Mike Loukides

Mike Loukides is Vice President of Content Strategy for O'Reilly Media, Inc. He's edited many highly regarded books on technical subjects that don't involve Windows programming. He's particularly interested in programming languages, Unix and what passes for Unix these days, and system and network administration. Mike is the author of System Performance Tuning", and a coauthor of "Unix Power Tools." Most recently, he's been fooling around with data and data analysis, languages like R, Mathematica, and Octave, and thinking about how to make books social.

Distributed science

In the future, we will solve biological problems by running experiments in parallel.

ScienceHack2014

Participants at #ScienceHack 2014, Synbiota’s Open Distributed Genetic Engineering event. Photo by Madison Matthews, courtesy of Synbiota.

In my post on biohacking and bioterrorism, I briefly mentioned the possibility of vaccines and other treatments developed outside of institutional research. That may be far-fetched, and I certainly hope we’re never in a situation where DIY treatments are the only ones available. But it is worth looking at how biologists outside of medical institutions are transforming research.

Perhaps the most ambitious project right now is Synbiota’s #ScienceHack. They are organizing a large number of volunteer groups to experiment with techniques to produce the compound Violacein. Violacein is potentially useful as an anti-cancer and anti-dysentery drug, but currently costs $356,000 per gram to produce. This price makes research (to say nothing of therapeutic use) impossible. However, it’s possible that bacteria can be genetically engineered to produce Violacein much more efficiently and cheaply. That’s what the #ScienceHack experiment is about: the groups will be trying to design DNA that can be inserted into E. coli bacteria to make it produce Violacein at a fraction of the cost. Read more…

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Full-stack developers

Developers who understand the whole stack are going to build better applications.

Large tree with branches. Photo by Alex, used under a Creative Commons license

Some see the full-stack developer as a unicorn, but it’s starting to look more like a tree, with tooling, cloud services, design, data, and networking added.

Since Facebook’s Carlos Bueno wrote the canonical article about the full stack, there has been no shortage of posts trying to define it. For a time, Facebook allegedly only hired “full-stack developers.” That probably wasn’t quite true, even if they thought it was. And some posts really push “full-stack” developer into Unicorn territory: Laurence Gellert writes that it “goes beyond being a senior engineer,” and details everything he thinks a full-stack developer should be familiar with, most of which doesn’t involve coding. Read more…

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Biohacking and the problem of bioterrorism

Natural bioterrorism might be the bigger threat, and the value of citizens educated in biosciences can't be overstated.

You don’t get very far discussing synthetic biology and biohacking before someone asks about bioterrorism. So, let’s meet the monster head-on.

I won’t downplay the possibility of a bioterror attack. It’s already happened. The Anthrax-contaminated letters that were sent to political figures just after 9/11 were certainly an instance of bioterrorism. Fortunately (for everyone but the victims), they only resulted in five deaths, not thousands. Since then, there have been a few “copycat” crimes, though using a harmless white powder rather than Anthrax spores.

While I see bioterror in the future as a certainty, I don’t believe it will come from a hackerspace. The 2001 attacks are instructive: the spores were traced to a U.S. biodefense laboratory. Whether or not you believe Bruce Ivins, the lead suspect, was guilty, it’s clear that the Anthrax spores were developed by professionals and could not have been developed outside of a professional setting. That’s what I expect for future attacks: the biological materials, whether spores, viruses, or bacteria, will come from a research laboratory, produced with government funding. Whether they’re stolen from a U.S. lab or produced overseas: take your pick. They won’t come from the hackerspace down the street. Read more…

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The backlash against big data, continued

Ignore the hype. Learn to be a data skeptic.

Yawn. Yet another article trashing “big data,” this time an op-ed in the Times. This one is better than most, and ends with the truism that data isn’t a silver bullet. It certainly isn’t.

I’ll spare you all the links (most of which are much less insightful than the Times piece), but the backlash against “big data” is clearly in full swing. I wrote about this more than a year ago, in my piece on data skepticism: data is heading into the trough of a hype curve, driven by overly aggressive marketing, promises that can’t be kept, and spurious claims that, if you have enough data, correlation is as good as causation. It isn’t; it never was; it never will be. The paradox of data is that the more data you have, the more spurious correlations will show up. Good data scientists understand that. Poor ones don’t.

It’s very easy to say that “big data is dead” while you’re using Google Maps to navigate downtown Boston. It’s easy to say that “big data is dead” while Google Now or Siri is telling you that you need to leave 20 minutes early for an appointment because of traffic. And it’s easy to say that “big data is dead” while you’re using Google, or Bing, or DuckDuckGo to find material to help you write an article claiming that big data is dead. Read more…

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Wearing the future

Current wearable computing technology is just scratching the surface — the really interesting tech has yet to be invented.

In an interview at SXSW, Google’s Sundar Pichai said something about wearables that I’ve been waiting to hear. Wearables aren’t about Google Glass; they aren’t about smart watches; they’re much, much more, and these technologies are only scratching the surface.

I’ve tweaked Apple a couple of times for their inability to deliver a watch, despite years of leaks and rumors. I suspect that products from competitors have forced them to pivot a few times, rethinking and delaying their product. But the bottom line is that I don’t care; I don’t wear a watch, haven’t for a long time, and I’m not about to start. Just not interested.

