Archive 2013

Any New Zealand schools want to help judge the Flame Challenge? Grant Jacobs Dec 13

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(Crowd-sourcing how best to let NZ schools join in the judging of the Flame Challenge.)

The Flame challenge is an international competition that challenges scientists to explain to 11 year-old students a question. The results are judged by children. (There is more on the Flame Challenge in my previous post.)

This year’s question is ‘What is colour?’ Explanations are in two categories, written or visual. The visual entries include short videos.

The question was drawn from more than 800 suggestions from around the world. Last year there were over 20,000 student judges.

I have been asked by the Alan Alda Center for Communicating Science who run the Flame Challenge for suggestions how New Zealand schools might get involved in judging — apparently no New Zealand schools have been involved in judging the entries before.

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Striking the flame of science in kids Grant Jacobs Dec 12

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Introducing this year’s Flame Challenge science communication competition.

Hawkeye, Alan Alda’s character in M*A*S*H, was a lanky wise guy with a serious edge—or was it the other way around?—always poking at serious matters. (M*A*S*H fans or the confused might try Footnote 1.) In front of the kids in this PBS segment Alda seems to have a sweeter version of his famous role in real life.


His subject is science. In particular, how to teach it to kids.

Alan has run a couple of science writing challenges now — What is a flame? What is Time? — inspired by his disappointment in his science teacher’s answer to the first question. Let’s let PBS tell that story,

YouTube Preview Image

His challenges are cleverly set up. A question that is easy to pose but deceptively hard to answer and a target audience of 11 year-olds. Old enough to take a fairly sophisticated explanation but need the explanation broken down. And, of course, the judge are kids – no adults guessing what kids might think is best.


This year’s Flame Challenge is, What is colour? You’ve until March 1st 2014 to get your entry in, to be judged by thousands of kids via on-line voting. (Accuracy is screened by scientists. Teachers should note that their classes need to sign up before the end of January.)

This year there will be two winners, one for a 300-word-or-less written entry and another for a video or graphical entry. (Videos must be less than 6 minutes long.) Winners will get a trip to the World Science Festival in New York.

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Book review: The Best Australian Science Writing 2013 Grant Jacobs Dec 11

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Looking for a Christmas present for someone who likes reading about ‘things’, how they work, why?

Or just generally musing about life.

I’ve had past success with anthologies of science writing as gifts, in my case Best American Science and Nature Writing or Best American Science Writing, both part of the long-established ‘Best American’ series that offers collected writing over many niche genres.


Now in it’s third edition I have only become aware this year of Best Australian Science Writing. Like it’s American counterpart it’s an edited collection of works previously published elsewhere, from newspapers, books, magazines and radio.

Among the entries are all short-listed articles from the 2013 Bragg[1] University of New South Wales Prize for Science Writing.[2] This year’s winner was Fred Watson’s, Here come the ubernerds: Planets, Pluto and Prague.

The collection is mostly of short to medium length articles on science-related topics, but also features poetry and biographical pieces. The authors, too, are a mixed collection. Some are scientists who write in addition their scientific work; many are full-time (science) writers.

The book is available as a paperback and in electronic form (EPub, Kindle or ePDF; this review is of the paperback format).

Among the reasons I feel these anthologies make for excellent gifts is that it’s a format that can be read in an hour here, half an hour there or an afternoon and can be left on the table or at the bach for visitors to pick up.

Another strength of science writing anthologies for gifts is they cover a very wide range of topics. There’s bound to be something for everyone.

Tim Minchin, a man of many talents but perhaps best known for his comedy including the excellent beat poem Storm, has placed his introduction, Not a Nobel Laureate,[3] on-line. It’s excellent and worth reading, even if you don’t buy the book. (Fellow sci-blogger Siouxsie will be disappointed with his description of pink-haired people.) It’s followed by the editors’ preface then the articles themselves.

My views on the individual pieces vary, as they will for any reader, a natural consequence of the variety on offer, but one that in many ways makes these anthologies better gifts: they’re likely to always include styles the recipient likes, even if you’re unsure of their reading tastes.

As a measure of this, among my favourites are some that didn’t make the short-list for the Bragg Prize. Each to their own.[4]

Over the whole collection I’m happy to say that I chose to skip few,[4] mostly those related to climate – partly a consequence of writing style preferences but also in part as it’s a topic that feels stale to me, important as the subject is. Others will chose differently. On the whole, the articles are excellent and fun reads.

