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23andMe

One of the stranger call-ins on my interview with Kathleen Dunn last month was when a woman who proudly declared that she was a math major in college asserted that 23andMe had told her she wasn’t at risk for many diseases which now in her 60s she had developed. I didn’t want to be too pointed about it, but if you are in your 60s you are at risk for developing many illnesses no matter what your “genetic risk.” This is clear from 23andMe’s statistics, which display high baseline risks for many common diseases. From reading comments on 23andMe discussion forums it seems that perceived false negatives are going to be a much bigger issue than false positives over the long run. If the tests are “wrong” in a direction which leaves you in a better state than predicted you might feel like you’ve dodged a bullet. On other hand if the tests are “wrong” in a direction which gave you false comfort, or add insult to injury when you’ve developed a debilitating disease, then you feel much more burned.

I don’t really recommend blogs too much anymore. But please check out The Stage and Social Evolution Forum.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Blog, Open Thread 
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Beginnings and endings.

(Republished from Discover/GNXP by permission of author or representative)
 
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Questions?

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I found this broadside against intellectual ignorance by Christoper Beckwith rather amazing and enjoyable. Long time readers will be aware that I am a fan of his Empires of the Silk Road. In any case, I have noticed that many of my friends and acquaintances use the term ‘ignorance’ to connote a set of views which they find normatively offensive. That is not my preferred usage of the term. Rather, I take it rather at its face value as denoting those who are lacking in the basic facts from which to even attempt audacious inference. The latter I appreciate. The former I detest.

(Republished from Discover/GNXP by permission of author or representative)
 
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How do people manage to keep track of the scientific literature in their area?

(Republished from Discover/GNXP by permission of author or representative)
 
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Don’t be shy

A few weeks ago I was asked on Twitter by someone for advice on how to write a science blog/do science communication. Since I was studying up for my qualifying exam I said I’d get back to him later. I passed, and now this is later.

First, you should probably read Sabine and Chad. Second, I’ll be up front and admit that I don’t give much thought in the details to this sort of thing (though I follow with interest the opinions of others, such as Bora Zivkovic, on this topic). I really only have one qualification: I’ve been doing this for a long time. Since spring of 2002. To my knowledge only Derek Lowe has been blogging continually and without interruption about science longer than I have (Chad Orzel of Uncertain Principles also started in the spring of 2002).

So in no special order, my “advice”….


Know your goal. This is such a vague and general admonishment to be almost vacuous. But I mean it sincerely. For example, what’s my goal? Basically to write about things that interest me, first and foremost. Obviously I can spin secondary goals out of this (educate the public, make some money, gain marginal internet fame, etc.). But what keeps me writing is that I’m chattering about topics and issues that are objects of intellectual obsession. This means that you sometimes have to read me going on and on about site frequency spectra, and in other cases my interpretation on the importance of the Byzantinze apogee under Basil II. Other people are more focused. Ed Yong worked really hard to get where he is now as a freelance science writer with a wide range of outlets, and he did it to a large extent by extremely high quality writerly blogging. At the other extreme you have someone like Michael Eisen, who offers his unvarnished opinions as a scientist on a variety of topics, though generally science and science policy related. I don’t think anyone assumes Eisen wants to become a writer, but obviously he needs outlets besides what scientific journals can provide. Then you have John Hawks’ model, a professional scientist in writerly garb. It’s more important that you have some internal raison d’etre than that it be coherent, consistent, or even attainable.

Know the web of 2013. You don’t have to be a systems administrator or web developer, but you have to have a minimal amount of web 2.0 awareness. To illustrate what I mean, say you go to PNAS and see an article you like, and want to link to it in your Twitter feed. It turns out to be rather difficult to find the appropriate widget to share, though it is there. But once you try to use it all it fills in for you is the link. Not the title. So you have to manually cut & paste the title, since people often don’t want to click a link if they don’t know what it is to. Or if you go to an abstract in Current Biology, there’s a Facebook like option, but not a Twitter widget. I’m not really picking on these journals, rather, I’m using them to illustrate that a lot of these publications don’t even know how to leverage social media to increase their exposure. And what applies to journals applies to you. This isn’t 2003, and traffic is not driven just through links. Much of the initial exposure you’ll get is via social networks like Twitter and Facebook, so make sure that those widgets are installed. This may seem trivial, but there are too many cases where people don’t bother to install them, while asking me how they could increase their web visibility. Make commenting not too much of a hassle. Don’t overwhelm your site with an enormous visual header which takes up a lot of bandwidth, and occludes much of the screen. Make your RSS feed link prominent so people can subscribe. In other words, reduce the energy that it requires others to find and relay the content you’re generating.

