New Zealand on-line news outlet Stuff has elected to present a science section. Yay!

Some might even say ‘about time’.

In a modest promotional effort, they’ve offered the first of what are to be daily science pictures.

It’s great to see support voiced in the comments. (Sharp readers will notice I have given a heads-up to readers there about our forum.)

“Finally a blokes version of your ridiculous fashion section…” says Peter (comment 10). Excellent sentiment, but I’ll oppose that science should be ‘for blokes’ – science is for everyone.

Image Credit: NASA / Tony Landis

Tony (in comment 8) writes:

“Great stuff! Looking forward to reading it, but please, no editorials on what you think is right/wrong, harmful/beneficial, just pure science please! For example, I’d hate to read about how someone “thinks” WiFi radiation is bad…”

I’d like to think what Tony is after is that he wants substantive material, work based around evidence, not opinion pieces ‘pushing’ a writer’s viewpoint based on their “thoughts”.^[1]

Good on them for taking it up – go over and encourage them. I’d be happy to see your thoughts on what you’d like to read, too.

Shades of how long is a piece of string, I know, but Tony’s plea leads this writer to wondering, again, just what is it that readers would like to see as ‘general science’ on-line?^[2]

This being one of those days^[3] let me indulge in some ruminations on science writing as soul food of sorts.

Some newspaper articles on science are light, almost fluffy. I use that word because to my eyes many newspaper articles outside of straight news in New Zealand seem to aim to be fluffy. There’s nothing wrong with being engaging with a lively use of language, of course, but it’s frustrating when there proves to be little real content. This style sometimes strikes me as self-endulgent – the writer is certainly exercising their writerly nous… but sometimes (often) damn-all else.

It’s like watching an old-time comedy with where a pert, if dotty, housewife stereotype busies around dusting what is obviously an absolutely spotless shelf, the polished surface gleaming flawlessly in the stage lights. She’s bubbly and charming as hell, but not actually achieving a sodded thing other than being bubbly and charming for the sake of being bubbly and charming. Itself not a bad thing – in small doses. It’s just if the entire movie is like that, well… You get to a point where you think “it’s very pretty, but… this is kind-of empty-headed” (I don’t mean the gal’s character, which might be right, but the movie.)

The real craft of science writing,^[4] to me, isn’t just about finding the latest good factoids or pictures. That’s fairly easy, if sometimes time-consuming: usually the factoid or picture is itself enough and the rest mostly padding. Science communication can be that, too, but to me it wants to be more.

The real meat is trying to bring the science to readers in an engaging way. That’s much harder. It demands understanding the background well enough to show what was behind that cool cyclonic twist on the Stuff website (shown above). This wants to go past the short press release material.

Image Credit: NASA/Chris Gunn

Or tell us what that testing of the James Webb Space Telescope shown (immediately above) is actually doing. Looking at the NASA caption, that big tank is a “Space Environment Simulator vacuum chamber” and the thing being lowered into it is Optical Telescope Element Simulator (OSIM). The Stuff website doesn’t point that what the tank is (nor does it link to the NASA site). There’s a story there. That’s a big vacuum chamber! What are the challenges making one that size? How cold do they make it and how do they make it that cold? Can they simulate rapid changes in temperature? Precisely what is the Optical Telescope Element Simulator? (I’m guessing it’s box of the same material as the external skin of the telescope with a bunch of recording gear in it – ?)

They’re great shots, but some might ask “where’s the beef?” What science are the pictures showing?

Without the background photographs are ‘science teasers’, teasers being short pitches used to draw readers in. Nothing wrong with the tease, but I like some food after I’ve seen the menu or those pick’n'choose photos some Asian restaurants have.

I like a mixture of styles and content type myself. I couldn’t name one particular thing that ‘is’ science writing, although I prefer that somewhere it has, or links to, more than the ‘surface’ veneer. I could better name what I don’t like to see in science material. (Hey, scientists are strong on criticism!) Stuff that‘s poorly researched or simply wrong. Writers whose material reveals that they don’t really understand how science actually works.

