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Archive for the ‘April 2014’ Category

Counting chromosomes

In April 2014 on May 14, 2014 at 9:49 am

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Sarah: Every time an egg and a sperm come together, its a bit of a lottery as to how the chromosomes from each contributing parent manage to recombine and form new life.

Occasionally errors in chromosomes occur – perhaps an extra copy sneaks in, or one is lost. Sometimes this means a pregnancy doesn’t even get started; sometimes the embryo will survive a few weeks or even months.

When parents look for medical assistance to achieve pregnancy through IVF (in vitro fertilisation), insemination of eggs often occurs under controlled laboratory conditions. If an embryo starts to grow, it is then placed into the uterus and everyone crosses their fingers in the hope that a baby will result.

But even if the embryo looks healthy, its chromosomes may contain errors. Just like when natural fertilisation occurs, such pregnancies will also fail in the early or even later stages. Many parents using IVF undergo repeated cycles of heartbreak and high financial costs until a baby finally arrives.

A new test has been developed by a biotech start-up company in Adelaide to screen the numbers of chromosomes in an IVF embryo before it is selected for a possible pregnancy.

Here’s a story I wrote on the test for The Lead SA (image thanks to Janine on flickr]

Adelaide biotech kit to improve IVF success

A screening kit developed by Adelaide biotech start-up Reproductive Health Science will reduce heartache and financial burden for couples seeking to become parents through IVF.

The kit is used to safely test an embryo for the correct number of chromosomes before it is selected to start a pregnancy.

Chromosome abnormalities are the leading cause of pregnancy failure and loss in women of all ages.

“As far as we know, for this kind of chromosome testing there are no other Australia companies developing competing products,” said Dr Michelle Fraser, the CEO and director of Reproductive Health Science.

“One of the advantages of our technology is its ease of interpretation. We’ve developed a kit that is easy to use and which does not require complex analysis by the clinician. The readout is also easy for the patient to understand,” she said.

The new testing kit relies on technology known as microarray, in which the chromosomes in a single embryo cell are laid out as a grid of DNA, and then amplified. Missing or extra chromosomes are identified using the procedure.

IVF, or in vitro fertilisation, offers couples medical assistance to achieve pregnancy.

Statistics from Reuters global analysts predict the global market in IVF will grow by more than 12% in the period 2012-2016 due to increasing infertility rates and greater uptake of medical tourism. However cost is one of the major barriers to IVF for many couples. The process can also be an emotional rollercoaster when apparently healthy embryos fail to successfully implant into the uterus, or don’t survive for the duration of a pregnancy. Current success rates for IVF hover around 20%.

“Being able to count the number of chromosomes in embryos before they are selected for a pregnancy is an important tool for doctors,” said Dr Louise Hull, a reproductive health researcher at the University of Adelaide and fertility consultant at Fertility SA.

“It’s an exciting approach that Reproductive Health Science is using. Providing accurate information about the chromosome component of embryos will offer greater confidence to couples having IVF, particularly those who have been through the heartbreak of repeated miscarriages or failed pregnancies in the past,” she added.

Improved success will also reduce the need for multiple cycles of IVF, and therefore result in lower overall costs for the couple involved.

Reproductive Health Science — which recently listed on the Australian Stock Exchange after a reverse merger in April — will officially launch their kit and related products later in 2014. The company was founded in 2003 on a patented technology for single cell chromosome analysis from the University of Adelaide.

“We’ve got a global product, and we’ll be going after the global market,” said Dr Fraser.

“Making sure you’ve got a really good quality embryo in IVF is something that’s important across the industry.”

Reproductive Health Science will stay based in Thebarton Bioscience Precinct in South Australia for the foreseeable future.

After the chocolate rush

In April 2014 on April 26, 2014 at 7:23 am

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Kirsti: Did you know you can make your own chocolate?  Fresh memories of Easter indulgence have got me wanting to try it.

How did you fare on the chocolate front this year?  Did you choose your chocolate? Or were you given some and ate indiscriminately? Before you unwrapped an Easter Bilby did you pause, think about the sugar content and plough in anyway? Which chocolate do you like best?

I would seriously like to hear the answers to these questions!

Me? I did not choose any chocolate for myself. I WAS given some, and I ate as much of it as was humanly possible while altruistically sharing with families and friends (read: I gave most of it to the kids). I didn’t pause, I just felt sick after too much.

