Saturday, January 10, 2009

Top science stories of 2008

Popular interest in science news just isn't what it used to be. That's a sad but apparent fact. However, one reason that some people will always be interested in science news is that it satisfies a deep-rooted need for novelty. We get bored with the same old, same old after awhile. Our brains even tend automatically to tune out stimuli that don't ever change, or that change very little.

Science, on the other hand, keeps on providing a steady stream of genuinely new, and sometimes even surprising, information. This was just as true in 2008 as ever. It's a fact that could be lost sight of amidst all the other chaos of the year. As we review this year's noteworthy events in science, take note of how often the interest of the story resides in the novelty of the information.

Last year we did a summary of the news summaries. It was fun, so let's do it again.

As usual, Science magazine again provides the most intelligent selection of significant developments (December 19 issue).

The number 1 story (in their opinion) was reprogramming cells from one type to another. This research was announced in August and published a little later (October 2) in Nature. I was plannning to write about it – haven't yet – may still do so.

Here's how Science describes it:

Reprogramming Cells
By inserting genes that turn back a cell's developmental clock, researchers are gaining insights into disease and the biology of how a cell decides its fate.

This year, scientists achieved a long-sought feat of cellular alchemy. They took skin cells from patients suffering from a variety of diseases and reprogrammed them into stem cells. The transformed cells grow and divide in the laboratory, giving researchers new tools to study the cellular processes that underlie the patients' diseases. The achievement could also be an important step on a long path to treating diseases with a patient's own cells.

And here's the whole Top 10 list:

  1. Reprogramming cells
  2. Direct visual observation of extrasolar planets
  3. Identification of specific genetic abnormalities in cancer cells
  4. New class of high-temperature superconductors
  5. Clarification of how proteins bind to their targets
  6. Discovery of a new, cheaper catalyst for splitting water into hydrogen and oxygen
  7. Real-time imaging of zebrafish embryonic development
  8. Discovery that cells of "brown" fat are more closely related to muscle cells than to cells of "white" fat
  9. Computation using quantum chromodynamics of correct (to within 5%) mass of a proton
  10. Much faster and cheaper genome sequencing technologies

References:
Could this list have been better? Yes. It doesn't mention anything in astrophysics or cosmology, where there was actually quite a lot happening in the areas of dark matter, dark energy, star and galaxy formation simulations, gamma-ray astronomy, high-energy cosmic rays, and more.

Several other print and/or online publications attempted to come up with similar lists. Here are some of the better ones:

News 2008 (Nature)
Nature's list of important stories gets a lower rating because their criterion was "newsworthiness" or something like that, perhaps in terms of social or political impact, rather than scientific significance. Polar bears? Eh. In terms of actual science the list includes genome sequencing, synthetic genomes, Arctic sea ice, and pluripotent stem cells (a year late).

2008: Science News of the Year (Science News)
A little disappointing, because it covers so many stories. But from another point of view, that's the biggest strength, if you have patience to go through longish lists in 13 different categories.

Top 100 Stories of 2008 (Discover)
This traditionally long list (couldn't they at least have separated out the best 20 or so?) is substantially improved this year by organization into categories. But then they spoil it and lose mucho points for referring to the Higgs particle as the "God particle". Ugh.

The Year in Science (MSNBC)
Good job by Alan Boyle. Intelligent choices, not too long, not too short. Nice mix of scientific results and political/social implications. Now we just need to convince Alan and other American science writers to stop using the name of a long-dead baseball jock in connection with an important neurological disease (ALS).

Year in science: Dig into DNA, out-of-this-world discoveries (USA Today)
Workman-like effort from Dan Vergano. This is the one to read if you want brevity. Genome mapping, extrasolar planets, ancient DNA.

Top Ten Physics Stories of 2008 (American Institute of Physics)
Pretty fair list, albeit in just one area of science. Covers superconductivity, quark physics, gamma-ray bursts, cosmic rays, and low-temperature physics.

The best of 2008 (Physics World)
Another decent physics list. Drawback is organization by month, which doesn't map well to topic areas – notable ones being superconductivity, graphene, quantum computing, and dark matter. Somehow they managed to miss the proton mass calculation, and anything in astrophysics except for dark matter.

Biggest Science Stories: Bloggers' Picks for 2008 (National Geographic)
Interesting concept: the magazine chooses bloggers to discuss the most important stories in several areas – anthropology, paleontology, energy, archaeology, psychology, and environment.


Lists of lists:

Unimpressive lists:

New Scientist did offer up a number of collections of its own favorite articles in various topic areas. You get to separate the wheat from the chaff.

It's unfortunate how little coverage there is in this, and most other non-professional media, of significant stories about cell and molecular biology, where scientific activity is frenetic.

