Supercomputers

You might imagine science experiments as taking place in a lab with test tubes and beakers. Although that’s sometimes the case, these days a lot of scientists use computers to run their experiments and analyse their results. And not just any old computer – many researchers actually use supercomputers.

What makes a supercomputer SUPER?

Supercomputers are scientific research machines. They are made up of thousands of separate computers, all wired together by specialised fibre-optic cables. When individual computers are set up like this, they can communicate among themselves at high speed, and share the workload on complex projects.

The fastest supercomputers in the world are tens to hundreds of thousands of times more powerful than a standard laptop or smartphone. They can do a quadrillion calculations per second, working through huge amounts of data in a short space of time. Calculations that might take weeks or months on a desktop computer can be done in a few hours on a supercomputer.

Hot machines

One of the big issues with supercomputers is the amount of heat they produce. Because they are running 24 hours a day, the computer chips use a lot of energy and require a lot of cooling.

NCI uses fans to cool the computers, and then water to carry all the heat away. On an average day, NCI consumes enough electricity to power a whole suburb, and goes through more than 2000 litres of water per hour. Other supercomputer designs have their own ways of dealing with the heat.

Australia’s fastest facilities

Australia has two major supercomputing facilities for research: the National Computational Infrastructure (NCI) in Canberra, and the Pawsey Supercomputing Centre in Perth. NCI focuses on environmental science, human genomics and chemistry, while Pawsey has a focus on radio astronomy.

NCI is used by researchers from 35 universities and five national science organisations, including CSIRO, the Bureau of Meteorology and Geoscience Australia.

Much of the work involved in designing our-next generation weather forecasting models is done at NCI. It also holds a large data collection containing the equivalent of millions of DVDs worth of satellite images, ocean models and geophysical observations. This makes the facility a crucial resource for researchers from almost every field of science.

Pushing the limits

Countries around the world are always trying to push the boundaries of supercomputing forward. The parts they use need to be replaced every four or five years just to keep up with progress. Currently, the fastest supercomputer in the world is the Sunway supercomputer in China, followed by those in the United States, Japan and Europe. Australia’s two supercomputers are around the top 100 in the world.

Research possibilities

Worldwide, supercomputers are being used for more and more scientific research every year. We all benefit from the science that gets done with these machines. Flip over to the next two pages for some examples of supercomputer research.

What can you do with a supercomputer?

Predict tomorrow’s weather

Weather forecasts help us live our lives every single day. For many people, forecasts are more than the difference between wearing a jumper or not. Airlines depend on forecasts to schedule flights, farmers use them to know when to plant and harvest crops, and they us stay safe during natural disasters.

The Bureau of Meteorology – Australia’s national weather forecasting agency – has been working with NCI and CSIRO to improve their forecasting methods. They record thousands of temperature, wind speed, rain radar and barometer measurements from across the country, and use them in computer models that can predict the weather for coming days.

The main computer model the Bureau uses is called ACCESS: the Australian Community Climate and Earth-Systems Simulator. It brings together separate atmosphere, ocean and land models to fully understand what’s happening in the atmosphere to produce our weather.

The three organizations are working together to improve the ACCESS model by shortening the time it takes to run the forecasts. Recently, they managed to reduce the running time by 30 per cent. This means that once the changes are incorporated in the next version, they will be able to fit more runs inside their schedule, or run more accurate models.

Map the stars

Astronomy research produces huge amounts of data each day: data that has to be analyzed and stored for later use. NCI is one of the places where many significant astronomy datasets are stored.

For example, a telescope in Coonabarabran, New South Wales, takes extremely detailed pictures of the Australian sky every night as part of the Skymapper project. Skymapper makes these pictures available to astronomers to use for their own research. In 2014, some of the oldest known stars in the universe were discovered using this data.

Other astronomers are trying to understand phenomena such as supernova explosions by modelling them on the supercomputer. This lets them test their understanding and compare it to observations they’ve made previously. If the models match the observations, it means the researchers are on the right track.