Writing is iterative, chill out. You really have to jump in and figure out your speed (or realize it isn’t for you). Different people have different styles. You won’t know what your style is until you actually go ahead and start writing. You won’t know if it is for you unless you actually try it. Many people flame out and leave behind a blogspot site with one or two posts because they don’t have the first two elements under control, but a minimal level of persistence is also necessary. To iterate means repeat, and you need to try again and again until you converge upon your personal golden mean. The process though is riddled with misfires. If you can’t tolerate that, then you might not be able to tolerate the process.

Write what you know, or what you want to know more about. Pretty self-explanatory. You don’t need to have a Ph.D. to have passion and interest in topics. But you better have those in the first place.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Blog, Blogging 
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The Way of the Sages

On occasion I recommend to friends reading what are to the public obscure philosophers such as Nietzsche and Plato. This is not because I necessarily think that these individuals had deep and/or true thoughts and ideas (though in some cases I do believe they did). Rather, I want to make it clear to angst ridden moderns that cognitive tail chasing has been around a long time, and others have done it with more thoroughness and aplomb, so there’s no point in wasting time and being original. Also, smart opinions from people whose world views are fundamentally alien toward our own allows us to consider what dogmas and orthodoxies we hold as self-evident truths. The reality is on questions of “meta” (physics, ethics) there hasn’t been that much progress on the margin over the past ~3,000 years, in sharp contrast to what used to be natural philosophy and logic/geometry. As an example, I don’t find our arguments against slavery particularly impressive compared the rebuttals of the ancients or basically any pre-moderns in favor slavery as a necessary evil or even a good. Rather, what I find impressive is our realized humanity. In most areas our advances have been in what we have done, not our justifications for what we have done.

(Republished from Discover/GNXP by permission of author or representative)
 
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Summer is coming!

(Republished from Discover/GNXP by permission of author or representative)
 
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A lot’s been happening. The human phylogenetic graph is looking curiouser and curiouser.

(Republished from Discover/GNXP by permission of author or representative)
 
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The usual.

I haven’t been able to blog much because of various other responsibilities, but I definitely do feel pent up posting energy. So when I come back I assume that I’ll have a lot of stuff to say. Meanwhile I’m chortling a bit about this bizarre attack on my friend Steve Hsu. Here’s the issue that I always have with this: Steve managed to get tenure as a theoretical physicist. When you’re talking to someone who is an academic theoretical physicist it is generally optimal to not assume a priori that they’re ignorant dullards. Unless that is you want to just engage in empty signalling rhetoric.

Though despite not having concerted time to write, I am tweeting a lot since that requires only minimal lengths of attention. Mostly it’s just repeating the functionality of my Pinboard, though I do comment and what not.

Finally, I keep hearing that the Big Five personality typology is much more scientific than Myers Briggs. So I took a bunch of tests which purport to analyze the Big Five categories.

Extraverted: Very high. Consistent. I was 90-99% on all tests.
Agreeableness: Low. Consistent. Generally in the 15-0% range.
Openness: Medium. This was not very consistent. 40-60% range.
Neuroticism: Erratic. For whatever reason I varied from 20-80% here.
Conscientiousness: Medium. But there was some variation.

Oh, and here’s a list of books I’ve rated for Good Reads.

(Republished from Discover/GNXP by permission of author or representative)
 
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Last week’s thread was rather informative.

(Republished from Discover/GNXP by permission of author or representative)
 
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For old time’s sake. The cats have a new companion….

(Republished from Discover/GNXP by permission of author or representative)
 
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With the impending expiration of Google Reader, I have been using Feedly, and I like it quite a bit. So if you’ve been procrastinating, check it out.