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posted by Charles Daney • 1/10/2009 11:23:00 PM
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Wednesday, January 23, 2008

Top science stories of 2007

Well, 2007 has been over for three weeks now. Must be time to look back and figure out what happened there. Overall, I'd say it was a good year, but not a great year. Let's have a look at what others picked for the "top" stories.

Science usually makes pretty good calls, as you'd expect. Since online access is by subscription only, here's my paraphrase of their list of top "breakthroughs":

  1. Recognizing human genetic variation – in other words, there's more diversity in human DNA than expected
  2. Making pluripotent stem cells by reprogramming
  3. Closing in on the origins of ultra-high-energy cosmic rays
  4. Determining the structure of a G protein-coupled receptor (for adrenaline)
  5. Investigating transition metal oxides as an alternative to silicon for electronics
  6. Exploring the prospects of materials exhibiting the quantum spin Hall effect for realization of spintronics
  7. Understanding how asymmetric division occurs in CD4 T cells
  8. Growing ability to synthesize complex pharmaceutical and electronic compounds
  9. Adding to the evidence that memory is an important ability for imagining future events and situations
  10. Proving that it is possible (for a computer) to never lose a game of checkers against a human (or another computer)

There are some surprising developments in this list – such as the extent of human genetic diversity or (especially) the apparent ease with which cells can be reprogrammed to behave like pluripotent stem cells. But what strikes me most about the list is that not much in it gives a sense of "closure" in the way that, say, determining the genetic code or proving the Poincaré conjecture (last year's top "breakthrough") was.

Instead, what we have are a number of developments that are merely the first steps towards much more impressive things to follow. We are just beginning to understand how genetic programs actually work, especially in disease conditions and in processes like metabolism and cell division. There will be much more meaningful developments with stem cells, protein structure determination, molecular synthesis, non-silicon electronics, spintronics, and nanoscale engineering.

I suppose this is why the items in the list are called "breakthroughs".

Here's a press release from the AAAS with a synopsis of their list: Human genetic variation -- Science's 'Breakthrough of the Year' (Physorg.com)

Many other lists of top stories could be found. Here are some of them, with my somewhat jaundiced opinion of most, as well as a bit of measured praise for the less awful.


2007: A year of stunning progress in the science of life (Guardian Unlimited)
Please read this one. It's not particularly lengthy, and it will be instructive to compare it with most of the other articles summarized below. It's lucid, and not larded with fluff.

In terms of what's actually noted as key advances, it covers genetics, synthetic biology, stem cells, cloning, and regenerative medicine. And despite the title, it also covers climate change and further improved evidence of dark matter.

Year in science review: Global warming, new species (USA Today)
The quality of this list is surprisingly good, considering the source. (Scientific American should be ashamed – fat chance.) Significant items include climate change (a perennial winner), stem cells, the extremely bright supernova SN 2006gy, and the Earthlike planet of Gliese 581. As a sop to the mass-market audience for "science" the list also includes dinosaurs, vanishing honeybees, and the discovery of many new biological species, alongside the looming extinction of others.

2007 News review (NewScientist)
The main list is sparingly presented in a few brief paragraphs. The selections are a bit odd (the dangers of noise pollution? really?). But in a sidebar there's a tidy list of links to separate additional articles, allowing you to easily avoid whatever you might regard as needless tedium. What I don't quite understand is the removal of, oh maybe 75% of science, to a separate article on 2007: The year in biology and medicine.

Top 25 Science Stories of 2007 (Scientific American)
Much of this list is in the nature of tabloid-style science "journalism" – all too pathetic a reminder of what is far too widely considered to be "newsworthy" in the realm of science. Not quite as bad as the printed birdcage liner found at a supermarket checkout station, but close. Daylight saving time redefined? Some guy with TB goes on a honeymoon to Europe? Poisoned pet food? Baseball jocks on steroids? Oh, please. They forgot to mention flying saucer or Yeti sightings – surely there must have been some.

See, the problem with this is that it tends to trivialize, by association, those few stories they included which were actually important, such as climate change, stem cells (the science, not the bogus controversy), and Earthlike extrasolar planets.

Top 10 Scientific Discoveries (Time)
Fortunately, this list is shorter than Scientific American's, so there's less tabloid-style dreck in it. And what there is of that isn't quite so egregious (dinosaurs, "kryptonite", an elderly clam). This makes for a somewhat higher percentage of actual science (stem cells, human genome, supernova SN 2006gy, extrasolar planets).

But here's the depressing thing about this list. Not so much the content, which doesn't quite treat the readership as unqualified imbeciles, but rather the presentation, which treats the readership as short-attention span consumer droids who will docilely plow through separate pages for each story, replete with stock photo imagery, brief text, and delightful time-wasting banner ads and "sponsored links".


Briefly noted: Here are some more specialized or other "best of 2007" lists that don't seem to require much further comment from me. Some are good; others are..., well, just other.

