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Strategies for Better Science Blogging: Part One, Best Practices & Guidelines

Scientific Communication Word Cloud (I Ching)

Last week, there was a kerfuffle around an IFLScience blogpost about rare diseases, and the responses from the rare disease community. In that post, I mentioned that I’d been looking for guidelines, checklist, style guides, and other similar types of tools for effective and appropriate science blogging, but that I wanted to make it a separate post. This is that promised post.

Before I get in too deep, here is a search strategy I used, and which you can use to poke around more in this, if you wish.

(“science blogging” OR “blogging about science”) (“style guide” OR checklist OR guidelines OR “best practices” OR rules)

(1)

Let’s start with the best introduction and brief overview I’ve found, written by Andrew Maynard. In these two posts, Andrew distills the most important lessons learned from years of working with graduate students and collaborating with other bloggers to give feedback on his “Mind the Science Gap” course and blog.

Anyone can blog about science. But it takes effort and diligence to blog well.

When I was teaching the Mind The Science Gap blogging course at the University of Michigan, it became clear early on that, no matter how enthusiastic or knowledgeable you are, there are some basic guidelines that can help make the difference between a great piece and a train wreck (thankfully we never had any of the latter). Over time, these developed into the Mind The Science Gap Good Practice Guide for writing Science Blog Posts.

So you want to write better science blog posts … http://www.riskscience.umich.edu/want-write-better-science-blog-posts/

Good Practice Guide for Writing Science Blog Posts http://www.mindthesciencegap.org/style-guide/good-practice-guide-for-writing-science-blog-posts/

Here is a distillation of his main points in my own words.

PREPARING:
Read broadly.
Read quality.
Skim beyond the basics.

GENERAL:
Don’t imply expertise you don’t have.
Don’t give advice.
If you give opinions, SAY THEY ARE OPINION.

WRITING:
Stick to the facts.
Include multiple voices & sources.
Report on controversies fairly.
CITE THEM.
Be generous with credit to others.

PICTURES:
Choose images to support the story.
Get permission.
Cite your images, also.

LAST STEPS:
Re-read your writing.
Find a proofreader.
Ask yourself if what you said was fair, accurate, scientifically defensible, and honest (FASH).

AFTER:
If you made a mistake, own it.
If you correct a mistake, say so in the post.
Say thanks to whoever raises useful questions.

(2)

Including many of the above, but enriching them with many practical tips from a rich set of interviews with successful science bloggers, this next one is also fabulous. I’d love to see “Blogging Tips” made into an infographic / checklist where I could post it for easy access.

Blogging Tips for Science Bloggers, From Science Bloggers http://www.scilogs.com/from_the_lab_bench/blogging-tips-for-science-bloggers-from-science-bloggers/

(3)

There are a lot of people concerned with the quality of science blogs right now. Andrew Maynard (1) has been teaching classes on science blogging. SciLogs (2) had that series of interviews with best practices. And at Science Online this year, there was a workshop devoted to the topic of standards in science blogging. They used the hashtag #SCIOstandards to extend the conversation through Twitter. I’ve picked just a couple example tweets with good points, but really, it is worth going to the #SCIO Standards Storify and reading through the whole thing!

There is a lot more! Here is one of several Tweets connecting to the Storify. There are also many spin-off conversations without the hashtag. You can see these by browsing from the individual tweets, and reading the replies to them.

For more background about this workshop, check out this link.

Background Reading in Science Blogging – #scioStandards http://www.scilogs.com/next_regeneration/background-reading-in-science-blogging-sciostandards/

(4)

Given that what started all this were questions of science blogging ethics and how blogging can work (or not) within a community, it seemed appropriate to draw attention to the community guidelines and harassment policy from one of the leading science blogging communities and forums, Science Online. It might seem a bit strange to include the concept of harassment in the context of science blogs best practices, but just think for a moment. What is your goal? If it is to inflame controversy and grab attention, then perhaps harassing people is one way to succeed in that goal. If your goal is, however, to accurately communicate science information in an engaging way, then you want to reach a broad audience and you want them to believe you. Making enemies may not be the best path towards that goal. In the case of last week’s IFLScience upset, it is unfortunate that there is a significant audience that felt persecuted and harassed. I don’t believe that was intentional, but it wouldn’t hurt for IFLscience (and the rest of us) to stop and consider whether or not our posts could be interpreted as willfully contentious or harassing as part of those final steps in our checklist before clicking “post.”