My favourite chocolate is Haigh’s peppermint dark chocolate frogs. Only slightly ahead of Whittakers milk chocolate with hazelnut….

But now I want to make my own. I want to prove to myself that with some science I can make Lindt-quality deliciousness. I also really want to use paint scrapers to mix something in my kitchen, preferably something from a cacao plant.

Theobroma cacao, the plant from whence chocolate comes, is native to Central and South America. I – for one – am really glad that someone discovered how to mix it with sugar and reduce the bitter flavonoids to make chocolate. First savoured as a drink by the Mayans and Aztecs in the 1500’s, cacao was deemed highly desirable across the globe within a century, and the French and Spanish set up plantations in the colonies wherever they could.

Now that it’s everywhere, making your own chocolate is the ultimate challenge, but apparently you can do it from scratch in your own kitchen. Although making chocolate is often described as an art, I say ‘bah!’ Given the requirements for very specific temperatures during the roasting process (at which the polymorphs of chocolate melt), the need for safety goggles and specific tools, it’s all pointing to science.

And it’s true – dark chocolate is probably better for you simply because it contains less sugar and milk solids, and has an ever so slightly higher concentration of theobromine (a vasodilator, diuretic and heart stimulator also found in black tea and the kola nut) and flavonoids (that have various health benefits including anti-inflammatory and anti-viral and anti-bacterial properties).

Happy chocolate making! I’ll post the results here when I try it!

 

A beachy boney fishy Easter mystery

In April 2014 on April 23, 2014 at 1:13 pm

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Sarah: Tucked away down here at the bottom of Yorke Peninsula, we solved an Easter mystery by social media.

The case began whilst on a family beachcombing foray.  My 6-year old niece ran towards me holding the item shown in the photograph above,

“Aunty Sarah, what is this?”

I did not know, but described to her the features I could see.

“It’s made of bone, and looks a bit like a vertebra, or one of the bones in a spine.  It is symmetrical, which means it would be the same on each side if you chopped it in half along its length. It has flat spines which stick out from one end, and has small holes on each side which you can imagine nerves might come out from in the living situation”

But it wasn’t a bone from a spine of any animal I knew; the unusual rounded end ruled out this possibility. We googled various bone images and came up with nothing. It had us truly flummoxed.

Not just us, but also a group of interested followers on twitter and Facebook. After I posted the following photographic angles….

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…the comments came rolling in thick and fast:

“Almost looks like the front of the scull of a bottle-nosed dolphin”

“Vertebra was going to be my guess too, overall I have no idea! I do hope it turns out to be a sperm whale tooth!!!”

“At the risk of being a total dunderhead, It looks like an occipital bone/saggital crest on a parietal skull bone but where is the rest of the skull?! Seal? Foetal something? I have no idea, but this is super fun”

“ALIEN”

“Looks like a beak of some kind of bird”

“It looks like mammal bone”

“Agree. Don’t know exactly what it is but it doesn’t look fish-y to me”

“Is it ambergris?”

“True looks like a vertebra. I’d only be guessing. But looks old and well worn. Whale?”

On a whim, I forwarded my images to the twitter account of the South Australian Museum (@SAMuseum). I sat, I waited, it was killing me!

Two days later, a JACKPOT response from the museum.

“Found! This is the bone that forms the hump on the head of a Snapper fish (Chrysophrys auratus)”

Mystery solved! Now I can sleep. Thanks museum staff and all who followed along.

P.S. You can see the bone above the eyes of this X-ray image of a snapper head here. This is the bone that sometimes undergoes abnormal growth and gives some snapper their famous ‘bumpy nose’ appearance.

P.P.S. And for the record, some of the people whose comments are shown above were actually very close. You know who you are!

 

When is a weed not a weed?

In April 2014 on April 15, 2014 at 3:22 pm

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A ScienceforLife.365 guest post by Dr Heather Bray* 

Heather: My garden needed a darn good weeding this morning. I spent a couple of hours on it, furiously pulling up or digging out the offenders, being careful not to disturb the plants I have nurtured since before the summer..

When it came to this little fellow however, I left him alone. I decided this one wasn’t a weed.

The best definition for a weed is the first one I learned in Year 7 Agriculture:

A weed is a plant in the wrong place.

