In my house, Wednesday night is science night: I often get a run of three or four science shows on my local PBS channel. While watching one of these shows, I saw a brief interview with author Sam Kean regarding his book, Disappearing Spoon, about chemistry and the periodic table. When I saw that he also wrote a book called The Violinist’s Thumb, described as the “stories of science, history, language, and music as told by our own DNA”, I knew I had to read it.
Is becoming a cat hoarder a viral disease? Can a scientist develop an idea so ahead of its time that it takes a generation before it is accepted? Sam Kean answers these questions and more in The Violinist’s Thumb.
The picture went viral very quickly – it was shared on Facebook over 37,000 times and it was viewed more than one million times in less than 24 hours. I received it as an attachment in several emails. At first I thought it was another in-joke among science fair supporters like the usual groaners about volcano or flying geese projects. Then I was horrified to see how much support it was receiving in various media.
I just read your latest Blog. I wanted to comment on it, but could not figure out how? Any suggestions?
Yes, an outbreak of bots, like a bad case of norovirus, was infecting our comment boxes with such explosive numbers that we had to disable them until we can develop the antidote. Meanwhile, you can send your comments directly to me and I will respond.
Almost immediately after my last blog on norovirus came the publication in the Journal of Applied Microbiology of a paper examining the mechanisms of action of oregano essential oil and its primary component, carvacrol, against norovirus. This research was directed by Kelly Bright from the University of Arizona.
I knew a professor whose research was in an area called natural products chemistry, the study of biologically-active natural products from plants and other living organisms. He said he got his inspiration looking at plants that were used medicinally by First Nations peoples.
I wondered if, in a similar way, Bright’s research interests in finding alternative disinfection technologies led her team to look at products found in a health foods store.
Let’s look at how oregano oil is used and marketed.
Right up until his final show on February 6, Jay Leno was making jokes about norovirus outbreaks on cruise ships. I watched Jay often enough to know that this was a very frequent topic of his one-liners.
Calling on all young scientists: Science Fair season in Alberta is here, and it is nearly time to showcase your research projects. Students are actively working on projects to be ready for presentation at their school and regional fairs. I’ve been talking to organizers at the regional level and they tell me they are busy registering students, contacting potential judges, and seeking sponsors. Once again, Genome Alberta is sponsoring awards and giving financial support for regional Science Fairs in Alberta. We are pleased to recognize the achievements of young student scientists. The Genome Alberta awards are presented to students with outstanding projects in the life sciences, and especially in genetics and genomics.
We know that it is extremely rewarding to interact with these young scientists. Here are our recommendations on how you can be involved during Science Fair season:
c.1600, from Greek heureka "I have found (it)," first person singular perfect active indicative of heuriskein "to find" (see heuristic). Supposedly shouted by Archimedes (c.287-212 B.C.E.) when he solved a problem that had been set to him: determining whether goldsmiths had adulterated the metal in the crown of Hiero II, king of Syracuse.
Don’t be the one to recommend the book Leonardo’s Foot: How 10 toes, 52 bones, and 66 muscles shaped the human world by Carol Ann Rinzler for your school library. Sexual fetishes are described in greater detail than I expected in the final chapter. Leave this one for your public library to put on their shelves. That said, I do recommend that you read it. Here’s why.
Wow! We have another year in the books! And 2013 has been a very active year when it comes to genomics, biotech and science in general. I once again have used Prezi to capture the highlights of our blogs. It’s always difficult to select just a few from among the many and varied topics that we write about, since there are many themes that carry through a series of blogs. I continued this year to write reviews of newly released science books. I also received positive feedback for my series written from my perspective as a delegate to the 2013 Canada-Wide Science Fair held in Lethbridge, Alberta. I also received comments and emails supporting my continuing science tourism series titled Seeking Science. This year my travels were around the Adriatic coast of both Croatia and Italy.
Mike took his radio skills to the 20th annual Biotechnology Industry Organization's International Convention and recorded interviews with people involved with the BioAlberta delegation. He also kept up his monthly Twitter Snips feature where he curates the best genomics-related tweets of the month.
Have you ever watched one of those movies about schools that frequent television channels from time to time? There were two on in my viewing area last week, both based on real-life teachers. For example, Dangerous Minds was based on the experiences of teacher LouAnne Johnson, while the experiences of Principal Joe Clark led to the movie Lean on Me. I’m sure there are many more that fit this genre, but here is the basic plot of all of them:
Young, innocent, and enthusiastic teacher comes into a school for a job
Teacher assigned the toughest classes that no other teacher wants or even has the skills to be successful with
Teacher overwhelmed by student antics the first day and almost quits BUT comes up with an inspiration for how to deal with these out-of-control students
Teacher uses unconventional methods and wins over students BUT ends up with administrators and/or parents in an uproar and demanding teacher be fired
Teacher fired; students cry and then protest – teacher brought back to much fanfare and we the audience cheer.
Why do they keep making movies like this and why is this trope so popular? Are they a sign of what is wrong with our education system?
We learned this week of the death of Frederick Sanger who has been described as the ‘father of modern molecular biology’ and more recently the ‘father of genomics’. He described himself as "just a chap who messed about in his lab". Sanger’s messing in the lab led him to many honours including two Nobel Prizes in Chemistry. High school and first year biology students learn about two of Sanger`s major contributions. In this blog, I will outline his methods.
In 2011, when blogging about Movember, I indicated that: “Research will continue through the year to get a clearer idea of the contributions of diet, heredity or environmental conditions to prostate cancer.”
Now that Movember is here again, I thought it would be a good time to examine what benefits we are getting out of the campaign which continues to occupy the month of November each year. Movember Canada certainly has some bragging rights when it comes to the way they maintain a fundraising and administration cost ratio of 8.5% (well below international best practice of 15-25%), but what results have come from the research?
I do not always need to be actively seeking science to find it. Case in point: I had part of a day to spend in Ancona, an Italian port city on the Adriatic Sea. Ancona does not appear in many guide books, perhaps because the authors think it has little touristic interest. Yet, right across the street from my hotel, I discovered an entrance to Parco del Cardeto, the largest urban reserve park in Ancona, officially opened in 2005. This 35-hectare park consists of the beach and cliffs along the Adriatic coast from Ancona’s port and old town section towards the south.
What happens when art and science combine? In Zadar, Croatia I was able to experience the result of a collaboration between the creative mind of architect Nikola Bašić working with hydrologist Vladimir Andročec and organ maker Goran Ježina to create a public art space called Sea Organ. It is meant to be “a place for relaxation, contemplation and conversation”. While I was visiting, it was definitely such a place, as many of the visitors seemed to be discussing the wonder of the power of the sea to produce a natural concert. The Sea Organ project was awarded the European Prize for Urban Public Space in 2006.
The success of Sea Organ led Nikola Bašić to follow up with the creation of Greeting to the Sun. I actually found his newer installation much more intriguing: it consists of a sun 22 metres in diameter at the far end of the sea walk, with the planets in apparent proportional size and distance as you approach. If you are able to visit this site at night you would observe the photovoltaic cells powered up during daylight, producing a significant light show. Alas, I had to move on before witnessing this display.
I became much more aware of the power of waves as I continued seeking science on the next phase of my journey. I remembered a physics teacher I knew who would never miss the opportunity to investigate waves. He would create wave patterns in a pond or puddle by disturbing the surface of the water with the dip of a finger or the toss of a small pebble. I don’t remember all the lessons I learned from his experiments, but I was fascinated by the variety of waves I observed while crossing the Adriatic Sea on a ferry. I was especially intrigued by the wave patterns set up in my glass of water which were created by the humming of the motors.
If you wish to know more about waves, here are a couple of resources of interest to teachers:
Physclips – from the Australian Learning and Teaching Council and the University of New South Wales
The Physics Classroom – a website authored by physics teacher Tom Henderson partially funded by a National Science Foundation grant
Plitvice Lakes National Park was among the earliest-named UNESCO World Heritage sites in 1979. My first awareness of them came through the photo sharing website Flickr. I was in awe of the beauty and unique landscapes I saw in some of these photographs. Last winter when we were researching our travel plans for the coming year, we selected a Croatia tour that would include a day at Plitvice Lakes. I spent the rest of my spring and summer anticipating my opportunity to hike the nearly 20 km of trails around the Plitvice lakes, waterfalls, and travertine barriers.
The beauty of Plitvice Lakes is in the landscape that results from the dissolving and then subsequent precipitation of calcium carbonate (CaCO3) in the form of travertine tufa dams. More than 10% of all sedimentary rock is limestone. Since it is made up of CaCO3, it has played a very important role in the geological sequestration of CO2. When CO2 dissolves in water, it forms carbonic acid. This weak acid running over limestone over a long period of time dissolves the rock and leads to formation of underground drainage systems we know as karst formations. The dissolved calcite can be precipitated out in a variety of forms.
Traditionally, geologists described this as a purely chemical process. Recent research is pointing towards biomineralization as an important component. In the Plitvice Lakes, for example, it is now believed that mosses, algae and microorganisms are essential to the process. Calcite microcrystals are trapped by the biofilm (gelatinous mucopolysaccharide exopolymers) while the gliding motility of the cyanobacteria allows them to escape becoming entrapped in the mineral deposits. A very recent paper reports that they have found four proteins that can spontaneously catalyze the precipitation of calcium carbonate in vitro. They are currently working on the genomics of the corals as they relate to the formation of limestone. I think that scientists will find the interaction between the biosphere and the lithosphere to be much greater than perhaps initially thought.
I found the Plitvice Lakes to be an area well-deserving of its UNESCO World Heritage status. Yet I realized that right here in Alberta you can also visit some awesome karst features.
Karst Spring in Kananaskis Country is one of the most striking manifestations of a karst formation that you can see. The water shoots right out of the side of the mountain with incredible force.
Rat’s Nest Cave under Grotto Mountain is a karst cave which has stalagmites that have been dated as old as 730,000 years. You can see a wide variety of other karst features made from the deposition of calcite in this cave.
Big Hill Springs Provincial Park may be the closest local analog to Plitvice Lakes. As soon as I was at Plitvice, I couldn’t help but recognize that, while smaller in scale, Big Hill Springs has many parallel features. On my return from Croatia, I revisited Big Hill Springs and spent time viewing and exploring the falls and the ancient tufa dams. I allowed my imagination to take me on a time trip to when the water might have backed up behind these massive dams to form lakes and falls that would have rivalled Plitvice Lakes.
I will look forward to developments in biofilm and biomineralization. I also hope to learn more about Big Hill Springs. I have not found much published on this unique Alberta resource.
Structure and Design was added as an element of the Alberta science curriculum about 25 years ago. It is introduced to students in upper elementary or junior high school. For most students, it seems to be a fascinating and engaging topic. As a teacher, I introduced the subject by having the students make paper snowflakes. This showed them that slight changes in cutting of the design could lead to dramatic structural differences. As a bonus, their finished work was great for decorating my classroom for the winter season. I finished the unit off with the building of graham cracker gingerbread houses. These activities allowed the students to go through the technological problem-solving model, part of the program of studies at the time. As an adult teaching this topic, it made me much more aware of observing and trying to read buildings.
Visiting the UNESCO World Heritage site of Diocletian’s Palace in Split (Croatia) is an excellent place to read buildings. In this one place you can see Roman architecture from the late 3rd century, 12th century Romanesque churches, and later buildings influenced by the Venetian and Austrian empires. Nearby you can also see buildings of the communist era. And you can experience this architectural mashup by walking less than half a kilometre in any direction.
Part of any visit to Diocletian’s Palace should include a tour of the space below ground level. Apparently it was not until 1956 that the centuries of rubble that filled the space was removed. This revealed the extremely thick walls, arches, and high-vaulted ceilings built by the Romans to support the structure above. The size and scale of the excavated area had me in awe of the construction skills and engineering knowledge of the ancient Romans. It makes me wonder which modern buildings will still be standing in seventeen hundred years.
One particular highlight of my visit to Diocletian’s Palace was encountering a group of archaeologists at work restoring mosaic flooring discovered within the palace walls. I had the opportunity to talk to them as they were painstakingly brushing off portions of the mosaics. Part of the process required that they carefully place the mosaic pieces back into the mortar. They indicated that in some cases they know where the pieces go, but they are also required to do some guessing in their restoration efforts.
A few years ago, I greatly enjoyed a book by Mark Kulansky called Salt. One of my lasting memories of this book was the important role played by salt in human history. He pointed out the irony of how, for thousands of years, people sought better and better ways to purify salt (NaCl) only to have our modern society return to using sea salt and other more natural forms of the product. I first saw the salt pans of antiquity when I visited Lokrum Island (described in my previous blog). Today, I was able to view working salt pans from high up on the Walls of Ston, locally known as the ‘European Wall of China’. The construction of the walls began in the 14th century, in part to protect the valuable salt works. By the 1920s there was an effort to take the walls down. Croatia has now nominated this historic area for UNESCO- World Heritage status, which should ensure its protection in the future. If you have time, it is possible to not only do a tour of the Ston Salt Works, but also to volunteer for a day of harvesting and working the salt pans. Volunteers get tickets to the evening concerts held in town and of course, a souvenir packet of salt.
Prior to my arrival in Dubrovnik, I had prepared a short list of things I wanted to see. I was joining up with a small tour group so I knew that I probably would not be able to see everything on my list, but then again I would learn about some new things not on my list.
Definitely on my list and included in the tour was a visit to the Franciscan Monastery, which boasts one of the oldest pharmacies in the world dating back to the 15th century. I had previously visited the Perfume and Pharmaceutical Works of the Santa Maria Novella in Florence, which claims to be Europe’s oldest, set up in 1221. Now I had the opportunity in Dubrovnik to see what may be Europe’s second oldest continuously operating pharmacy. It was an interesting yet short visit, and sadly, like so many historic sites, ‘no photos’ signs were posted.
I was pleased when visiting Dubrovnik’s museums to see significant pride shown in their early scientists. I made note of three whose contributions went beyond the borders of Croatia.
Marin Getaldić (1568 –1626) is known for his study of mirrors and developing some of the mathematics of optics. His name and research are associated with two places along the Dalmatian Coast. One such place is a cave along the shore just across the water from the island of Lokrum. He also studied on the Wall of Ston, a site I was to visit a few days later. Getaldić’s parabolic mirror is on display at the National Maritime Museum in London. He was a friend of Galileo, and both spent time in Padua at the same time as William Harvey (whose biography I discussed here).
Stjepan Gradić (1613 – 1683) was a polymath who also studied at Padua. He is probably best known in his own country for his description of the 1667 earthquake in Dubrovnik, an event which destroyed most of the city.
Ruđer Josip Bošković (1711 –1787) made contributions to atomic theory and astronomy, including how to determine the equator of a rotating planet and establishing that there is no atmosphere on the moon. In his own country, he is particularly recognized for developing the mathematics to predict tides. As a land-locked Albertan, I don’t ever even think about tides. However, when you live in a coastal area, and especially if you make your living from the sea, being able to accurately predict the tides is important.
Was it visitors with the plague or was it to protect the walled-up citizens from the plague? You can find both opinions on the internet. One of the guidebooks that I consulted prior to my trip led me to believe that the Onofrio’s Fountains were involved with the history of the plague, so I was delighted to not only see them, but to drink water from these fountains. Later, while researching this blog, I began to question the authenticity of the oft-repeated statement that visitors during the time of the plague needed to wash themselves at the fountain before coming into the city. I now lean toward the explanation that the fountains were built so that the walled city would have access to potable water during times of siege, and closing the walls during the plague was just such a siege, albeit from disease rather than an angry army.
I took a short boat trip to nearby Lokrum, an island just off the coast of Dubrovnik. Lokrum is now designated a UNESCO-protected nature reserve. No one is allowed to stay overnight on this island. As I stepped onto the shore, I was pleased to see that the entire island is a designated no-smoking area. The pathway system was a bit confusing to me: better signage would have helped. The botanical gardens have been somewhat neglected but there are indications that this will be improved going forward. There are clearly a lot of different species growing in the area surrounding the 11th century Benedictine monastery. There are at least 450 different species of trees and 400 species of succulents in the gardens, making this the biggest collection in the Mediterranean region. Peacocks brought to the island in 1859 roam freely and I watched with fascination as the mother hens tended to their little peachicks. I also noted a number of old salt pans which surely must have dated back to antiquity.
I’m sure there is a lot more science to see in Dubrovnik, but I was on a tight schedule and moving on up the coast.
In my previous blog, I expressed my desire to seek science on a journey to the Adriatic Coast. Ultimately I planned to end up in Italy, but the first portion of my trip involved visiting Croatia. I didn’t know a great deal about Croatia prior to this trip. I did know that I wanted to see Diocletian’s Palace which I learned about in my reading of Justinian’s Flea and I definitely wanted to visit Plitvice Lakes as I had seen many beautiful pictures taken at this UNESCO World Heritage Site.
Croatia is a country that is both very new and very old. New, in its current embodiment Croatia has only existed since 1991. New in that its current borders were only set in 1998, and it was just July 1 of this year that it became a member of the European Union. Yet this country is very old in that it was peopled by Neanderthals perhaps up to 300,000 years ago. And old in that three quarters of the Croatian males sampled carry the Y-chromosome haplotype classified as ‘Old European’ meaning that marker has been present in Europe since prior to the last Glacial Maximum more than 10,000 years ago.
As I sat at the terminal in Frankfurt, I was excited to see the shiny new Croatia Airlines jet taxiing up to the dock. On boarding, I was equally pleased when I sat in my seat and discovered a new copy of Croatia Airline Inflight Magazine. I would have some interesting pictures and exotic advertising to keep me occupied during the short flight.
And yet wait! What’s this? A diagrammatic DNA! Where is the English? Wow! I was finding Science already before the seatbelt signs went off. Here in an airline magazine is a feature article about the 8th ISABS Conference in Forensic, Anthropologic and Medical Genetics and Mayo Clinic Lectures in Translational Medicine. The magazine boasts that the scientific elite arrived in Split via Croatia Airlines. I also learn that this major scientific event dates back to the American forensic experts who came to Croatia to help identify the victims of the aggression against Croatia two decades ago. This year there were over 550 participants with over 80 speakers representing 45 countries at the event. The magazine proclaims this event to be the pivotal scientific event in Europe in 2013. The article highlights the work of several scientists like Dr. Manfred Kayser, a leader in the field of forensic phenotypisation. His work may establish gene maps to determine eye colour from DNA. Progress in the field of translational medicine and creating individual therapies based on individual genomes were also discussed in this inflight magazine.
As the plane began its descent into Dubrovnik, I considered the way the Human Genome Project led to improved techniques and breakthroughs in many fields. During this flight alone, I had already thought of how genomic studies led to advances in anthropology, archaeology, forensics and personalized medicine. I also thought that it will be a great day in Canada when our Genomics conferences receive the same support and wide-spread recognition as being highlighted in our inflight magazines.
During the past year, several key events helped me develop a plan for continuing my Seeking Science series. You may have read some of these in past years as I visited London, Rome, Florence and Assisi. This year, I read and reviewed for you the book Justinian's Flea. Later, I attended a special presentation by Dr. John Humphrey at the University of Calgary. He sparked my interest with his description of the Roman ruins that could be found around the Adriatic Sea. Realizing that I could actually visit some of the areas that I had read about in Justinian's Flea spurred me on to begin planning a trip to Croatia and Italy. This I knew would allow me to experience the context of some of the places that were so important in the history of Europe that were affected by the plague. Additionally, when I looked at possible trips, I realized that I could in the same journey visit the Plitvice Lakes, a UNESCO World heritage area that is formed by the extreme action of biofilm, a topic that I have also blogged in the past year. After planning my trip, I read and reviewed the biography of William Harvey. I realized that it was an easy side-trip to Padua where I could see the very ancient university town I had read about in the book. I made sure to compile notes as I was going through the biography so that I would know what highlights to look for in a visit to Padua.