To give some flavour of the book, here’s a peek at some (by no means all) of the contents, in no particular order of merit:

  • Fish that become gonads. (Not have gonads, become gonads.)
  • Some fairly (seemingly) off-the-wall ideas as solutions for climate change in Earthmovers: playing god with the climate.
  • Pregnancy testing, then and now (very entertainingly).
  • Darwin, a perennial favourite for science writers, turns up several times. I especially liked Janine Burke’s short account of rebelling her Catholic College teachers and Francesca Rendle-Short’s much longer article of her six day creationist father, mentor to Ken Ham—of Creation Museum infamy—and her father’s Alzheimer’s.
  • One writer rails against the characters (caricatures) in Big Bang Theory.
  • I like Elizabeth Finkel’s piece following an examination of Aboriginal art for it’s portrayal of the team work and fallibilities of research, showing an understanding of the reality of scientific work as you might expect from a writer with research experience.
  • There’s a neat account of a writer’s autistic son, told in a different style that you’d usually encounter – fresh and very effective.
  • One of this year’s big science features in the media was testing for the existence (or not) of the Higg’s Boson; one article plays on the media coverage. (Peter Higgs and François Englert won this year’s Nobel Prize for Physics.)
  • A longer piece spans the death of Pluto as a planet while wandering among other astronomical and planetary topics.
  • Female sexual desire.
  • Behind the scenes of organ donation. Written by a surgeon, the practical, hands-on knowledge comes through.
  • Chickens as sentinels of epidemics.[5] (By Nobel laureate, Peter Doherty; author of several popular science books.)
  • Flatology, the science of flatulence, opening with Charles Darwin’s concerns about his emissions.
  • Cigarettes and polonium-210, the radioactive element probably best known as used to poison former KGB officer Alexander Litvinvenko in London. Smokers and friends of smokers will want to read this.

There’s more that I can possibly list without driving the reader to distraction, if I haven’t already. But in some ways that’s half the thing isn’t it? Distraction with the curious and interesting. A watering hole for a few minutes or hours.

Brief bibliographies of each author are available in a section before the stories. (I missed this at first.) The source of the articles are given in the back, under the (to me, slightly misnamed) section Acknowledgements.[6]

Each article ends with an unusual cross-link feature, a short index of words found on other pages in the book, that I take to be a print version of links embedded in the text of the electronic versions of the book.

About the book

Title: The Best Australian Science Writing 2013

Editors: McCredie and Mitchell

Publisher: NewSouth Publishing (University of New South Wales Press Ltd.)

ISBN: 97817422 33857 (pbk), 97817422 41654 (ePub/Kindle), 97817422 46666 (ePDF)


My copy is courtesy of the publishers.

None of the entries are from blogs. I don’t know if they were ruled out, but, if so, it’s worth noting the American counterpart occasionally includes writing of merit from on-line, too.

1. The Braggs are a famous father-and-son science team, who together won the Nobel Prize in Physics, 1915 for their work in X-ray crystallography. The Bragg name features in several terms in the field such as Bragg’s Law and Bragg diffraction. They were Australia’s first Nobel Prize winners.

2. For writers wanting to try their hand, entries for the 2014 competition are now open.

3. Tim Minchin’s introduction title is reference to that the introductions of both previous editions were penned by Nobel laureates.

4. My own taste in reading these days, particularly when busy, favours clear, lean(er), writing with interesting things to think about leavened with humour rather than, say, the slower-paced descriptive prose of the opening piece, The weather of who we are. It might also relate to that I tend to tend to escapism at busy times, tackling slower reading when time is there for the killing. Bear in mind, too, that as someone who follows popular science some topics are old news to me.

5. Sentinel Chickens has been published and was also short-listed on the Guardian science writing books of the year. I’ve a library copy I may (no promises) review before Christmas.

6. While it’s understand their use of the word, I think of acknowledgements as thanks for support or inspiration, rather than publication credits.

Other articles on Code for life:

Mad on Radium

Ancient books (or I’d rather be reading)

The Panic Virus

Science-y reading

A Geek Nation reviewed

Book review – The Poisoner’s Handbook

The bosom serpent

What books do you think geeks should read?

Advent, chromosome by chromosome Grant Jacobs Dec 07

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Why not count down the days of the advent chromosome by chromosome? It’s a great idea and the Royal Institution’s implementation of it is excellent, try it.

When you visit their advent website, you’ll see a karotype,* with a microscope lens in middle.


We have 23 pairs** of chromosomes: one pair of sex chromosomes (XX in women, XY in male) and 22 pairs of autosomes (non-sex chromosomes) numbered 1 to 22.

We also all have a small organelle that is involved in ‘energy’ processing in our cells, the mitochondria. It has it’s own little chromosome, known for being passed down only from our mothers,*** that is counted as the 24th chromosome for this advent calendar.