A brief skim suggests the articles on Stuff’s main science page are a good start, although the lack of links or other pointers to the original sources and follow-on material bothers me. Its sort-of a print-edition sin brought across to the on-line world, the unwillingness to spare a couple of lines at the bottom for sources. For on-line material, there’s no real excuse and it denies the curious to follow the story further directly from the page.

Update

Since writing the above I’ve wanted to offer a closer, more critical, look at what’s on offer but simply haven’t time. Readers here may want to read fellow sciblogger David Winter’s take on one of Stuff’s recent science offerings.

Footnotes

1. By way of example, I try when examining claims in media or on other websites, etc., to base what I offer around scientific literature and so on, rather than writing solely in the ‘I think that’ sense. It’s the evidence that matters on these things, not a writer’s “instincts”.

2. Of course, I have a self-interested reason for asking this!

3. It’s been a frustrating day that has left me wondering about NZ internet services. First the IRD website was struggling, bailing out and not delivering content. (For many businesses GST returns are due today.) Later, Telecom’s SMTP server ‘decided’ to stop accepting out-going email. (At the time of writing [after 7pm] is still is not relaying out-going mail. For the moment I’m waiting it out.) I know it’s Monday, with all that comes with that, but businesses suffer when these sorts of things happen.

4. I’m not referring to the perennial science journalism v. science writing ‘debate’ here.

Animating our DNA*

Do TED lectures need better vetting?

Epigenetics overview (video)

“We’re so used to getting a prescription that’s it’s surprising when we don’t”

Dear journalists and editors,

Ken Ring & March 20th – let’s get back to science (Check the links at the end for lots of reading)

Haemophilia – towards a cure using genetic engineering

Initial reports are not a done deal

Homeopath says to treat a burn… burn it some more

Are bioinformaticians gods?

One of the most oft cited quotes on twitter is drawn from this passage from the abstract of Henry Sauermann and Michael Roach’s paper:

“We also show that the attractiveness of academic careers decreases significantly over the course of the PhD program, despite the fact that advisors strongly encourage academic careers over non-academic careers.”

Here‘s their abstract in full:

“Even though academic research is often viewed as the preferred career path for PhD trained scientists, most U.S. graduates enter careers in industry, government, or “alternative careers.” There has been a growing concern that these career patterns reflect fundamental imbalances between the supply of scientists seeking academic positions and the availability of such positions. However, while government statistics provide insights into realized career transitions, there is little systematic data on scientists’ career preferences and thus on the degree to which there is a mismatch between observed career paths and scientists’ preferences. Moreover, we lack systematic evidence whether career preferences adjust over the course of the PhD training and to what extent advisors exacerbate imbalances by encouraging their students to pursue academic positions. Based on a national survey of PhD students at tier-one U.S. institutions, we provide insights into the career preferences of junior scientists across the life sciences, physics, and chemistry. We also show that the attractiveness of academic careers decreases significantly over the course of the PhD program, despite the fact that advisors strongly encourage academic careers over non-academic careers. Our data provide an empirical basis for common concerns regarding labor market imbalances. Our results also suggest the need for mechanisms that provide PhD applicants with information that allows them to carefully weigh the costs and benefits of pursuing a PhD, as well as for mechanisms that complement the job market advice advisors give to their current students.”

Their initial statement that “most U.S. graduates enter careers in industry, government, or “alternative careers.”” is also seen from statistics taken on the situation here in New Zealand and in England, too. I think it might be fair to suggest this is a global trend, at least in ‘Western’ nations.

I’m a little too busy to explore this paper in depth, as I would like to, but I would encourage interested readers to read it – it’s open access and straight-forward. Below I’ve included a few quotes as encouragement and food for thought.

A key point about this work is that it surveys the preferences of the students, rather than ‘just’ where they ended up. A related issue is the advice given to students, also I topic I have raised in the past (suggesting that more attention to careers outside of academia might be needed):

“In this paper we draw on novel survey data to provide unique insights into PhD students’ career preferences, changes in preferences over the course of the PhD program, and faculty advisors’ encouragement of specific career paths.”

Their survey is dominated by the life sciences:

“Our sample includes 4,109 PhD students in the life sciences (59%), chemistry (18%), and physics (23%).”

