The Up-Goer Five Challenge – Thesis Edition

The Up Goer Five

The Saturn V, or Up Goer Five, depending on your jargon.

The Up-Goer Five Challenge was inspired by a xkcd comic titled “Up Goer Five” which sought to describe the design of the Saturn V Rocket, using only the one thousand (or “ten-hundred”) most common English words. AmericanScience: A Team Blog has a great description of the reaction to the comic, and the resulting challenge to scientists to translate their research abstracts using a special web-based text editor to contain only the ten-hundred most common words. The challenge was taken up by many people, including chemists, and a linguist  who beautifully describes Saturn, who displayed their efforts on Twitter #upgoerfive, which were collated into a Storify, and a Tumblr was created to showcase the entries.

I thought I would try the challenge as well, using the abstract from my thesis, titled Environmental Fate and Toxicity of Three Brominated Flame Retardants in Mesocosms. Before I start, I fully acknowledge that the abstract (presented below) is full of jargon, acronyms, and not very accessible, but it describes my work in a way that is accepted by my community. Here it is,

Traditional brominated flame retardants (BFRs), namely the polybrominated diphenyl ethers (PBDEs), have persistent, bioaccumulative, and toxic properties that have resulted in the phase out of their production and their being banned in certain jurisdictions. To meet regulatory flame retardancy requirements, non-PBDE BFRs have entered the marketplace. Much remains unknown regarding the environmental fate and toxicity of these emerging BFRs. The objective of this thesis was to use outdoor mesocosms to examine the fate and toxicity of three emerging BFRs; bis(tribromophenoxy)ethane (BTBPE), tetrabromobisphenol A bis(dibromopropyl ether) (TBBPA-DBPE), and BZ-54, which consists of two BFRs, ethylhexyl-tetrabromobenzoate (EHTeBB) and bis(ethylhexyl)tetrabromophthalate (BEHTBP).

While it was difficult to accurately determine degradation rates because of fluctuating concentrations, the estimated half-lives indicated these compounds are persistent (> 60 days in sediments). The partitioning of the compounds between the particulates and the sediment resulted in differential degradation rates (greater in the particulates), and products formed; those formed on the particulates were consistent with photodegradation products.

The effects of these emerging BFRs on Hyalella azteca and the benthic macroinvertebrate community were assessed through the use of in situ exposure and sampling techniques. The in situ Hyalella cages showed a high degree of variability for most endpoints, regardless of their placement (e.g., water column vs. sediment) in the mesocosm. BTBPE accumulated in the H. azteca (0.03 – 1.4 ng/g ww), however this was not associated with any changes in growth or reproduction. There was high variability in abundance and diversity between the mesocosms, which limited the ability to detect statistically significant differences. Interestingly, the BZ-54 treated mesocosms had the greatest abundance, and the least amount of community diversity.

This thesis examined the bioaccumulation potential of these compounds in fathead minnow (Pimephales promelas), as well as the associated effects on growth and development as measured through physical and biochemical endpoints. There was considerable uptake and persistence of BTBPE and TBBPA-DBPE, as well as indication of metabolism of these compounds, but limited physical effects observed. There were indications of increased oxidative stress in the BZ-54 treatment, and increased induction of vitellogenin in fathead minnow from the BTBPE treatment.

I could tell translating this into Up Goer Five language was going to be a difficult challenge, as from the title of my thesis, “and” “of” and “three” were the only words recognized by the Up Goer Five word editor. The description was made more difficult when words like “treatment”, “pond”, and even “fish”, were not allowed. So with a bit of working (e.g., fish = water cats, thanks PETA) here is my translated abstract using only the ten hundred most common words.

Old school fire slowing things are long lasting and bad, so new fire slowing things were made. We don’t know much about the new fire slowing things, like if they are long lasting or bad, so we tried to figure that out using small bodies of water.

While it was hard to find out how long they stick around, the best guess for half-lives says that these new fire slowing things are long lasting (> 60 days in the bottom of water). Where these fire slowing things ended up changed over time, with them liking to go into the bottom of the water. These fire slowing things changed into other things over time, these new things had been seen by other people too.

We wanted to figure out if these new fire slowing things would hurt the little life forms in water. Most of the little life forms were the same in all the bodies of water, no matter what new fire slowing thing was put in the water. One fire slowing thing made its way into some of the little life forms, however this did not change the growing or baby making of the little life forms. There were lots of changes in total number and make up of little life forms between the water bodies. The bodies of water that had one fire slowing thing in them, had the greatest numbers, but the least number of types.

This work also looked into the way the fire slowing things could move into water cats, and if they caused any problems in growing or making babies. Two of the fire slowing things moved into the water cats and stayed there for a long time, and did break down into other, smaller things. There was not much change in the growing, well being, or baby making of the water cats. One of the fire slowing things did look like it was causing some hurt, but only a little bit. Some of the boy water cats that were in the one fire slowing thing water body, had stuff in their blood that should only be found in girl water cats, but not so much that it was really important.