Move the lens around to locate each day’s calendar (you can change the focus, too). Days that haven’t yet come to pass aren’t labelled.

Each day has a short film exploring part of that chromosome and interesting genetics associated with it. If you’re thinking amateur science videos, don’t. Think more BBC documentary.

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Tsundoku Grant Jacobs Dec 04


Just hours before heading off the Dunedin’s annual fund-raiser for the Regent Theatre, the 24-hour booksale, I read this tweet from New Zealand science writer Veronika Meduna:

great, the Japanese have a word for “the act of buying books and not reading them, leaving them to pile up”: tsundoku 


I love that word. It’s neat, evoking such as specific thing.

I hate that word. There’s a guilty conscience for those books I haven’t read yet!

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The public and new research: peer review, initial reports and responses to extraordinary claims Grant Jacobs Dec 03


The recent and widely-reported retraction of a study on safety of genetically-modified (GM) maize has once-again raised the topic of what of peer-review offers.[1] This perennial topic includes what a scientific paper really is, how scientists respond to extraordinary claims (and what an extraordinary claim is) and, of course, what peer review contributes. With all the fuss the retraction of this paper has brought I thought it’s worth briefly looking what these mean, aimed at non-scientists.

What is a research paper?

Research papers present data along with interpretation of that data that argues a case for what the data might show.

Once it’s understood that conclusions drawn from research papers should be read as arguments for a case much of the rest of how research should be treated follows naturally.

Because they present an argument for a case, initial reports are rarely ‘a done deal’.

Research is more complex that the simple summaries you read in newspapers might suggest! Accounts for general readers usually present a ‘gloss’ of the broad questions the research hoped to probe.

By contrast, the validity of the conclusions often depend on details that are buried in the particulars of the methods used in the research. These methods are—understandably—rarely presented in accounts of research in media or press releases.[2]

Anyone who holds up a new paper in an argument, presenting it as definitive is most likely overstating the case; they are certainly overstating it if the claims made in the research paper are extraordinary. (By new research paper, I mean one that that has yet to followed up by further research, or criticism.)

Responding to extraordinary claims

An extraordinary claim is one that flies in the face of what is already thought to be correct. (It might also be a very strong claim being made using limited or poor evidence.)

Over-turning previous findings is a regular occurrence, something that is not greeted with dismay. While a scientist’s response to new findings is generally “that’s interesting”, the case has to be strong to over turn previous results. As a result, it’s a sound—and wise—response to extraordinary claims to pause and think “let’s look closer and make sure this thing is right.”

Taking extraordinary claims at face value, uncritically, is generally imprudent and can reveal a bias, a wish that the claim were true.

Here’s one response to an extraordinary claim that has just been published, that rats can pass on the memory of a smell to their offspring,[3] on twitter. As you can see, it’s focused on “let’s check this thing is right”, offering some specific issues that might want attention. (You’ll see from the writer’s profile he’s a specialist on olfaction, too.)

You can argue these things back-and-forth – that’s just how it goes. Uncertainty about how data should be interpreted can take time to resolve: think months even years. It’s not helped by that subsequent findings are often not reported by the media. Of course, we’d wish that media reported the initial findings with appropriate caution in the first place. (If they don’t an illusion of a ping-pong effect can take place, where science as presented in the media apparently keeps changing it’s mind about something.)

What peer-review offers

Peer-review by scientific journals is not a final arbitrator of truth and cannot be.

If reviewers were to rule that the conclusion were true for all time, they’d have to anticipate all future developments and objections. Obviously that’s impossible. (This is also why it’s reasonable for new findings to overturn older ones.)

That’s an unreasonable request, clearly. More reasonably reviewers might be tasked with ruling if the conclusions were ‘true’ to current knowledge. There are two problems with this. Firstly, it’s not the job of peer review to ask that all work be consistent with current knowledge. Some results simply won’t be. Work like that might remain a bit of a puzzle for some time, sometimes many years, even decades. Secondly, the reviewers would have to have an impossibly wide knowledge. Experts that they may be, reviewers cannot represent the wider range of expertise of the scientific community.

It’s a practical reality that reviewers simply can’t fully determine if a paper is ‘right’ and it’s not what is aimed for.

If someone presents a paper in an argument, saying that because it was published in a peer-review journal it “must” be ‘right’, or similar, they’re pulling a con. They’re not presenting the weaknesses and strengths of the argument, but putting something else in it’s place. (It had 5 peer-reviewers? So what.)

So what is aimed for in peer review?

In broad terms, they aim to eliminate papers that don’t meet the aim of the journal or it’s standards, and to try eliminate weak aspects of otherwise acceptable papers. Ideally you’d want high standards and to ensure that all the arguments are water-tight all of the time, but neither are truthfully possible.