We decide which plants are in the right place and which ones aren’t based on a whole range of factors; many of the reasons are based in science, but some are not. Some plants are dangerous and so we consider them weeds because they are toxic to humans or animals. Some weeds can affect nearby plants through competition for resources in the soils or by suppressing their growth through allelopathy. Some weeds are invasive and push out indigenous flora. Other weeds cause harm indirectly, and are considered a pest because their presence in association with other plants can reduce the purity, quality or price of an end product destined for market.

But some weeds are pretty, and so we choose to leave them where they are, or move them to another place and even help them to grow. Those of us who live in urban areas will be mostly familiar with this aesthetic idea of a weed as we arbitrarily decide whether a plant is in the right place to suit our own needs.

By some definitions, all the plants in my garden are weeds. The heartsease pictured above I spared quite simply because I like it. This particular one is an escapee, being self-sown from a plant in a pot.

I also have lots of arum lilies, the loveliest of all the weeds in my opinion. These remind me of the times I did practical work on dairy farms in NSW, where there were often clumps visible in the paddocks. All the ones I have now came from three lilies I brought from a previous garden, so I can see how they can ‘jump the fence’ and become a pest. There are also weedy tendencies in agapanthus, the species I used to re-establish the garden bed quickly (after the process of getting a new fence trashed what was previously growing).

I do feel a little guilty sometimes about both of these plant choices, but I’m planning on selling my house soon and needed something cheap, pretty and hard to kill. And they are everywhere in gardens around where I live. At least I haven’t planted lantana, a common Adelaide garden plant and ‘Weed of National Significance’ – I have vivid memories of seeing this species fill whole valleys of bushland in coastal NSW.

A weed is a wonderful example of something that is both a scientific concept and a social one. Ideas about what plants belong where can be constructed socially and culturally. There are others; for example ideas about food and naturalness are both influenced by factors other than science. It is important when we want to engage the community in discussions about scientific ideas that we don’t assume everyone will see things in the same way.

One person’s weed is another person’s flower, and so my little heartsease is safe … for now.

*You can find Heather on twitter as @heatherbray6

Getting active

In April 2014 on April 14, 2014 at 8:00 am

Kirsti Active voice Steven Hromnak

Sarah: A few days ago, I wrote a post on the peculiarities of verb tenses and personal pronouns in writing about science. I should have prefaced the article with the disclaimer that I have not actually published anything in the pure sciences for many years. I’m delighted that the more in-touch-with-real-science Kirsti has now written a response. 

Kirsti: The tradition of writing in passive voice, or in the third person, as a scientist is still as pervasive as stereotypes of scientists themselves.  Most scientists might still say that a sentence like this:

All stems greater than 10 cm DBH were sampled along the 100 m transect,

is more correct than:

We sampled all stems greater than 10 cm DBH in the 100 m transect.

But things are changing.

Many journals – including high impact journals like Nature – encourage authors to write in the active voice because they suggest that,

“readers find concepts and results to be conveyed more clearly if written directly. We have also found that use of several adjectives to qualify one noun in highly technical language can be confusing to readers.”

I couldn’t agree more.

Using active voice for scientific publications not only saves space and allows more articles to be published per issue, but it infers accountability. Who did the research? WE did the research. WE (the authors) do the stuff; design the study, collect the data, analyse and interpret the results, write the paper. Other people with specific expertise contribute too, and if significant enough, attributing an action to someone should occur in the paper too.

For example, in a results section, using active voice makes distinctions about who actually did specific parts of the work, like this:

We oven-dried (at 80oC for 50 mins) all ant samples, and Pacific Carbon Laboratories analysed stable isotopes 13C and 15N.

If those results were written in the third person, it might read something like this:

All ant samples were dried and weighed (at 80oC for 50 mins), and 13C and 15N were analysed for all individual ants.

This second example has no important attribution to who actually DID the stuff. Say the isotope analysis went wrong? You don’t know who to blame in the second sentence!

Sarah’s post about writing styles in science really piqued my interest, partly because I have been teaching bits of science writing at Monash University for the past 6 years. Here, we teach to write in the active voice. We critique examples in the literature of passive versus active voice, and active always comes out on top. We also review many of the journals’ instructions, which are now moving toward a requirement of active voice.