Science Online Community Guidelines: http://scienceonline.com/community-guidelines/

Mission:
“ScienceOnline cultivates science conversations both online and face-to-face. At our face-to-face events, we provide an atmosphere that encourages creativity, collaborations, connections, and fun. Through social media, we listen, support, share, recommend, and reach out. Through all of this, we celebrate science.”

Values:
“Respect. Generosity. Acceptance. Open-mindedness. Compassion. Kindness. Curiosity. Enthusiasm. Humor, Wit. Inclusivity. Collaboration. Open-mindedness, Humility. Support. Sharing. Cooperation, rather than competition. Encouragement, Transparency, Engaging all with science. Inclusive, Encouraging Individuality, Cooperation, Creative, Innovative, Engagement. Critical, challenging, enthusiastic. Passion, Great at connecting the dots in a pattern that makes sense 🙂 Principled, Generous, Profound, Profoundly fun.”

Science Online: Harassment Policy: http://scienceonline.com/scienceonline-harassment-policy/

Harassment Policy:
“Harassment includes offensive verbal comments related to ethnicity, religion, disability, physical appearance, gender, or sexual orientation in public spaces, deliberate intimidation, stalking, following, harassing photography or recording, sustained disruption of talks or other events, inappropriate physical contact, and unwelcome attention.”

(5)

I’ve said many times that my favorite piece on how to respond to negative comments on a blog post is the Air Force guidelines shared by Jeremiah Owang.

Air Force Blog Assessment

That said, while it provides a strong general foundation, there are special characteristics to science blogs that may benefit from a slightly different context or require different types of responses. This is especially true when you consider the community and culture of science, and compare that with the broader communities and cultures in which science occurs. Here is a recent post I found by Juliana Houghton, which discusses these issues from the viewpoint of students blogging about science. It’s worth reading.

Student Post: Science Blogging — A Veritable Troll Bridge for the Modern Age: http://www.engage-science.com/student-post-science-blogging-a-veritable-troll-bridge-for-the-modern-age/

“But when we’re writing about things like science, and especially the parts of science that we individually find inspiring and enlightening, we might not expect inflammatory comments that seemingly come out of nowhere. To complicate matters, in science we are trained to question and to respond to questions. It is doubt and questioning that pushes science forward and keeps us from resting on our laurels. Q&A sessions following scientific talks often contain questions that get at the very fabric of our research. We can (and should!) say “I don’t know” when we really don’t, but we also work hard to think carefully about those comments and not dismiss them just because we might prefer our present point of view.”

I loved that paragraph which placed science blogging in the context and culture of doing science. This next snippet is what echoes the Air Force policies mentioned above.

“Ask yourself, is this commenter presenting an alternate viewpoint or just a personal attack. If the latter, it’s ok to just leave a comment unanswered. Another way is to set up strict commenting rules on your site and follow through with moderating. If your rule is that comments must address the article’s topic and the comment simply calls the author a nasty name, then it never even needs to appear on the webpage (or can be quickly taken down by the moderator, depending on your settings).”

(6)

Last but not least, let’s look at science blogging in the broader context of academic and scholarly blogging. There are best practices and courses for those environments, also! Virtually all of what appears in the literature on academic blogging is relevant to science blogging. Jessie Daniels and Polly Thistlethwaite drafted a quite nice overview at Just Publics 365, which provides context beyond much of what has already been said — about the target audience, your readers, differences in writing styles between blogs and professional research venues, and more. They’ve made this available in a variety of formats.

A Guide to Blogging for Academics http://justpublics365.commons.gc.cuny.edu/2014/06/30/academic-guide-to-blogging/

1. Talk to Me: Acknowledge the Reader.
2. Just Say It: Don’t lead with a disclaimer or qualifier.
3. K.I.S.S. : Keep it Simple Scholar
4. Get in & Get Out.
5. No, It’s Not All Important
6. If You Have Something to Say, Say It
7. Don’t Let Perfection Be The Enemy of The Good
8. Scholarly Writing vs. Public Writing

The Academic’s Guide to Writing Online http://sociologysource.squarespace.com/storage/Academics_Guide_To_Writing_Online.pdf

Illustrated Blogging Advice for Researchers
http://justpublics365.commons.gc.cuny.edu/2013/09/11/illustrated-blogging-advice-for-researchers/

Media Skills for Scholars http://mediaskillsforscholars.pressbooks.com/

Just to connect that back to the science context, there is an older article about science blogging that has some similar insights, and which discusses why scientists blog. I found it interesting and useful to just break out the section headings from that article.

