access to much of the best technology. Micro-CT, microscopy, virtual dissection, chemical analysis, any of these things and more can be brought to bear.

    There's a lot more to this project than simply verifying (or refuting) that this stuff is soft tissue evidence. We need to know how it formed. If it's not soft tissue, we want to identify what it is, because there will almost certainly be more of it as the site is excavated and more specimens are prepared. If it is soft tissue, we need to know how it may have been changed as it was preserved, whether through drying, soaking in anoxic conditions, mineralization, or some combination of processes.

    We think the process of finding this out is even more exciting than knowing the result. We hope many of you see it the same way.

    If you write to us, you can expect that we may make your suggestion part of the website. This is an open project, and while we will be posting selectively, we will be sharing information as it progresses.

    Why would somebody want to participate in an open science project like this?

    We want to do the science right. We hope many people out there share this goal. It's a tremendous chance for people who don't normally operate within paleoanthropology to help us discover something fundamentally new about our evolution.

    People who perform analyses or contribute samples as part of this project happen will be full participants in the science and coauthors of any resulting publications. We want people to work together on this, and we think the best science will result from bringing together the best ideas and comparisons.

    How will the project work?

    That depends on what great ideas we hear from people. Lee's team will be carrying out analyses on these samples.

    Rachelle Keeling is coordinating the study, doing the research on what should be done, and what it will tell us about the samples. She and I will be reviewing the e-mails that the project receives, and will try to determine which approaches are feasible, and which order they should be carried out.

    As you send in ideas about what should be done, the more detail you can include about the analytical methods you can provide, the better. How much material (if any) does the method require? What hypotheses can the method test, or what information can it provide about the samples? How much time and preparation is required?

    If you have comparative samples that may be useful, what kinds of observations can you make on them? Can you point to references that have also used these samples?

    In other words, we want a bit of a plan if you can provide it. If you need more information from us to see if it's feasible, let us know -- we may be able to answer it, or have some team members carry out steps in advance.

    The project will be carried out over the next year, so the sooner we hear from you, the better!

    What is the Malapa site?

    Malapa is a cave site outside Johannesburg, South Africa, in the area where many other sites preserving remains of early hominins have been found. I have a Malapa page that gives a short introduction and links to many stories here about the fossils found at the site. I visited the site in July, 2011, and posted a narrative of the visit ("A visit to Malapa") that gives a good overview and several photos of the general area.

    Two of the most complete hominin skeletons ever described, both dating to 2 million years ago, have been discovered and described at the site. The site additionally includes further fossil materials that are still undergoing preparation and study. It is one of the most important fossil discoveries ever made in paleoanthropology, and will continue to produce new evidence about our origins for many years to come.

    How was the possible soft tissue evidence discovered?

    So far, the team at Wits has been working on breccia blocks recovered from the surface at Malapa. There has been no excavation yet at the site. The possible soft tissue evidence was discovered during the course of scanning and preparing these breccia blocks.

    The blocks are packed with bones. Many recognizable bones jut from the surfaces of the breccia, from antelopes, carnivores, small baboons and hominins. In several cases, hominin bones were recognizable at the surface, and these blocks were CT-scanned very early in the process of study and preparation. Scanning gives the preparators knowledge of what lies beneath their drill bits. In some cases, the best course of action is to leave the bones embedded within the breccia matrix, for further study by micro-CT.

    CT scan of Malapa MH1 cranium

    Initial CT scan of the MH1 cranium embedded in matrix block.

    In the initial CT-scanning of the MH1 cranium, team members noticed an area where the matrix surrounding the skull appeared irregular. As they prepared this out, it became clear that the breccia itself had pulled away from the cranium across a small region, and the breccia had a thin layer of material at its surface there. This is not the outer table of the bone (which is intact in the corresponding area), nor is it apparently an impression of the bone.

    Malapa MH1 breccia block with possible soft tissue

    Photo of breccia block including MH1 cervical vertebra (top). The smooth area, center, is a thin layer of candidate soft tissue on the surface the breccia.

    An additional section of possible soft tissue emerged as the female MH 2 mandible was prepared.

    Upon magnification, these pieces do appear to have a structure. As yet, no dissection or further sampling has been attempted. The team has no committed opinion about what these represent or how they were formed, other than that they do not appear to be simple impressions in the surface of the breccia. Disproving that they represent soft tissue may be just as interesting as demonstrating it, because either way we will discover important facts about the preservation and formation processes of this unique site.

    How could soft tissue possibly be preserved from 2 million years ago?

    Like other South African cave sites, the Malapa fossil hominins were preserved within a breccia, a cemented stone material packed with fossils, rock fragments, and other material. The Malapa breccia represents a remarkable snapshot of time, when hominins and other animals fell into a "death trap" and their complete skeletons were preserved.

    It is clear that Malapa preserves an extraordinary density of hominin remains, with nearly complete skeletons and articulated parts. These skeletons do not appear to have been disturbed after the bodies entered the site. Some plant and insect remains are preserved in the breccia as well.

    Beyond this, any explanation so far is speculative. If there was water in the site, which seems likely, it may have included an anoxic layer that preserved some of this material. A major goal of the project will be testing different hypotheses about the preservation environment of these fossils, to try to explain what these substances may be.

    Are you telling us everything?

    :)

    Synopsis: 
    The Malapa Soft Tissue Project is an experiment in open science, trying to uncover new facts about a unique discovery.
  • Open every box

    Thu, 2011-05-26 02:26 -- John Hawks

    Fascinating: "Unique Canine Tooth from 'Peking Man' Found in Swedish Museum Collection"

    Swedish paleontologists were the first scientists to go to China in the early 20th century, and they carried out a series of expeditions in collaboration with Chinese colleagues. They found large numbers of fossils of dinosaurs and other vertebrates. The material was sent to Sweden and the well-known paleontologist Carl Wiman, who identified and described the fossils. But when the direction of research changed after Wiman's death, 40 cartons were left unopened and forgotten -- until know. In recent weeks, they have been opened by Per Ahlberg, his colleague Martin Kundrát, and Museum Director Jan Ove Ebbestad, who had drawn attention to the cartons in the storeroom at the Museum of Evolution.

    You know, this is why open science is so important. When you have a small group of people working a collection, the information goes when they die. I hear about cases like this all the time. And we're talking about hominins in relatively well curated collections. The number of unique specimens of other fossil organisms sitting in boxes must be enormous.

    The more eyes you have on your collection, the more it is worth.

  • Public impact

    Mon, 2011-05-16 07:19 -- John Hawks

    Alice Bell on public engagement for social scientists and humanists: "Being professional about 'impact'."

    Me, I’m a public sector professional, and as such, I take pride in the ways in which I may cultivate an independent voice, but do so within a network of constraints provided by public service. Listening to outside voices is not a threat to my professionalism; it’s an expression of it.

    ...

    We are paid to do our research. Teaching a small set of kids privileged enough to go to university, or publishing in esoteric journals only a couple of people will read does not cut it. Moreover, it doesn’t challenge our ideas enough to make the sort of high quality work we should be producing. Earn public trust by showing off your worth. You may well learn something in the process too.

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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.