Satellite searches

One of the best ways of studying our environment is to use satellites to take pictures of Earth from space. Different satellites have their own instruments and cameras on board, to investigate things such as vegetation, ocean currents, geology and agriculture.

The trick with using satellite images for research is being able to get just the ones you want, for the specific region you’re interested in. The Australian Geoscience Data Cube makes it easy for researchers to find the images they’re after.

Programs running in the background can pick through the database of images and search based on whatever criteria the researcher wants. Then, the satellite images can be used for research into bushfire prevention, water management and the monitoring of coral bleaching.

In the future, science will rely more and more on these huge databases of satellite observations. In turn, supercomputers will become even more critical as a way to learn about changes in the environment and how they will affect us.


This short article was originally published in the June 2017 issue of the Double Helix Magazine, an Australian children’s science magazine.

I wrote it for work, as a new way of reaching out to young people and letting them know about a different kind of scientific research.

Advertisements

Peer-reviewed article published: Communicating science in English has unique challenges for non-native speakers

In the first half of 2014, nearing the end of my undergraduate studies, I completed a course called SCOM3003: Special Topics in Science Communication (now called Science Communication Research Project). The course lets students design their own research project around a science communication topic of their choice, with supervision from an academic in that field. The final product at the end of the semester is a seminar presentation to the research centre, and a mini-thesis detailing relevant literature, methods, results and conclusions.

Following my completion of the course, I worked with my supervisor to turn the mini-thesis into an academic article, to submit to a peer-reviewed journal. Progress was slow, and as with any scientific publication, involved a lot of waiting, but after 5 attempts, I’m pleased to say that our article, Communicating Science in English: a preliminary exploration into the professional self-perceptions of Australian scientists from language backgrounds other than English, has now been published in the Journal of Science Communication.

jcom_title

You can read the entire text here (Open Access for the win!). Here is the abstract for you to read. Please do let me know in the comments or on Twitter what you think.


Scientists for whom English is not their first language report disadvantages with academic communication internationally. This case study explores preliminary evidence from non-Anglophone scientists in an Australian research organisation, where English is the first language. While the authors identified similarities with previous research, they found that scientists from non-Anglophone language backgrounds are limited by more than their level of linguistic proficiency in English. Academic science communication may be underpinned by perceptions of identity that are defined by the Anglocentric hegemony in science, which dictates not only how academic science is communicated but also who can communicate it.

Huttner-Koros, A. and Perera, S. (2016). ‘Communicating science in English: a preliminary exploration into the professional self-perceptions of Australian scientists from language backgrounds other than English’. JCOM 15 (06), A03.

Growing up as a plant

Have you ever planted a seed in the ground and watched it grow? If you find it tough growing up, imagine what it’s like as a plant. The process behind it all is photosynthesis, and our survival depends upon it.

The building blocks of plant growth Photosynthesis (foe-toe-SIN-thuh-sys) is the way that plants use energy from the Sun to make their own food using carbon dioxide from the air and water from the ground. The energy that plants absorb from sunlight is used to trigger a chemical reaction. The reaction turns water and carbon dioxide into sugar and oxygen. The sugar eventually gets turned into plant fibre, while the oxygen is released into the air.

Our life depends upon it Professor Susanne von Caemmerer from the Australian National University specialises in the form and function of plants: in other words, what they look like and what they do. “Photosynthesis is universal,” she says. “All terrestrial [land-based] plants do it, and that’s what makes our life possible.” The oxygen we breathe comes from photosynthesis that has been going on for thousands of millions of years.

Knowing better Photosynthesis doesn’t happen the same way in all environments. This year, it’s time to celebrate our understanding of a type of photosynthesis best suited to hot and dry places. It’s known as C4 photosynthesis.

Fifty years ago, two Australian scientists – Dr Hal Hatch and Dr Roger Slack – were the first in the world to understand the details of the C4 chemical reaction. They found that sugar cane used a different process to photosynthesise than other plants they knew about. Since then, scientists have found that lots of other plants use C4 photosynthesis too.

Plants that handle the heat Plants that use C4 photosynthesis can use less water and deal with heat better than their cold weather cousins. They do this by managing the carbon dioxide in their cells differently to other plants. This ability makes it much easier for C4 plants to survive in places like north Queensland, where a lot of sugar cane is grown.

