Monday, December 2, 2013

Public Service Science Announcement (PScA): Posted Online Does Not Mean Scientifically Published.

Good Morning, Dear Readers!

I'm feeling annoyed with the Internet right now. Perhaps I woke up cranky. Perhaps I haven't had my usual dose of Earl Grey tea. Or perhaps it's all these tweets I've been seeing over the past couple of weeks. I don't feel right posting a link or showing a screen capture of just one tweet as an example, because it seems that my Twitter feed is filled with retweets from multiple people sharing this news article. I wouldn't want to seem as though I was singling out one re-Tweeter.

The subject of said article: humans originated from a pig-chimpanzee hybridization.

"Holy Flying Spaghetti Monster! Which journal is this published in?" was my reaction when I first saw the links.

I may be incorrect, but there does not appear to be any scientific journal in which this research appears. The documentation for this idea comes from the researcher's own website.

My reaction when from "Holy Cthulhu!" to "I'll wait for the paper."

Science literacy and atrophied critical thinking skills are not new topics. We have the cringe-worthy "It's just a theory" phrase when someone wants to discredit an idea without themselves having any knowledge or data to support said discrediting. We have several cryptozoology websites whose contributors have boarded the Circular Reasoning Merry-Go-Round and present only data that supports their claims (Bigfoot/Sasquatch is my favorite example because of the strong ichnology influence.)

Topical to this is my all-time favorite, the Pacific Tree Octopus, a seemingly well-researched website that decries the decline of an endangered species, but was really a social science experiment to test the online academic critical thinking skills of students. Turns out that we as a society are a bunch of suckers when it comes to information presented online.

This is a definite PR problem when it comes to science publication. We (as scientists) call for open-access to published research while simultaneously seeming to denounce those that are sharing their own work for the world to see. The big difference between open-access of published data and these "open science" websites is that the published data has been officially published. This is not a smart-ass comment. When the results of a research project are published by a scientific journal, it means there is a history of critical work that went into getting those results to a certain scientific standard. This is called the peer-review process. First (there are variations of this process), the editor of the journal to which the paper was submitted would send the paper to two or three experts in the field of that particular research. These would be experts who were not directly involved with the research.

Second, the experts would go over the results with a critical eye. When I review papers, these are the questions I ask myself (and I assume that researchers reviewing my papers ask themselves):
- Were the data collected carefully? Were enough data collected?
- Does the subject matter (e.g. a fossil footprint) show to me what the researcher says that it shows?
- What are alternative interpretations that I can come up with before I reach the interpretations and conclusions section of the paper?
- Did the researcher address all the possible alternative interpretations? In the case of identifying a fossil, did the author examine all the possible identities of said fossil before settling on an identification?
- Did the researcher thoroughly check all of the previous work and interpretations that have been done on the subject?
- Are the interpretations and the conclusions in proportion to the data presented? In other words, are the authors stretching an interpretation over too little data?

Third, the experts would write up their comments and recommendations for the paper. Their recommendation options run from "Accept with no changes" to "Accept with minor/major changes" to "Accept with major changes and re-review" or "Reject/Not acceptable for publication." In my experience, the information and/or interpretations presented in a paper have to be pretty shoddy to warrant a "Reject." My philosophy with reviewing papers is to help the researchers present the most sound interpretation based on the data available. A rejected paper is not meant to be a personal attack: it simply means that the researcher did not convince their fellow researchers of their interpretations. It means they need to go back to the drawing board (or the lab, or the field, etc.) and do more work.

Fourth, the editor for the journal reads these recommendations, adds some of their own, and then notifies the researcher about the decision. If the paper is accepted with any type of revision recommended, the researcher must address those recommendations before sending in the corrected copy (or provide a darn good reason why they are not applying said recommendations.) The version of the paper that is originally submitted is the equivalent of a first draft of an essay, and the revised version is the second draft, ideally with all the corrections made. The peer-review process can be long, complicated, and sometimes arduous, but it is the most thorough way the scientific community has of fact-checking research.

Here's the peer-review process for posting your unpublished work online. First, do your work. Second, acquire internet access and design a website. Third, post said work. [Note: there is a big difference between posting unpublished research and posting about research that has already been published.]