But I hadn’t really ever thought about it from a mental health perspective.

I’m really interested in reading Sarah’s third person perspective. My head tells me I won’t like it, but my heart totally understands the need to separate oneself from difficult concepts. Kind of telling yourself “it wasn’t really me there, and if I write about it like it was someone else maybe I’ll see things differently……”

Therapy. By writing.

I totally get that.

[image thanks to Steven Hromnik on flickr]

Staking a claim

In April 2014 on April 11, 2014 at 2:28 pm

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Sarah:
Scientists can be brushed aside as just another cultural group staking a claim on our resources.

It’s a concept which occurred to me whilst reading Flight Behaviour by Barbara Kingsolver.

The young bored mother Dellarobia Turnbow feels anger and resentment when a group of scientists arrive to study an unusual (and climate change-driven) aggregation of monarch butterflies she discovered in the hills above her house.

“Why did the one rare, spectacular thing in her life have to be a sickness of nature? These butterflies had been hers. She’d found them, she’d showed them to her son, in her name they were becoming beloved and important. They seemed to matter, like nothing else she’d ever possessed.

So how did an outsider just get to come in here and declare the whole event a giant mistake? These people had everything. Education, good looks, boots whose price tags equaled her husband’s last paycheck. Now the butterflies were theirs too.”

This kind of emotion arises when natural resources hold value for multiple stakeholders in the real word too. Governments, industries, farmers, mining consortiums, food producers and recreational groups fight with scientists to stake claims on forests, oceans, reefs, inland waterways and fertile land. Often, the guys with the biggest budgets and loudest voices win these battles.

Quite simply, scientists need to be more effective in running campaigns to explain, justify and garner support for their claims and thus compete on a level playing field with their opponents on the ‘other’ sides.

One step towards achieving this end is for scientists to get out into the community and listen to the experiences and views of the people they feel they are fighting against. To know your enemy, you must become your enemy, right?

Will Grant and colleagues at the Australian National University recently conducted a dialogue project, bringing Australia’s leading climate change scientists to round table discussions with local people across regional Australia. Called Up Stream, the story of the project has been documented in a series of four 7-8 minute video clips:

Ultimately, it’s only with the help of unique and multi-faceted projects like this that science even stands a chance.

[image thanks to John Haslam on flickr]

It was written. I write. She wrote.

In April 2014 on April 10, 2014 at 8:44 am

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Sarah: Classically-trained scientists communicate in a very particular way. When writing articles for professional publications they are taught to always remove any sense of ‘personhood’ from their descriptions of how experiments are conducted, and the passive tense is usually applied.

Hence, rather than write,

I used a microscope to count the skin cells.

The perfect scientist would say,

Skin cells were counted using a microscope.

It’s indirect, apparently no actual person was involved, and in long sentences it can get messy. But – for historical reasons – it’s just the way things are done in science. It’s rather fitting I guess, given that science is supposed to be removed from any subjective influence.

It’s because of this requirement for a very specific and removed style of language that many scientists find it hard work to communicate through platforms other than their specialist journals. For example, creating enticing and punchy articles for blogs and newspapers can be nigh on impossible without the use of personal pronouns – I, we, she, he, they – and the active forms of verbs. This is something I’ve had to think about quite a bit in writing posts for this blog, as even now habit can lead me to using the passive voice on occasion.

But it turns out there are also implications according to whether one writes using the first or the third person i.e. I versus he or she. This I learnt through reading a fascinating article by Jane Turner Goldsmith: entitled The Psychology of Writing, it appeared in the March 2014 edition of Southern Write, the quarterly magazine of the SA Writers Centre.

Jane says,

“It matters who is telling the story and how it is told. We know this matters to a reader of course, but it turns out to also matter to the writer – from the point of view of mental health.”

And then,

“Writers who use the third person are also less vulnerable psychologically than their counterparts who write in the first person. It makes sense – there is more psychological vulnerability in that exposed first person voice, commonly (but not always) employed by poets, than there is in the more distanced third person point of view. Some kind of mastery over difficult or traumatic emotions is thought to result from the distancing.”

As someone who has been writing daily or weekly blog posts in the first person for the past 20 months or so, this struck a chord. Writing from the perspective of ‘I’ often feels heavily self-indulgent, and can be especially difficult when writing about very personal matters.