I am not sure that this Up Goer Five version is less jargon filled or any more readable than the original but it certainly illustrates the point about how the language we use, and the restrictions that are placed on that language, to communicate science can have a big difference. AmericanScience notes “what’s at issue is how the language in which we conduct and communicate science—though essential—can be a handicap both to public understanding and to scientists’ own abilities to work out problems together. How much this hits home will depend on the area you’re talking about, of course, but there’s a certain truth to how technical terminology can impede—rather than expedite—collaboration, especially across subfields”. Effective science communication can be tricky, and the Up Goer Five challenge is an interesting way to get people to thinking more carefully about how their word selection impacts readability.


Remembering Challenger

27 years ago today, the space shuttle Challenger exploded shortly after takeoff, killing the seven member crew. Here is a short Storify I put together to remember the day.
  1. ad astra per ardua RT @NASA: Remembering the Challenger crew. The NASA family lost 7 of its own on 28/1/86
  2. The #photography side of my brain still can’t get over these photos. NASA’s darkest moments – #Challenger
  3. When Challenger exploded 10 miles up I lost friends, colleagues. Our nation lost heroes. In their spirit we keep exploring.
  4. S. Christa Corrigan McAuliffe, Teacher in Space #challenger
  5. Remembering Concord’s own Christa McAuliffe & the heroes who were lost aboard the #Challenger 27 years ago today.
  6. Today honors the life and death of Christa McAuliffe. “Reach for it. Push yourself as far as you can.” ~ Christa McAuliffe
  7. This Day in History: 1/28/1986 – The Challenger explodes after takeoff, killing all 7 crew members including WA-native Dick Scobee
  8. Ellison S. Onizuka (Lt. Col. USAF), Mission Specialist #challenger
  9. Today we mark 27 years since the #Challenger disaster took the life of the first #Jewish female astronaut Judith Resnik.
  10. Remembering Challenger astronaut Ronald McNair, the multi-talented kid from South Carolina who dreamed of going to…
  11. As with any great tragedy many people have strong memories of where they were when it happened, and somehow sharing those memories becomes a part of the story. I am not sure how reliable my memory is but I am quite sure that one of my first memories is watching television with my Mom and seeing the Challenger explode. I was probably too young (23 months old) for this to be an actual memory, but it is so deeply ingrained I feel that it might be. It seems to be a first memory for others as well.
  12. Challenger was lost 27 years ago. Probably my earliest memory.
  13. Weird, one of my first memories was of the Challenger showing up on tv in the middle of my viewing of Seseme Street as a kid.
  14. #Challenger I watched it from outside of my elementary school. It is burned in my memory. Also the first time I watched the news…
  15. I was age 3, in the backyard with Mom, and watched the #Challenger blow up. Yes, I remember it. #SadDay
  16. Remember getting news in 4th gr class. I’m as old as the teacher on board was. MT @borenbears: 27yrs ago this moment. #Challenger. Remember
  17. 27th anniversary of Challenger explosion. I’ll never forget it. My babysitter made me turn off Empire Strikes Back to watch the coverage.
  18. Hard to believe it’s been 27 years since the Challenger fell from the sky. The @ChicagoBears had just won the Super Bowl & I was home sick!
  19. The footage is hard to watch. Remembering those on this day #challenger
  20. Rather then remembering the Challenger as an explosion in the sky, I think it is better today to remember Challenger with the image below.
  21. We will never forget the last time we saw them…as they slipped the surly bonds of earth to touch the face of God.

Round Up Ready – Moon Edition

40 years ago Gene Cernan left the last bootprint on the Moon.

To commemorate that occasion here is a round up of Moon related stories.

The correct phase of the Moon is frequently ignored in Christmas illustrations.

The correct phase of the Moon is frequently ignored in Christmas illustrations, above, the phases are read from right to left, top to bottom.

Unfortunately, a study titled “Santa and the Moon” revealed that when it comes to Christmas imagery on gift wrapping paper and children’s books, the Moon is frequently depicted incorrectly. The paper (which despite focusing on visualizations of the Moon, has the most visually unappealing figures) notes that there are typically two ways of depicting the Moon, either a full Moon, or crescent Moon, on its first or last quarters. A crescent Moon on its way towards the first quarter is called a waxing Moon, which can be observed in the afternoon twilight and in the evening with its right hand side illuminated (for observers in the Northern Hemisphere, the top row in the above figure). A waning crescent Moon, which is illuminated from the left hand side, rises early in the morning (around 3 a.m., bottom row in the above figure) and can only be observed late at night and in the morning twilight. A full Moon is directly opposite the Sun in the sky, and hence it will rise at sunset. The paper sought to “quantify the level of ignorance concerning the phase of the evening Moon” by examining the depiction of the Moon on illustrations from children’s books, wrapping paper, and Christmas cards from the USA and the Netherlands. The paper found that designers of Christmas related illustrations, tend to draw the Moon according to their own taste and with disregard for astronomical precision, with the most common mistake being the depiction of a waning Moon (observable in the early morning) in an evening scene (as depicted here, as opposed to the correct waxing moon for an evening scene, as shown here). For shame Hallmark, for shame.