Bonetta, Laura. Scientists Enter the Blogosphere. Cell 129 (May 4, 2007):443-445. http://www.cell.com/abstract/S0092-8674(07)00543-0

Meet the Bloggers
Blogging to E-ducate
What is the Impact?
Why Aren’t You Blogging?
Blogging to Talk Shop
Communities of Bloggers

Closing thoughts

Do you know why you are blogging? Are there any of these best practices that you wish you did better? There are for me! We all have strengths and weaknesses, may be good at one thing and not so strong in other areas. I don’t usually have anyone read over my work before it goes live, and there are likely to be a lot of possible errors as a result of that. So far, I’ve scraped by, and I’m grateful that this is just a personal blog and that I don’t face the kind of audience and attention that IFLScience have. I’m not sure I’d do any better with the scrutiny than they are currently.

I did find many other resources along these lines. These are more the high profile pieces and overall context. I hope to have another post to simply share a lot of links that might be of further interest.

Good Lord, People, 23andMe is NOT Dead!

Reposting from my personal genomics blog because I think it is important also for the audience of this blog.


23andMe

Good Lord, people, 23andMe is NOT dead! Or closed, or no longer taking orders, or anything like that. I hear this a lot.

“You know, I always wanted to get my genome tested. I was going to try 23andMe, but then the FDA shut them down. Oh, well, missed my chance. [sigh]”

NO! You did NOT miss your chance. Firstly, 23andMe is not closed for business. They still will take your money and your sample. They still will analyze the sample and give you results. From what I’ve been seeing in the results from folk I’ve been helping to look at their data, 23andMe seems to be running the test exactly the same way they always did, for the same SNPs.

They simply are, at this time, not offering their health reports to new customers. It isn’t the data that has changed – it iw what analysis is shared with the customer. Old fogies like me who got their tests done before the FDA folderol” still have access to our old 23andMe health reports, and they continue to improve them.

I have heard nothing to indicate that 23andMe are not working with the FDA to try to make it possible to release health reports again in the future. Issues around that get complicated and I’m going to save them for a later post. Right now, what if you wanted a test for some genetic health information? Can you do it? How long will you have to wait to find out the answers to your health questions?

You can still do it. It isn’t as easy as it was before, but it can be done. I’ve been spending a lot of time talking people through how to do this, and it is time to write it down. If nothing else, it will save me time. This will be the short short version, and I can answer more detailed questions and describe specifics, maybe give an example or two or three.

FIRST, THE DISCLAIMER

Risk is Not Just Genes

Making sense of genetic information is complicated even for experts, which most of us are not. Of course, part of the irony of looking at genetics for health conditions is that most of the time what causes the condition is not just the genetics, but genes PLUS something else. If you don’t find the genes for something, that doesn’t mean you can’t get it; if you do find the genes for something, it doesn’t mean you will get it. It is hardly ever a case of this=that.

What Does Risk Mean, Anyway?

There is also the challenge of figuring out how important the risk is, and whether or not to do something about it. So, my personal risk of celiac disease is over 4 times normal. Wow! That sounds like a lot, doesn’t it? But 4 times normal for celiac risk is still only 1 in 20 people, because normal is about 1 in a hundred. I know someone with celiac risk 17 times normal, which is 1 in 4 people. That’s getting to be pretty serious! But, while celiac is dangerous, it isn’t one of those conditions that is immediately deadly or painful. And my friend still has a 3 in 4 chance of NOT getting celiac, and that is a lifetime risk.

On the other hand, my risk of venous thromboembolism (VTE) is 1.5 times normal. That doesn’t sound like much does it? It’s higher, but only a little bit. So we don’t really need to worry about it, do we? Well, yes. VTE can kill you on the spot, and it is incredibly painful. And normal is 1 in 10 people for lifetime risk. For me, the risk is closer to 1 in 7.

Given that, according to 23andMe, my genetic risk of celiac is roughly 1/20 and my risk of VTE is 1/7, and adding in the comparative dangers of the two diseases, my docs got all excited about the VTE, and not terribly about the celiac. I hope you understand why now, and also a bit more about why genetic risk is complicated.