Over the next few days, I will be blogging my adventures in Seeking Science around the Adriatic Sea. I hope that this either inspires you to plan your own seeking science holidays, or to use my series as a jumping off point for discussions with your students and/or your friends. I have quoted Neil deGrasse Tyson before, and I probably will again. He said: “Science is not a subject you took in school. It's life. We are wrapped by it, in it, with it”. Over my next series of blog postings, I will reveal to you how exciting it is to be always seeking science.
Click here for the my entire Seeking Science Series.
Is it possible that summer is over and another school year is about to begin? Wow! It sure seemed to go by quickly. I hope that your year planning has gone well, and your students are excited to be there and in the mood to learn. I had a note from a friend who told me that in his school division, 300 teachers working together created over 1000 new courses in just under 48 hours. He noted that was one busy combo of software and server. I know that teachers have been putting in this extreme effort to be ready for the new school year.
In Alberta, for more than 25 years science has been taught from the perspectives of science, technology and societal impact. Foundation 1 of the program of studies is as follows:
Science, Technology and Society (STS)—Students will develop an understanding of the nature of science and technology, the relationships between science and technology, and the social and environmental contexts of science and technology. “
You may be well aware that the catch-all acronym STEM stands for Science, Technology, Engineering and Mathematics. The discussion of STEM Education has become much more prevalent in both the United States and in Britain. In both countries, STEM is referred to in their official education documents. I have not seen this acronym formalized by Alberta Education yet, but I know that educators throughout Canada are tending to refer to STEM education when talking about the courses they teach.
We at Genome Alberta are now going into our eighth year of blogging designed to encourage STEM education. We strongly support the use of project-based learning and our blogs introduce a variety of ideas that can lead to class discussion in science, technology and societal decision making. Some of our blogs are inspired by questions sent by teachers and students looking for clarification or explanations. Other blogs anticipate the hot science topics and issues.
Here’s another idea: follow me on twitter. I tweet a variety of science and technology-related links to help you encourage scientific literacy in your classrooms. You can also follow the official Genome Alberta twitter stream, @GenomeAlberta, or that of Genome Alberta’s communication director @Mikesgene . The hashtag #STEM will alert you to STEM-related tweets. Educational topics are under #edchat, while #scichat signals general science topics of interest.
One of the first things you could put on your school-year calendar is National Science and Technology Week in Canada, which runs October 18 to 27 this year. Check out the events: there may be opportunities for field trips in your area or you could suggest possible learning opportunities for your students’ families.
Best wishes for a fantastic school year!
I recently posted one of my flower pictures to the website Flickr. I like to make sure that my descriptions on the site are accurate. For this picture, I wanted to know the common name for Gaillardia aristata. In my family, we’ve been calling this flower a Brown-Eyed Susan for as long as I can remember. Yet, when I looked in my newest field guide – Alberta Nature Guide (reviewed here), I found it was called Great Blanketflower. Then I did a quick check on Wikipedia and sure enough Gaillardia aristata is called Blanketflower.
Since I read it on the internet, it must be correct. Right?
Why were we calling these flowers Brown-Eyed Susans? Had we learned the name from our parents who were unaware? Did we learn this name from uninformed friends? There was no doubt that we had the Latin name down correctly. Had we spotted the alternate name somewhere else?
I decided to go through my personal library of guidebooks to see if I could learn the common name of Gaillardia aristata.
I checked E.H. Moss, Flora of Alberta. My 1964 edition was considered the ultimate authority on vascular plants by the botanists at the then-named University of Alberta at Calgary. This book provided a rigorous description of the plants of Alberta with keys to their identification. At one time I may have known how to interpret this description; now, alas, I would need a refresher course to know if the plant is hirsute or villose. I agree that it is showy, but I’m not sure if I can tell if the setae are longer than the achene. E.H. Moss does not give any common names for Gaillardia aristata Pursh.
And who is Pursh? Frederick Traugott Pursh (February 4, 1774 – July 11, 1820) is the botanist credited with giving the official binomial nomenclature name to Gaillardia aristata. At age 24, after receiving his education at the Dresden Botanical Gardens, he moved to the United States where he eventually became involved in classifying specimens collected by Lewis and Clark on their 1804 to 1806 expedition. Among the specimens he was classifying was a flower most likely collected by Lewis somewhere near Lewis and Clark Pass – the continental divide in Montana. Pursh was not without controversy. He worried that he was not going to get the funds to finish his project, so he packed up, specimens and all, moved to England and published his definitive work on North American plants in Europe.
The E.H. Moss book does not have a single picture or drawing in it. Luckily for me, picture book taxonomy became a reality for Albertans with the publication of R.G.H. Cormack’s Wild Flowers of Alberta (1967). Cormack, like Moss, arranged his book into families. I think that almost every flower book I’ve purchased since groups the flowers by colours, making picture book botany even easier. I used the Cormack book for many years to help me identify plants in the wild. He gives Gaillardia aristata the common name Wild Gaillardia, but in his description he states “whether the Gaillardia or Brown-Eyed Susan as it is commonly but incorrectly called…” At last I’ve come across some indication that we were not totally making this up.
High school students learn that Carolus Linnaeus (May 23, 1707 –January 10, 1778) developed the classification system that we still use today. It was originally based on structural similarities. Now, scientists can use genomics as well to help define biological relatedness. Linnaeus avoided using common names that might change from place to place or time to time. Instead, he used Latin, the language that was used by scientists in his time period. He probably knew that Latin would not change over time as it was no longer a spoken language.
The system developed by Linnaeus is called binomial nomenclature. The first part of the name identifies the genus and is written beginning with a capital letter; the second part names the species and is written all lower case. In handwriting, both genus and species are underlined; when in print, they are italicized.
I collected a series of books edited by Herbert Zim called Golden Guides. In The Rocky Mountains (1964) we learn that Gaillardia is also called Fire-Wheel. Ben Gadd in his 1986 Handbook of the Canadian Rockies tells us that true Brown-Eyed Susans belong to the genus Rudbeckia, but that the name fits the wild Gaillardia so well that he says “I guess we’re stuck with it”. In 1999, Andy Bezener and Linda Kershaw in Rocky Mountain Nature Guide refer to Gaillardia as Brown-Eyed Susans, but do in fact say they are also known as Blanketflower. Yet, in her 2003 Alberta Wayside Wildflowers, Linda Kershaw calls Gaillardia the Great Blanketflower and explains the name comes from the fact that “the vibrant wildflower displays the bold colours of blankets from the American Southwest”. No mention of Brown-Eyed Susans this time. Neil L. Jennings’ Uncommon Beauty (2006) clearly labels Gaillardia aristata as the Brown-Eyed Susan.
As of this writing, my picture received 42 comments from viewers. Several of the comments indicated surprise that we would have called them Brown-Eyed Susans. Only one person allowed that he also had called them Brown-Eyed Susans. After six weeks of doubting myself on the common name of a flower and doing a lot of additional reading and talking to people, I think there is no single correct common name. There appears to be regional variation: for example, I think Americans tend to call these Blanketflowers, while we in Alberta prefer Brown-Eyed Susans. In the future, perhaps I’ll follow the advice of nature photographer Rob Lean. When I asked him he said he simply calls it Gaillardia. That’s what Linnaeus would have wanted. I now realize what a tremendous contribution to the advancement of science was made by Carolus Linnaeus in giving us a (near) universal way of naming living things. .
On the ‘new book’ shelf at my local library, I spotted Thomas Wright’s Circulation: William Harvey’s Revolutionary Idea. When I picked it up and looked at the Preface I became immediately engrossed. The first paragraph tells me that William Harvey’s “theory demolished centuries of anatomical and physiological orthodoxy, and introduced a radical conception of the workings of the human body that had profound cultural consequences influencing economists, poets and political thinkers.”
Many times in my career as a high school science teacher, I helped students recreate Harvey’s experiment which demonstrates that the valves in the veins allow blood to flow in one direction. After reading Thomas Wright’s book, I have an infinitely better understanding of the life and times of William Harvey and what led to that being such a significant demonstration.
Thomas Wright helped me put the life and times of William Harvey into the perspective of the period when our current idea of how to do modern science was in its infancy. At the time of Harvey’s university education in Padua, the theories and ideas of Galen were considered supreme, and the development of new theories had to comply with the processes put in place by Aristotle. When William Harvey questioned the work of Galen, it was tantamount to heresy. Wright uses a series of thematic essays interspersed between the chronological chapters to enrich our experience and help us relate to the Zeitgeist of William Harvey’s time.
One of the thematic essays is about the experimentation and empiricism advocated by Francis Bacon. Although they were contemporaries, William Harvey was not in the camp of the new wave of ‘scientists’ manifested by the scientific method. I never really thought about how science was done prior to the development of what we call the scientific method. Through Wright’s book, I learned that during Harvey’s time extreme rigor was required to prove a theory. It was not that a theory had to be falsified to be rejected; rather, it had to receive the approval of significant recognized people in authority to be accepted. William Harvey took great pride, for example, in showing his proof to the king; but he felt crushed when his theory was publicly rebuked by Caspar Hofmann, considered a significant authority in anatomy during the mid-1600s. William Harvey clung to the idea that theory had to comply with the Aristotelian interplay between data and ideas.
This was a time period when what was seen in the body was expected to be mirrored in what was seen in other aspects of life and the outer world. Wright illustrates this view with examples demonstrating that when William Harvey’s ideas regarding circulation began to be widely accepted, the application of the idea of circulation was also taking hold of our view of the universe and solar system, in the traffic on city streets, and in the flow of money through commerce and trade.
I thoroughly enjoyed reading Thomas Wright’s book Circulation – William Harvey’s Revolutionary Idea. If you teach biology, then I highly recommend this book for you. If you are interested in one of the major ideas that helped transform the way we think about the functioning human body, this book is for you.
Note: When I reviewed the book Age of Wonder, I was writing about the explosive developments in science and scientific ideas that began in the late 1700s. The Royal Society was founded in 1660, with Sir Joseph Banks becoming President in 1778. Thomas Wright’s book about William Harvey describes the scientific thinking at a time that was almost two centuries earlier.
Even though it seems a bit early to me, I recognize that early August is already the time of year for back to school sales. This past week, I was totally stunned as I was walking through Costco when I saw that they already had Christmas trees on display. I was equally stunned when I read a recent news feature on Canada.com: Weird science: STEM fields face image problem in K-to-12 schools.
I think of myself as a strong advocate for science and science education, so why did I find this article so disturbing? Well, here’s the first sentence:
“When people meet lab analyst Alana Hill — an attractive blonde who looks more Hawaiian Tropic than Revenge of the Nerds — their first reaction is usually that she doesn’t look like a scientist.”
Now I’m already asking myself: who decided a scientist has to look like a nerd? Why can’t an attractive blonde be a scientist? And should the description of any scientist be defined by their physical attributes? No wonder scientists have image problems.
Science, Technology, Engineering and Mathematics are collectively called STEM subjects these days. In this article, author Misty Harris claims that the STEM subjects are underrepresented in our education system, and furthermore that students start to opt out of the STEM track in middle schools. In our Alberta schools it is not possible to opt out of any core subjects in Junior High. In my experience as a high school teacher I found that many students put together education plans that allowed them to take all the science courses available. If anything, it was the arts and especially the industrial arts classes which suffered from enrolment problems. For many students, that is not a lack of interest, but forced priorities and graduation requirements. In a previous blog, I expressed my confidence in science education based on my analysis of 2012 enrollment data in science and engineering at the University of Calgary.
To me, the most troubling part of the Weird Science article was that it reported teacher Murray Park advocating against science fairs. Was he misquoted in this article? He can’t possibly be serious! Surely his suggestion to eliminate science fairs has been taken out of context. Science fair research is no more formulaic than real science research. Communication of science fair results does have a format just as real science communication has specific guidelines for submission depending on the journal. Surely Park knows about ‘differentiated curricula’ or ‘multiple intelligences’ or whatever is the current educational jargon for personalizing the curriculum.
I believe that most informed science educators are likely to side with Terry Godwaldt, quoted in the article as supporting less teaching to the test and more hands-on activity-based learning. Thank goodness! According to Youth Science Canada, “Every year, over 500,000 young Canadians participate in project-based science – as many as are registered in minor hockey”. We want to teach students to become not just consumers of knowledge, but producers as well. Through participation in a science fair, students take their projects that extra step of communicating what they have learned.
Science fair develops not only scientific and mathematical literacy, but also develops language arts skills, organization, oral and written communication and technical writing skills. Science fair gives the students an opportunity to be evaluated and receive feedback from independent non-school based professionals. Science fair requires an interdisciplinary approach and may lead to work with mentors. Science fair projects require the use of creative ways to solve problems and to approach problems from many different perspectives. Science fair adds a means of providing excitement to projects. Science fair allows students to be fully in charge of designing, assessing and trouble-shooting their own project. Science fair projects are real world problems in many cases with real world solutions. Science fair projects at the high school level certainly concentrate on the higher level functions of Bloom’s taxonomy.
Listen to Shari Worobey, Regional Coordinator of the Canadian Rockies Regional Science Fair, describing a student participant: “his positive experience with Science Fair has helped his self-confidence, has provided an opportunity to practise research and presentation skills, in addition to encouraging him to continue his life long journey, learning in the field of science”.
There should be no image problems in your classrooms with STEM. As Neil deGrasse Tyson said: “Science is not a subject you took in school. It's life. We are wrapped by it, in it, with it”.
QR codes (originally Quick Response Code) are those series of black and white patterned squares that seem to be popping up everywhere. One very good reason for this is that there is now a very large portion of the population that has a smart phone device. Here is a case where we may not remember, or perhaps never knew, that the codes date back to 1994 when they were developed by Toyota so they could track a vehicle’s production.
With your QR code reader, you can directly go to the destination website without needing to type in anything to your browser. Depending on the availability of technology, teachers have the possibility to use QR codes in a variety of ways to enhance the learning of their students. One way would be to post codes around their classrooms and create a bit of a digital scavenger hunt, directing students to a series of web pages and asking them to complete questions based on their reading.
To illustrate my point, I have created a short 5 question quiz about Genome Alberta. Give it a try and if you want your answers verified, email them to me (firstname.lastname@example.org). Also, email me if you want more details on the steps I took to create this QR quiz.
1. Genome Alberta is partnered with Genome Canada. Who are the other two partners?
2. A new Genome Alberta project aims to speed up the detection of which organism?
3. What does Genome Alberta call its news website?
4. What role did Gerry Ward play at the 2013 Canada-Wide Science Fair?
5. Which high school team did Mike Spear interview?
Bonus Question: In what year was Genome Alberta established?
Pretend these codes are posted around your room. Or for complete authenticity, print them and post them to your walls.
I want to draw your attention to two owls described in the Alberta Nature Guide which I recently reviewed on this blog. Our most common owl is the Great Horned Owl, Bubo virginianus. It is found throughout the province and is such a powerful predator that it can take on a cat. It is also one of the few predators capable of taking on a skunk. The other owl of interest is the Snowy Owl, Bubo scandiacus. This is a bird which lives in the northern tundra, but works its way south when winter hunting in the Arctic becomes difficult. It can be seen in Alberta especially November through April in a variety of locations such as forest clearings and agricultural areas where mice and other rodents replace the usual diet of lemmings.
I have a special affection for the Great Horned Owl. In my early teaching career, I was involved when the children of Alberta were asked by the provincial government to select a bird to represent the province. It was a crowd-sourcing decision, but not in the way we know it today. Can you imagine? This was in 1977 and schools did not even have access to photocopiers, let alone computers and the internet. No Twitter, Facebook or Survey Monkey. As a teacher, I received an envelope that contained ballots for the students. I don’t remember which birds were on the ballot, but I remember that there was a brief description representing a campaign speech for each bird species. The result of the ballot announced the winner a few months later. Thus, the Great Horned Owl became Alberta’s provincial bird.
Québec’s National Assembly chose the Snowy Owl as their official bird in 1987. I am not sure if students were involved in this decision, but in both cases, provinces chose these symbols not only as signs of strength and tenacity, but as a strategy to enhance the quality of the environment and make the public aware of our wild species.
DNA has played a big role in helping us learn about the relatedness of these two birds. In 1758 when Carolus Linnaeus first came up with his classification scheme, he put the Snowy Owl into a genus all its own, Nyctea scandiaca. Linnaeus based his decisions on the apparently unique features of this magnificent bird. With our knowledge of biochemistry and specifically our ability to sequence DNA, we can now make comparisons at the molecular level. Scientists like to use cytochrome b gene sequence to distinguish at the genus and species level. This gene is found in the mitochondria of all animals and searchable databases were set up so that cytochrome b gene sequences could be stored and compared. Through this work, more objective classifications can be made for closely related species. These kinds of studies gave scientists the confidence that Snowy Owls were indeed so closely related to the other horned owls that they were put into the genus Bubo. The previous genus Nyctea was no longer deemed appropriate for classification which is meant to show phylogenetic relationships.
The day after I reviewed Alberta Nature Guide, where I suggested we are involved in a movement towards becoming aware of nature again, I received my July 2013 issue of National Geographic. I was delighted to learn that farm families living in Transylvania can name more than 120 species of plants and that even their children can identify as many as 50. I had a sense that I was justified in advocating we learn more about the species that inhabit our own province.
Summer as defined by the solstice has already arrived and with the Canada Day weekend coming up, the real summer is about to begin in Alberta. For a lot of us, that means heading out to hike the trails in Alberta’s biologically diverse areas. We have 6 distinct natural regions, 5 national parks and more than 30 provincial parks. Alberta is a fantastic place to be for nature lovers in the summer.
If you go looking for wild flowers, you probably take a flower guidebook with you. If you are into birding, you probably have a bird book. There are guidebooks for mammals, trees, shrubs and even insects. It is not really practical to take your entire library with you when you go out to just admire and appreciate Alberta’s natural history. That’s where the Alberta Nature Guide from Lone Pine Publishing comes in.
Natural history is the study of plants and animals in their natural setting. Documented interest in natural history dates back to the time of the Greeks. Deep knowledge of natural history must certainly be associated with hunter-gatherer societies predating the Neolithic revolution. Now in the 21st century, we may wish to regain a sense of the wonder and knowledge of natural history as we head out on the trails.
What I like about Alberta Nature Guide, authored by Krista Kagume and Gregory Kennedy, is that in one small and light paperback guidebook, I can find information about the most frequent and likely to be seen species in Alberta. Realistic drawings and helpful descriptions illustrate representative samples of mammals, birds, amphibians, reptiles, fish and invertebrates as well as trees, shrubs, vines, forbs, ferns and grasses. I can leave it in my vehicle or take it in my pack. I know that it will provide me with the information I desire at the level I require when I’m getting back to nature in Alberta this summer.
I’m not going to write a review of Dan Brown’s Inferno, for to do so could lead to spoilers. I will say that when the movie version comes to the theatre, I will go to see it. Like Dan Brown’s earlier thrillers, this book is part travelogue, this time set mostly in Florence and Venice. I challenged my family to join me in a game - getting points for the photos we already have in our archives of the iconic sites noted by Brown as he describes the action and movement of our hero Professor Robert Langdon. I found a lot of excitement and entertainment in the suspension of disbelief.
Spoiler Alert: I have tried my best to discuss the science of Brown’s Inferno without providing spoilers. If you have any doubts, read this blog after you have read the book.
Brown starts off this book of fiction with the claim that the science is real. Let’s look at four major scientific topics in the book and judge for ourselves.
In the late 1960s and early 70s, there was a great deal of discussion about planetary overpopulation. Paul and Anne Ehrlich authored The Population Bomb, while the newly-formed Club of Rome published Limits to Growth. These books helped form population growth as a major theme in environmental courses of that time. Sustainability then referred to controlling overpopulation and the subsequent disappearance of limited resources.