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posted by Charles Daney • 1/23/2008 02:48:00 AM
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Tuesday, December 26, 2006

Nature's review of 2006

Nature is one of the world's two premier science journals, the other being... Science. Sadly, their review of this year's science developments is, to this observer at least, simply underwhelming.

Oh, they mention Perelman's work on the Poincaré conjecture, and a couple of developments in biology (stem cells, and genetics). But as far as fundamental science is concerned, that's about it. Their emphasis is predominantly on stories that made big newspaper headlines for social/political reasons, such as global warming and natural disasters.

Sure, that stuff is very important for its human impact. No argument about it. But it's been covered endlessly in the popular media. Does Nature think they've added much to what you could read in, say, the New York Times? Or Newsweek, for that matter.

My advice to Nature, not that they've asked: Put the main emphasis on the fundamental science – in some serious depth we can't find elsewhere – instead of the yakety-yak one can hear from any talking head on the news shows.

That said, if anyone reading this still wants to read a little more from Nature's editors about what they considered scientfically important in 2006, here are some of their top 10 lists:

Editor's choice stories
A "vegetative" patient who showed signs of consciousness. That was number 1! A social scientist who could glibly discuss gravitational waves. (Number 3.) The world's smallest vertebrate. (Number 4.) Demise of the world's "most infamous" iceberg. (Did you know there was one?)

Reader's choice stories (most clicked on)
This list is better than the editor's choice. But not by much. Example: "Sexy pictures and lacy underwear take men's minds off getting a good deal."

Most commented on stories from Nature's news blog
This is probably the most interesting list. Lots of good arguments here, if you care for that sort of thing. Does gender matter? Islam and science. Delusions of faith.

Longer news features
Ranges from the genuinely important (climate change) to the "why did they bother?" category. And you'll have to buy a subscription to read most of them. Betcha no one does.


For the record: here's the home page for Nature's "review of the year's top stories and pictures".

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posted by Charles Daney • 12/26/2006 02:04:00 AM
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Science's top 10 "breakthroughs" of 2006

Science Magazine's selection of the top scientific developments of the year is basically the grand prix of scientific competition. And the editors usually make pretty good calls, though in truth there are many, many important scientific developments over the course of a year. Recognizing only 10 just leaves out too much. But it seems like a limitation we have to live with. Fortunately, there are other, if less prestigious, commentators who offer similar lists on science in general or on specfic fields. Taken all together, we get a more comprehensive picture of what happened during the year.

Anyhow, you can find an index of Science's articles on the top 10 (from the December 22 issue) here. (Access is free, though you will have to register at the site.)

Their choice for top breakthrough of 2006? It's the proof of the Poincaré conjecture. It is rather unusual for a development in mathematics to rate so much attention, but then this is no ordinary breakthrough. Something like this comes along in mathematics only every 10 or 20 years. It was written about on this blog here, here and here. (And in a few other articles besides, which you can find by searching the archives.)

Science's choices for runners-up were interesting too, of course. Among those are some that have been discussed here, such as macular degeneration (this), memory (this, this, and this), and small RNA (this). There's a steady stream of developments in the latter two areas, in particular, so stay tuned for more.

Just as interesting as the list of this year's breakthroughts were Science's list of areas to watch in 2007. Prominent in this list are the areas of planetary science (both our own solar system and others) and genome mapping and comparison.

It's also interesting to note areas that are not on the list, for either this year or next. Where, for instance, are topics in cosmology, astrophysics, and extragalactic astromomy – such as dark matter, dark energy, black holes, the cosmic microwave background, and gamma-ray bursts? Some very fundamental results have been obtained this year, with more surely to come in 2007. They've been discussed extensively here – search the archives for plenty of examples. Just goes to show how much has to be left out of a "top 10" list.

Additional references:

Maths solution tops science class – from the BBC

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posted by Charles Daney • 12/26/2006 12:42:00 AM
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Tuesday, January 03, 2006

Top science news stories of 2005

This is the time of year that everyone in the news business offers an opinion on the top stories of the year, so we're not going to be any different.

Science Magazine selected "Evolution in Action" as the year's top story.
Equipped with genome data and field observations of organisms from microbes to mammals, biologists made huge strides toward understanding the mechanisms by which living creatures evolve.

To round out the top 10, the runners-up were:

  • 2. Planetary probes - missions to Mars, Saturn and its moons, and others
  • 3. Plant development - molecular biology of flowers
  • 4. Violent neutron stars - magnetars and short-duration gamma-ray bursts
  • 5. Genetics of brain disease - schizophrenia, Tourette syndrome, dyslexia
  • 6. Earth's differentiation - meaningful differences between earthly and extraterrestrial rocks
  • 7. Potassium channels - molecular structure of an essential component of nerve and muscle cells
  • 8. Climate change - a crescendo of evidence that it's real
  • 9. Systems biology - understanding cells as complex systems
  • 10. ITER - a site for the International Thermonuclear Experimental Reactor is finally chosen


We don't disagree with these choices, but our own list is mostly different, if only because it's limited to stories we have written about (or plan to soon). In the following list, there are references to some (but not all) of our relevant articles.