The Feedburner address for this blog is:

http://feeds.feedburner.com/GeneExpressionBlog

The blog content is of course pushed to Twitter:

https://twitter.com/razibkhan

Also, if for whatever reason you want Razib-curated-content, my Pinboard is public (RSS). I also push content to a Facebook account. And the best way to contact me is using one of the options on my personal website. And with that I end this irregularly scheduled administrative post.

(Republished from Discover/GNXP by permission of author or representative)
 
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St. Patrick was just one man!

(Republished from Discover/GNXP by permission of author or representative)
 
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A citizen of the Republic of Letters

Many people have been talking about the Patrick Dunleavy and Chris Gilson piece on why academics should blog. In my own opinion it’s a little hyperbolic, not everyone is the same, whether it is in inter-individual differences in attributes, or the circumstantial point where one is in their career (e.g., if you are a graduate student or postdoc then your boss/mentor’s attitude matters a lot). With that out of the way I think it is important to reiterate that more academics should blog sometimes. I suspect one issue is that the image of academic bloggers is dominated by people such as Jerry Coyne or the guys at Marginal Revolution. They blog in huge quantity on a wide range of topics. Obviously this is not suitable for everyone’s temperament or situation (it seems that after tenure there is a greater obligation to engage in communication because the biggest hurdle of impressing one’s colleagues is over with, though that’s just me).

But there are other models. There are many times on Twitter where I am party to/or interact with someone where the format becomes tedious and uninformative, and yet the individual still has very strong opinions on the subject. At this point I’m prompted to ask “do you have a blog where you could elaborate your position?” Most of the time the answer is no. And my question here is why? Many academics seem satisfied with 1999 vintage web pages with a short list of qualifications and publications. Often these are years out of date. I’ve met aspiring graduate students who approached a professor from afar to do research after browsing lab websites, only to be told that the lab’s research focus had totally moved in a different direction, they just hadn’t updated their page (this is why it is useful to do a literature search to supplement the lab web page, but shouldn’t the lab web page ideally actually inform you about the state of research in said lab?).

I don’t think it would be productive to have thousands more Jerry Coynes or Tyler Cowens. But, I think it would be productive to have thousands more Michael Eisens. Eisen can go months without posting, but when he does post it often gets a lot of people’s attention. That’s because he talks about what he knows about and what he is passionate about. It doesn’t matter that he doesn’t generate a stream of content, when the wadi that is it is NOT junk turns into a raging torrent, you better take notice (and most people do).

Mind you, I am aware that Michael Eisen is gifted with a particular personality profile (which seems to be shared by his brother, Jonathan) which make trenchant blog posts to be expected, and likely relatively easy. But I think a huge number of academics fall under the intersecting conditions of:

1) Specialized knowledge
2) Passion about that specialized knowledge

To give a concrete example of why I think more academics should be blogging: I’m sick of hearing selective quotes in the media from specialists who are consulted after a big splash is made by some result in the popular press. I want to hear the specialists at length in their own words. And don’t tell me it would take too much time, from what I can tell most of the time one is interviewed by the media 95% of the content is not transmitted. Not only that, you don’t have a choice on which quotes are excised out of the full context of your assertions.

Finally, I want to concede that at the end of the day many, many, academics will never blog. And that’s OK. I just think that many more have the aptitude/inclination than currently blog due to cultural inertia. Especially if you can burn time on Twitter, you can afford to blog every few months on some topic that where you add value to the information ecology.

WordPress is easy and it’s free.

Related: The first steps towards a modern system of scientific publication.

Addendum: Here are three blogs which I follow because of my personal interests which illustrate the variety of communication styles, Evolutionary Genomics Blog, Genomes Unzipped, and Haldane’s Sieve.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Blog, Blogging 
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I’ve observed the rise of Ezra Klein out of the corner of my eye for years. Political blogging is not really my thing, but I’ve been “around,” and I’ve brushed up against the “Juicebox” now and then (though I interacted with Matt Yglesias as early as 2003, usually I get on the radar of Washington policy types when my friend Reihan Salam picks up something I say). So I thought I’d point you to a profile in The New Republic, Ezra Klein: The Wise Boy, A tale of striving and success in modern-day Washington.