Regardless of how it is depicted, the Moon is always awesome, mysterious, beautiful, and hundreds of other adjectives, and we cannot return to it soon enough. Goodnight Moon.

Round Up Ready – Education Edition

This year holds many neat anniversaries, and oddly enough each of them have had an impact on my education, in a quasi-related way.

First up, pretty much any student in elementary or high school would always love the day that the science teacher would pop in a Bill Nye the Science Guy video. This year marks the 20th anniversary of the first airing of his television show. On a recent podcast, it was revealed that Bill Nye will be returning to the airwaves so to speak, with a new series of videos that will be broadcast on YouTube as part of Nerdist Industries.  Bill Nye has always been an advocate for science education and promoting continued funding for space and exploration. He is definitely a personal role model, not just for his science awesomeness, but for his bow-tie wearing prowess.

The space program, for which Bill Nye is such a great advocate, is also celebrating a unique anniversary this year. September 5th marked the 35 years since the launch of Voyager I. After that short 35 years Voyager I is about ready to leave our solar system, which is an amazing accomplishment, some say that is on par with the Magellan travels and the moon landingWired has complied a photo retrospective of Voyager I ‘s journey, they are quite stunning, and something that I think we have come to take for granted. Voyager I (and many other space missions) are such an inspiration to me and have in their own round about way encouraged me to pursue an education in the sciences.

In addition to the role Voyager I has had in revealing some secrets of our solar system and universe, it also had a supporting role in Star Trek: The Motion Picture.

Star Trek: The Original Series is also celebrating this year, as it celebrates 46 years since the original airing of the first episode. To mark this occasion Google, made one of its best Google Doodles yet.

While TOS wasn’t my series (although I have come to enjoy it), I was still inspired by the great vision of Star Trek. I know those days of watching Star Trek: The Next Generation inspired me to pursue science, and I am very happy about that.

While I didn’t end up following any of the engineering sciences as would be suggested by my inspiration from Bill Nye (former Boeing engineer), or space, or Star Trek, I did end up pursuing an education in Environmental Toxicology. It was during this time that I learnt about Rachel Carson, whose ground breaking and seminal work, Silent Spring, is this year marking 50 years since its first publication. In her book, Carson drew the public’s attention to the consequences of indiscriminate use of pesticides, mainly DDT and its effects on non-target organisms such as birds. Her book was, and continues to be, very controversial, but its strengths lay in the way it was written. It was written in a very accessible and eloquent manner, and was backed up with an extensive reference list. Carson’s book is largely credited with the launching of the modern environmental movement, and the banning of the use of DDT. Rachel Carson is a true inspiration to me, not only in terms of her science, but for her gift of communicating that science to the public, and ultimately having an impact of so many people.

Inspiration to pursue education can come from anywhere. There are lots of other people, experiences, and television shows that have helped guide me towards this path, above is just a very small sampling, I will do my best to draw attention to the others at another time.

9.63 Seconds vs. 7 Minutes of Terror

Over the weekend, there were two great news stories, first Usain Bolt defended his Olympic 100 m sprint title, then NASA successfully landed the Curiosity Rover on Mars. Much of the world collectively watched  (slightly delayed in the US for Bolt’s race) as Usain Bolt (he has one of those names that must be said in full) broke his Olympic record.

After his victory Usain Bolt showed just how classy of a guy he is by stopping mid interview to listen and respect the American National Anthem. That class and excitement that he brings to the sport is part of the reason his fame is so widespread, and that his signature pose can be seen around the world.


The New York Times has a great feature, showing how impressive Usain Bolt’s performance was, and how the 100 m times have changed over the past 116 years. While the improved times are impressive, they pale in comparison to the changes made in the Olympic Gymnastics Vault competition.

The gold medal gymnastics vault of 1956 Olympics vs. the best vault of the 2012 Olympics, click to see in action. Source

Yet for all the excitement of Usain Bolt’s win, perhaps the most exciting thing this weekend was the successfully landing of the Mars Rover, Curiosity, to which Google alluded to in their daily Olympic themed Doodle. To watch the landing in full, click here, but for the abridged version, complete with animation, click here. The landing of Curiosity involved what was known as the “7 minutes of terror“, where for 7 minutes the complicated landing maneuver was performed on autopilot, and engineers at the Jet Propulsion Laboratory had to wait. Engineers like Bobak Ferdowsi, who became one of many memes to pop-up in light of the successful landing. Once news of the successful landing reached JPL the engineers celebrated much the same as if they had just won the Gold medal.