It is interesting to note that in the 40 years since the publication of these books, the authors now claim that they did not specifically make predictions. The Club of Rome now states on its website that “The Limits to Growth did not offer predictions, rather it portrayed different scenarios based on trends and different policy decisions”. Paul Ehrlich also denies that he made predictions while lamenting the nearly doubling of the human population since he wrote his book.
Matt Ridley in The Rational Optimist provides a much more positive spin on “escaping Malthus’s Trap”, but he also admits that “demographic transition theory is a splendidly confused field”.
Will Dan Brown’s Inferno lead to a renewed discussion of population growth? I don’t want to make a prediction; in fact, I won’t even present a scenario.
The Plague - Black Death
I had to give my head a shake after reading Dan Brown’s Inferno because I had almost convinced myself that the virus on which the plot turns was going to be a new strain of the Black Death. Then I remembered that Yersinia pestis, the organism responsible for the high mortality plague epidemics, is a bacterium. In a previous blog, I reviewed Justinian’s Flea where that author speculated that the plague played a major role in the shaping of the human history of Europe. A more recent paper examining the DNA of Y, pestis notes that these bacteria have probably been around a long time and that the same Y. pestis strain was responsible for all three major historical pandemics:
Justinianic Plague - 6th century Europe
Black Death – 1348 – 50 Asia to Europe
Third Plague Pandemic – 1855 Yunnan Province spreading worldwide.
We are told that Bertrand Zobrist, our main villain in this novel, is an extremely talented geneticist: and extremely talented he must be! In less than a year while remaining hidden away and on his own, he was able to develop a diabolical virus.
Zobrist knew that viruses make a good tool for genetic engineering as they are naturally able to inject their own genetic material into a cell and take over the genetic apparatus of the infected cell. Zobrist was therefore able to use a virus as a ‘vector’ in his genetic engineering scheme. Zobrist would have had to isolate or synthesize the gene he wished to insert into the virus. Then he would have had to develop/find a virus that would not trigger an immune response in human hosts. He would have needed the virus to target the germ cells of the host to realize his diabolical plot, and he would have needed to ensure that the gene insertion was not random or he would not get the results that he wished for. He needed to do all of this without doing any actual trial experiments.
Oh sure, use your search engine to do a search for virus detection and it will display thousands of results - all about computer viruses. What kind of equipment would you buy to detect a real virus? After the swine flu scare and the SARS outbreak of a few years ago, the demand for a quick way of determining the presence of a virus seemed imperative. Small devices were developed to quickly determine from blood or saliva if a person was infected by a virus. Nanotechnology was developed to detect the presence of virus particles in the air. The viral detection done in the novel by Elizabeth Zinskey’s SRS team apparently used individual PCR machines that started blinking after a few minutes. A PCR machine is really a type of thermal cycler that puts the samples through a series of heating and cooling. I’ve seen PCR machines that can act in as fast as 15 minutes, but from what I have read, viral detection requires having a very specific targeted sequence to start with.
It was amazing to see how quickly the science fiction from the movie GATTACA became real, so perhaps I should not be too skeptical of the real science in Dan Brown’s Inferno. It is certainly an entertaining read.
Social media and smartphones have really improved the way we can work with groups of people, whether business or volunteer colleagues, or students and their parents.
If you have been following my blog you know that I recently spent a week as a delegate at the Canada-Wide Science Fair (CWSF). I’ve been involved at this level a number of times over the past 20 years. What a difference technology has made to accompanying a group of students away from their home – some perhaps for the first time.
Using the theme ‘Sharing the Trail’, I have previously helped teachers use social media to keep up with science education. This time when I was chosen to be the delegate for the Calgary Youth Science Fair, I welcomed the opportunity to test out a few ideas that had been percolating in my mind. I was going to be travelling with 12 students and 3 adults to the Lethbridge CWSF.
When I initially met with the parents and student finalists prior to our trip, I suggested that if they were interested, I could set up a Google Circle for us to share information. I have prided myself in being what I considered to be a power G+ user for some time. For several years, I have been using the sharing features even before it was named G+. I use shared calendars with both my family and with others for volunteer activities. I had used Google Drive (formerly called Google Docs) in a group setting to facilitate collaborative information sharing. I’ve used small G+ circles to share ideas and photos with committee members.
Here are the steps I went through to set up a G+ circle for the science fair finalists and their parents. First, I went into Drive and opened a spreadsheet to record the pertinent student information. Now, instead of needing to carry a binder with all this data, all I needed was my smartphone. By sharing this document with the other adult supervisors of the group, they also had full access to the information in case it was necessary.
Next I was able to take the list of student and parent email addresses and incorporate them into my contacts as a Gmail group. Now, all my email correspondence to the group could be sent to me with bcc to the group, thus maintaining the privacy of the individuals and their email addresses.
At this point, I sent an invitation to all of the students and their parents to join me on G+. Once about half of them had joined, I was able to create and share a private Team Calgary circle. I taught the participants how to save the circle, and how to share information only within our circle.
Through the week, I was able to share my photos with the circle, while keeping them out of the public domain. I received positive feedback each time about this method of sharing information. At the end of the week, several of the students asked me to keep the circle going as they thought they might have stuff to share after getting home. In actual fact, it wouldn’t matter if I had removed the circle from my G+ if they had already saved it as their own circle. G+ circles are self-moderated.
I also found that Twitter was actively encouraged at the CWSF. Several of my student finalists had accounts, and many of the other people at the fair were actively tweeting. Throughout the fair site, we were encouraged on posters and at meetings to use the hashtag #cwsf. I used both my own Twitter account @gwardis and I also tweeted on behalf of Calgary Youth @sciencefairCYSF. Based on my experience at the fair, I recommend Twitter for sharing information that you don’t mind being public. The G+ circle was still the best way to share private information within the group.
Once we were back from the fair, one of the student finalists used YouTube to post a video collage of photos from the fair. She asked me to share it with her fellow students. Naturally, I posted it on my G+ circle for the team, but as a backup, I also emailed the link out to the rest.
When I wrote about stromatolites and biofilm last year, I speculated that the spacecraft Curiosity would be looking for biofilm as a sign of life on Mars. At that time, I did not know that there is a major joint project of the Canadian Space Agency and NASA which has astronauts working directly with scientists on microbialites. As part of their training to go into space, the astronauts do ‘real science rather than just simulations’ so they will be much better prepared when they travel into the future.
I recently attended a geoscience open house at the Canmore Museum and Geoscience Centre. The feature presentation “Early Earth and Outer Space” by Ben Cowie and Allyson Brady, was described as a talk about microbialites. I knew immediately that I was in for a treat. Ben is a PhD candidate at the University of Calgary. Allyson, with a doctorate from McMaster University, is science lead and principal investigator for the Pavilion Lake Research Project (PLRP). Both are keen, enthusiastic scientists wanting to share their excitement over working on such a unique project.
Microbialites are rock structures created by single celled organisms that live on their surface. Fossil microbialites would be a sign of life since the rock is formed by living things. It is important for scientists and astronauts to be able to distinguish between rocks formed by biological processes or through physical processes alone. This is one of the reasons that astronauts are being trained at the PLRP. You can imagine that it would be very useful to have an astronaut who could tell at a glance if a rock on the surface of the moon or a planet is worth further examination.
Some of the oldest fossils on earth are stromatolites. Stromatolites, one type of microbialite, can still be found growing in hypersaline marine lagoons. The major surprise was also finding microbialites growing in the fresh cold water of a British Columbia Lake. The lake does not look any different from any other glacially formed lake in interior British Columbia. Yet this particular one hosts a unique form of life: fresh water bacteria which form into microbialites. According to Ben, these were first noted by scuba divers in 1997. Scientists began research at this site in 2005. In 2010, astronauts became part of the research project. Allyson showed us pictures of the submersibles that put the scientists into the driver’s seat and allow prolonged mapping and filming at Pavilion Lake, which is much too cold for scuba divers to do detailed work. She also told us about MAPPER – a citizen science project which allowed more than 4,000 online volunteers to contribute to the analysis of over 1.1 million photographs taken by the scientists at the PLRP.
Allyson calls this project “extreme microbiology”. She told us how data and samples are shared with ecologists, biochemists, microbiologists and geneticists. I found one such project described when I spent time on the PLRP website, where Joe Russell from the University of Delaware has blogged his work on DNA of the microbialites.
I know that we will hear a great deal more about this major project being done at a small cold glacial lake in British Columbia.
Today was the last day full day of the 2013 Canada-Wide Science Fair (CWSF). And a very busy day it was. After breakfast, the finalists were once again at their projects for the last school tours and public viewing. The top of the fair Platinum award winners had been moved overnight to a prime location to accommodate the anticipated crush of viewers. Adam Noble, top of the fair, certainly draws a crowd. A tab was placed on the winning projects so that one could tell at a glance which projects received medals.
I spent time walking around the projects and looking at ones that caught my eye. During the latter half of the morning the delegates from Alberta got together at the tables above the exhibit hall and continued the networking process required to establish a strong provincial organization. One major goal of Youth Science Alberta will be to assist Alberta students in getting to the CWSF. Larger fairs probably don’t need the financial help, but for several of the smaller regionals in the province, the Genome Alberta support is the only cash funding that allows them to help bring their kids to the fair. Hopefully this will change into the future.
After a quick lunch it was take down time. With the new backboards, the process this year was sort of a reverse of the safety check. The students who properly followed procedures and used the designated tape were able to peel it off quickly leaving a clean backboard. Then they got an official to check and sign them off. With all takedown sheets in hand, each delegate was able to have their region checked off by their zone rep and received the money for taking the students for a night out on the town.
The city of Lethbridge has much to offer. Our group started off at the Galt Museum where we got a personalized tour from the curator, Wendy Aitkens. She began by explaining the central history of Lethbridge, pointing out the sights we could see through the windows of this marvelous facility. Then Wendy took us through the highlights of Discovery Hall. After seeing the permanent exhibits, we made our way to the travelling exhibit ‘Canadian Science and Engineering – Hall of Fame’. I found the panel on Raymond Lemieux. He was my uncle’s brother and I knew from the time I was a child that he was a significant Canadian scientist. We then worked our way down the hall to see some of the artifacts of Senator Joyce Fairbairn, the first woman to be named leader of the Government in the Senate. The exhibits that pay tribute to her are housed in what was once the men’s dorm at the old Galt Hospital which opened in 1891.
After the obligatory trip through the gift shop we made our way out of the building for a few pictures near the views from the grounds. Next, we bused the eight blocks to Galt Gardens, a park where we were able to take in the final portion of a concert. Any interested finalist or delegate could learn to line dance from some leaders at the concert. My own finalists were not keen so we went over to Park Place shopping mall where we spent a little time and money.
We had already made a booking for dinner at the nearby Boston Pizza. We joined two other Alberta regionals for dinner. All of our finalists submitted their menu choices the day before, and when we stepped into the restaurant we were escorted to our reserved section. The food started coming almost immediately. It took less than an hour for 30 hungry people to be served and out. Some of the other regional groups went to possibly higher-end restaurants and spent the whole evening waiting for food. We have learned through experience to choose a known franchise for our young students as we know that they will all find a food choice that they can eat. All happy, no complaints.
After supper, we were back at the university campus for a carnival night housed at the finalists and delegate lounge. All our finalists were there. None stayed back in the room to study, prepare or even watch videos. This was the final event of the fair.
It seemed that 11:30 p.m. came early, and for some it was. The regionals from eastern and central Canada either stayed up, or woke up in time to catch a bus for Calgary at 2:30 a.m. They had early flights out of Calgary to the east. Another set of buses left at 4:00 a.m. Chris Roedler and his committee did not get any sleep, but they sure looked relieved when they boarded us on to our bus back to Calgary at 9:00 a.m. on Saturday. This was the last bus out of Lethbridge. For the organizers, it was finally over. For us, we have a bus ride back to Calgary to meet parents at the airport and then for us too, it will be really all over for another year.
Time this morning seemed to fly. After breakfast, the finalists were at their projects by 9:00 a.m. for public viewing and school tours. The University of Lethbridge had again filled the hallways with displays and demos for the close to 2500 students who would be touring the Canada-Wide today. When the yellow buses arrived, there was enough electricity in the air to light the city as the elementary aged students started bouncing off the buses and into the exhibition.
I overheard one of my students talking to a VIP from one of the big sponsors and realized immediately that she is the one I would ask to represent us for the CBC interview coming up at noon.
The delegates spent the morning either viewing the displays or attending professional development-like forums to learn about various aspects of science fairs. I attended one on how to improve your local regional fair and realized how lucky I am to be associated with Calgary Youth, a regional with more than 50 years’ experience putting on science fairs for students. Just before lunch, all the delegates and finalists from Alberta grouped up in their dark citron team jackets for a picture on the knoll overlooking the Old Man river valley under the stylized U of L sculpture.
At 2:00 p.m. precisely, the buses were loaded and departing for the Enmax Centre. Brilliantly, the organizers had the delegations sitting at the same numbered table assigned for the opening ceremonies. They had however rearranged the placement of the numbers so that we were sitting in an entirely new place. Then the lights went down, the music went a little louder and a deep voice announced in French and English that the awards would start in 2 minutes.
As a delegate, you want your team to do well, and provincial rivalries naturally exist, but in the end you find yourself cheering for all of these young scientists being honoured for their curiosity and perseverance to get to this level. By the end of the event, more than half of the Calgary Youth finalists received a medal. All four of the Alberta finalists who had previously won a Genome Alberta award crossed the stage to receive a medal. Best of fair goes to Adam Noble from Peterborough, Ontario. The experienced finalists from my region indicated they were not surprised as they said that Adam’s project was a quantum better than anyone else. I must make sure to take a look again at public viewing on Friday.
After the awards ceremony, we cleared out of the Enmax centre briefly so that the tables could be set for the banquet. As the banquet drew to a close, the stage was filled for a final time with the volunteers from all the committees:
National Judging Committee
National Science Fair Committee
Board of Directors of the National Science Fair
Ambassadors for the Finalists
Youth Science host team.
Youth Science Canada has only 3 paid employees. They were also introduced. It was impressive to see the large group of people on the stage that work pretty much the entire year to make sure this is a major event for our young scientists. We gave them a standing ovation.
We bused back to the University campus in record time where the finalists quickly changed from their best dress clothes to their casual attire and the finalists lounge was a rocking good time for the rest of the night – ending with the #CWSF version of the Harlem Shake.
I had no trouble falling asleep after doing the final room check to see that all my finalists were safely back in their rooms for the night.
When I first saw the planned tours for the Canada-Wide Science Fair in Lethbridge, I didn’t know how I was going to make my choice. I was thrilled when I found out that I did not have to make a choice because the Lethbridge host committee set up the tours so that every participant visited every venue. I don’t know the entire history of Canada-Wide tours, but I do know that this is the first time I have been able to visit two UNESCO World Heritage sites on the same tour day.
We had been previously assigned bus numbers. On tour day, we went straight from breakfast to the bus staging area in a parking lot near the exhibit hall. As we passed by numbered tables, our box lunches were set out and ready to be picked up. Then on to the bus.
The buses departed Lethbridge at 8:15 a.m. and our cycle took us through Cardston to Waterton where we arrived by 10:15 a.m. The park is not normally opened this early in the year, but they made an exception for the Canada-Wide tour day. The woman in the Welch’s Chocolate Shop was smiling from ear to ear when she saw 5 bus loads of kid’s coming through her door. Yes, that was the first stop every one of them made. Once stocked up on ice cream, candies and fudge, we wandered around the town and taking in the sites. I especially like seeing the awesome power of Cameron Falls. I have not seen it during spring run-off before. We were back on the bus by 12:15.
Next stop for us was the Head Smashed In Buffalo Jump. We were met at the door by our guide Edwin. He is a great story teller and had the ability to engage the larger group of us assigned to him, or to pull aside someone with a very specific question. Just as we were about to leave, Edwin pulled me aside to show me some details of the buffalo skeleton. An hour and a half was only time to see the major highlights, and having a guide to point them out really made a big difference for so many of us. A person probably needs more than a day to see all the exhibits on display.
Two UNESCO World Heritage Sites done and we still had a third stop to make – The Alberta Birds of Prey Centre. They call it an interactive experience. That is an excellent description. As soon as we were on the grounds at the centre, there were guides helping excited finalists and delegates get close-up to observe and even gently touch several baby birds of prey. I was fascinated with the month old baby Great Horned Owl. It was abandoned by its parents at a construction site near its home. The guide told me that these little guys have such long legs to jump among the branches developing their strength and balance in preparation for their first flight which takes place by about two months of age.
We were all very tired by the time the tours were over. Super lasted until almost 8:00 p.m. as some of the buses got back quite late from their tours. Just before doing the final room checks for the night, I discovered that Mike had posted the interviews he had done on Sunday. When I checked with Atulya, I made sure he knew his interview was up. I sent an email to the delegates so that they could pass that information on to the other two finalists.
I think everyone will still be a little tired in the morning. This was a long day. Tomorrow - the Awards.
Wow! Today was a busy day. I hardly recognized our finalists. When we met to go for breakfast, they were so dressed up. The guys were in their best suits and ties, the young women were all in their most business formal attire. It was time for the judges.
Delegates are not allowed anywhere near the exhibition hall on the Judging Day. Instead, a series of workshops was available for us in the morning. I went to hear Dominic Tremblay talk about the newly revised and improved SMARTS program. He described it as “the first social network for young scientists, created by young scientists”. Actually, he said it is an online community, not a social network. Apparently, social networks get blocked by school administrators, online communities do not. I came out of the session very excited about this opportunity for teachers. I could write a lot more now. In fact, I have over 5 pages of written notes taken during Dominic’s session, but I think that I will try it out first and then do a much more detailed blog telling you what I learn.
During the second half of the morning, we had a Zone meeting. Alberta and B.C. make up the Western Zone. This meeting was an opportunity to give feedback about how things are going so far, and to learn the details about transportation for the big field trip coming up tomorrow.
The organizers were clever enough to make sure that the lunch today was the least messy possible alternative. There were lots of rolls and sandwiches, the type of foods that could be eaten while all dressed up in best clothes. One delegate told me of the time that spaghetti and meatballs in tomato sauce was served on a judging day a few years ago. Many of those students went back to be judged with red blotches all over their clothing. That did not happen today.
Right after lunch, the delegates attended a special meeting of Youth Science Canada. The very talented people who make up the board was introduced. Three of the existing board were retiring or terms were up. That meant three new members to be elected. Each region is allowed one vote. The three of us from Calgary came to a quick consensus after the speeches, marked our ballot and sent it to the front. Once the results were declared, the special meeting was over.
Next year’s fair will be held in Winsor Ontario, and their regional hosted a Social so that all delegates could get a feeling of what to expect if they went to the Canada-Wide in 2014. It seemed we had barely finished the snacking there when it was supper time. Considering how large the group is, the food has been very good. Tonight as a treat for the finalists after going the stress of judging, they actually had carving stations with large baked hams being sliced to order. I think one could gain weight if they keep feeding us like this.
The finalists and delegates had an opportunity to wind down in the lounge with games and music, or to go to one of 10 movies being shown in some of the lecture theatres. The Alberta delegates got together to talk about the formation of Youth Science Alberta, a foundation which will look at ways to help and coordinate funding for Alberta regionals.
Tomorrow will be another big day. The delegates were glad that the finalists were ready to hit the hay early. Wake-up tomorrow for the field trips is at least an hour earlier than it has been so far. I made sure to have everything ready for the trip tomorrow before lights out for myself.
Our team met this morning in the hallway of the dorm before heading down the hill to the dining hall for breakfast. When I got there, I was a little apprehensive when I discovered that all the coffee was gone. I settled for a cup of decaf. The servers soon brought out a couple of large urns of the real stuff and when I got my refill, I was ready for the day. It must be quite the challenge to feed such a large group of people who are all on the same time schedule.
