Episode 1: Manuscripts, mushrooms, and methylation

IT BEGINS.

A HUGE thank you to Jai Ranganathan, host of the podcast Curiouser and Curiouser, and to the guys at Science…sort of (especially Ryan!) for help getting this podcast off the ground.

Our fabulous theme song was created by the always amazing Paul Smaldino.

Links from the show

Manuscripts

Arxiv.org (the open access system we discuss)

The SciFund Challenge

Mushrooms

Mystical Experiences Occassioned by the Hallucinogen Psilocybin Lead to Increases in the Personality Domain of Openness (link to the article)

Methylation

Disease-associated epigenetic changes in monozygotic twins discordant for schizophrenia and bipolar disorder (link to the article)

What is epigenetics?

Michael Meaney (the professor we discussed who studies epigenetics in rats)

21 thoughts on “Episode 1: Manuscripts, mushrooms, and methylation

  1. InfernalXerxes

    Amazing, just amazing. So many things to think and talk about, but if I had to pick one, it would be the last discussion about cross disciplinary discoveries being necessary to allow advancement on a given subject. It reminds me of an idea I first encountered on an episode of the 90′s Outer Limits. In 4×16, Final Exam, the idea is presented that at a given point in history, an advance will be made in a subject, e.g. cold fusion, because the collective consciousness and state of knowledge in the world is right for that advance to be made.

    I have always found this interesting and looking back throughout history, there have been numerous cases of independent scientists making the same discovery around the same time. You mentioned that the thought that an advance in a field you are studying is unknowingly dependent on an advance in another field may be discouraging, but I look at it from the other perspective. One day you may wake up, read an article, and suddenly realize how to make cars fly.

    Reply
  2. PBJ Platypus

    Sorry to take away any seriousness expected on these comments, but… perhaps Bruce Wayne’s parents’ death triggered some sort of methylation that made him have the hero complex he needed to become Batman. Wild Mass Guessing and all that, I suppose.

    Reply
  3. Carl Troein

    Ooh, another podcast for me to fall behind on! But this one has +Inf% more Weiners than, say, SGU! Yay for awesomness and brain-altering parasites! (And parasprites; now THOSE are brain-altering for real!)

    Oki, I’m done with the exclamations now. :-D

    Reply
  4. Tom

    It’s just weird listening to you guys when I’m just hearing some of the characters from SMBC theater that you guys play.

    Reply
  5. nick

    Zach and kelly
    i happy to hear you two talking about epigenetics. my father is involved in epigenetic research and i could probably get him to talk to you about it further if you would like.
    send me an email and i can probably arrange something.
    cheers
    nick

    Reply
  6. Mark S. Everitt

    I’m hearing very similar talk on peer review in many places, and for quite some time now. I tend to think of review as a chore, but I always do it thoroughly. In most cases when I get reports back for my papers, the job done was much less thorough.

    Now it so happens that I enjoy washing up, which is a chore too, but it gets shared fairly anyway. ;)

    Perhaps one thing to do would be to make this fair. Similar to what is discussed, on uploading a manuscript, I’d like to be presented with a list of papers open for review. You get to choose two or three (depending on how many referees are the norm on a submission). Perhaps some weighting toward those papers that are ageing. i.e. you can review two papers, or one that’s gathering dust.

    Another line of reasoning now… At the risk of giving all of science to Google (and giving up my beloved LaTeX) how about Google Docs as a platform for publications? Image this; Collaborative paper writing, potentially simultaneous editing, along with publication and a system like the above for peer review. Google loves doing graph based metrics and this would be a lot of fun. As long as the papers are free to upload and download, this is a virtually limitless resource. The more I think about it the more advantages I can see. This could be very disruptive. arXiv+

    Reply
  7. Todd Carpenter

    in regards to the discussion about a peer review website/how to balance things out..

    Seems like their could be a way for people who are just not into doing reviews to still ‘cancel’ out the papers they put up: If you are a prolific reviewer/commentator, you have an excess of ‘points’ built up compared to the amount of papers you put out. Scientist A wants his paper on the website submits directly and ONLY to scientist B, who has a large excess of points. Scientist B can read the paper/etc and decide to use his/her own points to ‘post’ the paper, leaving the original authorship intact.

    That being said one can never create a system that cannot be gamed in some way shape or form. I had ideas for this sort of peer reviewed online database stuff a couple of years ago, though I though of a sort of cross-discipline database that would include invention and design as well as theory and studies. Sounds like people who actually have talents are doing it already, which is very cool.

    Reply
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  9. Deno

    Mighty mighty Weinersmiths:
    Awesome! Now I have yet another procastinatory tool. This is awesome :-)
    I wanted to add something to your Arxiv comments:
    Arxiv has massive issues. Whichever Internet Rule states that ‘just because you can doesn’t mean you should’ is not in effect. Now, because I’m in astronomy grad school, I subscribe to the astronomy Arxiv RSS feed. That means I have to wade through over 300 posts a week, and about 5% are crank-y papers. I guess that’s an ok fraction of good to suck, but it still hurts to think that the cranks can put their rantings on Arxiv and then claim they’ve had published papers (technically not a lie…but only technically).