But I want to preface it with a weird incident that happened last year. My high school history teacher, now retired, and a self-identified moderate Democrat (his background is urban Midwestern white working class), passed along an Ezra Klein column and observed, “even the conservative Ezra Klein thinks….” Not everyone is a political junkie, or has watched the ideological perceptions of people change over time, but this was really bizarre for me. Four years ago I talked to Klein on the phone while working on my profile of Reihan Salam. I didn’t use anything Klein said because he kept pulling the best stuff “off the record.” Since I’m not a journalist this struck me as kind of strange, but I respected his preferences. I always think it is really weird to think that circa 2013 Ezra Klein is saying anything good about Republicans, when circa 2008 Ezra Klein had very little positive to offer when allowed to be candid (sugarcoating the tone and content; and to be clear, he had only good things to say about Reihan).

And yet who I am to judge? Archives of my stupid thoughts go back to 2002. That’s 11 years, and I’ve changed quite a bit, though not in all ways. Many people who become “public intellectuals” today are not going to have the luxury of being stupid anonymously, to get prominent you have to put yourself “out there” in the first place. When people ask me how to become a decent blogger, I always say, “get over your fear of saying stupid things in front of people.” Of course at some point you can start to pull things off the web, but it is highly likely that your comments are cached somewhere, and are going to be retrieved if one is persistent. I found the profile of Klein interesting, and appreciated that the author brought to light his older comments…but really who doesn’t have plenty of contradictory opinions over a decade? If you put a lot of them out in public in a journal form it isn’t hard to construct juicy juxtapositions.

This is of course just an elaborated version of what everyone is going to go through with the “death of privacy.” We’re in the awkward transition where digging up old quotes or embarrassing photos still has shock value. The trick will get old soon enough.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Blog 
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As some of you may have noticed, Neuroskeptic has joined Discover. I am rather pleased. There will be others soon enough.

Chris Chabris has a blog. I reviewed his book The Invisible Gorilla a few years back. Here’s one thing I would say about Chabris: I read him very closely, because he is very careful. And I’ve been doing so since the late 1990s, when I first encountered his writing.


Ruling Islamists, Under Attack, Reject Blame for Tunisia’s Woes. Tunisia was, in my pinion, the Arab Spring’s first best hope.

Paper: Men and Women Are From Earth: Examining the Latent Structure of Gender. Most people who believe that there are differences between groups, who are not totally stupid, don’t conjecture that they are categorical and dichotomous classes. Men are taller than women in a pragmatic sense does no entail that all men are taller than women.

DIY biotech spreads to community. In many ways I think “DIY” is going to become a buzzword with less meaning in the near future. With the proliferation of information appliances we’ll do lots of things ourselves, bu we won’t be amateur about it.

Fears of the Future Haunt a Budding Generation of Afghan Strivers. American economic stimulus driven by taxation causes prosperity somewhere.

Isotopic data show farming arrived in Europe with migrants. We need to be careful of projecting two exclusionary models.

Inside China’s Genome Factory. BGI may have great publicists, but I suspect to a large extent they are the real deal.

Honey Boo Boo’s Mom is Actually Doing Something Smart with Her Reality Show Money.

Zen Groups Distressed by Accusations Against Teacher. One of the most annoying thing about sincere and zealous “spiritual seekers” and they often end up worshiping “teachers” in a cult-like manner. Call me an old fashioned Whig, but true wisdom isn’t found in ancient books or over confident charlatans.

The Dice Are Rolling on Dell’s Legacy. There are no eternal winners in capitalism.

God Made A Factory Farmer.

When E-Mail Turns From Delight to Deluge. Facebook has siphoned off a lot of the inter-personal email.

Michael Bloomberg, Tireless Champion of Civil Liberties. Yes. You read that right.

Why Are There So Few Vegetarians? I found out about these stats a few years ago.

uBiome. I think I’m in.

(Republished from Discover/GNXP by permission of author or representative)
 
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I’ve been saying for a few weeks that this weblog’s comments are going to be improved with a Disqus system. Worry no more, I have a “hard date.” I’m not going to give it to you because my personal experience with hard dates in I.T. is that things come up, and delays are routine. But, it won’t be much longer. In the range of weeks, not months. All the features that I missed will be back, and you should be able to leave comments with Twitter or Facebook authentication.