At 9:00 a.m. all the finalists were expected in the exhibit hall as the school tour groups were about to begin. Soon, students from every grade level were excitedly roaming the halls of the University of Lethbridge taking in the atmosphere of a Canada-Wide science fair. By hosting this event, the University of Lethbridge was also able to showcase their campus and all the programs and activities that are available here.
Delegates used this time block for their once a year formal meeting. When asked to raise your hand if this was your first time as a delegate, nearly two thirds of the hands went up. We were introduced to the executive and the structure of the organization was explained. It takes a lot of work and organization to bring together students representing every part of the country. For me, this event always reminds me of just how big Canada really is. Additionally, we learned about the arrangements and requirements for the rest of the week.
I had lunch with a friend of mine who has worked at the University of Lethbridge for more than 30 years. Since he is judging at this year’s fair, we did not speak about any specific projects or finalists, but he did mention how amazed he is by the quality of research shown in the 5 page reports that he has been reading. After we said our good-byes, I headed to the meeting area for what is called ‘Discovery Day’. These were a series of talks and lectures on a very wide variety of science research areas from cell biology to digital music. When we registered by computer a few weeks ago, we made choices from a long list of these topics. On our name tags there were a couple of numbers printed out under the word ‘discovery’. That told us which group to join up with. It was all organised and run with excellent efficiency. My first session had a small group of finalists learning how to make measurements of very small specimens using sophisticated microscopes. Unfortunately I was called away to do the final set-up and safety check for one of my finalist who had been unable to arrive with the team on Saturday.
As the entire group of finalists gathered in the dining hall for supper, you could feel a peculiar vibration in the room. Could it be that judging day is tomorrow? As soon as dinner was over, most finalists headed back to their room for final preparations and going over their ‘seven, four, one’. They need to have a seven minute presentation for the first round of judges, a four minute presentation for the second round of judges and a one minuter for anyone else who wants a quick summery of what they did. By 7:30 p.m. the delegate and finalist lounge was almost empty. You could actually talk and listen in that room. And talk we did! Most of the delegates from Alberta hovered around a table swapping stories with a members of the host team. The major topic of discussion was about how to create a strong and useful provincial organisation similar to what we see in other provinces like B.C., Ontario and Quebec. Each province has its own unique structure and funding model, but with the same goal – get students to the Canada-Wide fair. We want to make sure that Alberta students have the same science fair support.
There was no noise in the halls even before lights-out. I guess all the finalists are getting a good night’s sleep before judging day.
After a hearty breakfast and a couple of cups of coffee, we headed out for a campus tour with guide Lucas. He apologised for all the construction, but noted that the University of Lethbridge has been undergoing massive expansion over the past few years. The campus is built into the hillside of the Old Man River valley. Lucas cautioned us he does not try to talk and climb at the same time. We soon learned why as we reached new heights going from cafeteria to the exhibition hall. Besides learning about the strong academic and research program offered by the university, we also learned how to spot tracks for their mascot – a colourful little pronghorn. He is hiding around the campus and there is a prize for spotting him.
After lunch as I headed into the exhibition hall for the first public viewing, I heard my name called out. It was Mike Spear, Genome Alberta’s director of corporate communications just behind me. The two of us headed into the buzz of the exhibit hall. I was able to point him towards the projects which I knew were winners of our Genome Alberta awards at their regional fairs. Mike interviewed several of these finalists and he will be posting those interviews on our website. Check back in the next few days. As I walked around through the exhibits, I was impressed with the number of excellent projects in all areas of science. I talked to several students who had outstanding biotech projects, some had already competed in the recent Sanofi BioGENEius Challenge Canada (SBCC). The judges are going to have difficult decisions to make on Tuesday.
After public viewing, all the finalists and delegates rushed out to the parking lot to be transported by bus to the Enmax Centre for the Opening Ceremony. Dominic Tremblay, as master of ceremonies, got the proceedings underway and after the expected speeches and welcome from hosts and sponsors and politicians, we were treated to Alberta Beef and entertained by the talented hoop dancer Maria Livingston. The highlight for many students was the presentation of the Microsoft Alumni Award to Ben Gulak and hearing him describe how science fairs transformed his life.
Finally the Chem Guys, Wayne Lippa and John Eng came out on stage with a bang and showed in some powerful ways that chemistry is the study of changing matter. Of course for a science fair, the two competed to make the biggest volcano, but showed their greatest success when they combined their efforts. I was glad to be a slight distance from the stage. They ended their presentation with the finale of Tchaikovsky’s 1812 Overture, playing the classic volley of cannon shots with exploding balloons.
Ceremonies over, it was back on the bus to campus and a wrap up at the finalist and delegate lounge.
The Canada-Wide Science Fair (CWSF) is happening this week in Lethbridge. This is the first time in 10 years that the event is being held in Alberta. When the regional science fair winners arrive at the CWSF, they are called finalists. The adults that chaperone and assist them are called delegates. This year, I am one of them. I thought I would share some of my observations and experiences with you.
Of course it did not start with Day 1. Since our regional fair in mid-April, I have been busy collecting information and managing the data for my finalists. I have had a great deal of assistance from previous delegates from my region with coaching the finalists in preparation for their ultimate competition this year – the Canada-Wide Science Fair.
Science fair teams from all across Canada flew into Calgary and then were transported by bus the 220 km to Lethbridge. Team Calgary met on the arrivals level at YYC, and waited briefly for the plane carrying the Newfoundland finalists to arrive. We then boarded our bus and in a little over 2 hours were being warmly greeted by our hosts at the University of Lethbridge.
First up, get our room keys, stash our luggage, then hurry off to find the registration desk, collect our goodies and attend the orientation session. We put all the important phone numbers for the week into our contacts. We learn that this year the fair has its own social media team and they want to see all our tweets #cwsf. Blackberry is one of the major sponsors, so their devices were subtly in evidence being used by all the national and host committee members.
As soon as the orientation was complete, our team grabbed their projects and we went to the exhibit hall to set-up. As we were there relatively early, our finalists had lots of space and time. Most of them had reduced their project displays to two large printed sheets so that with only a few lengths of double sided tape their displays were up and beautiful. They then had to obtain a safety check and once that was complete they were set for the week.
While my team was setting up, I was able to meander through the exhibit space and meet up with other delegates I knew from previous fairs or working with them on the Genome Alberta Awards. I have the Calgary Youth - Genome Alberta Award winner already on my own team . In a short space of time, I had been introduced to two more of this year’s Genome Alberta award recipients. We did take a break for supper at the University Hall Atrium and afterwards took in a session of Judging 101 given by the CWSF ambassadors. Then back to the exhibit hall to finalize the set-up by closing time - 8:00 p.m.
We spent the rest of the evening at a meet and greet, and soon the Alberta delegates were all gathered at a table outside on the patio away from the loud music but taking in the warm dry air of a spring night in Lethbridge. We didn’t solve all the problems of the world tonight, but we certainly had some reminisces about past Canada-Wide’s and how exciting it is for this year’s fair to be back in Alberta.
Once again in the next few weeks, both the Super Bowl and the Grey Cup of Science Fair season are about to take place. The Intel International Science and Engineering Fair (Intel ISEF) will take place in Phoenix, Arizona from May 12 - 17. The Canada-Wide Science Fair (CWSF) happens in Lethbridge, Alberta May 11 - 18. Canadian students participating in the CWSF are called finalists since they have to qualify by already winning at the level of their school and regional science fairs. For Canadian students to be considered for Team Canada ISEF, they must already have been CWSF finalists. Only 18 students make up this team: six are from Alberta, and two of these are Genome Alberta award winners.
Genome Alberta sponsors awards for all Alberta science fair regions. Many of the Genome Alberta award winners will be representing their region with competitive projects at this year’s CWSF. We support independent research project-based learning and we are very proud of the outstanding students who are recipients of this year’s Genome Alberta Awards.
Here is a list of the 2013 Genome Alberta award winners.
Today was DNA Day in Canada. So let’s talk DNA! And talk we did, starting with the question: “how do genetics affect an individual’s personality?” and ending with:” "Hi! Can you explain how sunlight both causes skin cancer and is required for the body's normal repair processes. What are the implications in sunscreen choices?”"
The scientists were praised: “we love what you're doing here! great experience for us to learn!” Some participants were in awe: “You guys are respected scientists!”
There was discussion of ‘spiders from space’ and questions about the reality of ‘Bigfoot DNA’. How can you beat that? Well, with the serious questions and discussion about Duchenne muscular dystrophy, amyotrophic lateral sclerosis, Ehlers-Danlos syndrome, triple X syndrome, and a wide variety of forms of cancer.
I felt that this day was a success as there was nation-wide participation. It appeared that entire high-school classes, especially in Ontario and Manitoba, were signed in and asking questions online. That was something I suggested in earlier blogs, so I was glad to see that happening. Individual teachers, students, and student teachers logged in and were asking questions. I saw tweets and retweets about the event emanating from coast to coast. The number of participants in the chatrooms was up considerably from last year. At one point there were over 80 participants signed in, and if some of these represented classes of students, the number of individuals jumps considerably.
Using the hashtag #DNADay2013, I sent out tweets on the questions and answers that interested me, and this led to over 50 retweets and mentions, a number that exceeded my expectations. When I looked at the stats on my bit.ly, I found that besides Canada, I was getting clicks from around the globe, including the US, Australia and Italy.
I really liked the format this year with a bigger range of experts available and moderators who frequently reminded participants what the specialty of the experts was. I think that helped focus the questions and keep everyone interested in following the discussion as we all celebrated DNA Day in Canada.
A couple of days ago, I tweeted an article I read in Futurity featuring the issues raised by Stanford bioethicist Hank Greely. I wasn’t too surprised that my friend and fellow science tweeter Philip Mulder pushed back asking me if it were safe. Since I had watched Jurassic Park several times, I said that if we were to do it, we had better start with very small organisms. Indeed, that may actually be happening. Let me explain.
The day after my reading about de-extinction online, my April issue of National Geographic arrived in the mail and the cover story was again on de-extinction: Reviving Extinct Species – We can but should we? This article was an even more comprehensive examination of the issues involved in de-extinction than the Futurity piece. The author, Carl Zimmer, describes some of the latest bio-techniques being explored; as well, he outlines the ethical issues raised by Greely and others.
In the Gospel according to John, Lazarus of Bethany had been dead and Jesus brought him back to life. Paleontologists use the term Lazarus Taxon to describe a species or group of animals that disappear in the fossil record, only to reappear at a later time. Medical literature describes the Lazarus Syndrome as auto-resuscitation after failed cardiopulmonary resuscitation. You can imagine the ethical issues implied in determining when post-mortem procedures can be undertaken when there is a remote chance of the Lazarus Syndrome occurring after an apparent death. Now a research team in Australia is working on the de-extinction of gastric brooding frogs in what they appropriately name the Lazarus Project. (Not to be confused with The Lazarus Experiment, the sixth episode of the third series of Dr. Who). These little gastric brooding frogs do meet the criteria I tweeted to Philip in that they are very small creatures.
Not de-extinction exactly, but certainly we have experience with re-introduction of organisms into habitats from which they vanished. While still somewhat controversial, probably the most successful of these is the reintroduction of wolves into the American northwest. It has been observed that there is increased biodiversity in Yellowstone National Park now due to the wolf control of elk populations.
There is a strong movement to reintroduce Plains Bison (buffalo) to Banff National Park. I realize that there are positives to this endeavor, but I do hope that such an exercise examines all the potential unintended consequences as these guys are a lot bigger than a gastric brooding frog.
Wouldn’t it have been nice if there were only the positives when John Hammond built Jurassic Park. As Hank Greely said about sabre-toothed cats, “It would be neat to see one of those!” In the meantime, Jurassic Park in 3D just opened in my local theatres. I will feel safer sitting in the seats to watch it with the special glasses knowing that the dinosaurs don’t really still exist anymore …. or do they?
DNA Day in Canada is coming soon. Do you have your questions ready? There has been a great opportunity in the last month to formulate your questions based on all the many exciting genomic announcements. Unlike sports, where there are all kinds of statistics based on trivia, science moves along at its own unmeasured pace. My own feeling is that this was a record breaking month for genomic breakthroughs being announced. Here are some of them:
This one is significant because it is a large scale genomics research project funded by Genome Canada with cofunding provided by Genome British Columbia and Genome Alberta. It is also significant because the Mountain Pine Beetle infestation has infected an area of Canada’s forests which by some reports is larger than England. The initial goal of the research is to help understand and predict the spread of the Mountain Pine Beetle. Another highlight I noted is the discovery of new plant cell wall degrading enzymes, which may have biotechnological applications leading to the conversion of cellulose plant cell wall sugars into biofuels.
Note to Teachers: In 2008 I made available a Mountain Pine Beetle 'primer' on all aspects (at that time) for teachers wanting to use a real world problem and an inquiry approach to learning. Contact me if you wish further details.
By setting up insect traps and then sampling all the crushed-up bugs, researchers were able to determine the biodiversity in large urban areas. In most cases it represented a verification of what was known to be present, but there were also several examples of species not currently known to be in that area. This is a technique I am sure we will hear more about.
Here is a cute little guy that lives in Madagascar and fills the niche of a woodpecker. Probably because it is nocturnal, it has very large eyes. It also has a disproportionately long ring finger. First it taps on the wood, listening for the movement of grubs under the bark. Then it gnaws through the bark and finally digs out the grubs with its long finger. The lemur may have lived in Madagascar for close to 10 million years, but has undergone range pressure since the arrival of humans 2300 years ago. DNA sequencing will play an important role in terms of classifying and maintaining the biodiversity of this organism. It should also be noted that one of the researchers contributing to this work is Dr. Steig E. Johnson of the University of Calgary.
Could falcons be the fastest animal in the world? If the speed associated with their hunting skill is considered, they can dive through the air at close to 390 km/h. No other animal comes close. The genomic research also indicates that they may be among the fastest evolving birds with respect to gene loss. To maintain their top predator status, these falcons require unique morphological, physiological and behavioral adaptations that are being investigated by the research group. The authors of this study hope that: “The genome sequencing data presented here provide a resource for the future examination of evolution and adaptation in birds and in raptors in particular.”
From the ancient domestication of the aurochs in the Middle East and India to the Moorish invasion of Spain, and then to Christopher Columbus sailing west, DNA sequences have travelled along in domestic cattle. Now DNA sequencing shows that the Texas Longhorn encompasses that fascinating history. With cattle ranchers using increasingly sophisticated genetic data, the genome of the Texas Longhorn will provide the tools to develop herds which can survive in hotter, drier climates and provide lower fat, grass fed beef to consumers.
For nearly 4000 years, humans have cultivated and selectively bred members of the Rosaceae family clad. While the classification boundaries are in some flux, there are at least 95 genera and over 2800 species of plants in this family which includes peaches, apples, strawberries, roses, apricots, almonds, plums and cherries. As with the Texas Longhorn, the sequencing of the peach genome has the promise of tracing the history of domestication and helping somewhat in our interpretation of peopling the globe. And, as with the Mountain Pine Beetle, the sequence of the peach genome may provide valuable clues to future use of biofuels.
The eye worm is restricted geographically to equatorial west and central Africa. It is spread to humans through the deerfly vector. The study of Loa Loa has recently acquired some urgency “because of the severe adverse events (encephalopathy and death) associated with ivermectin treatment during mass drug administration campaigns”.
As with the Mountain Pine Beetle problem, which requires consideration of the genome of the beetle, the pine tree and the blue stain fungus (thus the Tria Project), the study and control of the eye worm requires knowledge of genomic interaction between the worm, its vectors and its acquiring of genes from former endosymbionts. The authors of this paper explain the complexity: “Each filarial parasite interacts with both its definitive mammalian host and its intermediate arthropod host during its life cycle. The parasite is thought not only to have its own innate immune system to protect itself from microbial pathogens but also to have evolved mechanisms to exploit and/or subvert host and vector defense mechanisms.” With an estimated 13 million people affected, this is indeed important research.
In 1950, HeLa cells became the first human cells to be successfully grown in vitro. More than 60 years of research has been done using these cells, but there has been a clash between advances in biotechnology and bioethics. This controversy was explored in detail in the 2010 best-selling book The Immortal Life of Henrietta Lacks by Rebecca Skloot. The recent announcement of the sequenced genome of the HeLa cells led to a striking set of reactions questioning the ethics of not only of the release of the genome sequence without consulting the family, but of continuing to work with these cells at all.
Neither Henrietta Lacks nor her family was involved in the decision to release her family’s genetic data. I wonder now, what if I were to release my own genetic data. Do I have the right to release this information without consulting my family? What about my obligations to future generations? How can we predict what might happen in another 60 years of genomic research?
I hope I have provided you with a few ideas to pursue with the experts on DNA Day in Canada. Make sure you mark April 18, 2013 on your calendar, and set aside the time to participate in this once-a-year opportunity.
Luckily for me, Calgary was the location for the world premiere production of Sequence, a play by Arun Lakra. It was the Grand Prize Winner of the 2011 Alberta Playwriting Competition, and a finalist in the international STAGE Competition (Scientists, Technologists & Artists Generating Exploration). And through a lucky series of events, I found out about it in time to get tickets and go.
The play was presented by Downstage Theatre, a Calgary-based company dedicated to producing Canadian theatre that creates conversation around social issues. Sequence is indeed a play that initiates a lot of thinking about social issues. Like looking at a two-dimensional sketch of DNA, the complementary strands of the play weave back and forth. The viewer must focus carefully as luck, religion, science and coincidence form the complex strands of the play, all delivered with rapid-pace dialogue. At the end of the performance, the folks at Downstage moderated a deconstruction of the issues among the audience and the actors.
It was intriguing to see how the two complementary stories were staged. In the one story we have Theo, described as Time Magazine’s luckiest man in the world, and his interaction with Cynthia, a lucky member of his audience who won the draw to see him at the end of his book-talk presentation. Their interaction takes us through a discussion of mathematical theories and the probabilities of coin tosses. As an aside, I saw that Dr. Lakra’s top choice in books includes The Drunkard's Walk and his inclusion of the Fibonacci series in the play makes me think he probably read Mathematicians of LIfe as well.
The second story gives us the intense interaction between Dr. Guzman, a near-blind stem cell researcher who has been scooped while looking for the gene responsible for her illness, and the seemingly very unlucky Mr. Adamson, a wheelchair-bound student who believes his actions are controlled by God guiding his decisions. Through her discussion with Mr. Adamson, Dr. Guzman informs the audience about the importance of the sequence of DNA, and how small changes in the sequence may lead to serious genetic diseases.
If you go, listen carefully: there are lots of humourous one-liners in the play. In the discussion period afterwards, the actors indicated that they can almost determine where the various disciplines of scientists are sitting by the location of the laughs. I enjoyed this play tremendously and I hope that it gets wider distribution so that many more people get a chance to see it and discuss the issues of luck and destiny.
I just finished reading a book recommended to be of interest to me: Justinian’s Flea by William Rosen, published in 2007. It has been a selection of both the History Book Club and the Scientific American Book Club. With that combination of ancient history and modern science, it was a great read.
I know that we all read books based on our individual background and perspectives. When it comes to history, it has been a long time since I was a student in high school, and the canon at that time included learning about Egyptians, Greeks and Romans. We then jumped ahead about a thousand years to the Renaissance. My knowledge of history has been supplemented somewhat in subsequent years through movies, documentaries and docudramas, but generally along the same lines as school. I developed a greatly renewed interest when I read Bryan Sykes’ book Saxons, Vikings and Celts which I reviewed in a previous blog. About the same time, I visited Hadrian’s Wall and was stunned to realize that the Romans were in Britain for almost as long as Europeans have been in North America. Needless to say, my perspective on history was changing rapidly.