Generally students favoured academic faculty as their preferred career option:

“Across all cohorts, students in the life sciences and physics most often rate a faculty career with an emphasis on research as extremely attractive (34% and 38% of students, respectively), followed by teaching careers and R&D positions in government.”

Some, thankfully, expressed a preference for careers outside academia:

“Figure 1 also shows that some respondents find “other” career extremely attractive. We asked respondents to specify which particular career they were thinking of, and the most commonly mentioned careers include science communication/writer, science policy, non-university teaching, working for a non-profit/NGO, and consulting.”

The authors looked at the change of preferences during the course of the PhD studies:

“the share of life sciences students finding a faculty research career extremely attractive is significantly lower in the late stage versus the early stage of the PhD program (33% vs. 39%, p<0.01). Similarly, the share of life sciences students finding a faculty teaching career extremely attractive declines from 25% to 21% (p<0.05). In chemistry, we observe a significant decrease in the share of students finding teaching careers extremely attractive (21% vs. 16%, p<0.01) and a sharp increase in the attractiveness of careers in industry (37% vs. 23%, p<0.01). There is some evidence that the attractiveness of startup careers increases in all three fields, although these changes are not statistically significant at conventional levels of confidence.”

“[…] the share of students finding a faculty research career most attractive drops in all three fields, from 57% for the early cohort to 50% for the late cohort in the life sciences, from 45% to 32% in chemistry, and from 60% to 53% in physics.”

“we find that the share of students who find a faculty research career “unattractive” or “extremely unattractive” increases from 11% to 21% (p<0.01) in the life sciences, 22% to 38% (p<0.01) in chemistry, and 7% to 14% (p<0.05) in physics.”

While these changes might seem modest, it’s perhaps worth remembering this is over the space of just a few years. They note that while the preference (on the whole) remains for academic careers, those that favour this still out-number the opportunities (at least within the USA):

“Despite the decline in the attractiveness of faculty careers over time, our data show that the faculty research career remains extremely attractive to a large share of graduating students in the life sciences and in physics (see Figure 1). As detailed in the introduction, however, NSF data show that the share of graduates who are actually able to obtain tenure track faculty positions is significantly smaller [5].”

The authors also surveyed what the students thought their advisors encouraged, concluding that their data

“shows that the faculty research career is indeed by far the most often “strongly encouraged” career. A small number of students feel that certain other careers are explicitly discouraged, mostly teaching careers and careers in industry. It is notable that encouragement for faculty careers and discouragement for industry careers are especially pronounced in the life sciences, where the share of graduates obtaining tenure track faculty positions is smallest and where much of the discussion around labor market imbalances takes place [5]. Even in chemistry, where industry careers are very common and where students express a strong interest in industry careers, students feel that research careers in academia are much more strongly encouraged.”

“[…] a considerable share of students feels that non-academic careers are neither encouraged nor discouraged. One possible interpretation is that these careers are discussed between students and their advisors and that the latter explicitly take a “neutral” stance with respect to these careers. Alternatively, these career options may not be very salient in student-advisor discussions, and the neutral ratings in Figure 4 may reflect a lack of guidance and information regarding these careers rather than an explicit neutral position.”

In a somewhat similar theme to a recent post on my blog (What kind of scientist are you?), the authors also

“asked respondents how interesting they would find each of 5 different types of work in the future”

finding it notable that

“notable that many students in the life sciences and in chemistry have a strong interest in research that solves concrete problems”

I will leave readers to read the author’s discussion for themselves.

There has been a lot of commentary on science careers, Ph.D. studies, job prospects and related aspects, online including here at sciblogs. Let’s hope that this and other quantitative studies can inform this discussion and give it more clarity.

There are currently two comments on the article on the PLoS One website, the first pointing to media coverage of the article, the second wondering if it is “necessarily a decline in interest, but rather, an increase in responsibilities.” Share your thoughts at PLoS One or below.

Other articles on Code for life:

Career paths, redux – the academic research career is the exception

On alternatives to academic careers and “letting go” (with links to other articles on this topic)

“Other” career paths – #IamScience

Changing the Ph.D.

Teaching students to write scientific papers

More inclusive re-entry to encourage departure to businesses?

Free for this month (May, 2012) is an e-Book version of Carl Zimmer’s popular science book, A Planet of Viruses.