  1. Accelerating progress on cancer - here, here, here, here
  2. Climate change is real - here, here
  3. Gamma-ray bursts - here
  4. Dark matter and dark energy - here, here, here, here, here
  5. Gene expression and epigenetics - here, here, here
  6. Star formation - here, here
  7. Video conferencing - here
  8. Quantum computing - article coming real soon now


Other lists of top science stories for 2005

Top Science Stories of 2005 - Scientific American

Review of the year - Physics World

The Top Physics Stories for 2005 - Physics New Update

NewScientist.com's top 10 news stories of 2005

2005: The year in astronomy - New Scientist

2005: The year in the solar system - New Scientist

2005: The year in biology and medicine - New Scientist

Most Overlooked Science and Tech Stories of 2005 - by RJ Eskow - also here

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posted by Charles Daney • 1/03/2006 12:38:00 AM
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Monday, January 02, 2006

What is your dangerous idea?

Edge has posted its Annual Question for 2006. This year it's a real doozy: What is your dangerous idea?
The history of science is replete with discoveries that were considered socially, morally, or emotionally dangerous in their time; the Copernican and Darwinian revolutions are the most obvious. What is your dangerous idea? An idea you think about (not necessarily one you originated) that is dangerous not because it is assumed to be false, but because it might be true?

John Brockman -- founder of Edge, literary agent par excellence for science writing, and agent provocateur working on behalf of what he calls the Third Culture -- provides background about Edge and the Annual Question at this article on the Huffington Post. (There are many interesting replies to this article.)

There are 117 essays written in answer to this question, by such people as Steven Pinker (whom Brockman thanks for suggesting the question), George and Freeman Dyson, Brian Greene, Martin Rees, Leonard Susskind, Craig Venter, Richard Dawkins, Daniel Dennett, Ray Kurzweil, Lynn Margulis, Lee Smolin, Jaron Lanier, Stewart Brand, Rudy Rucker, Gregory Benford, and... well you get the idea. Quite a roster. Interested yet?

It's simply impossible to pick out the most interesting ideas from the list, let alone to discuss adequately even a few of them right here, right now. Instead, of course, these questions will form inspiration for thought all year, and beyond. (Even if -- or because -- most of the essays leave plenty of room for disagreement.) As Brockman aptly puts it, quoting Ernst Mayr (shortly before his death), "It's a conversation."

An idea may be considered dangerous for several reasons. It may be an idea that one agrees with, and which one considers to be capable of having seriously destabilizing effects on the world. Or it may be an idea that one disagrees with -- but expects the same sort of effect. So one should not assume that any of the ideas suggested are actually favored by the suggester. It could be either way, though most people can't help tipping their hands.

Many who responded discussed ideas with which they themselves are closely identified. But by asking for ideas that are "dangerous", Brockman challenges everyone to contemplate ideas that are dangerous precisely because one fears they might be true -- whether or not one wants them to be true.

Putting the question this way is especially important for a simple reason: It forces thinkers to consider ideas seriously even though the truth of those ideas might be contrary to what one has invested heavily in.

This is how science should work. We should not stint on thinking about those very possibilities that contradict our favorite beliefs. At least, the thinking process will better equip us to better defend and substantiate those beliefs. We must be careful not to hold a belief simply because we want it to be true.

I expect to examine many of these ideas here over the coming months. This is more than just a little food for thought. It's a substantial smörgasbord.

Just to give a taste of how this can go, here's one comment that struck me, from Haim Harari:
When, in the past two years, Edge asked for brilliant ideas you believe in but cannot prove, or for proposing new exciting laws, most answers related to science and technology. When the question is now about dangerous ideas, almost all answers touch on issues of politics and society and not on the "hard sciences". Perhaps science is not so dangerous, after all.

Perhaps it's not the science and technology we humans produce that is the greatest threat to our continued existence. Maybe it's us. We're our own worst threat. We have met the enemy, and it is us.

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Already (and unsurprisingly) there have appeared discussions of Edge's question for 2006. Here are a few of them:

Not Even Wrong: What is Your Dangerous Idea?

Cosmic Variance: Dangerous, stupid, or simply dishonest?

Luboš Motl's Reference Frame: Dangerous ideas

The Slimmer List of Edge Dangerous Ideas

Other reports:

Gene discoveries highlight dangers facing society

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posted by Charles Daney • 1/02/2006 10:20:00 PM
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