In Justinian’s Flea, Rosen considers the period of time leading up to and following the end of the Roman Empire. Furthermore, he observes that there was a contemporary Chinese Empire and he asks “why China remained a coherent nation at precisely the same time that Rome’s empire was atomizing into the nations of Europe?”
I found the history portion of the book to be a bit of a struggle as there were lots of unfamiliar names which made the reading difficult. Alemanni, Agapetus, Aigan, and Aeitus of Amida are just a few of the historic figures I had to juggle in my mind, and these are just the ones that start with the letter A. Even when the names were familiar to me, I still had difficulty keeping track of them: there was John Chrysostom, John of Ephesus, John of Troglita, John the Cappadocian, and John the Sanguinary. Then too, there were many peoples in the book: there are Huns, Goths, Visigoths, and Ostrogoths; also Burgundians, Alans, Suevi, Vandals, Lombards, Parthians and generic barbarians. He tells us of the historical importance of the various types of Christians including Catholic, Chalcedonians and Eastern Orthodox; in addition, he challenges us to understand the difference between monophysitism and diphysitism as it was viewed by 6th century holy men.
My reading speed increased when Rosen moved into the history of biology at the same time as arranging an understandable timeline for the evolution of Yersinia pestis as the major disease-causing organism in a virulent pandemic. He tells us that the host flea, Xenopsylla cheopsis, was probably confined to a narrow bracketed range in East Africa until a global cooling period allowed it to escape its natural boundaries. Luckily for the flea, the rat, Rattus rattus had also escaped from Goa and back to the Roman Empire thanks to the movement of pepper ships.
Rosen gives us details of the mechanism of infection of Y. pestis and how its genome allows it to be so dangerous. He tells us about how the bacteria produce a “demonic set of compounds” which render our immune system almost defenceless. Other authors have noted that Y. pestis has undergone large-scale genetic flux which “provides a unique insight into the ways in which new and highly virulent pathogens evolve”.
When Rosen cycles back to his question of “why China remained a coherent nation at precisely the same time that Rome’s empire was atomizing into the nations of Europe?” the answer seems clear to him. It was “the plague – Justinian’s Flea”.
After I finished reading the book, I discovered that Rosen has created a website for Justinian’s Flea as a companion resource to the book. I particularly enjoyed the Q&A page with the author.
I learned a lot by reading this book. Many times I found myself thinking about what might have gone through the minds of the people who lived through the terror of the times -- battles, sieges, wars and the plague.
The 2013 Science Fair season is well underway. Students are actively working on projects to be ready for presentation at their school and regional fairs. Organizers at the regional level are busy taking in student registrations, seeking out sponsors, and contacting potential judges. Genome Alberta sponsors awards and financial support for regional Science Fairs in Alberta. We are pleased to recognize the achievements of young student scientists. The Genome Alberta awards are presented to students with outstanding projects in the life sciences, and especially in genetics and genomics.
I indicated in a previous years’ blog that it is extremely rewarding to interact with these young scientists as they showcase their scientific work. Here are our recommendations on how you can participate:
Parents of school-aged children: get your children involved by taking them to see a regional fair or by encouraging them to participate in the process.
Interested adults: take the time to volunteer as a judge or on a committee which puts on the fair.
Teachers: inspire your students to pursue science fair projects. These projects build skills and confidence in cross-curricular areas including language arts, oral presenting, artwork, mathematics and science.
I have listed below the locations and dates of the fairs in your region of the province. Please take this opportunity to become involved or just take in the excitement of your local Science Fair.
2013 fair date
April 17 to April 20
Olympic Oval, University of Calgary
Banff Community High School
March 15 to March 16
Bower Place Shopping Centre
Red Deer, AB
Red Deer Lake School
April 6 to April 7
Northern Alberta Institute of Technology
April 12 to April 13
University of Lethbridge
March 13 to March 14
GPRC - Fairview Campus
Medicine Hat College
Medicine Hat, AB
Fort McMurray, AB
You can find the location and links to your nearest Science Fair here.
In addition, this year the Canada-Wide Science Fair will be held in Lethbridge. This will be the first time since 2003 that the Canada-Wide will be held in Alberta. Additional information and a call for judges were sent out in our February GenOmics Newsletter.
“When you know how to look, almost anything can become a thermometer, a barometer, or even an anemometer. “
Neil Shubin, in his new book The Universe Within, takes us on a time trip from the formation of the universe to evolution in a time of genomics to help us learn how to look.
Almost a year ago, I reviewed Neil Shubin’s Your Inner Fish, so when I found that he had a new book coming out I marked the date on my calendar to make sure I read it hot off the press. I really like Shubin’s story telling ability. His engaging and exciting style along with his personal anecdotes and behind-the-scenes look into the world of science made me want to talk to people about what I was reading in the same way I might had I been reading an exciting detective novel. I was several chapters in before I realized the brilliant chapter illustrations forecast the segment of time to be discussed. Shubin acknowledges his illustrator Kalliopi Monoyios and recommends her Scientific American blog: Symbiartic. I immediately started following her tweets.
I was already familiar with many of the scientists profiled. Happily, the book also made me aware of the contributions of many more prominent scientists previously unknown to me. For example, reading about Walter and Luis Alvarez evoked thoughts of science shows I watched long ago that explained their new and exciting theory. I knew about Milankovitch who proposed the heating cycles of the earth, but I was totally ignorant about Camp Century, built in Greenland during the Cold War. I knew about Alfred Wegener and John Tuzo Wilson; I didn’t know the role played by Harry Hess, Bruce Heezen or Marie Tharp. Neil Shubin brings together all their contributed pieces and arranges them to show the picture we have.
What I found most significant about Neil Shubin’s The Universe Within, was how he was able to weave together the 13.7 billion years of history of the universe along with 3.4 billion years’ history of life on earth and bring it all together in such an absorbing way. This is a great book for anyone interested in the wide swath of science from the macro of astronomy to the molecular of genomics.
“The idea that your DNA, the fundamental building blocks of life, may not necessarily be your destiny is not a new one. The French biologist Jean-Baptiste Lamarck (1744–1829) coined the notion of soft inheritance as an alternative to Darwinism.”
I’m trying to imagine Jean-Baptiste able to coin soft inheritance as an alternative to Darwinism in the year of Charles Darwin’s birth (1809) and a full 50 years in advance of the publication of Darwin’s On the Origin of Species (1859). He must have been clairvoyant as well.
As I outlined in my previous blog on this topic, Lamarck still believed in spontaneous generation. He explained the transmutation of species through the use and disuse of the organs as the way organisms adapted to their environments. Charles Darwin, on the other hand, developed a model of natural selection inspired by the artificial selection that he saw in domesticated organisms:
“Slow though the process of selection may be, if feeble man can do much by his powers of artificial selection, I can see no limit to the amount of change, to the beauty and infinite complexity of the coadaptations between all organic beings, one with another and with their physical conditions of life, which may be effected in the long course of time by nature's power of selection.”
It does not matter to Darwin whether natural selection is a result of either genetic or epigenetic expression: the resulting action on the phenotype is the same. Neither Lamarck nor Darwin knew about genes, and they certainly didn’t consider DNA methylation or histone modification when proposing their theories.
Epigenetic regulation is certainly a new and exciting way of looking at how organisms adapt to change in their environment. I want to learn about it without the skepticism I get when I am being asked to view epigenetics as somehow a vindication of Lamarck over Darwin.
PTC tasting has been used as an example of a Mendelian trait controlled by a dominant gene. This paper shows how a teacher can go beyond Mendelian genetics to:
demonstrate pedigree analysis,
make Hardy-Weinberg calculations,
determine student genotypes through the use of cleaved amplified polymorphic sequence analysis, and
encourage students to examine evidence for evolution at the molecular level.
But before implementing this lab in your classroom there are some issues to consider. Since PTC is a toxic substance, its permitted use in the classrooms of Alberta has gone through a range of regulatory acceptance. Science teacher resource books published in the 1960s gave recipes for teachers to prepare their own PTC paper (A Sourcebook for the Biological Sciences – Morholt Brandwein and Joseph). Throughout the 1970s to the mid-2000s PTC was not permitted in many Alberta schools. Although it is still not included as a part of the Alberta Program of Studies, a 2006 Safety in the Science Classroom once again spelled out that PTC paper could be used under extremely controlled circumstances. PTC is classed D1 (materials causing immediate and serious toxic effects) in WHMIS. Furthermore, it classifies PTC under class B – Chemicals, i.e., not appropriate for student use in schools except in junior and senior high school science courses under highly controlled conditions of use. To be in compliance, a teacher would need to hand the paper directly to each student, “check that students do not have bleeding gums or open wounds in the mouth”, and collect the used papers into a biohazard container for disposal.
Teach.Genetics, a Genetic Science Learning Centre based at the University of Utah, indicates that many schools have (in their opinion) needlessly banned the use of PTC paper in schools based on toxicity reports. They suggest PTC is no more dangerous than table salt. They include various calculations to justify their stance. Regardless, salt (NaCl) has a median lethal dose (LD50) of 3000 mg/kg whereas PTC is 3 mg/kg. This is not a trivial difference: it is several orders of magnitude.
Here are my questions:
Were we in Alberta previously far too cautious?
Are we now being far too imprudent?
Is it even wise for a teacher to suggest that students taste something described on Wikipedia as being twice as toxic as potassium cyanide? (I’m imagining the hushed tones of the breathless reporter on the evening news as I type this).
Please take the time to let me know what you think of using PTC in the classroom.
Our blog comments are moderated and do not show up immediately. Your email address is not revealed. You can also let me know directly by email or send me a tweet.
2012 has been a very busy year in the field of genomics. We at Genome Alberta have been keeping you up to date with the latest happenings through our blogs, our GenOmics News, and with micro-blog postings on Twitter. (@MikesGene, @gwardis, @GenomeAlberta)
As a review of the year, I’ve once again put together a fun little presentation to remind you of the wide variety and scope of our blogs. For each month, I chose one blog to highlight.
I used Prezi to create this presentation. Prezi is a tool “that helps you organize and share your ideas”. Here are some hints if you have not used Prezi before:
click your way through using the forward and back buttons on the bottom; or
choose ‘autoplay’ from the ‘more’ menu on the lower right; or
explore ‘freeform’ using your mouse as you might in Google maps.
You may remember some or all of the blogs. You can revisit all the blog entries on our site by selecting Blogs > Archive.
Happy New Year! Stay tuned in 2013 as we continue to keep you informed about the promise and the power of genomics.
Fifty years ago, on December 9, 1962 the Nobel Prize in Physiology or Medicine was awarded jointly to Francis Crick, James Watson and Maurice Wilkins "for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material". The importance of their contribution becomes clear when we look at how much additional progress and understanding has taken place in genomics, genetics and molecular biology since their initial publication almost 60 years ago. Below is a timeline which I first included in a blog when I was preparing for DNA Day in 2009.
Genome Alberta, partnering with the Ontario Genomics Institute and Let’s Talk Science, will once again be celebrating DNA Day on April 18, 2013. Every year, this is a great opportunity for students, teachers and all others who are interested in science to become involved directly with leading scientists in the field of genomics. I hope you will include this date on your planning calendar.
You may also be interested in the activities associated with Nobel Week this year. To celebrate 50 years since the award-winning work on DNA, there is a “brand new one day meeting [December 9, 2012] dedicated to exploring the impact of genetics and genomics on us all and promoting discussion between the traditionally separate domains of science and society.” Take the time to explore their website, see and read the discussions or get yourself set up to watch the videos or live stream the conference. From what I read, I suspect they may be tweeting this event from @NobelWeekDialog. You can even amuse yourself with an online game: DNA - The Double Helix.
Continue monitoring our Genome Alberta blogs to keep up to date about Genomics. We will have additional information regarding DNA Day 2013 as that day approaches.
We had a couple of sets of Magnetic Poetry® on our fridge when my daughter was a teen-ager. One was the original version, the other Shakespearean; later we added the chocolate version. From time to time, she and her friends would rearrange the little ditty so that it read something completely different. It was fun to see what would appear next. The individual words remained much the same, but the expression was completely different.
Traditionally, we learned that there are two types of RNA:
Informational - plays a role as the messenger (mRNA) when DNA is transcribed and translated into protein.
Functional non-coding - plays a variety of other functional non-coding roles (ncRNA). The first ncRNA described and studied in detail was the RNA molecule which acts to transport the amino acids for protein assembly, appropriately named transfer RNA (tRNA). There have been a number of other functional RNAs discovered over the past few years. One of the significant assumptions which must be made then is that there are at least two types of genes: one which codes for protein, and one which codes for the RNA. The old aphorism, ‘one gene, one protein’ does not work.
The 2006 Nobel Prize in Physiology or Medicine was awarded to Andrew Fire and Craig Mello for their work on ncRNA. They found that some small RNA had a regulatory role in transcription. They also suggested that these ncRNAs may be related to protection from retrovirus invasions.
I previously blogged that many retroviruses are incorporated into the genome. I learned the importance from a lecture by 2008 Nobel laureate Dr Luc Montagnier who has been making major contributions to our understanding of RNA since 1962.
A wide variety of transcriptional control mechanisms have been found in recent years. For example, Wang, Crutchley, and Dostie have written about the roles of ncRNA in ‘Shaping the Genome with Non-Coding RNAs’. In their paper, they describe a variety of roles played by ncRNA in gene expression regulation. Kelley and Rinn in a paper published very recently (Nov 2012) explain how ncRNA is more varied between species than are the actual genes. They also note that endogenous retrovirus insertions are implicated.
We have been trying to understand how the genome works since well before the Human Genome Project (HGP) began. Research and advances in knowledge since the publication of the HGP seems to be taking place at a very rapid pace. How do you explain how the genome works? Are you still using the metaphor that the genome is a series of pop-beads and each bead leads to the production of a protein? You may want to update your view to that of fridge magnet poetry. The number and kinds of words remains similar, yet the order and expression can greatly change the expression not only from species to species, but from cell to cell.
I posted my thoughts In advance of this conference to a YouTube video. Additional remarks about the power of genomics are posted on Genome Alberta’s YouTube channel.
A Sonar image on Bottlenose shows that prior to the conference there was a buzz about the #powerofgenomics, but once the conference got going, it turned into an explosion.
I’ll be monitoring #powerofgenomics for the rest of this once-in-a-decade conference.
This is Canada’s 50th year in space. It was in September 29, 1962 that Canada entered the space age, launching the scientific satellite Alouette 1 and thus making Canada the third country in space after the USSR and the USA . Now, 50 years later, Canadian astronaut Chris Hadfield is preparing to launch aboard the Soyuz spacecraft heading for a 5-month mission on the International Space Station.
On its website, the Canadian Space Agency asks students if they have ever wondered how things behave in space. Students are invited to submit science experiments that could be done by Chris Hadfield while in space. Those students selected will get to ask Chris about the experiment and his work in space through a personal phone call from the orbiting International Space Station. This opportunity is described as being ‘out of this world’.
This may be a great opportunity for an individual or groups of students to design not only an experiment that can be done in space, but one where data may be collected in a parallel or complementary manner here on earth. With appropriate experimental design, you could end up with a fantastic project to enter in your local science fair.
This is a win/win opportunity that is truly out of this world.
There are three types of people who should visit the Museo Galileo in Florence:
People interested in the history of science
Junior high school students and teachers, and
A number of years ago, I began my teaching career in an older school that had two storage rooms full of outdated science equipment, some of which I was only familiar with from pictures in the old texts. Sure, I had worked in research for a few years and was familiar with the latest (at that time) high-tech equipment such as ultra-centrifuges, electrophoresis equipment, freeze driers and sterile cabinets. What I had never used were bell jars, galvanometers, hydrometers and hygrometers. Over the years, curriculum changes had relegated most of this stuff to storage. Still, I was fascinated and when the students went home, I stayed late to try some of the old experiments. Then, when appropriate, I would bring out the old equipment and give the students an opportunity to explore the past. Now here I was in Florence at Museo Galileo which houses one of the oldest collections of historical scientific equipment.
Perhaps we should be much more aware of the contributions of the Medici Family to the support and development of sciences. In an earlier blog, I mentioned that in 1545 Cosimo I established the botanical gardens which are now associated with the University of Florence. Cosimo I also began a collection of scientific instruments and maps representing the known universe, which he displayed at the Palazzo Vecchio. His son Francesco I built the Uffizi Gallery and began collecting works of art. His brother Ferdinando I moved the scientific collection to the Uffizi Gallery in the 1580s; here it remained until a reorganization in 1775 led by physiologist Felice Fontana on behalf of the Habsburg-Lorraine rulers. The collection was greatly enhanced with the addition of the most advanced instrumentation from all over Europe. A library and workshop were also added. After additional alternating periods of support and neglect, the scientific collection moved to its current location in 1930. It was modernized and renamed Museo Galileo in June 2010. One floor of the museum is dedicated to the Medici Collections and another one to the Lorraine Collections. Near the well-stocked gift shop, there is an activity room with hands-on stations that permit the visitor to repeat some of Galileo’s experiments and other cool demonstrations. I thought that students might find some of these set-ups fun to build for independent studies or science fair projects.
There is so much to see that I spent the better part of a day in this museum. Let me tell you about two of the exhibits that made the greatest impression on me.
First, I came away from the museum with an entirely new impression of the Law of Parsimony (aka Occam’s Razor). I recalled that when I was a teacher, I followed the textbook explanation that one reason the model of the Copernicus heliocentric system won out was that it was much simpler than Ptolemy’s geocentric system. I had no idea of the extreme difference between the two models until I saw the various Ptolemaic armillary spheres side-by-side with the solar system models. The Santucci Ptolemaic armillary is almost 4 metres tall, very complex, and very impressive.
Second, I was very impressed to see the large collection of microscopes and telescopes that were used by some well-known scientists of the past. One telescope is known to have been used by Galileo in 1610 as he prepared for the publication of Sidereus Nuncius considered to be the first scientific treatise based on telescopic observations.
I discovered after my visit that the Museo Galileo has an extensive web presence as well. If you cannot get to Florence, you can do a virtual tour of the museum. I know that I will revisit in this manner.
Yes, I indicated I passed all the iconic tourist sites in historic Florence in my recent blog when I was exploring the botanical gardens associated with the University of Florence. What I did not mention was this was not my first time in the city. Naturally, if you have an interest in science, and if you are going to Florence for the first time, visiting the Duomo is a must. Let me give you some tips.
The dome of the Basilica di Santa Maria del Fiore, built between 1420 and 1436, was the largest dome in height and span until the Houston Astrodome was built of much lighter materials in 1965. Both the design and the special equipment required to build it were carried out by Filippo Brunelleschi, who is considered to be the father of modern architecture. Prior to a visit, I highly recommend doing some background reading and Ross King’s Brunelleschi’s Dome is an excellent resource. I have learned from seasoned travellers that you can almost have the dome to yourself if you are travelling in mid-winter. However, if you are in Florence anytime during tourist season, you can expect that there will be a steady line of people with varying degrees of physical fitness climbing the 463 steps to the top. I got there about 20 minutes prior to opening and was the seventh in line. That gave me an excellent opportunity to look for the structural features described in King’s book, and to have pretty clear views from the top.
A visit to the Duomo is not really complete without taking in the Museo dell'Opera del Duomo. In this museum I was fascinated by the original rhombus-shaped panels from Giotto’s Bell Tower depicting the science of that time, as well as models made by Brunelleschi when building the dome.
Florence was also the home of one of the best known Renaissance polymaths: Leonardo da Vinci. He is known primarily for his art work but he also made many contributions to the sciences. Fiesole is an interesting town in the hills above Florence. It is reachable by a 20 minute bus ride from the historic centre. Once in Fiesole, it is possible to hike out to the actual spot that Leonardo da Vinci used to study the mysteries of flight. It is rather awe-inspiring looking out over the cliffs knowing that Leonardo da Vinci once did the same thing.