C4 photosynthesis first came about around 40 million years ago, when the carbon dioxide level in the atmosphere dropped to what it is today. Plants started to evolve to deal with the change. Since then, more than 70 different kinds of plants have evolved this C4 photosynthesis mechanism.

“The transition to C4 is mind-bogglingly difficult, so the fact that it happened 70 times is quite incredible,” says Hal.

Food for thought Photosynthesis of all kinds is an important process for researchers to understand, because all our food ultimately comes from plants. C4 plants make up more than 30 per cent of the worldwide food supply, including crops such as corn and sorghum. Australia has lots of C4 grass species, such as kangaroo grass and lovegrass.

Looking a little bit deeper, we see that many plants do things in their own distinct way. But no matter where they live or how they get their energy, remember that it’s plants that make it possible for us to breathe and eat, and therefore survive.


This short article was originally published in the October 2016 issue of the Double Helix Magazine, an Australian children’s science magazine.

This year is the 50th anniversary of the discovery of the C4 photosynthetic pathway, and I was lucky enough to talk to Hal Hatch, one of the discovers, about it. The parallel evolution of this cell mechanism in 70 distinct species is incredible, because as he puts, it is “mind-bogglingly difficult.”

Susanne von Caemmerer is part of a team trying to do just that, artificially convert a plant from C3 to C4. Their aim is rice, a plant that could grow in far more places, far more efficiently, if it’s photosynthetic pathway was a bit different. Their huge ambition is amazing, and the potential is tremendous.

Endangered tongues

When WordPress notified me that Mother Tongues had linked to one of my posts from a while ago in a piece about endangered languages, I checked out the whole thing, and thought it was great. So without getting too recursive (what I said about what they said about what I said) about it, I’m linking to the whole piece for you to enjoy.

Mother Tongues

You’ve probably heard of the plight of the orang-utans and cries to “save the whales” but have you heard of Ixcatec or Tharkarri?

They’re not cute and cuddly animals you can touch, but they’re still capable of living.

They’re the vanishing mind-music of people: critically endangered languages.

Ixcatec and Tharkarri are just two of the 2,465 languages included on UNESCO’s Atlas of the World’s Languages in Danger.  

Enveloped in silence

Languages can die out – just like plant and animal species can become extinct.

On an archipelago off the western coast of Canada, just 20 speakers of the Haida language remain – a mere fragment of the estimated 15,000 speakers at the time of European contact.

haidapost4-01.png In the Haida language, guusuwàa means “someone who likes to gossip or talk a lot.”

In a tiny town called Tabasco in central Mexico, the Ayapaneco language persists in the minds of two elderly men…

View original post 595 more words

Huh? Do you say that too?

When someone says something you didn’t hear, what do you say? It turns out that most people around the world say ‘Huh?’, just like we do.

Linguists from the Max Planck Institute of Psycholinguistics in the Netherlands listened to recordings of people speaking in 10 languages from around the world and found that every language had a word like ‘Huh?’ to fix misunderstandings in conversation.

Although words in most languages are hugely different from one another, the research found that this particular word sounds and works almost exactly the same in all languages.

“Our explanation is that it’s the same because all languages have the same need for a short and sweet word for quickly asking the other to repeat what we didn’t quite catch,” says linguist Mark Dingemanse.

So if you don’t follow what someone’s said, don’t worry. People all over the world are saying the same word with you: ‘Huh?’

Adam Huttner-Koros

This short article was originally published in the January 2016 issue of Double Helix magazine. I wrote it to inject a bit of language and linguistics into this children’s science mag, and thought that the topic made for an interesting and accessible article. The research won one of the (in)famous Ig Nobel prizes, and the findings are incredible. The broader, follow-up study provides a lot more detail about the conversational act of “Other Initiated Repair”.

There are whole worlds of research out there, about things we don’t even know exist. Yet even the simplest conversations and utterances contain thousands of beautiful, intricate details.

Your audience is more diverse than you think.