Perhaps it could be time to move to the third person to explore some aspects of the science in my life. Could this be my first inkling of a foray into narrative or creative writing? With science in it, of course*.

*Don’t panic, I despise science fiction

[image thanks to Jorel on flickr]

 

 

 

Read a great science book?

In April 2014 on April 9, 2014 at 12:17 pm

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Sarah: Have you read a great science book lately?

If your answer is no, look no further than Science Book a Day, a site produced by George Aranda. George explains why he set up this resource:

“My aim is to engage people in science via books and for them to bring their own ideas and experiences to science. To me, science isn’t about being told by scientists that “this is science” but for people to build an understanding and engagement with science in their own way.”

I was very pleased to contribute a book review for George earlier this year: The Curious Country, edited by Leigh Dayton (and an accompanying interview with Leigh herself).

George has also been kind enough to allow me to reproduce the review here. And yes, I highly recommend you all read it! Scientists and non-scientists alike, it’s very easy to pick up and grab a bite of science here and there, depending on your areas of interest. And it’s free! (links to download are shown in the review below).

Review: The Curious Country edited by Leigh Dayton

What do Australians think about science? It’s an issue that interests – even plagues – many of us who conduct scientific research, or communicate science outside of specialist environments. In 2012 Australia’s Chief Scientist Professor Ian Chubb decided to seek an answer to this question. By surveying ordinary Australians and asking them to identify the important issues they wanted science to address, a book was born – The Curious Country (freely available as a PDF at http://press.anu.edu.au/titles/the-curious-country/pdf-download/). The book was launched on December 3 2013.

Edited and introduced by science writer and broadcaster Leigh Dayton, the book is presented as a series of essays addressing common issues identified in survey responses. The work is further organised according to key societal challenges that had been previously highlighted by the Office of the Chief Scientist. Thus chapters are entitled:

  • Living in a changing environment;
  • Promoting health and wellbeing;
  • Managing our food and water assets;
  • Securing Australia’s place in a changing world;
  • Lifting productivity and economic growth;
  • Sustainable energy and productivity; and
  • Curiosity.

The book is a thorough, diverse and balanced guide to science in Australia – past, present and future. The 26 essays addressing each of the important issues across the chapters have been written by some of the best communicators of science this country has to offer. Pleasingly, the authors include not only professional writers and journalists highly familiar with science – such as Amy Corderoy, Wilson da Silva and Elizabeth Finkel – but also research scientists, research leaders and those with experience of science in a broader context. The Fruits of Science – a piece which describes innovation and the difficult journey from the lab to the real world – comes from Dr Craig Cormick, the newly-crowned recipient of the 2014 Unsung Hero of Science Communication award. Ecologist and scientist Professor David Bowman presents a call to action in response to extreme weather events such as bushfire, torrential rain and drought in Adaptation is the Key to Survival. Epidemiologist Professor Tony McMichael considers diseases, their occurrence and their impact at a population level in Population health: Understanding Why Disease Rates Change Over Time. Former Minister and diplomat Dr Brendan Nelson offers Science Diplomacy: in essence an Australian case study showing that engaging other nations in the pursuit of knowledge promotes international relations and national wellbeing.

While some of our politicians, business leaders and indeed journalists continue to question the existence of human-induced climate change, writers in The Curious Country know that it is happening. It appears as a challenge and influence requiring current and future action in many of the book pieces, even those not directly addressing climate.

All essays in The Curious Country are pitched at an interested reader who may or may not have any prior experience with science. While many readers will devour the content over a few sittings, the book could (should!) easily sit on coffee tables in homes and businesses across Australia, to be picked up and read as interest and time allow. It certainly deserves a position alongside other more popular and glossy compilations themed around art, design, literature and sport. The Curious Country would also form a fantastic set of reading material for high school and tertiary teachers and students looking to explore science, medicine, education, society, technology, innovation, futures thinking and philosophy. To that end, the office of the Chief Scientist has recently distributed the book e-link to 8000 schools across Australia, and has arranged an on-paper print run for distribution to politicians and other decision makers. Free downloadable versions in e-reader format will soon be available.  The book content has been released under a Creative Commons Attribution – Noncommercial – Share Alike 3.0 Australia license.