On Asking for Help

Last part of the disclaimer.

For both of these, celiac and VTE, 23andMe looks at SOME of the genes and SNPs known to be associated with the condition, but not ALL of them. So whatever 23andMe tells me about risk is only part of the picture. It looks at the most important genes, but is still only part of the picture. That’s why you need experts to put all the pieces together, and get more information to fill in the gaps from the 23andMe test.

Everyone always says, “Ask your doctor,” when it comes to finding something puzzling, confusing, contradictory, or worrisome in your genetic tests. I did, and found that most of my doctors didn’t have the expertise to make more out of it than I did. Some poohpoohed the 23andMe results, others made clinical decisions based on them without verifying with other tests, some asked for more medical tests to expand upon what 23andMe had, and one said, “You know more about this than I do, but I’m going to learn.” Here is a quote from an NEJM article a few months ago about the risks and benefits of trusting direct-to-consumer personal genomic services such as 23andMe.

“Clinicians will be central to helping consumer–patients use genomic information to make health decisions. Any regulatory regime must recognize this reality by doing more than simply adding the tagline on most consumer ads for prescription drugs: “Ask your physician.” That is insufficient guidance unless your physician has ready access to a clinical geneticist or genetic counselor.” Annas GJ, Elias S. 23andMe and the FDA. N Engl J Med 2014; 370:985-988. http://www.nejm.org/doi/full/10.1056/NEJMp1316367

Some of the personal genomics service offer phone-in access to genetic counselors. I tried that, and didn’t get helpful answers there, either. Even worse, one of the answers I got was blatantly wrong. It may have been just the genetic counselor who I happened to be talking with, so don’t judge the whole profession by that one person, but do be prepared to keep looking for info if needed. Where I found the most helpful information was in the 23andMe forums, BUT a lot of the info there was unreliable, and I had to sort out what was helpful and what wasn’t.

So, my recommendation is, absolutely DO ask your doctor, ask a genetic counselor if you can, but that might not be enough. You might need to do more research on your own, or find someone you trust to help you with this.

What Good Is It?

So, what good is it then? It gives you clues. Like a detective, you take the clues and look for more information, or ask for more thorough testing, or raise questions that weren’t being asked or addressed before. Some of the clues will be red herrings. Some of them may lead you to a prized solution. For me, these clues ended up dramatically improving my quality of life, and may have even saved my life.


So, now, the short short version. And PLEASE, if someone more expert than me with genomic data reads this and spots any errors, please say so!

PART ONE

1. Get your 23andMe test done.

Pic of the Day - PGenPGEN, Take 2

2. Log in at the 23andMe web site when you are notified that your results are ready.

23andMe

3. Click: Browse raw data.
23andMe: Getting to your raw data

It should look like this:

23andMe: Browse Raw Data

4. Click: Download raw data.
23andMe: Download Raw Data

5. Complete security procedure (log in again, answer security questions, etc.). It should look like this.

23andMe: Downloading Raw Data

6. Answer the question about what type of data and format you want. NOTE: I always choose ALL DNA, unless you have something else specifically in mind.

23andMe: Downloading ALL Your Raw Data Or ...

7. Find the file (which will be named something like genome_Firstname_Lastname_Full_12345678901234.txt)

PART TWO (A): Easier Way

Genetic Genie

Now you have choices. You can dig into the information the easier way, or the less easy way. Let’s start with the easier way.

1. Select a tool to do what you want with your data. There are LOTS of tools people have built to do useful things with 23andMe data files. One of my favorites is Genetic Genie, because it tells you about the MTHFR gene which has become so important in my life. I also am spending a lot of time with Promethease because it is so complete compared to most other 23andMe analysis tools. Lets start with these.

2. Go to the tool of your choice, such as:

Genetic Genie: http://geneticgenie.org/

Promethease: http://www.snpedia.com/index.php/Promethease

3. Follow the directions at the tool, but this almost always requires you to upload your 23andMe data file. Here are more details about doing this with Genetic Genie.

4. Last come what is always the tricky part — making sense of the information you get. That’s worth several posts, but for starters the main point to remember is that the 23andMe test is a place to start, not a final answer. In Genetic Genie, the code, analysis, and text are written by engaged amateurs, not by doctors or genetic counselors. They worked hard, collaborated with a lot of other people, and did a lot of research, but it isn’t going to say the same things your doctor might.