    There is no peer-review requirement to load your article onto Arxiv, which is both good and bad. Good, because peer-review is inherently biased and very conservative; nepotism is rampant, and god help you if you have an interpretation that disagrees with one of your reviewers – no paper can survive a reviewer who knows that their treasured interpretation is right. Bad, because ANYONE CAN PUBLISH.
    I’ve read abstract after abstract that contain poor, not-science, CRANKERY (for example, panspermia cosmology, which totally displaces the wrong LCDM and explains life’s presence EVERYWHERE: http://arxiv.org/abs/1109.1262 Who knew!)

    So while I approve of the idea of restructuring peer review, I don’t know if a votey system would work all that well. What if the votey gets Pharangulated (or Xtianized or whatever)? The internets are a scary thing…

    Reply
  10. Randy Rockwell

    re: peer review balance

    What you have here are two markets. There is a supply of peer review and demand for peer review: the review market. There is a supply of papers submitted and demand for papers submitted: the submittal market. As I understood your arguments, Zach would like a system where individuals were not compelled to participate in both markets, leaving the good reviewers to review and the good submitters to submit. Also, Kelly would like a system where individuals were compelled to participate in the review market if they participate in the submittal market to prevent a shortage of peer review. This is a problem of free will vs shortage. This is the kind of problem that free markets solve.

    Solution (two commodity version):
    You would need an exchange rate between the two markets, for example: for every paper you submit you must review three papers. (Kelly’s plan) What is important here is to not fix the exchange rate, so that if there is an excess of reviewers, the rate would fall until people could submit without reviewing papers that twenty others have already reviewed, but not so much that all the papers were not receiving reviews. Likewise if there is a shortage of reviewers, the exchange rate would rise until the same temporary equilibrium is met.

    Solution (three commodity version)
    Introducing a new commodity: money. I know, I know, money is the root of all evils that corrupt the research process and such, but hear me out. By having exchange rates between submittal and review listed in dollars (or whichever), we now open up the possibility that individuals could submit papers without needing to review (Zach’s plan). We also open up the possibility that reviewers could spend time reviewing and be paid for their time if the task is as onerous as Kelly believes. Also, anyone who dislikes the idea that money is involved could simply ‘net out’ their account by reviewing enough papers to have a positive balance on their account before submitting their own paper.

    Thanks for the podcast and for listening to a Chemist turned amateur Economist.

    Reply
  11. Morris Keesan

    I wonder if this DNA-methylation stuff could be at all implicated in the development of multiple personality disorder? Everything I know about MPD I learned from Daniel Keyes, in his book The Minds of Billy Milligan, but if, as Keyes suggests, long-term systematic abuse of a child can trigger this kind of dissociative syndrome, could there be some epigenetic effects at work?

    For more on epigenetics, there’s this BBC radio programme, which mentions interesting results showing that epigenetic effects can persist across generations, and even across more than one generation (e.g. a woman’s diet while pregnant can affect her grandchildren, and, surprisingly, epigenetic changes in the FATHER can persist into his offspring).

    Reply
  12. Lynda

    I feel smarter having listened to this!

    And a little freaked out about parasites again. I just started to forget that dude I saw on TV in 1985 with the wicked case of trichinosis. GET THEM OFF ME.

    Reply
  13. Vasiliy Sharapov

    There is a simple solution to the peer review balance problem (which reminded me a lot of BitTorrent for obvious reasons).

    – Users earn reputation with high-quality reviews and high-quality submissions.
    – Submissions in need of review are ordered by submitting users’ reputations.

    Einstein and Erdős might have to put in a couple hours of work to get the first paper off the bottom of the list. After that, assuming their papers were very good, the reputation returned should keep their future work immediately visible (at the top).

    The problem with enforcing a 1:1 or 2:1 review:submission balance is that some users willingly work at a 100:1 or even 1000:0 ratio, leaving new users without an easy way to advance. With reputation coming from _both_ reviewing _and_ great work the system will encourage _both_ reviewing _and_ great work.

    Reply
  14. John

    You mentioned the idea of a system like arXiv where people vote on papers. Such a system exists for astrophysics, wherein people at a variety of institutions vote on papers they would like to discuss at their (daily, semi-weekly..) discussions. It doesn’t affect whether your paper is published, but it does give a gauge, even before citations, of how influential a paper will be.

    http://voxcharta.org/

    Also, as a practical matter, if you do not review the papers you are asked to review, the editors of the journals will know and make it more difficult for you to publish in their journal…

    Reply
  15. Cliff

    If you think that psych articles have lower standards, you should read some education articles some time. Even articles from the esteemed Journal of Research in Mathematics Education (JRME) are often nothing more than “I taught my students this way and they did better on this test that I built than students from other classes.”

    Reply
  16. Sean

    Not sure if this was addressed at some point (if it was and I missed it I apologize for this post), but I heard Kelly remark that methylation was of the histones. DNA bases can also be methylated, although the sequence is still the same in the sense that the underlying bases are not changed, and will still be passed on.

    http://en.wikipedia.org/wiki/DNA_methylation

    “DNA methylation is a biochemical process that is important for normal development in higher organisms. It involves the addition of a methyl group to the 5 position of the cytosine pyrimidine ring or the number 6 nitrogen of the adenine purine ring (cytosine and adenine are two of the four bases of DNA). This modification can be inherited through cell division.”

    The cited articles seem to be referring to it, as they refer to “DNA methylation”.

    Reply
  17. Juniper Hunter

    I know this is old but can you please provide the citation for the whole ‘adenosine receptor allowing large molecules to crossthe blood brain barrier’ dealio you mentioned?

    Reply

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