While in Fiesole, it is very worthwhile to visit the Roman-Etruscan Archaeological area which includes the Civic Archaeological Museum since 1873. They have much to be proud of at this museum. I especially liked the individual Lombard warrior display, which included a skeleton excavated from a tomb in 1986, and speculation regarding his lifestyle.
Back in Florence I was able to find tributes to da Vinci as well as many other scientists and artists in the niches of the courtyard of the Uffizi Gallery.
I also visited the Perfume and Pharmaceutical Works of the Santa Maria Novella. I learned that starting in the 1200s, Dominican friars worked with flower petals and perfumes developing medicines. By 1612 the Grand Duke of Tuscany declared this a “pharmacy” and now it is in its 400th year of continuous operation under the name Officina Profumo - Farmaceutica di Santa Maria Novella. This is still a working pharmacy, but it is possible in their sales rooms to see antique instruments as well as historic vessels and glassware on display. The museum rooms (unfortunately ‘in restauro’ when I was there) house an extensive collection of antique ceramics, tools, and scientific equipment.
Nielsen provides us with a brief history of science communication, noting that scientists in the 1600s carefully revealed their findings in code and in anagrams so that they could later prove their primacy if someone else claimed the same discovery. Then, by 1665, Henry Oldenburg founded the first scientific journal, the Philosophical Transactions of the Royal Society. It probably took another century to get to the point of scientists publishing their work. By the late 20th century, the phrase ‘publish or perish’ had real meaning in terms of grants and jobs. There have been some successes in open science, but “the scientific community, which ought to be in the vanguard, is instead bringing up the rear”.
Nielsen got my interest early in the book telling me about the chess game ‘Kasparov versus the World’. It was a chess match played online in 1999 which involved collaboration of 50,000 people from 75 countries matching wits against world-ranked chess champion, Garry Kasparov. Nielsen continues to weave lessons learned in the match as he describes other collaborative efforts like Wikipedia. Another significant portion of the book explains Galaxy Zoo and the use of online volunteer ‘zookeepers’ to classify tens of thousands of galaxies. Nielsen does note that astronomy has always been an area of science with a significant proportion of knowledgeable amateurs. Another area where collaboration has met with amazing success is the PolyMath Project which, after a slow start, produced many advances in mathematical challenges.
Another interesting collaboration described by Nielsen is the Foldit Game which predicts protein shape from the primary sequence of DNA. Gamers are challenged to contribute to science by playing the game.
Nielsen praises the development of Open Source journals like PLoS and arXiv that are freely available to all, and he contrasts the access of these to the pay wall of most major science journals. He also likes the fact that granting agencies are helping to move science forward by requiring all papers to become freely available within 12 months of publication.
I found myself making extensive notes for discussion when I read Michael Nielsen’s Reinventing Discovery. It is both stimulating and exciting to read. I won’t give away all of his arguments, but I do recommend this book if you are interested in how scientists are using the internet in new ways of problem solving.
Sure these are iconic tourist sites in Florence, but I passed by Il Porcellino, the Duomo, and the Accademia di Belle Arti which houses David. These were all lined with tourists waiting for their opportunity to see these world class attractions. I continued on up the street past where David has been kept since 1873, all the while dodging the large art prints strewn on the pavement by the street vendors who hope you will make a purchase. Soon I was past the hustle and bustle of the historic centre, and I was entering an area where only a few other keeners go: the Giardino dei Semplici of the Museo di Storia Naturale.
The botanical gardens are now associated with the University of Florence, but were originally established by Cosimo I of the Medici Family in 1545 as a garden of medicinal plants. The gardens have a long and interesting history. I was not there at the right time of year to see one of their featured plants, the Amorphophallus titanium in flower. That would have been nice to see as it is considered to be the largest unbranched flower in the world. Perhaps I was lucky not to smell it though, as I heard it lives up to its other name – corpse plant – in that it has a very strong fragrance of dead carrion.
Moving along through the garden, I was able to see some intriguing herbariums containing very fine and healthy specimens of carnivorous plants. The gardens are set up in a series of thematic plots, some containing poisonous plants, and some with specimens of coffee, tea and a whole lot of other useful plants. I spent a lot of time studying each section, but perhaps for me, the most interesting beds were the evolutionary garden and the fescues. In the evolutionary garden, a small knoll has been built up, and the plants are organized so that as you proceed along the path, you walk through the ‘living fossils’ like the cycads, ferns and horsetails and make your way to the conifers.
I wondered why I was so fascinated by the fescue plants growing in tiny pots along the back wall of the garden. Perhaps it was because we define our biomes in part by the climax species, and much of Alberta is in the fescue grasslands biome. Perhaps it was because rough fescue (Festuca scabrella) was adopted by the province of Alberta in 2003 as our environmental emblem for grass. Or maybe the reason I found this display so interesting is because this garden’s collection of over 300 specimens of fescue is used for scientific and genomic studies, including the 2007 paper that examined the divergence of fescue as chromosome and genomic size expanded and then contracted.
Online, Michael Brooks can be found on twitter, on his website, or on his Free Radicals blog. I also found his writings in a new and entertaining book The Secret Anarchy of Science. This book is not a history of science, yet it exposes the behind the scenes account of many stories in the history of science. He talks about Newton, Galileo, Watson and Crick. We hear about the precarious journey towards a Nobel Prize for a wide range of Nobel laureates from Svante Arrhenius to Robert Wilson. We learn what inspired scientists such as Albert Einstein and Kary Mullis to come up with their ideas. The book is full of anecdotes about well-known names such as Faraday, Fermi, McClintock and Tesla. I also learned of scientists whose names are not familiar to me, yet I realized that I was well aware of their work when reminded by Brooks as he portrays many of the battlegrounds for ideas which had ultimate winners and losers. Brooks relates to us many a story of scientists who took a long time to gain recognition by their peers. He quotes Max Planck to illustrate: ‘A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die’.
Brooks worries that scientists may become straightjacketed by their lab coats and the society’s expectation of what science is all about. He wants us to know that “This book is a call for more scientific anarchy, and for the creation of a culture in which it can thrive.”
One of the major themes Brooks weaves through the book describes situations where scientists break the rules to get their ideas accepted. He gives examples of where the model is so pleasing that the data is either gently massaged to fit it, or ignored entirely and left for future generations with better measuring devices for verification. I’m not sure that Brooks intended this, but I was getting the impression that he thinks a successful scientist might be a cross between a liar and a thief whose inspiration comes while high on drugs and then fights with the establishment when sober. Science teachers or school librarians would need to be aware of this aspect prior to ordering this book for a school library.
Brooks suggests that science education should let students know “what science and scientists are really like” so that it avoids being a dull and dismal road. I agree fully with him that children learn better by doing. If you have been following my blog, you know that I am a long-time advocate of inquiry-based learning to support critical thinking in science. Like Brooks, I believe it is not as important for students “to learn all of the scientific information on the science curriculum”. However, even he chronicles how some anarchists read and know everything on a topic prior to adventuring out on their new paths of knowledge. I think that it is still important to teach children how to apply scientific problem solving so that they develop the appropriate thinking skills. We know that a student driver does not start off learning to drive by intentionally breaking rules whereas an experienced driver knows that there are times to take appropriate and safe risks.
Michael Brooks in his book The Secret Anarchy of Science succeeds in presenting more than a “string of entertaining anecdotes”; in fact, he leads us to additional thought and discussion.
Growing up in Alberta, I often have the feeling (correct or not) that I am the first human to walk through some places. As a youngster living near the edge of the boreal forest, I explored with my friends what we thought were the extreme outer limits of civilization. Now, as an adult hiking in the national parks or Kananaskis country, I have (inadvertently) bushwhacked where no trails exist. Surely I was among the first humans to walk in that area.
Now in Umbria, I’m on a trail that is known to have been walked by Saint Francis of Assisi starting in about the year 1208. The trail which takes me out of Assisi towards the top of Monte Subasio has been hiked by reverent pilgrims and other hikers continuously since the mid-13th century. Yet looking out from this area I was not thinking about those who hiked this trail during the past thousand years; instead, I was thinking of the first hunter gatherers in this area at least 40,000 years ago - the Neanderthals. As I looked out into the valley, I tried to imagine Neanderthals moving along this very ridge system scouting out possible hunting locations or searching for the plant bounty offered in the underbrush.
Geologically, the hills were here more or less as they are now. No doubt the last ice age had some effect on the biota on these slopes, but the permanent ice did not reach this part of Italy. Did the advancing ice lead to the demise of the Neanderthals? That is one possible explanation. It surely had some impact. Or did they assimilate with the rapidly advancing Homo sapiens arriving out of Africa? Very recent DNA evidence suggests that some genetic mixing took place.
I think that there has been a lot more discussion of Neanderthals in the media since it was revealed that there is possibly as much as 4% Neanderthal DNA found in non-African humans. Some of the personal genome companies will provide you with your exact Neanderthal percentage if you are curious enough to find out what is in your genes.
Across the valley near Gubbio on the lower slopes of Monte Ingino traces have been found of both Neanderthals and early Homo sapiens. There has been almost constant occupation of these hills and valleys for over 30,000 years.
Perugia, the capital city of Umbria, is also home to one of the world’s oldest universities: the University of Perugia founded in 1308. Perugia is also home to the National Archaeological Museum of Perugia. This museum has many exciting and modern displays. One of the newest and most prominent exhibits is Origini del genere Homo (Origins of the genus Homo). Through a series of panels and glass cases, I got to see some of the stone tools and other artifacts of the Neanderthals. I left this museum keen to learn more about Neanderthals especially the ongoing discussion regarding the admixture of Neanderthal DNA with modern Homo sapiens.
On June 18, 1178, five monks from Canterbury observed a flaming torch sprouting out of the moon. It is now believed that they actually observed the formation of one of the craters on the moon. That crater is named Giordano Bruno in honour of the Italian philosopher who was burned at the stake in part for his early support of Copernicus and the idea of the existence of a plurality of worlds and their eternity.
When I read Gerald Weissmann’s Epigenetics in the Age of Twitter, he drew my attention to Giordano Bruno when he described “a statue dedicated to him in 1889 by a progressive Italian government that wrested Rome from papal rule. Bruno’s statue still presides over the Campo de’ Fiori of Rome. ”
I thought, hey! I’ve seen that statue before. I probably even took pictures. Now, while seeking science in Rome, I had a chance to revisit both the statue and why Giordano Bruno is important.
Many Rome guidebooks suggest a visit to the busy scene and lively market at Campo de’ Fiori. DK Eyewitness Travel describes this “field of flowers” as being in Medieval and Renaissance times one of the liveliest and roughest areas in Rome. DK points out that it is still a hub of secular activity, although it was once the place of execution and that the statue of Giordano Bruno marks the spot where he was executed for suggesting the earth moved around the sun.
In Rome: A Cultural, Visual and Personal History, Robert Hughes begins his book discussing how Bruno was Italy’s most brilliant and unorthodox mind of the sixteenth century. Bruno had the audacity to propose that the universe, far from being a tight and limited system of medieval cosmology, was in fact infinitely large – a vast continuum consisting of sun after sun, star upon star. Hughes continues that when the statue was put up in 1889, it was stated that the fruits and vegetables would renew themselves forever in freshness as his best memorial. Even now, by day this space is full of vegetable, fruit and flower stands, and transforms each evening into a food and entertainment centre.
Each time I have been there, I see people sitting at the base of Bruno`s statue eating gelato or munching on goodies from the market. I wonder how many of them even notice the statue above them. When I moved around the statue examining the panels portraying his life and trials, I thought about the extreme risks to scientists in the 1600s.
We probably don`t know as much about Bruno as we do of other early scientists like Copernicus, Galileo, Newton and Tycho Brahe. Is it possible that Bruno`s work was hidden or destroyed after he was burned at the stake for his ideas on February 17, 1600?
While some accounts indicate that Bruno and Galileo never met, it is known that they both taught mathematics at the university in Padua at the same time. Surely they were aware of each other’s ideas. Dava Sobel in Galileos’s Daughter suggests that the treatment of Bruno probably had an influence on Galileo’s response to the same inquisitor, Roberto Cardinal Bellarmino aka the ‘hammer of the heretics’.
Bruno is described as a heterodox, i.e., his beliefs were not in agreement with the principles of his society or religion. He is portrayed as a martyr to free thought who paid the ultimate price, a fiery public death. Bruno may not be a household name in the pantheon of scientific heroes, but he serves as a reminder that while scientists today may have opposing interpretations, they no longer need to worry about being burned at the stake for those ideas.
From a science tourist’s perspective, Rome is all about ancient history and archaeology – so if you are a modern day antiquarian you need only to open your eyes. There are a great many sites ranging in antiquity from pre-Roman times through the Renaissance up to the unification of Italy.
In my previous blog, I was seeking science at Lux in Arcana, the exhibit at the Capitoline Museums. At the time of my trip planning, the number one attraction in Rome according to TripAdvisor was the Roman Houses of Palazzo Valentini. It is no wonder that this relatively new museum is so highly rated, as it is the most effective and spectacular use I've seen of multimedia to create a time travel experience. As you proceed on plexiglass walkways over the ruins, you experience computer graphics and laser lights rebuilding the excavations before your very eyes as they would have looked in their original splendor. There is a requirement to book your visit because the tour’s multi-media exploration is done in different languages at different times of the day, and tour size is limited to 15 due to the small size of some of the exhibit spaces.
Ostia Antica is a short distance by public transport from the historic centre of Rome. It has some of the features of Pompeii as an archaeological site that preserved a great deal of a highly-populated port town from Roman times. The difference is that Ostia Antica was filled with silts and muds rather than volcanic ash. These have been removed to reveal the ancient buildings right down to the details of the mosaic floors. Surprisingly, it is not on the list of many tourists, so you can explore this area in relative solitude.
A short trip on subway and bus took me to the nearby town of Tivoli which has two UNESCO World Heritage Sites. I wandered around in awe at the engineering and architectural marvels from the 16th century at Ville d’Este. The gardens and fountains became the model which influenced the future of European garden design for centuries to follow. In the heat of the summer, this is a fine place to enjoy some shade and explore the many magnificent fountains. I was lucky enough to be there at the right time to experience the Fountain of the Organ which uses water to power a pipe organ and music plays briefly throughout the grounds. The French organ builder, Claude Venard, developed and installed this organ in 1571. By16th century standards, this was considered a novelty, the first in modern times to perfect the techniques and the automatisms of Greek and Roman models of antiquity. Venard’s design did not produce the sound from the pressure of the water like the ancient models, but rather from the separation of an air-water mixture.
I knew I was not through seeking science in Tivoli when I heard about the recently reopened Parco Villa Gregoriana. This woodland area has been the site of civilization as far back as the 3rd century BC when the Greek temples were built over a deep gorge along the river Aniene. It seems like a wilderness hike that takes in two major waterfall systems, but these falls are not entirely natural. After a devastating flood in 1826, Pope Gregory XVI commissioned a project to prevent future floods by redirecting the river, thus transforming the gorge by sending the water over falls and through a tunnel. I have attempted to capture the majesty of this place in the attached video.
I was unable on this trip to visit Tivoli’s other UNESCO World Heritage Site, Villa Adriana. I did however find a personalized video tour given by a virtual Hadrian himself.
The Roma Pass which I described in my previous blog covers all the sites and the public transportation mentioned above.
Perhaps our planning process started with a tweet. Something along the lines of “see 100 documents from the Vatican Secret Archives – 12 centuries of history”. The exhibit would be on only until early September. I wanted to see this important exhibit, but what else could I see in Italy. I began seeking science even before we purchased the airline tickets.
One of the first stops I make prior to any trip is TripAdvisor. I know that there are numerous review sites, but TripAdvisor was an early adaptor of user-generated content, and I’ve been a member since 2007. I trust that when I look at ‘Things to do’, I will be able to create my own checklist of what I want to see. Next, I’m off seeking science in Rome.
List in hand, I purchase a 3-day Roma Pass, which allows me into the first two sites at no cost and all others at a reduced price. Now I am ready to be first in line at the Capitoline Museums to see “Lux in Arcana – The Vatican Secret Archives Reveals Itself”. It is billed as an event of unprecedented scientific, cultural and media importance, and is the first and possibly only time in history that these documents leave the confines of the Vatican City walls. Inside the museum there are no photos allowed, so I’ve made notes from the displays and from the exhibit catalogue.
Of the 100 fascinating documents on display I will focus on the six that moved me the most.
Ten days were eliminated from the 1582 calendar
I first learned about calendars and their connection to astronomy when this was a topic included in Alberta’s science curriculum. Then, just prior to Y2K, I read a great book by David Ewing Duncan called Calendar which examined the history of calendars and how we measure the flow of time. In 46 BC, Julius Caesar directed the development of a calendar which made the equinoxes and solstices consistent and predictable. The Julian calendar had 365 ¼ days, but it was 12 minutes short per year. Thus, by the fourth century AD, the calendar was about 3 days behind at the equinox. In 1575, scientists were brought together by Pope Gregory XIII to solve this problem. On Feb 24, 1582, Gregory issued a bull* eliminating the days October 5 through 14, 1582 from the calendar, and removing three out of four century leap years. The copy I was seeing of this new Lunario Novo was among the first ones off the press.
Nicolas Copernicus: A Canon who studied the stars
I probably have a rather simplistic impression of the issues leading up to the acceptance of the heliocentric model of the solar system. Here was a papal bull issued in 1542 which indicates that Mikolaj Kopernik (Nicolaus Copernicus) was held in some esteem prior to the controversy of his revolutionary ideas. After years and countless hours studying the solar system, he was starting to lose strength in his old age. He hoped to dedicate his work De revolutionibus orbium celestium (On the Revolutions of the Heavenly Spheres) to Pope Paul III. On June 1, 1542 he asked Pope Paul III for permission to have his 12-year-old nephew, Jan Loytz, appointed his permanent coadjutor. The papal bull was issued without apparent question. On March 24, 1543 Copernicus was shown a published copy of his work. It is said that he looked and smiled and then shortly afterwards passed away.
A machine for sailing through the air
This story was new to me, and it’s a good one. An 18th century scientist named Bartolomeu Lourenco de Gusmao sent in his design for a Passarola - a flying machine. According to the display, this was either a “big bird” built to fly, or it was a hoax built to throw the curious off the results of his actual experiments. Regardless, the plans for this flying machine conceived in 1709 are part of this exhibit. In 1936, the airport in Rio de Janeiro was named Bartolomeu de Gusmão Airport after this early pioneer of flight.
Proceedings of the trial of Galileo Galilei
Galileo’s story is one I think many of us are familiar with. There have been innumerable books and movies made about his life and contributions to science. When considering Galileo’s times, it is important to remember that Italy was not a unified country, and that some of the moving around is what kept him safe. He was born in Pisa on February 15, 1564. By 1588, he was teaching mathematics in Pisa, and then he moved to Padua in 1592. In 1604 he observed a supernova and in 1610, he described the moons of Jupiter. When he published Sidereus Nuncius (Siderial Messenger) in 1611, some Dominican fathers started preaching against him. On February 26, 1616, Cardinal Roberto Bellarmino formally instructed Galileo not to advocate, defend or teach the Copernican Theory. Between 1616 and 1623, Galileo published a couple of additional books in Rome which continued to support Copernican Theory. He was confident that his friend Maffeo Barberini (now Pope Urban VIII) would understand the science and defend him. That was not to be, as his persecutor Bellarmino was a cardinal member of the Inquisition who held considerable power. Galileo’s book, Dialogue Concerning the Two Chief World Systems, published in Florence in February 1632, provoked the indictment for heresy and forced him to stand trial. Galileo was subjected to four interrogations before the Inquisition Tribunal. On April 12 and 30, and again June 10 and 21, Galileo defended himself as well as he could, often citing his old age (70) and forgetfulness as his excuse. Ultimately he was pronounced guilty and forced to accept the verdict against him. I simply stared in amazement to see his actual signature at the bottom of these trial documents.