This is why I always lectured my students in any writing classes I taught on the pitfalls of relying solely on the Internet for researching scientific writing assignments. There is no peer-review of the Internet. If I want to create a website that states Tyrannosaurus rex is a 40 meter long fish, I can do that. I can make it look official. I can present realistic looking data. Sure, I would be open to the mocking of my peers, but that website would remain up for as long as I wanted it to, and students everywhere could write about the wonders of an aquatic T. rex.

The fact that an image of an aquatic T. rex exists does make me less cranky. Image source:
A less hyperbolic example of this is the discussion around the website it is presented in such a way that the layperson or student would not be able to distinguish its information from peer-reviewed sources. Darren Naish at Tetrapod Zoology does a thorough examination of the site: it's a lengthy read, but worth every word. It is critical without being personal. Another example is despite being told by countless paleontologists that the specimens in question are in fact glacial erratics with no bones in them whatsoever, the person who made the website insists that they represent the remains of a frozen "Sea Dragon."

This is why websites like the pig-chimp hypothesis,, and annoy me. Regardless of the intent of the authors of such "open science" websites, they do take advantage of a society that is hungry for scientific information but has atrophied critical thinking skills. The authors of these sites are already convinced of their ideas, but have not convinced their research peers. What are almost never presented on these sites are the rebuttals to these ideas, which only serves to make the ideas seem accepted by the scientific community.

Back to the chimp-pig topic. I don't think that I can do a better dissection than PZ Meyers on Pharyngula (who does poke fun, but also presents thorough counters), but from what I have read of the Macroevolution website, there is one misperception that I know for a fact is not accurate, and has the effect of making the lay-person reader more accepting of the hypothesis. [Note: I have to hat-tip the Macroevolution site here. They do not say this is a theory, but a hypothesis. The science-reporting world is the culprit for attaching the ever-misused "theory" moniker to the stories.]

This misconception is the non-acceptance of hybridization in tetrapods by the scientific community. At least in the avian world, there are several examples of hybridization that are not only accepted, but are the focus of scientific research. My favorite examples come from Dr. Darren Irwin's website on his lab's research at the University of British Columbia Department of Zoology (complete with links to published papers).

"You'll do." MacGillivray's Warbler (Geothlypis tolmiei) to the Mourning Warbler (Geothlypis philadelphia) during breeding season, producing the "MacMourning Warbler" above. Image source.
Not only do some bird species within the same genus interbreed, but they also produce fertile offspring. This is why there is such consternation among conservationalists regarding the Spotted Owl (Strix occidentalis): those darn endangered owls are known to get freaky with a closely related competitor species, the Barred Owl (Strix varia), which makes their conservation even more frustrating.

"Owl just have to settle for a Barred Owl" said the punny Spotted Owl during breeding season. Image source.
While this topic does give me an excuse to post bird (and specifically owl) images, there is a point: hybridization is not a verboten topic in biology. Hybrids can happen between closely related species. In other words, hybridization is not unheard of between species whose genetic lines have had only a short (few million years) amount of time to accumulate differences. As PZ Meyers details, approximately 80 million years worth of accumulated genetic differences is a different hybridization hurdle to overcome. This is just the one example that stuck in my mind. Other scientists with different research foci will likely find others.

Why this Public Service Science Announcement (PScA)? Unfortunate for the pig-chimp hypothesis and other sites like it, it has received a great deal of attention before receiving the "SCIENCE" stamp. For this idea to break into actual science, it has to go past a compilation of literature review and comparisons to a peer-reviewed published paper. All of the supporting data have to be critically viewed by other geneticists and evolutionary biologists, specifically those that have familiarity with the evolutionary history of the subjects in question. Both the argument and the data have to be convincing.

This is a PScA for students. If you plan to use an online source when doing research for your school projects (or even for your academic work if you are a grad student), please check with your teaching assistant or your professor. Chances are they have a list of sources that contain peer-reviewed information that will not lead you astray, and can also warn you about sites that seem legit but actually do not contain peer-reviewed information.

Always remember: just because the nice website offers you the intellectual version of candy doesn't mean that you should get into the vehicle with it.

Shaman out.

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