For both of these great feats that happened this weekend, I think this picture of Bill Nye pretty much sums up my feelings.


Robot Scientists

Increasingly it seems that anything a human can do, a robot can do better (except love). Buzzfeed has a list of 15 Robots That Will Change the World, they include bots that can play violin, juggle, wash and cut your hair, and even solve a Rubiks cube. While many of these feats may seem trivial (except the Rubiks cube one obviously!), robots are also capable of performing meaningful tasks. The field of chemistry is seeing robots become lab assistants, and they are pretty good too. The robots are faster, more precise, and presumably less whiny than any summer student. These robot assistants can also work with very hazardous materials, like virulent strains of influenza or radiation, with little worry of exposure and death.

Similar robots are making great headway in the field of toxicology. The USEPA’s Computational Toxicology (CompTox) research program has developed Tox21, a program which uses robotics technology to screen thousands of chemicals for potential toxicity. This robotic system (seen below) can screen upwards of 10 000 chemicals!

Tox21’s robot system significantly reduces the cost and duration of chemical testing- a typical researcher may expect to work on 10-20 chemicals a year. Tox21 is testing chemicals found in industrial and consumer products, food additives and drugs, for evidence they might lead to adverse health effects. It does this through the use of microplates. Each plate contains 1536 small wells that can hold various living animal cells, (typically skin, liver, or brain cells of rats or humans), and a sample of a particular chemical. The robot then scans the wells using a digital imaging device, to detect any abnormalities in the cells, as pre-determined by the human researchers. Any positive results are flagged, and it is then up to human researchers to do further studies on the compound in question. Another example of high throughput automated lab robot performing the Ames test, is shown below.

The future of space exploration (left, or right?).

While these advancements are pretty amazing, they pale in comparison to the advancements robots have made in the field of space exploration. The future of space exploration currently belongs to robots. Mars is getting ready to receive its latest rover, Curiosity (which has a neat Guelph connection), the latest in a great line of robot explorers. The question of who is better suited to explore outer space, robots or humans or cyborgs, is a heated one. Many believe that the practical, economical, and ethical reasons, make robotic missions the clear answer for future space missions. Others believe that the sense of awe, inspiration, and even long term survival of the human race, are the main reasons why manned missions should continue. Ultimately, these space exploring robots will serve as the trailblazers for human exploration, and that is a good thing, I just wish we still had manned explorations happening, I am part of a generation that has never seen man on the moon, or really any further out there than in the low earth orbit. It sure would be amazing to feel that sense of wonderment the world felt as they watched those intrepid explorers of the Apollo missions walk on the moon. For all the jobs that robots can take away (e.g., violinist, barber, chemist, lab assistant, toxicologist), I hope astronaut is never one of them.

To Australia…and Beyond

Last week I mentioned the movie The Rescuers Down Under, and it got me thinking about my top 5 favourite movies that take place in Australia, so here they are (in reverse order);

  1. Crocodile Dundee
  2. Mission Impossible II
  3. A Cry in the Dark
  4. The Rescuers Down Under
  5. The Dish

The Dish tells the amazing story of a remote Australian village that has a satellite dish, that will provide radio and communication support for the Apollo 11 Mission. While the movie takes some artistic liberties, it does an amazing job of capturing the the excitement of culmination of the space race. Watching the movie it is easy to see how the events of this era inspired a generation of young people to engage in the sciences, even watching the trailer for this movie makes me want to go join NASA (maybe this attempt would be more successful than my first try). But sadly things at NASA aren’t so great these days. The Space Shuttle Program is over, and the future of manned missions to explore beyond low earth orbit looks very uncertain. The last shuttle mission was the STS-135, which ended on July 21, 2011 when Atlantis touched down. Matt Mira, a contributor to one of my favourite podcasts, made the trek down to Florida to watch and document the launch. His coverage of the event is great, and nerdy, and truly captures the excitement of someone who has long been interested in the space program. Check it out here, here, here, and here.

The sadness that is the current state of NASA has been thoroughly discussed by Neil deGrasse Tyson, and is part of the subject of his new book, Space Chronicles: Facing the Ultimate Frontier. He discusses the problems with NASA, its legacy, and a whole bunch of other great things with Ira Flatow on NPR’s Science Friday (listen or read here).

While the prospects of going into outer space might be grim in my lifetime, there are still ways that the individuals can pretend to be astronauts. Although who knows, maybe under a President Gingrich administration, we will get back to the moon sooner than later. That is by no means an endorsement of Gingrich, but rather an endorsement of the moon.