To get your copy, go to the University of Chicago Press website for the book and enter your email address in the space provided. You will be sent an email with a link from which you can download a copy. The book is displayed using Adobe’s Digital Editions software, of which I have little experience (but see first Footnote).

Carl Zimmer is a long-time science writer and author of several books including The Tangled Bank, (evolution), Parasite Rex (parasites), Science Ink (a collection of tattoos with scientific themes and their stories), Brain Cuttings, More Brain Cuttings (the working of the mind) among others.

Footnotes

I hope to have this blog back into more regular activity next week.

In local news, the main campus* of the University of Otago lost power this morning. According to reports on social media, the power outage is restricted to the campus area:

Paul Le Comte ‏(@five15design)
Massive boom & the power has gone out to a big part of #Otago Uni Centre for Innovation is dark – home time via the wood & coal shop

Paul Le Comte ‏(@five15design)
By all accounts St David St block, Centre for Innovation & all of Registry is without power

Tom Tremewan ‏(@TomTremewan)
Complete power outage all over @otago campus right now.

Pippa Mackay ‏(@pip_pip_pippy)
@BioinfoTools @five15design @otago power has just come back on in central library, unsure if it’s just back up or restored completely

Other self-reporting on social media indicate that surrounding suburbs were unaffected. There is no word from the University of Otago on social media at this time.

Of course, there is the inevitable joke:

Thomas Hedderwick ‏(@NinjaLikesCheez)
Whats the bet a noob pressed the big red ‘don’t press’ button in the Admin building? #OtagoUni

My sympathies to any whose experiments were ruined by this outage.

Anyone with more on-the-ground knowledge is welcome to contribute in the comments.

Footnotes

* The University of Otago is also represented in other cities in New Zealand, e.g. the Christchurch School of Medicine and in Wellington and Auckland.

Just a quick heads-up for New Zealand readers, tonight at 8:30pm Prime will be showing the British drama Hawking, produced by the BBC, which covers cosmologist Stephen Hawking’s earlier years from the initial stages of his diagnosis of motor neurone disease. The production features Benedict Cumberbatch, who starred in Sherlock.

Hannah M’s review at Rotten Tomatoes reads

I first saw Benedict Cumberbatch in the BBC TV show “Sherlock” and decided to look up what else he’d done. In this made-for-TV movie, he does an *excellent* job playing Stephen Hawking in the early days of his diagnosis. The movie’s writer, Peter Moffat, also wrote the fairly-entertaining Einstein and Eddington, but the writing is sharper and more interesting in this older one. Well worth checking out for fans of biographies, science stories, or Benedict Cumberbatch.

An astrophysicist, Sarah H, offered her thoughts:

I came at this movie from two perspectives: First, as a fan of Benedict Cumberbatch, and second, as an astrophysicist and high school teacher. I thought the film had a good combination of “hard science”, but wrapped up in understandable terminology and a sweet human story. Benedict’s physical work as Hawking is

I can’t vouch for this, not having seen it before, but most reviews praise Benedict Cumberbatch’s efforts - it might be worth checking out.

What do scientists look like?, redux

The littlest chameleon?

Epigenetics overview (video)

Do TED lectures need better vetting?

“We’re so used to getting a prescription that’s it’s surprising when we don’t”

Are bioinformaticians gods?

Media loves those romantic, emotionally appealing, stories of someone rediscovering their favourite lost toy or book from their youth. What if that favourite thing was the computer source code of a project you put your all into?

This story could win a geek’s heart. Jordan Mechner, writer of the early graphical computer game* Prince of Persia, gets sent a box by his Dad. In the box is a 5¼” floppy disk containing the original source code, something though he’d lost. A trans-continential flight over a weekend, others’ work on hardware setup to read the disk, ensue – it’s a saga.

It’s all on his blog – read it, he writes well, recounting the arrival of the box and a post-event exploration of “why?” ArsTechnica also has coverage.

Aside from the story itself, some of the technology appeals to me.

Source wikipedia.org; author Bill Bertram (CC-A).