A key thing that peer-review does is to try check if the logic, the statistics, the experimental methods are reasonable. Not if the conclusions are ‘right’ or not, but how those conclusions were arrived at—the bits making up the argument for the case in the paper—and if the conclusions are in fact consistent with the data.[4]

The standard of review will reflect the journal in question.[5]

From time to time peer review will fail, basically because people are fallible. We’d like to be perfect and all-knowing,[6] but we’re not. Ditto for reviewers.

Philosophically we might argue that peer review always fails – just by different degrees. Short of a purely mathematical paper or computer algorithm given with a proof, rigorous unfettered truth is hard to find.

Once a paper is published the wider range of expertise of the scientific community quickly points out any issues missed by the scientific journal’s reviewers – usually more vocally the more prominent a research paper and it’s claims are! (In cases, especially for less prominent research, specific issues can be known informally by the niche group working in the specific topic without it reaching wider recognition by those outside of the niche. This can be a problem for newcomers to an area of research.)

The final peer review of a research paper is it’s acceptance by the scientific community as a whole.

That can’t be over-emphasised. The peer-review of a paper by a journal is not it’s acceptance by science, the community. The peer review in journals is basically an attempt to eliminate the inappropriate, the obviously bad and to ensure reasonable arguments, and that’s all. The acceptance of the work — the conclusions offered — comes later, after the community has seen it and had time to explore any issues with the argument for those conclusions.

One more: putting right wrongs

Frequently research that draws attention to peer review in media are research being touted by advocates for a topical issue or cause, GMOs, climate change, a particular medical condition or illness.

One of the frustrations of seeing advocacy groups using initial findings to support their causes is that claims made (by advocates of a particular position) based on early reports that subsequently prove wrong are incredibly difficult to put right. A few persist in clinging to their original claim no matter that the research it is based on has been overturned. These can circulate on-line for years, misleading others.

You’d wish that people, including scientists, who promote research to advocacy groups would put the same effort to putting out word about something they espoused earlier having since been shown to be wrong, as they did in their original espousing of the now-incorrect claims.

Readers can help themselves by asking if the person presenting a new research ‘finding’ is (strongly) expressing appropriate caution and to remember that research papers are arguments for a case, not ‘a done deal’, and it is the acceptance by the wider scientific community is the true peer review of research work, and that that can take time. (As Yoda said, patience you must have my young padawan!)


1. I originally started on this at the time a report arguing that a species of arsenic-tolerant bacteria incorporates arsenic into it’s chemistry was published. That extra-ordinary claim received a lot of (justified) criticism, and promptly.

The ‘GMO’ paper in question is Séralini et al, Long term toxicity of a Roundup herbicide and a Roundup-tolerant genetically modified maizeFood and Chemical Toxicology Volume 50, Issue 11, November 2012, Pages 4221–4231. As you can see it’s preceded by a number of letters to the editor. It received considerably more fuss in the media, in part because of the unusual approach to reporting the authors’ views of the conclusions (which prevented the journalists from obtaining independent comment from other scientists).

2. An example might be research claiming that tiny (really tiny!) amounts of small RNAs in rice might affect humans; recent work aimed at testing this claim was unable to reproduce the original findings.

3. Put more correctly, it’s retention of a fear-conditioned response to an odour in the offspring. I’d like to get a copy of this paper (it’s pay-walled…) to check one thing that bothers me from reading the abstract (author’s summary of the research). One thing I felt in two minds about was this work was it being presented on-line before the research paper was available, as no-one (at that time) could look to see if the claim made might be sound or not.

4. You might think data just “is”, but data also has standards, standards set from exploration of the methodology. I’d elaborate on this but I don’t want to clutter the article.

5. The standard of a journal is a fraught question. Some appear to have no standards! Others set very onerous review standards, but get their share of papers that prove unsound. Suffice to say here, it’s a topic in it’s own right.

6. Not many people really would, but let me run with it. You got my point, right?

Related articles on Code for life:

Initial reports are not a done deal

Media reporting of subsequent findings

Arsenic life – more criticism, formally published

Trust science, not scientists

When the abstract or conclusions aren’t accurate or enough

XMRV-CFS, further retraction

Reproducible research and computational biology

What the audience are really thinking during your talk Grant Jacobs Nov 27

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Looking down at the faces as you rattle off the talk that you’ve nearly gotten down off pat, you sometimes find yourself wondering just what the audience is actually thinking about,


What do you think about when you’re at conference talks? (C’mon, don’t tell me you only ever think about the talk itself!)