Seed Money

How Kevin Folta got entangled with Monsanto, created a shady podcast alter ego, and spurred a hot public debate over conflicts of interest in big ag.

Seed Money: True Confessions Of A Monsanto Apologist – BuzzFeed News.

This article by Brooke Borel from Buzzfeed does a really good job of pulling apart the fragments of a complicated and messy situation. Stepping away from the industry funding issue, let’s focus on audience.

Talking about GMOs in public is hard, no matter which side of the fence you’re on (even if you haven’t taken a side). More than most other science topics, you need to be aware of who is listening to what you say, how they might perceive it and where they might be coming from.

Most importantly, I think, you need to be even more generous than normal in assuming that the people you’re supposedly “fighting against” have reasonable motivations, fears and worries. Their disagreement with you does not make them evil. Breaking down a multidimensional and complex discussion (such as GMOs) into a for-or-against mentality is bad for every single person in that discussion.

The only way to progress both science and our science communication practices is to actively acknowledge the diversity of our audiences in the work we do and things we say.

It’s more work in every single way to continually add nuance and perspective to your communications, to make your work accessible to ever more people, to turn a simple statement into an accurate portrayal, but that’s what is required of science communicators. Acknowledge your audience. Really truly acknowledge your audience, in all of its diversity and complexity. That’s where effective communication comes from.

Traditional knowledge combines with scientific methods for Nobel Prize win

Article from CNN: Nobel Prize winner Tu Youyou combed ancient Chinese texts for malaria cure

I love everything about this story. Using the knowledge built up over centuries by  people not so different from us to inform the problems AND solutions of today is awesome. I wish we did more of it. There are so many people with so much knowledge out there that don’t have access to the validation systems of science, but this shows just how much things could change if those people were included in the scientific system which often excludes them and their form of knowledge.

As problematic as the Nobel Prizes can be, this is the kind of discovery and scientist I am 100% happy to support as a deserved winner.

Indigenous Australian storytelling accurately records sea level rises

In yet another example of indigenous stories having a much greater value than we (non-Indigenous western types) like to think, this story from the Guardian explains that there is a tremendous amount of historical scientific knowledge kept within the stories of Indigenous people.

It’s pretty incredible to think that the Indigenous Australian people who tell these stories have managed to keep the message unchanged for thousands of years.

When we listen to these stories we’re hearing eye-witness accounts of sea level rises, 7000 years after they happened. 

I find it fascinating that the way this comes about is not through any particular feature of the language, but rather the storytelling culture of the population. Because retelling and checking the stories at every step is so important for the family and community units, all of the people listening today can hear essentially the same stories that their ancestors heard when they were told back then.

 Indigenous rock art in Kakadu national park in the Northern Territory. Researchers say stories about sea level rises in Australia date back though more than 7,000 years of continuous oral tradition. Photograph: Helen Davidson for the Guardian

Indigenous rock art in Kakadu national park in the Northern Territory. Researchers say stories about sea level rises in Australia date back though more than 7,000 years of continuous oral tradition. Photograph: Helen Davidson for the Guardian

I love learning about how Indigenous cultures know so much, and I love seeing coverage of them in popular media. Another article that I saw recently was this one, a great narrative about the stories of earthquakes and tsunamis that the Indigenous people of the Pacific North-West tell.

It’s a very similar tale, but one that we should try to remember: there is so much that the Indigenous people know, all over the world, and we would do well to listen to them speak.

I read the comments on my recent article and this is what I learnt

As a new-to-the-game freelance science writer, publishing an article in The Atlantic a few weeks ago was a huge accomplishment. Even more so because it was my very first bit of paid freelance writing. Despite my lack of experience, they took me on to write them an article, which speaks in part to some level of writing ability on my part AND mostly to the quality of the idea that I pitched to them.

The idea that the language in which science is done (ie. English) might have negative impacts on the discipline seems to me at the same time fascinating and obvious. It’s clear to me that there are people and ideas that can miss out because of an Anglophone and Anglocentric science. Not all ideas, not all people, but some of them some of the time. That’s what my article talked about. Discussions of this kind -interdisciplinary and unusual, with wide-ranging interest- are what The Atlantic likes to cover, so apparently they thought that the fit with their magazine was good.