(Republished from Discover/GNXP by permission of author or representative)
 
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Well, I don’t have as much time for these anymore…but here it goes….

Haldane’s Sieve. A must if you are interested in evolutionary/population genetics/genomics (not that you can keep up with it all, but interesting for a taste). Since it only posts on pre-prints you don’t need academic access to get into the academic literature.

Human Varieties. A blog which discusses relatively taboo topics such as psychometrics (well, OK, topics which are taboo so long as you don’t have children who are entering elementary school, at which point you examine average test scores with the same acuity as Alfred Binet).

Reaction Norm. He’s been hibernating for a few weeks. Perhaps he’s found a job?

America’s Real Criminal Element: Lead: New research finds Pb is the hidden villain behind violent crime, lower IQs, and even the ADHD epidemic. And fixing the problem is a lot cheaper than doing nothing. Obvious why it’s important.

Lead and Crime. Jim Manzi’s response.

My Mom Was Too Old: She had me at 42. She got frail before I was ready. There seems to be a trend of such stories. If you read it in detail you observe that delaying child-bearing has positive results in some ways (e.g., more financially stable). But as your own children grow up and mature their own freedom and self-actualization is hampered by the fact that they have to tend to their parents. I think one major strand of inter-generational tension which is going to become more prominent is the resentment of the children of the baby boomers who delayed parenthood. Because the boomer’s own parents had them relatively young they did not pay the cost of delayed parenthood which they are incurring upon their own offspring.

Did the Pro-Life Movement Lead to More Single Moms? This reminds me of Eric Cartmenez.

GQ’s Hottest Women List Separates Out the Indian and Asian Chicks. One of the weird things as the 21st century progresses is that the public discourse holds that race blindness in attractiveness in normative, but in their personal lives people tend to go with their inner Bull Connor. In fact I’m 99% sure that my friends who admit privately that they are only attracted to race X (usually their own race) would express public outrage at this sort of thing.

How academia betrayed and continues to betray Aaron Swartz. In your heart you know Michael Eisen’s right, even if you do go ahead and publish in Nature!

Harvard professor blasts Neanderthal clone baby rumor on Web. The whole George Church story is a weird fiasco. On the other hand a journalist friend told me a few months ago that Church was floating this idea of recreating Neandertals, at least in a speculative sense, so I’m not surprised that things got lost in translation.

Rump Faker: Is imitation calamari made from pig rectum? A charming urban legend gets its start. No comment.

Web Tell-All on an Affair Brings Down a Chinese Official. With greater transparency due to technology hypocrisy is going to get much more difficult in some domains.

Mathematicians aim to take publishers out of publishing. Now my question is why many humanities don’t follow suit.

War was central to Europe’s first civilization, contrary to popular belief. The Minoans were not peace loving goddess worshipers. I’d already assumed this, but I’ve encountered people who keep telling me that Minoans were matriarchal.

Comments Suck Right? So Why Do You Have Them. The comments of many opinion journals are a cesspool. So what’s the point?

Is the Neurodiversity Movement Misrepresenting Autism? For some reason we have a difficult time calling a pathology a pathology. I know people who have Asperger who have “trained” themselves to be functional. It can be done, but you need to acknowledge the problem in the first place. The issues for low functioning autistic individuals are far different of course.

Scientiam Consecemus!! The Ronin Institute is a cool idea.

Consider public archiving for your dissertation. This seems like an obvious thing to do. Unless Monsanto is funding your whole project.

Study: The New Less-Social Psychology of China’s Generation Without Siblings. One of the biggest social engineering experiments out there in the world today is the trend toward smaller families. China is the logical extreme of this. Why is this social engineering? Societies dependent upon nepotism and familial networks are going to find in the near future that the “circle of cousins” is going to be much smaller and more fragmented.

Germs Are Us: Bacteria make us sick. Do they also keep us alive? Microbiomes are going to be the “next big thing.” So you might as well start reading about it.

Let’s face it: New arrivals are draining the economy. No comment.