I’m more interested in Glass, but I’ve been amazed at how few people are listening to what Google has said about it: it’s an experiment. It’s not the endpoint, not the product. Given the excitement it has produced, Google would be foolish not to sell it. But really: it’s ugly, it’s a prototype, it’s a mockup. Five years from now, will we all be walking around with Google Glass hanging from designer frames? I doubt it. And I bet Pichai, Brin, and Page doubt it, too. It’s an experiment; it will show us what’s interesting, and point toward what to build next. It’s not the end result. Read more…

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Academic biology and its discontents

Disaffected grad students and postdocs increasingly turn to DIYbio to do work that makes a difference.

When we started BioCoder, we assumed that we were addressing the DIYbio community: interested amateur hobbyists and experimenters without much formal background in biology, who were learning and working in independent hackerspaces.

A couple of conversations have made me question that assumption — not that DIYbio exists; it’s clearly a healthy and growing movement, with new labs and hackerspaces starting in most major cities. But there’s another group mixed in with the amateurs, with a distinctly different set of capabilities and goals. DIYbio doesn’t mean exactly what we thought it did.

That group is what I broadly call “disaffected grad students and postdocs.” They’ve got training, loads of it. But they’ve spent the last few years working in a laboratory under a faculty member, furthering that faculty member’s agenda. They have their own ideas and their own research projects, but they can’t work on them within the context of academic biology. They’re funded by a grant, and the grant will only pay for certain things. And, as Anthony Di Franco points out in “Superseding Institutions in Science and Medicine” (in the current issue of BioCoder), grants are primarily given to people who already know what they’re going to find, and that is not how you get truly innovative and creative research. Read more…

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Bluetooth Low Energy: what do we do with you?

Why the dearth of imagination — we need to get beyond different flavors of spyware.

“The best minds of my generation are thinking about how to make people click ads,” as Jeff Hammerbacher said. And it’s not just data analysts: it’s creeping into every aspect of technology, including hardware.

One of the more exciting developments of the past year is Bluetooth Low Energy (BLE). Unfortunately, the application that I’ve seen discussed most frequently is user tracking: devices in stores can use the BLE device in your cell phone to tell exactly where you’re standing, what you’re looking at, and target ads, offer you deals, send over salespeople, and so on.

Color me uninterested. I don’t really care about the spyware: if Needless Markup wants to know what I’m looking at, they can send someone out on the floor to look. But I am dismayed by the lack of imagination around what we can do with BLE. Read more…

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Cheese, art, and synthetic biology

Christina Agapakis discusses the intersection of art and science in the new edition of BioCoder.

We’ve published the second issue of BioCoder! In this interview excerpt from the new edition, Christina Agapakis talks with Katherine Liu about the intersection of art and science, and the changes in how we think about biotechnology. It’s one of many reasons we’re excited about this new issue. Download it, read it, and join the biotechnology revolution!

Katherine Liu: What can art and design teach us about biology and synthetic biology?

Christina Agapakis: That’s a great question. There are two different ways you can think about it: first as a way to reach different groups of people and have a different kind of conversation or debate around biotechnology. The second way that you could think about it is more interesting to me as a scientist because I think using art and design helps us ask different questions and think about problems and technological solutions in different ways. To make a good technology, we need to be aware of both the biological and the cultural issues involved, and I think the intersection of art and design with science and technology helps us see those connections better.

Read more…

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The reason everyone should learn to code

It isn't to produce a nation of coders.

Why do we want everyone to learn to code? It’s certainly not to produce a nation of coders. I have no delusions about everyone learning to code: it’s not going to happen, and may not even be desirable.

But the underlying rationale behind a slogan isn’t the slogan itself; it’s what the slogan enables. I’m not terribly interested in whether or not ex-Mayor Bloomberg learns Python. I hope that helps him in his new career, but I suspect he’ll do just fine, regardless of his programming skills. I am much more interested in the excitement behind organizations like Black Girls Code, excitement that derives directly from the “everyone should code” meme. Read more…

Comments: 8

Is Valve’s SteamBox a contender for the next developer workstation?

Valve might be positioned to do to Macintosh hardware what the Mac did to the PC market over a decade ago.

A scenario started playing through my head the other day. In the late 1990s, Apple looked dead. Then they released OS X, plus very cool shiny hardware. That put Apple back in the game and gave them the life they needed to bring about the iPod, etc. Apple’s revival didn’t come from iPods and iPhones; it came because they made a deep connection to the software developers. In 2000, if you went to a developer conference, everyone was carrying some kind of PC laptop, probably running some version of Windows, possibly Linux. But almost overnight that changed, and it changed completely. By 2003, any self-respecting developer was carrying a MacBook, preferably the one the size of a small aircraft carrier. Apple did an undeniably brilliant job of growing this beachhead among the developer community into a dominant brand. Everyone wanted what the cool kids had. Apple had a winning product: they had the most beautiful version of Unix ever, with a user interface that beat anything that had ever appeared on Linux or Windows.

But now, Apple is looking more and more hostile to the developer community that enabled their revival. OS X is evolving into a slightly more capable version of iOS, and we’re all dreading the day when the only way we can compile and install our own software is by using Apple’s proprietary tools and going through the App Store. If you look closely at Apple’s work, it’s clear where they’re putting the effort: there’s a race condition in basic text editing (TextEdit, Mail, etc.) that’s been around since at least OS X 10.6, and I suspect goes all the way back to 10.1. It’s not something arcane that only crops up in strange circumstances; I run into it every day (and on several different machines). And that’s only the start.

I know loads of developers who are saying, “yeah, I’m assuming I’ll be off Apple in a few years.” But that’s a problem: it’s one thing to talk about leaving Apple; it’s something completely different to know where you’re going. Read more…

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