Screenshot of my article's headline

My article with its bold headline.

However, some people on the internet aren’t so sure it was worth it. I read through a fair chunk of the comments in the days after publication, and thought there was stuff in there worth responding to. I was not surprised to see a diversity of views, but the passion of the responses was unexpected. Here are a few points I want to address from the comments:

  • There were several racist statements about the capacity of Indigenous people to contribute to science. This is unacceptable. Some examples: So we go from “people should be encouraged to do science in their native language” which is okay to “we should listen to a bunch of primitives who’s conception of science is ‘shit go boom.’; As for the scientific “value” of the deadly sky devil of the naked people of nevernever land …first, they don’t contribute to science, and second, English prevalence has nothing to do with their illiteracy. I’m pretty sure they were illiterate long before the British Empire arrived and they’ll remain illiterate until someone teaches them English. People are welcome to have opinions about the state of science and whether its global language is a good or a bad thing, but words like primitives, naked people of nevernever land and remain illiterate demean indigenous people, their cultures and their heritage. I was sad to see these statements appear in the comments.
  • It seemed like my criticism of the language of science prompted a lot of defensiveness from readers. There were flippant responses about my experience or knowledge posted that served to delegitimize my argument, instead of refuting my argument with better points. For my part, instead of believing whole heartedly in science without looking at where it can be improved, I think the best way to improve science is to try to pick out the things that need fixing, which was the aim of my article. I may not have pointed the way to specific solutions, but pointing out a problem within it does not mean that I am invalidating the whole endeavour of science.
  • I noticed a lot of people think that English has become the universal language of science because of inherent features in the language that make it easier to speak and use. While there may be some value to this idea (which would need to be looked into much further with large comparative studies between many languages) on its own it seems like an easy way out of the difficult situation I describe. It makes it easy to ignore the problem and instead take pride in our ability to already speak the-best-of-all-the-languages.The question is this: given that English as the global language of science is here to stay (at least for the meantime), how can we better include ideas and participants from different world views into the discipline?

The last thing that I noticed is an issue that I need to deal with in my writing. If you’ve read my other blog posts, you know that this is an issue that I’ve been focused on for a while. Whether it’s from a scientific or a linguistic perspective, the intersection of those two things, specifically in regard to the English language is fascinating to me. However, reading some of the comments has shown me that my main point, underlying the rest of what I write, still lacks nuance and subtlety. It’s not yet inclusive enough of non-native English speaking scientists, and doesn’t articulate the major benefits of having a universal language.

My work definitely has room to improve, but fortunately there remains a lot to say about this topic, so I’ll definitely be working on it. In the mean time, I’m grateful to all the people who read, shared and commented on my article. I look forward to writing more of them in the future.

Why English as the Universal Language of Science is a Problem for Research

In non-blog related writing, an article that I wrote entitled Why English as the Universal Language of Science is a Problem for Research in The Atlantic is now published. In it, I talk about the effect that having English as the language of science has on the way that science is done. Here’s an extract:

Science’s language bias, in other words, extends beyond what’s printed on the page of a research paper. As Perera explained it, so long as English remains the gatekeeper to scientific discourse, shoehorning scientists of other cultural backgrounds into a single language comes with “the great cost of losing their unique ways of communicating ideas.”

“They gradually lose their own voice,” he said—and over time, other ways of understanding the world can simply fade away.

The way I see it, there are two kinds of impacts: impacts on the people in science, and impacts on the ideas in science. It was a lot of fun to write, and I used a bunch of research from previous blog posts when providing examples. There’s (of course) a lot of stuff that didn’t fit in there though, so I’ll see what I can wrangle into a new post some time soon.

On a personal level, it’s really exciting to have my first freelance article published, especially in such a well regarded publication as The Atlantic. If you’re interested in the article, you can check it out here. I’d love to read your comments and see what you think about all of this. To me, science’s language problem is a fascinating and important topic, but one that we often ignore. Let’s start talking about it now.