Subtleties of science

In April 2014 on April 8, 2014 at 8:10 pm

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Kirsti: In 1999 I lived in Narrabri, NSW, and worked for the CSIRO in the cotton industry. A keen rock climber, I spent many a weekend in Mount Kaputar National Park, Warrumbungle National Park and other great climbing places around the region.

In addition to the climbing in Kaputar however, I was fascinated by the red slugs there. My friends and I would often go bush walking and slug spotting, and I always felt that all was right with the world if we spotted a bright red Triboniophorus aff. graeffei.

So last year when a series of news articles, reports and blogs about a “new species of bizarre blood-red slug” discovered in a remote area of Australia came out, I was intrigued. A NEW species? ANOTHER red slug?!  Where? How big? Near the Kaputar red slug?

Headlines included:

It turned out that it WAS the Kaputar red slug they were talking about. The one I knew and loved. The research that was picked up by the media apparently found that the Kaputar red slug and cannibal snails were distinct species and endemic to Kaputar National Park, not colour variations of already described species.

What constitutes a distinct species has traditionally been a group of organisms described using morphological differences and that are capable of producing viable offspring. However, defining a species is fraught with difficulties. Currently, and most often, information used to split species is found in an organism’s DNA; if nobody has looked at an animal’s DNA, descriptions of species will stand until that research is done.

So the Kaputar red slug was a newly confirmed distinct species in that it was given a new name, but not a newly discovered organism, which is the angle most pieces were taking. But the slug itself had been known to scientists, locals and tourists for decades. It was not, as one Australian Geographic blog wrote,

“only discovered in the last few years……..because they are in such a remote location”.

The intricacies of recognising distinct species is a fundamental aspect of any biological science, and it frustrated me that those who had written the articles had not been specific enough to explain the full story behind the science, including the importance of taxonomy.

It’s fabulous that someone wrote about these slugs in the first place, but communication leading to misunderstandings about science is not good for anyone.

[image thanks to Vinni on flickr]

I’m popular, I’m never picked last

In April 2014 on April 7, 2014 at 12:47 pm

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Sarah: While we’re talking People’s Choice awards, let’s look back over the most popular posts of 2014 so far.

Just by way of reminder, ScienceforLife.365 started as my year-long daily blogging project to show how science can frame the ordinary, every-day decisions in life. Now in its second phase, the blog features weekly contributions from both myself and ecologist/educator Kirsti Abbott. Other guest writers also pop up (and if you have a great idea which would fit under the ‘science for life’ motto, please be in touch).

For me, one of the most interesting aspects of the blog is that it attracts two separate audiences (because it appears in duplicate on two platforms, WordPress and Facebook). I’ve presented analysis of the differing interests of the two audiences in the past: at the 100-day mark of the first year, and at day 360, as the 1-year anniversary approached. Over phase 1 of the blog, WordPress readers preferred posts on art, food, fashion, literature, writing and discussions around journalism and communication. By contrast, Facebook friends were interested in animals, science humour, new ways of thinking about science and the more personalised aspects of science and learning.

Differences in content preferences by audience are not so strong so far this year, with many posts appearing in both top ten lists, as shown below. In general however, it is still clear that readers who enjoy the blog through Facebook continue to prefer posts with more personal content (whether that be from myself or Kirsti). It’s also great that Kirsti’s colleagues, friends and family members have strongly supported her move into weekly blogging, as evidenced by their ‘likes’ and comments. Many readers also seemed to particularly enjoy the stories around how Kirsti and I met for the first time earlier this year – happy moments!

Here are the top 10 posts for 2014 (so far) on WordPress:

  1. Knock knock
  2. Water leaked from my face
  3. Part time everything
  4. Getting uncomfortable
  5. It’s another scorcher
  6. Tick tick tock
  7. Sharing the love
  8. Information is beautiful
  9. You want more heat??!
  10. Multiple ways of knowing

On Facebook, the top 10 posts for the year thus far are:

  1. Water leaked from my face
  2. Knock knock
  3. Bone picking
  4. Getting uncomfortable
  5. A new woman
  6. From rocks to vegetables
  7. Friendships in science, part 1
  8. Friendships in science, part 2
  9. You want more heat??!
  10. Tick tick tock

What is your favourite ScienceforLife.365 post?

*title taken from this song

[image thanks to Klearchos Kapoutsis on flickr]