I can relate to the appeal of the source code, as I imagine all programmers could. You don’t just see that something worked, but how – the thinking and strategies that went into it. More than that, I once did a little coding in 6502 assembler** (and later in 6508, 8086, etc). Writing in assembler you build up things from a very low level, moving numbers (‘words’) in from RAM into the registers in the CPU, then ask the CPU to perform operations on the values in the registers and push the results back out to RAM. You’ve got this mental imagine of hardware at your mastery in a way that high-level programming languages don’t evoke. Today even work that is at least nominally closer to hardware, say using CUDA to get a graphics processor to parallel execute some task, is abstracted away from this intimate feel of moving individual words around inside the world of a computer.

There’s also his reference to paper backups. I still have mine, in my physical archive. Paper copies of the source codes from my undergraduate days and my Ph.D. thesis work. Although he refers to them as lasting longer than magnetic media, one catch is that the dye used in printing can fade – best to keep them out of the light (as I do). If you’ve got those old heavy cardboard folders that 132-column print-outs can be filed in, they help keep the light off the paper when lying closed on a desk.

Footnotes

Thanks to tu2thepoo for the link to Mechner’s blog!

* I’ve added ‘graphical’ because there were text-only games before the graphical ones – something younger folk might not realise. One in particular I used to play, the text interactive puzzle adventure Zork. These proceeded in interactive story fashion, with the gamer typing in simple English-like instructions to move around, pick up objects, look at them and so on. In fact, the class a head of me in computer science had to write a interactive text game. As far as I know the department decided not to do it again as some students were a little too dedicated to the task. (Our year-long project was to write a text-processor. Later editions of Zork had graphics.)

** Those that have never programmed in assembly language and want to explore, or those that just want a trip down memory lane, might try download the full text of Randell Hyde’s The Art of Assembly Language. (There’s also an on-line HTML version.) It‘s based around 80×86; those looking for the earlier 8-bit languages will want to look around more, e.g. at 6502.org.

Other geek stuff on Code for life:

Sinclair ZX envy

Are bioinformaticians gods?

Animating our DNA*

Clay tablet science

C’s founder is no more

Research project coding v. end-user application coding

This discovery is mine (for a little while)

Last night local current affairs program Campbell Live ran a story comparing two staff members and their decision to vaccinate or not, “of course” choosing one ‘for’ and one ‘against’ for balance.

You can view the footage* and read the comments they quoted and subsequent comments on-line. (To get back to the quoted comments from the video footage, you’ll need to keep pressing ‘View previous comments’ until you’ve got them all displayed – there’s a few hundred of them now!)

Overall the story seems well done. We’ve discussed communication of vaccine issues before here – what do think of Doctor Cameron‘s efforts?

Here’s what Aspiring Health, from twitter, thinks: “Seriously Dr Cameron on @CampbellLiveNZ is the jolliest GP ever!” He certainly presents with gusto and exudes bonhomie. Personally, I think he did an excellent job.

Their presentation leads with a few quotes from their Facebook page (linked above). The first two are opinions. The next two make claims, neither of which are correct. Unfortunately I’m out of time to address these properly so I’ve excepted them below for readers to take my place. (I’m flat out here… but I can’t help make a couple of brief comments.)

The third quote in the video:

No, if we have a healthy diet our body should be able to look after itself and build up our own immunity to the flu, I believe our bodies will become ‘lazy’ and unable to fight off new strains if it can’t cope with strains we have now, if i do get the flu i’ll take echinachea and i’m usually ok within 24hrs!

Our bodies gain immunity to illnesses through exposure to either the infection or preparations based on parts of the infectious organisms – what vaccines are in essence. To gain immunity in the way Nichola suggests, she would have to become infected. (A healthy diet will not prevent you from catching a viral illness.) That those who are ‘run down’ from a poor diet may be more vulnerable once infected but does not mean that those with a good diet will not suffer.** The mention of 24 hours makes me think Nichola has had colds (i.e. not a ’flu) that have recovered naturally. These also bring up a point Tristram Clayton and Dr. Cameron made – influenza is not ‘just a bad cold’, it’s more severe. Dr. Novella at Science-based Medicine has reviewed evidence for/against use of echinachea for colds and flus; he finds studies come out against its use. Developing immunity to one strain doesn’t ‘tire’ or make your immune system ‘lazy’.

