How Would Mark2Cure Expedite Scientific Discovery?

How would thorough annotations improve information extraction from biomedical research literature? To illustrate one of the issues Mark2Cure aims to address, we’ll start with an example drawn from history–the undiscovered public knowledge that an information scientist named Don Swanson successfully mined in the 1980’s.

At that time, there were 2,000 research articles on Raynaud’s syndrome, a disease characterized by feelings of numbness and cold in some parts of the body in response to cold temperatures or stress. There were also about 1,000 research articles on fish oils, but there were no articles that spanned, joined, or linked both subjects.

In the case of Mark2Cure, citizen scientists will annotate abstracts of these research articles since the pace of research publication is much higher now than it was in the 1980’s.

This post was originally written for Mark2Cure and can be viewed in its entirety here.

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Neat Science Thursday – Misleading headlines can affect science policy

If you’re in the US, you can probably tell by the deluge of unwanted political ads in your mailbox and voicemail that it’s election season. These ads (especially the printed ones) serve the very important function of wasting a resources because few of these ads are printed on 100% recycled paper, even if 100% of these ads (that I receive anyway) go straight into my recycling bin.

I don’t even look at these ads any more because I don’t expect any of them to pass a fact check and they are usually full of false or misleading information. I am NOT disappointed that so many of these ads are misleading, simply because I have really low expectations for information coming out of the political arena.

But I don’t have such low expectations of science journalism, which is why misleading science headlines really irk me!

FAST Co recently published a really great article by Eric Jaffe on some recent findings on how misleading headlines can leave lasting impressions–even if you read the article!

    “A misleading headline can thus do damage despite genuine attempts to accurately comprehend an article,” the researchers, led by psychologist Ullrich K. H. Ecker of the University of Western Australia, conclude in a new paper in the Journal of Experimental Psychology: Applied.

    Ecker and colleagues believe the big problem with misleading headlines is that they’re just that–misleading, as opposed to downright wrong. Correcting misinformation requires a lot of mental work. People are perfectly capable of doing that work once they recognize the need, but in the case of misleading headlines, that need isn’t always clear. After all, the misleading headline about genetically modified food is true in a very strict sense: the foods may possess long-term health risks, in the same way the world may end tomorrow. As the researchers put it, misleading headlines may have served to nudge behavior “without readers noticing their slant.”

    “[C]orrecting the misinformation conveyed by a misleading headline is a difficult task,” they write. “Particularly in cases of nonobvious misdirection, readers may not be aware of an inconsistency, and may thus not initiate any corrective updating.”

Even worse is that highly viewed misleading articles in the news often leads to other news sources giving similarly misleading reports in order to capture more attention. This creates a widespread impression that the misleading headlines are not actually misleading and helps cement the misinformation.

Case in point for the day:

Unfounded fears about Ebola transmission through the air are already making for really strange policy. We don’t need such wonky policies to go with genetic screens.

Now get out there and vote.

Chocolate chia seed pudding

What do PhD’s do in their spare time? In Jenna’s case, it’s helping other people get healthy and fit. She just started her own site at: http://jenerallyfit.com/index.html and has posted some fabulous recipes.

This looks ridiculously tasty: Chocolate Chia Seed pudding

This pudding is rich and creamy and only takes a few minutes of prep time. Chia seeds (yes, like from the Chia Pet!) can absorb up to 12 times their own weight in water, which helps keep you hydrated and feeling fuller longer. They’re also a great source of protein, fiber and Omega-3 fatty acids. Here is the recipe:

  • 2 oz Chia seeds
  • 8 oz almond milk
  • 2 tbsp cocoa powder
  • Stevia to taste

Mix together ingredients and let sit in the fridge for at least 15 minutes to overnight. The longer it sits the thicker it will get. Makes 2 servings at around 180 calories per serving. You can definitely mix it up by using your favorite milk (coconut, skim) and/or sweetener (honey, agave). If you’re not in the mood for chocolate you can add almond or vanilla extract with cinnamon and raisins instead of cocoa power for an easy rice pudding. Top with your favorite fruit and enjoy for a healthy breakfast or dessert.

Chocolate Chia Seed pudding courtesy of JenerallyFit

Neat Science Thursday – More reasons to use twitter in science

In case you missed it, there was a great post on why you should use Twitter during your PhD on The Thesis Whisperer.

Excerpt:


    Twitter has changed the ‘stuffy’ image of academia. Twitter allows for opinions, debate, and input from others. The conversation that is stimulated is often thought provoking, and helpful when forming your own opinions, especially as a PhD student. It is not often that we are privy to the conversations between experts in our fields, or to their opinions. We often see only their rigorous scientific articles and presentations.

    Live tweeting from conferences, tweet chats, and the opportunity to share personal views has opened up the scientific community to greater interaction through an ongoing conversation. Twitter allows the opportunity to have your ear to the ground, and this is invaluable for a PhD student.

    Finally, Twitter is likely to play an even bigger part in our academic careers than many of us realize. This tweet from @AstroKatie is a testament to the new paradigm of academic impact “My supervisor wrote down huge Twitter presence: 7000 followers on my performance review. Social media outreach FTW!”

If you’re still unconvinced, check out the data sets and presentation slides from ASHG that were released via twitter:

And the jobs and post-doc position notices:

Need any more reasons?

NoB Hackathon

The Network of Biothings is aiming to alleviate the problem of too much information using a number of different approaches such as:

  • Crowdsourcing
  • Natural Language Processing
  • Citizen science
  • Microtask markets
  • Professional biocuration
  • Scientific publishing
  • Open Innovation Challenges

With resources already devoted to (and making incredible progress on) some of the citizen science aspects (ie-Mark2Cure) and some of the scientific publishing (ie- GENE/Gene Wiki) it’s time to draw attention to some crowdsourcing/open innovation challenge effort that is already underway–The NoB 2nd Hackathon taking place on 11/7/2014-11/9/2014 at UC San Diego on the 5th floor of the CALIT2 building.
To join in on the fun, you will first need to register, but scholarships are available to cover registration expenses. Details here.

edit: Here are some ideas for the NoB hackathon, feel free to add your own.

This post was originally written for The Su Lab and Mark2Cure. The post can be viewed in its entirety here.