Vandana Shiva: Brahmin in Shudra clothing. This post is probably too harsh, but Ron Bailey years ago pointed out that Vandana Shiva is a rather plump woman. This matters because anti-GMO activism is often an a lifestyle choice of the affluent post-materialist set. In developed nations this is one thing, but in nations like India where a significant proportion of the population is malnourished it’s rather galling that the well fed are attempting to constrain the choices of the ill fed.

How a quarter of the cow genome came from snakes. This is one reason GMO does not scare me too much.

Apple Killed the Netbook. I came close to getting a Netbook, but balked at the feature set for the price.

Derailed: The Rise and Fall of Diederik Stapel. I doubt there are that many Stapel’s in science, but even a few can ruin the whole enterprise.

Egg-Laying Mammal: Scientists Discover That for Australia the Long-Beaked Echidna May Not Be a Thing of the Past. The sort of thing that gives cryptozoologists hope.

Maybe “The Big Sort” Never Happened. Reanalyzing social science truisms is important.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Around the Web, Blog 
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John Hawks, Online communication biases upon the public perception of science:

Anyone who reads comments sections following news articles surely will have noticed the rotten wealth of trolls and other idiots who inhabit such forums. I thought about Brossard and Scheufele’s piece again today when I read a post by Dan Conover at Xark: “Why I shut down comments”. The post reflects on how blog communities have changed since the early days of blogging in 2005. This timeframe has coincided with the growth of social media of other types, such as Facebook and Twitter, which have given many people a closed community for sharing comments and perspectives with like-minded folks. Conover observes that the trolls and spam are more persistent, causing a rapid degradation of the value of comment sections of many blogs.

This isn’t of course universal. Many blogs continue to have rich and varied comment sections with their posts, and some (like mine) never had any comments at all….

To which Chris Mims graciously observes:

Unfortunately, due to the switch to a backward comment system this is applicable, if at all true, in the past tense. Before moving to the new set up I spent ~50% of my time related to this blog on the comments. I’d say now that that has gone down to ~10%, being generous. One might surmise from this that more time is devoted to generating content, but if you’ve kept track of this weblog you know that that’s not true. Rather, what seems to have happened is that the pulling away of engagement from the comments dampened my enthusiasm to write. This is a side aspect of my life, and I have other professional and personal commitments. I can see that plenty of people are reading from the Analytics, but the feedback seems critical to motivating me.

So what happened? In a proximate sense a few minor changes in technology resulted in a shift in the human dimension of engagement, and the whole system’s equilibrium was thrown off! I find it somewhat amusing that people talk about 2005 as the early days of blogging. This is technically true, but I’d been blogging for 3 years then, and some of the commenters on this weblog even go back to that 2002 era. Over the past 10 years I’ve developed a set of heuristics, but the new system makes it much more difficult for me to enforce them. Why?

First, I don’t know when comments are coming in. Clicking each post, and waiting for the comments to load is onerous. There isn’t even a sidebar where new comments are displayed. In the old system whenever I logged into the dashboard I could see comments, including the first sentence or two. In other words gauging the temperature of the commentary was extremely easy, with a low barrier to entry in terms of time commitments. Second, initially I couldn’t even moderate the comments rapidly (as I can now, finally). So the two essential activities relating to comments were hobbled by the new system: read & response.

For young comment threads I would at least see very quickly the beginnings of almost all posts. And when a response was necessary I would react very quickly. What sort of response was needful? I removed trolls and banned them immediately without any warning. This happened every single day. Extremely low quality comments drive away engagement. Second, I also tended to draw commenters out, and demand more of them, than they might be willing to give initially. Why? Because people need to see that their contribution to a discussion will result in genuine dialogue and exchange. If commenters got out of line, but not necessarily in a conventional trollish fashion, I felt it within my rights to track them down on Facebook and demand answers. This was usually trivially easy, and those who took upon haughty airs invariably expressed humility or remorse when called out by their real name by another human being.

And it is the synthesis of the human and technological that is critical. Technology needs to enable genuine human engagement. It can’t force it, though it can squelch it. The current registration system sets the bar too high, and the blog has been beset a bit by empty restaurant syndrome. Once the switch to Disqus happens I’ll try and kickstart discussion again by reengaging. We’ll see if there’s still life in the comment community.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Blog 
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"