The fourth:

So basically you’re jabbed with last years flu…..hmmm? No thanks.

Influenza follows a pattern of emerging from South-East Asia; this is monitored and the vaccines we receive are based on what is emerging from SE Asia that are anticipated might predominate here.

One thing I’d add to what was presented was that those who are self-employed, work in small companies or in important positions might want to consider the effect of be laid out of work for a week when they consider the value of the influenza vaccine. In the case of the self-employed, for example, you don’t get paid while you’re sick. You can leave aside the ‘medical’ arguments (not that I would myself) and look at it from a financial/employment/productivity view too.

Footnotes

* I’d embed this in this post if it were possible, but you’ll have to trek over there I’m afraid.

** Anecdotally I’ve ‘been there and done that’, too. From personal experience the ’flu is not a nice illness, it really knocks you flat.

Some of the other vaccine-related articles on Code for life:

Immunisation then and now

Fact or fallacy, a survey of immunisations statements in the print media

Sources for medical information for non-medics and non-scientists

IAS talks about vaccination

In his novel COSM Gregory Benford describes* four types of scientists -

1. I want to know – “Prying into Mother Nature’s secrets.”
2. Theory predicts – Exploring what theory says ought to happen.
3. This is what I do – “Habit often rather mindless. More deeply, it means This is who I am.”
4. A sweet experiment – Doing a well designed/executed experiment itself.**

What kind of scientist are you?

Footnotes

Gregory Benford is really writing about physicists (he’s a physicist himself) but the categories are basic enough they ought to apply to other fields.

Lest anyone think that computational biologists (my field) don’t do experiments – quibble about it, as I’m sure many will, but you can conduct ‘dry’ experiments on datasets. (Or at least I can wave my hands around a little here…)

If you’re a fan of hard science fiction and haven‘t read Gregory Benford’s work, do. His work is grounded on ideas taken from physics/astronomy/cosmology played out with strong lead characters. There’s a chat on the lablit forums opened by the author, with more thoughts elsewhere on the same forum. Reviews of COSM can be read at Suite101, goodreads and elsewhere.

* p33.

** It’s a bit harder to pick Gregory’s intentions on this one; this is my interpretation.

What is your relationship with your research notebook?

Scientific article download costs

New academic visas for New Zealand

The 24/7 lab: in praise of time out

Describe your fantasy institute

Below Jessica Tyler, from the University of Texas MD Anderson Cancer Center, introduces epigenetics, a topic I’ve touched on a few times and would like to elaborate further on. Her introduction is fairly gentle; hopefully some of the essence of the thing will come across to non-specialists!

Click here to view the embedded video.

You may need to wait until the video is buffered before it starts displaying. Feel free to ask questions in the comments below.

(Excuse the back-to-back videos and no articles – I’m very busy until at least Friday!)

Other articles on Code for life:

Epigenetics, growing old and identical twins becoming unique

Doggie ERVs

Transcribing a gene, free poster

Autism – looking for parent-of-origin effects

Coiling bacterial DNA

Epigenetics and 3-D gene structure

Weekend video – for general readers.

This TEDxCambridge lecture by Professor George Church* offers an informal look at progress in genomics and personalised medicine. While very informal compared to some TED lectures, but it does give glimpses of where genomics and personalised medicine might be headed in a series of quick snapshots.**

In the middle of his talk you’ll hear about some kids sequencing genes for their own interest or school projects. For some like me who has been doing computational biology from before the genome projects*** it’s a measure of how far things have come.

There are some examples of new possible treatments being explored.

Click here to view the embedded video.

His talk assumes a bit of background in places – he’s giving a high-flying overview. Feel free to ask anything in comments below.

Footnotes

* Prof. Church is well-known as a leader in the genomics (and applications of computational biology, my field).

** I personally would like to offer a more detailed talk on the subject, as it deserves it, but then it’d also be longer! This might be better suited to a lazy long weekend, perhaps.

*** More accurately, before eukaryote genome projects.

More genome-related articles on Code for life:

Genetic tests and personalised medicine

Boney lumps, linkage analysis and whole genome sequencing

Metagenomics-finding organisms from their genomes

Autism genetics, how do you copy?

Online lecture series on genomics and bioinformatics