Alexander VI Inter cetera bull – dividing up the world
When I was in school, I learned that the reason that people in Brazil speak Portuguese while the rest of South American countries speak Spanish was related to a line drawn by a Pope. The line was actually drawn by Pope Alexander VI and issued in a papal bull on May 4, 1493. Here was the actual document that divided up the world on a line one hundred leagues west of the Azores, and led to the Treaty of Tordesillas between Spain and Portugal. This effectively portioned the new geographic discoveries being made, and marked a major transition between what was called the Middle Ages and the Modern Era.
Papal recognition of the University of Cambridge
I was thrilled to find a document with a connection to DNA. Yes, it is a stretch but here is a document which predates Watson and Crick by 635 years, yet it indirectly allowed them to collaborate together to announce the structure of DNA. Here is what we know. In the twelfth century, teachers at cathedral schools and their students needed to join in a kind of association – these groupings became what we call ‘universities’. This academic initiative was quickly backed by Pope Innocent III. In the academic year 1208-09, an Oxford student accidently killed a woman with a dart. Local authorities could not arrest him as he was protected by the university status granted to students. The authorities then ruthlessly seized three other students outside of the city walls and hanged them. The rest of the students soon fled, thus disbanding Oxford University. Many escaped to Cambridge where Saint Giles Cathedral had a teaching tradition. Cambridge gradually acquired all the features of a university including a multiplicity of teachers and curricula. In March 1317, King Edward II asked Pope John XXII to formally acknowledge Cambridge as a University. On June 9, 1318 the pope issued the bull requested by the king. The original document which was stored at Cambridge has been lost. The copy transcribed for John XXII is thus the only evidence of the pope’s recognition of one of the world’s leading universities, the one where Watson and Crick did their work in the early 1950s.
Check back on my blog soon as I continue Seeking Science in Italy.
* A papal bull is a document issued by the Pope. The name comes from the distinctive lead ball (bulla) which is appended to the end of the document to authenticate it.
As I walked along the shelf of science books at the bookstore, I saw Gerald Weissmann’s latest book, Epigenetics in the Age of Twtter. I knew that I had to read it immediately. It bills itself in the subtitle as “Pop culture and Modern Science”. This book is composed of a collection of 28 modified essays first written for The FASEB Journal which is the official journal of the Federation of American Societies of Experimental Biology.
As soon as I started to read this book, I reached for my sticky notes so that I could mark easy access to the references section. There are 37 pages of references, and I found that I was flipping to see the sources constantly. It is amazing how Weissmann brings together such a very wide range of material in this book. He pulls facts and quotes from material dating from the mid-1800s to very recently accessed websites.
In each of his essays, Weissmann makes many connections of ideas and personalities. Some of his examples were familiar to me, others totally new. It was an easy book to read, but certainly not a quick one as I found myself going for background knowledge and increased awareness of some of the scientists, authors and politicians who may be more familiar to an American audience.
In one chapter, Weissmann discusses the ugly politics of Nazi science and then demonstrates through the way history unfolds that “science is and remains international”. In a subsequent chapter he takes us through time travel to see how the Nobel Prize was awarded to women very rarely, and then only reluctantly, until 2009 when this “aberrancy ran into equality on the podium in Stockholm. “
I looked at some of my brief notes that I sketched out while reading the book. Among the ideas I noted for my further thought:
macrobiomes and microbiomes
why do we need operational definitions in science
Hellman and Hamett
microRNAs and ‘Lock and Key’
Oliver Wendell Homes - Junior and Senior
Omics – the advancing edge of science and technology
Hair loss and grayness
If you read this fascinating book, you may create your own list. My favourite chapter, Voodoo Economics and Voodoo Healing: Witchcraft Persists in Massachusetts, compares conditions in Angola and the state of Massachusetts with regard to sorcerers and witches. After a quote describing healing touch therapy, Weissmann despairs “reading this twaddle”. Weissmann’s book is neither pretentious nor silly talk, it is a fine and challenging read.
I was lucky enough to be part of a group invited to participate in the inaugural guided hike by the Burgess Shale Geoscience Foundation (BSGF) to study the Helen Lake Stromatolites. This was a chance to satisfy my curiosity about the geology of the area around Helen Lake where the many faces and faults expose a great range and age of rocks. Dr. Rob Taerum, our guide, was well prepared to lead us on this adventure. Although not necessary for a BSGF hike, I prepared myself in advance by learning as much as I could about Stromatolites.
I was surprised when Rob revealed that these stromatolites had only been described in 2004, even though people have probably been scrambling over them since the first explorers came to this region in 1899 when Ralph Edwards as guide led Rev. C.L. Noyes, Rev. Harry P. Nicholls, Charles S. Thompson, and George Weed over the Dolomite Pass. Charles D. Walcott, best known for discovering the Burgess Shale formation in 1909, later found stromatolites across the mountains near Field on one of his many trips to the Canadian Rockies. In work he published in 1914 he proposed that there was a relationship to cyanobacteria.
Stromatolites are now regarded as among the earliest life forms, dating back 3.4 billion years. Fossil stromatolites were being described even before the beginning of the 20th century, but living stromatolites were not known until 1956 when they were found in Shark Bay, Australia.
To the delight of biologists, geologists and paleontologists, stromatolites are the prokaryote cells that lived nearly 2 billion years before eukaryote cells arose. They are the life form that, through their metabolic processes, released enough oxygen that it built up in the atmosphere, allowing the development of aerobic metabolism responsible for life as we know it today. And they are the organisms that help us determine what the oceans, seas and continental shelves were like over the many eons of deep time.
Stromatolites are predominately made up of cyanobacteria. Historically cyanobacteria were called blue-green algae, but clearly these prokaryote organisms do not belong in the same classification as the other ‘colours’ of algae as described in older text books. All the algae became problematic with respect to classification and newer classifications moved the various algae around (perhaps I will blog more on this at another time). Ultimately many cyanobacteria are now being defined by their metabolomes and transcriptomes rather than their phylogeny. Genome sequencing of cyanobacteria has been considered an important step towards developing a model of the evolution of photosynthesis. Since stromatolites are complex communities rather than a single organism, metagenomic techniques are being used to study them.
Biofilm is what holds the stromatolite community together, and it is the substance that sets up the conditions for the deposition of limestone material through the precipitation of calcite. Amazingly, biofilm was first described by former University of Calgary professor Dr. Bill Costerton* in 1978. He is considered to be the “father of biofilm”. His pioneering work led to our current understanding that, on a global scale, 98% of all bacteria live in biofilm and more than 50% of the biomass is actually biofilm.
Here is a thought: will Curiosity find any biofilm on Mars? Will that be the sign of life it is looking for? Will Curiosity transfer biofilm to Mars? Will that become the first case of interplanetary invasive species induced by man?
I hope that the BSGF gets the approval to guide hikes like the one I was on to the Helen Lake area. That way, if you wish to learn more about the geosciences related to stromatolites, you can go with them on one of their hikes. Keep following my blog for more information on developments in genomics, biotechnology or biofilm on Mars. There is much of interest happening now in studies of biofilms and cyanobacteria relating to topics from dentistry to biofuels. I will let you know more as I find out myself.
*Dr. Bill Costerton was a huge supporter of science teachers when he lived in Calgary. He was a great resource for me when I needed a scientific answer, and he was always excited to tour me and other science teachers through his lab. Dr. Costerton left Calgary in 1993 to become the Director of the Center for Biofilm Engineering at Montana State University. In 2008, he became Director of Biofilm research at the Center for Genomic Sciences in Pittsburgh. I was sad to learn that Dr. Costerton passed away in May 2012.
We are warned when we go out into the backcountry to go in groups and beware of bears, cougars, wolves and coyotes. Perhaps we need to be more aware of much smaller living things. Ticks and mosquitos have the ability to attack and infect us without us even knowing about it. In western Canada, mosquitos can carry West Nile Virus, while ticks can infect us with a variety of diseases including Lyme disease, Rocky Mountain Spotted Fever (RMSF), and now a new and as-yet-unnamed disease from the Lone Star Tick.
Here’s what to look for:
West Nile Virus – If you develop fever, headache, body aches, nausea, vomiting, swollen lymph glands, or a skin rash on the chest, stomach and back, you may have been exposed to West Nile Virus. It is possible to develop even more severe symptoms such as high fever, neck stiffness, stupor, disorientation, coma, tremors, convulsions, muscle weakness, vision loss, numbness and paralysis. (Centers for Disease Control and Prevention)
Lyme Disease – If you get a rash on your body that looks like a bull’s eye, you may be a target for Lyme disease. If you leave it untreated, you may go into the second stage of illness with symptoms including spread of the rash, arthritis, heart palpitations, fatigue, generalized weakness and central/peripheral nervous system disorders. (Alberta Health: Lyme Info)
Rocky Mountain Spotted Fever (RMSF) - If you have a sudden onset of moderate to high fever, significant malaise, deep muscle pain, severe headache and chills, you may have been exposed to RMSF. If you leave this untreated, it may last for two to three weeks. The rash can appear on your wrists and ankles and may even spread to the rest of your body. (Alberta Health: Rocky Mountain Spotted Fever)
Lone Star Tick-related – You may initially have symptoms similar to Lyme disease, but if the tick that caused this was a small tick called Lone Star, you may have Southern Tick-Associated Rash Illness (STARI). Most worrisome of this tick illness is that you may further develop a life-threatening allergy to red meat. (Scott P. Commins et al.) Thankfully this tick is not found (yet) in Alberta. They are wide-spread and abundant in the south and east of North America.
Lyme disease was recognized and named after Lyme, CT where the first outbreak in humans was noted in 1975. We know now that the bacterium was present long before this. Recent reports note that Ötzi the Iceman, who lived 5300 years ago, had Lyme disease. We know this because in 1997 the genome for the bacteria responsible for Lyme disease was sequenced. So by the time Ötzi’s DNA was studied, the Lyme disease bacterial DNA sequence was found as a systemic infection in his joints.
Nearly 5300 years ago, Ötzi treated his joint pain with medicinal tattoos. We don’t know how well that worked out for him as he was apparently suffering from atherosclerosis, joint pain, and some arthritis when he was murdered. Today, we treat the early symptoms of Lyme disease with a variety of antibiotics that usually lead to a rapid recovery. Research is ongoing into the treatment of persistent Lyme symptoms.
Here is another reason to be ticked off. Your dog can get a vaccine against Lyme disease, but you cannot. Two vaccines were once approved for human use in Canada, but a series of extremely controversial class action law suits in the U.S. resulted in these vaccines being withdrawn from the market. Most vaccines work by causing our immune systems to create antibodies to fight off foreign invaders. The Lyme vaccine was designed to neutralize the Lyme bacteria in the tick preventing it from entering your blood system. You can learn more about the vaccine controversy by reading The Lyme vaccine: a cautionary tale.
When I am hiking during tick season, I try to stay on the trail and I avoid stepping off into junipers or near the base of spruce trees. I also do a preliminary tick inspection before getting back into the car to drive home. Early detection and removal of ticks is definitely the best solution to avoiding tick-borne diseases.
This summer, don’t get ticked off. Keep the ticks off you.
Since I published this blog, I received a note from Ben Gadd reminding me that "In your list of places to avoid, you might add grassy spots frequented by bighorn sheep or other hoofed animals. Experience has shown that, in the Rockies, wood ticks prefer to climb up on the seedheads of grasses and thereby hook a ride on the heads of grazers. Or the shoes and socks of humans!"
Two very good websites for additional Tick Information can be found at:
Each time I read an explanation of epigenetics written for the non-specialist, I cringe if I see that the writer makes the claim that epigenetics is a demonstration of Lamarckian evolution and that Darwin could be wrong. Neither of these scientists knew about Mendel and genes, de Vries and mutations or Watson, Crick and DNA.
For many years our heuristic model of inheritance was based on genetics. In this model, genes were the mode of transferring biological traits from generation to generation. Now this model has been challenged with the advent of epigenetic research. There has been an increase in the number of examples of what is called non-genetic variation. Environmental signals may lead to phenotype changes that are expressed in subsequent generations.
So, does this mean that Lamarck was correct?
Lamarck was doing his work in the early 1800s. At that time, the scientific view proposed by Linnaeus was that life was organized in hierarchical form. During Lamarck’s life, spontaneous generation was still an accepted idea, although it was limited to microscopic organisms. The aspect of Lamarck’s work that we are most familiar with is that he was perhaps the first to propose a mechanism for change. He believed in ‘use and disuse’. The parts of the body used by an organism to cope with the environment will tend to increase and improve, and then be passed on to the offspring. This was no doubt a very daring proposal on Lamarck’s part in a time when species were deemed to be fixed and immutable. Lamarck proposed that evolution was the best explanation to link the fossil record with observed current biodiversity.
Our modern model is made up of knowledge gained from the fossil record, geographic distribution of biota, comparative anatomy, studies of embryology, and molecular evidence. We consider genes, genetic regulation and population genetics, all interacting with the environment.
Issac Asimov in The Relativity of Wrong cautioned that: “The basic trouble, you see, is that people think that "right" and "wrong" are absolute; that everything that isn't perfectly and completely right is totally and equally wrong.”
Although our current model will be assisted by the knowledge that comes from epigenetic studies, there is so much more. It is not explained individually by either Lamarck or Darwin. It will not be explained by just the genome or epigenome. It will continue to be a synthesis of many ideas.
I remember years ago someone telling me that they must be related to Genghis Khan. The storyline went something like this: if you were of European heritage and you had lactose intolerance, then you must be related to Genghis Khan or one of his tribesmen. Lactose intolerance was prevalent amongst people from the east. The Mongol Empire of the 13th and 14th centuries was the largest contiguous empire in history, stretching westward to the borders of Poland and Hungary. Lactose Intolerance must have travelled westward with them.
We know a great deal more today about lactose intolerance. Current models of genomics and epigenetics make us realize that lactose tolerance is a short stage in the lifecycle of mammals. The gene to make the enzyme lactase* is turned on in gut cells of young mammals who are feeding on their mother’s milk. When it is time to wean, the lactase gene turns off and the mammal youngster gets turned off of wanting milk. From a biological perspective, lactose intolerance is the “wild type”.
Coincidentally with humans moving from being hunter gatherers to becoming farmers, a mutation allowing lactose tolerance arose. From my reading, this is still a chicken and egg argument. The mutation is such that lactase does not turn off at the weaning stage. Lactose-tolerant humans can continue consuming milk throughout their entire lives, a very convenient adaptation if your food comes from raising cattle or goats.
Is lactose tolerance another example of neoteny in humans? Neoteny is the word which describes the retention of juvenile traits by adults. Neoteny is considered a feature that supported human evolution. Human lack of body hair is an example of neoteny.
At a recent birthday party, the father warned his now 40-year-old son that as a result of reaching this more mature age, hair would no longer grew where it was supposed to, yet it would sprout in places that it should not. Everyone laughed, but it made me think: maybe in humans moving from the juvenile stage just takes a little longer. Perhaps too, late adult lactose intolerance is another example of neoteny. In this case, the genetic switch finally shuts down the production of lactase.
As for Genghis Khan, I don’t know if anyone is seriously looking at his contribution to lactose intolerance in Europeans, but I do know that there are some interesting stories out there about his contribution of Y chromosomes. I’ll keep you posted.
* You can distinguish between an enzyme and a sugar by the word ending:
An –ase ending indicates an enzyme, thus lactase.
An –ose ending signifies a sugar like lactose.
Lactose is a double sugar (disaccharide) made up of the single sugars (monosaccharides) glucose and galactose. Lactase breaks the bond between the two single sugars allowing for digestion of milk.
To solve this riddle, we must go back in history to the middle of the 19th century. Long before Watson and Crick suggested a model for DNA, Professor Hans Winkler devised the word ‘genome’ in 1920 to describe the pertinent protoplasm which defines a species. He was pretty sure that this hereditary material was made up at least in part by the chromosome. Typical wisdom suggests that he combined the words gene and chromosome to come up with ‘genome’. That may well be true; but it is also possible that, since he was a botanist, Winkler would have been familiar with such terms as rhizome and biome, so he could have attached the -ome ending to the word gene to come up with an inclusive word describing everything to do with genetics.
Our quest for the answer takes us back even further to the 1880s. Simultaneously, Johann Friedrich Miescher was working on the fluids in pus while Gregor Mendel was breeding pea plants. Miescher isolated nuclein (DNA). Initially, he thought that it might play a role in heredity.
Gregor Mendel presented his major paper at a symposium in 1865. Miescher published the discovery of nuclein in 1869. Amazingly, neither was taken very seriously at time of publication. It was not until 1900 that Mendel’s work was rediscovered, and it was not until 1953 that Watson and Crick suggested the model for DNA.
The Oxford English Dictionary credits T.H. Roderick for coining the word ‘genomics’. The word came out of a brainstorming session to determine a possible name for a new science journal. The first known print usage was in September 1987 when Victor McKusick and Frank Ruddle announced in Volume 1, Issue 1, page 1 of Genomics: “A new discipline, a new name, a new journal”.
Genomics came to Canada in a big way in 2000 when the Government of Canada established the mandate for Genome Canada to develop and implement a national strategy for supporting large-scale genomics and proteomics research projects. Since 2005, Genome Alberta is one of the Genome Centres established by Genome Canada to focus on genomics as one of the central components of the Life Sciences Initiative in Alberta, and to help position genomics as a core research effort.
Make sure you keep up with all the latest developments, riddles and puzzles in the field of genomics by visiting GenomeAlberta.ca.
Let’s Talk Science recently published a Spotlight on Science Learning and asked the question ‘Is Canada’s science talent pool at risk?’ I’m an optimist. In my teaching career, I tried to approach every student as a unique individual. I had one student who, after a Bachelor’s degree in science, found a total interest in the arts and has become a renowned artist in his specialty. Another student that I taught went to the Masters level in the arts, and now she is an expert in the field of artifact restoration. It is impossible to know from a Likert scale what paths students may follow as they pursue their passions.
I learned a long time ago that most children up to about Junior High have no idea of what they want to do when they ‘grow up’. One day, they may wish to be a cowboy, the next a firefighter or policeman. It is only as they approach graduation and need to start making serious choices that students start to think about becoming ‘Doctors and Lawyers and Such’. The ‘such’ may include engineers, accountants, dentists, pharmacists or teachers. It does not include careers like bioinformatician, volcanologist or astrobiologist. Since the television series CSI: Crime Scene Investigation, I noticed an increased interest by students in genetics and DNA fingerprinting.
I took a look at the enrollment statistics from the University of Calgary in 2012. If we compare science and engineering to arts, there are approximately 1.2 times as many students pursuing the sciences at the undergraduate level. If we consider the same comparison at the graduate level, we see that the ratio increases to 2.3 times as many students preparing for careers in science and engineering as the arts. Is the University of Calgary an anomaly, or does this express the enrollment trends across the country?
I totally agree with the recommendations that come from the Spotlight on Science. I believe that a great many of these practices are already in place. I don’t think that it is as worrisome as indicated in their release. Many students are not aware of the wide range of science-related employment opportunities available to them. If we wish to improve the outlook, then we must provide a lot more information to spur student interest. Teachers at the high school and undergraduate levels should be bringing in examples of careers on an ongoing basis. I believe that would make a greater difference than the once-a-year career day.
It is interesting that while we in Canada are worried about not producing enough science and engineering graduates, the Americans are examining if they produce too many, and that there should probably be more emphasis on producing more generalists. I hope that all students will discover a meaningful path to find their passion in life. Let me know your thoughts.