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Frederick Sanger 1918-2013 Chemist who pioneered protein and DNA sequencing Grant Jacobs Nov 21

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Two-time Nobel Prize winner and pioneer of techniques that brought on modern biology, Frederick Sanger, died yesterday, aged 95.

His DNA and protein sequencing techniques are early steps to the world of high-speed DNA sequencing we have today, with whole genomes reported frequently and diagnosis of genetic components of disease, to mention just two applications. Knowing the sequences of molecules lets scientists learn what changes are associated with disease and to build evolutionary trees showing the ancestry of present-day species. Molecular sequences are central a part of modern biology.[1]

Fred Sanger is one of the few people to hold two science Nobel Prizes and one of the ‘greats’ of the MRC Laboratory of Molecular Biology.[2] (The others to have held two science Nobel Prizes are Marie Curie in physics, for work on radiation,[3] and chemistry, for her discovery of radium and polonium, and John Bardeen in physics for the invention of the transistor and for superconductivity theory.)

His first Nobel Prize was awarded in 1958 “for his work on the structure of proteins, especially that of insulin”, involving a method to sequence proteins; his second Nobel Prize was awarded in 1980 for the DNA sequencing method named after him, ‘Sanger sequencing’. This is sequencing method used in automated form to sequence the human genome.[4]

It might surprise non-biologist readers, but molecular biology didn’t start with DNA. A lot of the focus of early work was on proteins. This work on proteins is a key to the start of my field, bioinformatics or computational biology.[5]

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PhD students and young researchers – 800 words to win an iPad Grant Jacobs Nov 14

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The Access to Understanding science writing competition is back. You’ve 800 words or less to explain in plain English one of 10 Europe PubMed articles.


The competition is open worldwide.

The prizes are:

Winner: an iPad.

2nd place: an iPad mini

3rd place: an £100 Amazon voucher

All of last year’s winners were from the UK. Come on New Zealanders… We can’t leave this just to the Brits!

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What does a chromosome look like? (Not Just DNA #2) Grant Jacobs Nov 14

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Aside from the fun of peering at the stuff that codes for the parts that make up us, knowing how a chromosome is arranged inside a cell nucleus might tell us a lot about how our genes work. Understanding the structures of genomes might well be what is needed to make sense of the genetics of complex diseases.

So just what does a chromosome look like?

Are our genomes stuffed into the cell nucleus like loose string jammed into a bag or are they arranged in an organised way? Is the arrangement of genes that are being used in the cell different from those that are not being used? Are genes that are controlled in similar ways near each other? Do different chromosomes interact with eachother?

Mitotic chromosomes (via: The Pavellas Perspective)

Mitotic chromosomes (via: The Pavellas Perspective)

You’ll have seen images of chromosomes looking like two rods pinched together in the middle, like in the electron micrograph to the right, or perhaps as part of a karyotype (karyogram or idiogram)- showing the collection of chromosomes in your cell stained to revealed a banding pattern shown below.


Karyotype of person with Down Syndrome - note the extra chromosome 21 (See Footnote 1 for more).

Karyotype of person with Down Syndrome – note the extra chromosome 21 (See Footnote 1 for more).

Karyotypes, like that of a person with Down syndrome below, are typically used to investigate loss of large parts of chromosomes (deletions), or swops of large portions between chromosomes (rearrangements), that can be associated with different diseases or syndromes. Small changes can happen and affect genetics, too, but are too small to be seen this way.

Chromosomes can also change shape, depending on what genes are being used and what stage in the cell’s lifecycle they are in.

Just like us, our cells have a lifecycle, growing and producing offspring (daughter cells[2]). The chromosomes seen in karyotypes and the classic ‘X’ are from cells that are from cells about to divide into two daughter cells. In this stage of a cell’s lifecycle, chromosomes aren’t doing the work of a growing cell, but are tightly packed and aligned up against each other ready to be pulled apart into the two daughter cells.[3] (Also, these cells have been broken apart so that the chromosomes can float free.)

During the ‘growth’ part of the cell cycle, the cell does the chemistry that type of cell gets up to. If you were to look down a microscope into these cel, you couldn’t see how chromosomes are organised, even if you added chemicals that stain DNA or the packaging proteins (histones) that our DNA is wrapped around. What you’d see is an opaque mess that you couldn’t make much sense of.

Staining for specific features can tell scientists if those features are near the edge (periphery) of the nucleus or the middle, or if the features seem to be clustered together inside the nucleus, but you couldn’t really make sense a whole chromosome this way, it’s just too confusing.

This is a classic problem in science: trying to create a picture of something you can’t see or make sense of directly.

What to do then?

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