More Tools

23andMe: Tools for Everyone http://www.23andyou.com/3rdparty
NOTE: When 23andMe took out the health reports, they also edited this page to remove links to tools that provide health data from 23andMe data. So, this is interesting and useful, but not sufficient. You’ll have to look somewhere else for most tools.

23++ Chrome Extension: Get more from your data:
http://23pp.david-web.co.uk/getting-more-from-your-data/

Confessions of a Cryokid: Top 10 things to do with your FTDNA raw data (2011) http://cryokidconfessions.blogspot.com/2011/06/top-10-things-to-do-with-your-ftdna-raw.html

Genetic Genealogist: What Else Can I Do With My DNA Results: http://www.thegeneticgenealogist.com/2013/09/22/what-else-can-i-do-with-my-dna-test-results/

International Society of Genetic Genealogy: Autosomal DNA Tools: http://www.isogg.org/wiki/Autosomal_DNA_tools

Resqua: Q: What should I do after generating my Gene variance report? http://resqua.com/100005927200207/what-should-i-do-after-generating-my-gene-variance-report

Think Exponential: Get SNPd! http://thinkexponential.com/2013/01/10/why-you-should-get-snped/

PART TWO (B): Less Easy Way

Linking Disease Associations with Regulatory Information in the Human Genome

Actually, there are a LOT of different “less easy ways.” You can open the raw data file in a text editor and search manually for specific pieces of information. Or, if you code, you can write a little program to do some of the hard work for you.

Basically, it comes down to doing a lot of research, the hard way, by hand. But, believe it or not, I am doing it. I’ve had a lot of help from people who offered tips or comments in the 23andMe or MTHFR.net forums, on Facebook, on Twitter, and comments on these blogs. I am NOT an expert, but like most readers of this blog, just someone who wants or needs to know more. This is what I’ve learned and figured out on my own, offered as an example, nothing more.

Critical Background

23andMe gives SNP-based data. SNP stands for single nucleotide polymorphism. Polymorphism means something that can be itself but in different ways, our eyes are eyes whether they are blue or brown or hazel or violet or any other natural eye color. I won’t give an introduction to genetics here, but there are several online resources that explain these ideas, with one of the best resources being Genetic Home Reference from the US government. Depending on how much you want to know, you may wish to take the Coursera courses Introduction to Genetics and Evolution (Duke U) or Experimental Genome Science (U Penn).

1. What SNPs do you want to know about? Check here:

RegulomeDB (Stanford): Linking Disease Associations with Regulatory Information in the Human Genome: http://regulomedb.org/GWAS/

I have also found SNPs of interest in research articles, PUBMED, and other places, but this is a good start. The SNP identifier (what you need) will look something like this:

rs2187668

2. Find out which polymorphism is the one considered “healthy” or “normal”, and which one is the one associated with risk of disease? These maybe called “risk alleles” or
simply polymorphisms.

For example, for SNP “rs2187668” (one of the celiac risk SNPs) the risk indicator is (T), while the normal is (C).

3. Open your 23andMe raw data file in a text editor, like WordPad (Windows) or TextEdit or TextWrangler (Macintosh).

4. Search for the SNP you want to know about. The data will be in four columns:
– RSID
– Chromosome
– Position
– Genotype
You need to know about the first and last columns, RSID and Genotype. It will look a little like this.

rsid…..chromosome…..position…..genotype
… [many other rows of data] …
rs2187668…..6………32605884…..CT

So, this person (me) has for that SNP one risk allele “T,” (which I happen to know is from my dad, by comparing it to his scan) and one normal allele “C,” (which must, by default, be from my mom, since for every gene pair we have gotten one from each parent).

5. Repeat for all the other SNPs associated with the condition you are researching.

6. Search for more information and articles about those SNPs, the condition, and more. You can’t make sense of this without more information. And ask lots of questions.

More Tools

ENCODE:
About: http://www.genome.gov/encode/
Data: http://genome.ucsc.edu/encode/

ENSEMBL Genome Browser: http://useast.ensembl.org/

OpenSNP: https://opensnp.org/ OR https://opensnp.org/snps/

SNPedia: http://www.snpedia.com/

UCSC Genome Browser: http://genome.ucsc.edu/