Fear not! Alberta students are world class in reading, mathematics and science. It has also been reported that Canadians who are between the ages of 25 and 34 lead the world in “educational attainment”. Our students are in top place because they learn by doing, and they learn the language necessary to explain what they are doing. And yes, they also perform well on international test standards.
In Alberta, we recognize that the science program cannot be formulaic; we also recognize that there are at least three curricular emphases with their own particular problem-solving approach:
From the earliest grades, we introduce students to the skills of a scientist:
Making operational definitions
In Alberta, we recognize that science education provides a framework for students to understand and interpret the world around them. They develop both knowledge and skills through the processes of inquiry and problem solving. Since language plays a role in developing the skills of inquiry and problem solving, it is important to introduce students to a language framework. An algorithm such as the scientific method leads to strategic thinking. The actions of identifying problems, asking questions and proposing ideas require the use of a particular kind of language whether it be called the scientific method or just “doing science”.
I attended a session given by William H Leonard in 1980 where he advocated what he called the extended discretion approach to science. He justified this through his research showing that students were bored with non-productive, recipe-like activities. Leonard suggested that students become involved in the laboratory investigation by actively planning and then carrying out the experiment.
In the extended discretion approach, working from general goals and techniques, students plan their own experiments. Leonard reports that students who were accustomed to following detailed instructions during lab investigations found the approach hard at first because it required the students to conceptualize the problem. Once the students plan their experiments, they carry out their plan after teacher approval. I suggest that research-granting organizations handing over a great deal of money expect the scientists to go through a similar process in their grant applications. Variations of Leonard’s extended discretion approach are part of the learning cycle used with success throughout Alberta.
Note: I wrote this blog in response to a comment about students using the scientific method, as expressed in my previous blog. Since then, I have come across another concern: Canadian students, while strong in science performance, do not pursue science careers. I intend to explore this question in my next blog.
Is it time to add a new step to the traditional scientific method? The answer is a definite yes! Students are typically presented with a version of the scientific method wherever science is taught. Why? The scientific method is an approach to problem solving, a system we use to create new knowledge, and overall, a way of thinking. Yet, the way this framework is taught to students often misses a very important set of issues that professional scientists face: ethics.
Both in classrooms that I have observed and in science fair projects I have seen, students seem to have a very good grasp of planning experiments linking the manipulated and responding variables to the problem, hypothesis and data collection. Now, I would like to see inclusion of ethical considerations in the planning process. It could be inserted just before or just after the method/procedures. That way the student can demonstrate that ethics was part of the thought processes prior to carrying out the experiment. Even though this is probably more important for planning independent projects, all activities involve potential ethical considerations. This is especially true in projects that involve human or animal subjects.
Why not teach students to consider ethics from the start, rather than having them try to justify their experiments after the fact. Youth Science Canada identifies projects involving humans as being either Low Risk or Significant Risk. They provide guidelines to distinguish between the two and make available a template to create a letter of informed consent for students to use for the significant risk projects. Since many students like to do experiments that involve surveys, tests, or behavioural observations that can involve tasting or ingestion of food, teachers can make this an opportunity to discuss the ethics of human research in context.
In Alberta, ethics is taught as a separate component in Grade 8.
“The study of the acceptable standards of a society is a component of schooling that is essential in helping students to become contributing, responsible and ethically mature persons. Humans, by their very nature, are moral beings.” (1)
“The aim of the ethics course is to help students to become more thoughtful, to think of the interests of others, and to see the ethical implications in their daily lives.” (2)
By including ethics in the scientific method, it integrates ethics into the daily lives and habits of students rather than isolating ethics in an episodic course.
Genome Alberta through GE3LS has shown leadership in bringing “Ethical, Economic, Environmental, Legal and Social” aspects into the context of genomic research and innovation by addressing questions that lie at the interface between science and society. It is time to bring ethical concerns into the daily language of the science curriculum by including it as a step in the modern scientific method.
You probably knew that some of the vegetables that we eat are, from a botanical perspective, fruits. Did you know that it took a U.S. Supreme Court decision in 1893 to define which fruits are vegetables?
If there were a form of analytics on my television, it would discover that I watch a lot of science programs. I don’t know which station gets most of my attention, but I certainly like PBS, Discovery Channel, National Geographic channel and Space. If I’m not watching the science networks, then my television is tuned on to the History network. I also have some favourite shows on Food Network as well. You can imagine my excitement, then, as I found all the elements of science, history, gardening and food in Rebecca Rupp’s How Carrots Won the Trojan War.
In 20 entertaining and informative chapters, Rupp takes us on a journey through history, botany, genetics, culture and cultivation of the vegetables we eat. She lists over a hundred General Sources, and the Notes section contains many pages of specific references and additional information. It is an academically researched book, yet Rupp writes in a very entertaining and engaging fashion. Her sense of humour, suggested in the title, comes through on every page. Almost all chapter titles are alliterations, plus a small series of simple snippets suggesting several sidebars.
Rupp takes us on a historical journey reaching back to Neolithic times and the original cultivation of the vegetables. We visit the gardens and kitchens of ancient civilizations such as the Egyptian, Roman, Aztec and more, and move into modern genomics and the introduction of new crops. As a Canadian, I found some of the cultural and historical references in Rupp’s book may be more familiar to an American reader. That is certainly not a big enough impediment to prevent me from highly recommending this book as a great read.
Both the Super Bowl and the Grey Cup of Science Fair season are happening this coming week. The Intel International Science and Engineering Fair (Intel ISEF) will take place in Pittsburgh, Pennsylvania, from May 13 – 18. The Canada-Wide Science Fair (CWSF) takes place in Charlottetown, PEI the same week. Students who participate in the CWSF are called finalists since they qualify by already winning at their school and regional level. Students must already have been CWSF finalists to be considered for Team Canada ISEF. Only 18 students make up this team.
Genome Alberta sponsors awards in all 10 Alberta regions. Many of the Genome Alberta award winners will be representing their region with competitive projects at the CWSF next week. We support independent research project-based learning and we are very proud of the outstanding students who are recipients of this year’s Genome Alberta Awards.
Here is a list of the Genome Alberta award winners.
Sarthak told me that he “believes Genome Alberta does an amazing job spreading the work of high school students”. In thanking him, I indicated that I would be pleased to see something about his Intel ISEF project. He immediately sent me the following video description: Potential of Schwann Cells – a look at peripheral nerve regeneration.
We wish him well in his endeavors in Pittsburg and know that he will be a remarkable representative of Canada’s best student scientists.
Tomorrow, “Let’s Talk DNA” Day presents live chat from 11:00 a.m. to 1 p.m. EDT. That is 9:00 a.m. MDT for me, and I will certainly have my computer warmed up and ready. I’ve already established my user name and password so that I can have all four chatrooms open when the live chat begins.
Last year I was prepared with a couple of questions in my mind. Once the chat began and I could see all the other questions coming in, I realized that I had many more questions to ask. I found it to be a lot of fun and a wee bit of a challenge keeping all the conversations straight. Sure the script is rolling, but not so fast that I couldn’t keep up. What a great experience to have four of the top DNA experts at my fingertips to be able to ask any question about DNA, genetics and genomics. How fascinating to see the questions that other people have that I may not have thought of myself!
You may decide to sign-in and lurk, but from my experience, I bet you get caught up in the excitement and find yourself sending in the questions that come to your mind. See you on line in the chatrooms!
CurioCity’s DNA Day Website
“The instant I saw the picture my mouth fell open and my pulse began to race. The pattern was unbelievably simpler than those obtained previously (“A” form). Moreover, the black cross of reflections which dominated the picture could arise only from a helical structure.” James D. Watson, The Double Helix, 1968.
The instant Watson saw the pattern on the paper, he immediately had an idea of what it meant.
As a judge at Science Fairs, I have observed that some students make beautiful graphs, but unfortunately, the graphs are wrong. What I mean is that some students either do not use the correct type of line, or worse, they draw the wrong type of graph entirely (e.g., a pie chart instead of a line graph).
How can we help students learn these skills? When I taught science in a grade 7 – 12 school, I realized that it was worth my effort to spend time reinforcing the importance of graphs with my students. The key part of the Alberta curriculum regarding this says that the students shall “interpret patterns and trends in data, and infer and explain relationships among the variables”. That should be a full stop. But the curriculum goes on to say the student should do this by predicting “the value of a variable by interpolating or extrapolating from graphical data”.
Yes, data points are important, but not nearly as important as the shape of the graph that they produce. Like Watson, students need to be able to determine the implied relationship between the variables at a glance from the shape of the graph. Alternately, the students should be able to sketch the shape of the graph that shows the relationship that they wish to describe. In addition, students should be able to sketch the shape of the graph they expect from an experiment. That is a very clear way to show their prediction and therefore their understanding of the problem. After completing the experiment and graphing the actual data, they should be able to determine if their data confirms or refutes their prediction.
At the high school level, there are a limited number of graph shapes that students need to know. From an operational perspective, the manipulated variable is always on the horizontal axis and the responding variable is always on the vertical. The numbers should always get bigger left to right and bottom to top.
I have compiled a gallery of graph sketches that would be useful for students to know.
Sketch A) The first sketch shows a situation where, as the manipulated variable increases, the responding variable also increases and at a constant rate.
Sketch B) The second sketch shows the responding variable decreasing as the manipulated variable increases, still at a constant rate.
Sketch C) Here is a sketch where the responding variable is increasing at an increasing rate as the manipulated variable increases. This is sometimes called an exponential curve.
Sketch D) Many students never contemplate this result. Here is an example where there is no apparent effect of the manipulated variable on the responding variable. There are some interesting variations on this graph which I describe below.
Sketch E) In this example, the responding variable increases as the manipulated variable increases, but only until it reaches a maximum. In some ways, this graph represents a combination of both Sketch A in the first portion, and Sketch D in the last portion. I have seen student experimental designs where they predicted this type of outcome, and sketched it out in advance of collecting data. When that data came back appearing to support only sketch D, the students were then alerted to take more careful measurements at the lower end of the range resulting in verifying their original predictions. Without this level of understanding, a student may miss very critical measurements.
Sketch F) Similar to Sketch E, this graph combines elements of sketches A and D. This one though has Sketch D in the first and the third portion with Sketch A sandwiched into the middle.
Sketches G and H) These two similar graphs result when the responding variable has an optimal maximum or minimum. These graphs can result from direct data collection such as enzyme activity versus temperature, or they can result from re-graphing rate of increase of the responding variable in Sketch F back to the manipulated variable.
Have your students improve their graphing skills through simple sketches that demonstrate their understanding of the relationship between manipulated and responding variables. You can have your students learn more about DNA and the Double Helix by participating in DNA Day on Friday April 20, 2012.
I am very excited because DNA Day is coming soon. On April 20, 2012 we will be celebrating the 59th year since the publication of the paper by James Watson and Francis Crick which described their model of DNA. Their model related the structure to the function of the molecule and became the foundation for increasing our knowledge of genomics in the years since.
This year, Genome Alberta, along with the Ontario Genomics Institute and Lets Talk Science, brings you a two hour live chat with some of Canada's top experts in the field of genetics. You can also ask questions of Jay Ingram! This will be an excellent opportunity to take part in a cutting-edge educational experience. Want to get involved? Here are some suggestions:
Teachers: You want to show your administrators and parents how you use the latest in educational technology. This day is for you! Treat this day like a field trip. Forget the bell schedule, book time for your science classes and have the students participate in the online chat. If you can’t have each student at their own computer, you can set up one for the class and have your class participate as a group.
Students: Tell your teacher you want to participate in DNA Day. You will learn more today on this live chat than you will by doing questions 3, 5, 7 to 9 and 14a from Chapter 7 in your textbook. Besides, those questions can be done for homework. Convince your teachers that if this is a day scheduled for a class discussion, why not have that discussion online with some of Canada’s top geneticists.
Parents: After you have made the morning coffee, gather the family around the computer and sign into the live chat. You have seen Jay Ingram on TV. Now is your chance to directly ask him a question.
Retired Folks: You want bragging rights with your Grandchildren! Well, this is it! You will be able to have four simultaneous chat-rooms open on your desktop at the same time. You can follow the discussion about DNA, and you can ask your own questions too!
DNA Day live-chat: April 20, 2012, 9 - 11 a.m. MDT. There will be more about DNA Day on this blog as the information becomes available.
I was looking at the TV listings guide yesterday and noticed that the 1980 movie The Elephant Man was coming on. I didn’t have time to watch it, but I remembered that it was a well-known film in the early 1980s and I used to refer to the movie to illustrate the difference between a ‘dominant gene’ in the Mendelian sense and a ‘pre-dominant gene’ in the Hardy-Weinberg sense.
Some students expect that the phenotype most widely expressed in a population indicates the dominant gene. In their introduction to Mendelian genetics, they learned that using Mendel’s thinking, they could predict that there was a 100% chance in the F1 generation of the dominant allele being expressed in the phenotype. Even in the F2 generation, there is a 3:1 chance of finding the dominant phenotype in the offspring. The beauty of Mendel’s contribution is that he provided us with a method of making predictions about genotypes and/or phenotypes when considering specific traits of individual parents and their offspring.
On the other hand, population genetics allows us to gauge genetic variation within populations. Through knowing the number of individuals exhibiting the recessive phenotype, calculations can be made which predict the frequency of the specific alleles in the total population. At the time the movie was made, Joseph Merrick was thought to have suffered from neurofibromatosis-type I (NF- 1). I recall when the movie was current there was discussion that NF-1 was the result of an autosomal dominant allele which occurs in about 1 in 3500 births. I explained to students that this was a good illustration of the fact that just because an allele is dominant, it is not necessarily the most frequent. Indeed, using Hardy-Weinberg calculations, students determined that the frequency of the recessive allele is more than 99.98%.
While the calculations made by my students in the 1980s were accurate, much more has been learned regarding Joseph Merrick and what lead to his disease since then. According to trivia on IMDb “The NF Foundation used the movie as a fund-raising tool and credited it with making the disease more widely known.” We know that only about half of those with NF-1 inherited the alleles, the rest result from spontaneous mutations.
Most significantly, we now know that Joseph Merrick probably did not have NF-1. In 1996, additional studies changed his diagnosis to the much rarer disease, Proteus Syndrome. Proteus syndrome, which has fewer than 150 diagnosed cases worldwide, is caused by a somatic mutation in the oncogene AKT1. The gene codes for an enzyme involved in the regulation of cell proliferation and apoptosis, and is a somatic mutation only passed to direct descendant cells. In fact, a recent paper in the New England Journal of Medicine verified a long held hypothesis that Proteus syndrome is a mosaic disorder, and would be a lethal mutation if found in all cells of the body.
It may no longer seem relevant to talk about The Elephant Man in a biology class. Most students are probably not aware of the movie unless they caught it on the old movie channel. It is certainly relevant to use Joseph Merrick as an example of someone who lived his short life undiagnosed but remains 120 years after his death an inspiration for research, especially in genomics. Next time the movie is on, I’ll make the time to watch it.
Christa McAuliffe said “I touch the future, I teach”. When I think about her quote, I know that I’ve been very lucky. I have actually seen the future through many of the students that I have met. Eden Full is one such student. I first met Eden when she was a Grade 7 student keen to do a science fair project using little solar panels. In the years since, I have seen her refine her ideas and now she is making a major impact in developing communities through her SunSaluter technology.
I was delighted when Eden told me that she wanted to reach out to educators to help them inspire their students. Here is her guest blog:
Dear Educators Who Inspire,
My name is Eden Full and I was born and raised in Calgary. I graduated from John G. Diefenbaker High School before studying at Princeton University for two years. Now, I am taking a leave of absence with the support of the Thiel Fellowship to pursue my lifelong passion full-time. As a proud Albertan, I am writing to you today because I would like your feedback on how I can contribute to our province’s efforts to improve education and outreach.
I like solar panels. Working on the application of solar energy in off-grid and developing areas is my full-time job. I am passionate about bringing appropriately-designed technologies to different markets. For the past few years, I have been developing a low-cost, intuitive technology called the SunSaluter that rotates solar panels to optimize their energy collection without using any electricity. This technology has now turned into my company, Roseicollis Technologies Inc., and I am working on a strategy to implement it in as many areas as possible. The SunSaluter’s first pilot project was deployed as a community charging station in a small village called Mpala in central Kenya.
I have been exploring solar for more than half my life now. When I was ten years old, my first project “Make Way for Solar Cars!” at the 2002 Calgary Youth Science Fair evaluated how the brightness of a lightbulb affected a miniature solar car’s performance. Although I moped about the disappointing bronze medal I received, the experience inspired me to continue pursuing my passion for science and engineering projects. I went on to compete at CYSF for all eight years and received gold medals at the last six, earning trips to the Canada Wide Science Fair and the Intel International Science and Engineering Fair. It was through these opportunities that my childhood interest transformed into something I wanted to do for the rest of my life.
Through the magic of the Internet, I sought unconventional opportunities not available to most other students my age – not because I was smart, but because I was hungry to do more and be different. I emailed university professors, I applied for scholarships to different summer institutes (like Space Camp!) and I found all the knowledge I needed through Google. Most importantly, I learned through these experiences of self-exploration to never give up, never take no for an answer from adults, and look beyond what was obvious in my everyday life because the best opportunities are always hidden.
Here’s the secret: You do not need to be a genius to make your most ambitious goals happen. You just have to try. Every student is capable of transforming his or her childhood interest into a lifelong passion. My story should not be this unique. As someone who is only a few years older than your students, I believe there is an opportunity here for me to share my very relatable story as a fellow peer.
How can I help you continue to inspire your students to think outside of the box? I greatly welcome your feedback and ideas. I blog about some of my thoughts at my website, so please reach out to me there. I look forward to hearing from you. Thank you very much for your time.
In Alberta, students learning science are involved with more than science facts and the scientific method. The rationale for Alberta’s science program is to develop scientifically literate students thorough knowledge of science and its relationship to technologies and society. The science teachers I know are always aiming at informing themselves about societal issues that may come up in class discussions. It is not an easy task to always be aware. Canmore, Alberta based author Stephen Legault in The Darkening Archipelago demonstrates that it is possible to examine societal issues in an entertaining and intriguing manner in an installment of the Cole Blackwater mystery series.
Legault describes himself as a social and political activist, and his environmental consulting company advises on social and ethical practices for business. I met with Stephen over coffee and besides discussing a variety of environmental topics, we talked about his long devotion to writing. He spoke of hearing his characters’ voices in his head, and how when he sits at his keyboard, he can clearly see the story unfold as if it were a movie. I came home from that meeting with The Darkening Archipelago tucked under my arm, anxious to sit down and start reading. Sure enough, as I began my way through the book, I could picture the characters and the scenes in my head. It was a mystery alright, and it had me guessing right up until almost the final page.
Stephen writes the mystery, but he develops the story within the framework of having the reader examine societal issues that have arisen from increasing development of aquaculture off the coast of British Columbia. Although he does not totally hide which viewpoint he supports, he infuses a variety of characters into the book who support or question all sides of the issues. Thus, we learn of the scientific and environmental perspectives, as well as the ethical, political, economic, technological and recreational viewpoints. A number of characters also display strong egocentric opinions.
Walk down any high school hallway, and you may hear language that would make your hair stand on end. Reading Stephen Legault’s The Darkening Archipelago you will come across very little strong language; and when it is used in context, it is still less conspicuous than some of the language on TV or in movies. That said, just as when I reviewed Michael Crichton’s book, Next, I cannot recommend teachers assign this book or school libraries purchase it unless they have read it and make a choice to defend the language if challenged. On the other hand, I highly recommend that science teachers treat themselves to a great escape all the while developing talking points for the next lesson plans on ecology, populations, genetics, or parasites and their hosts.
As the cold arctic wind whips and ruffles against the microphone, the scientist strains to explain hunting for fossils in Canada’s far north. I look up at the TV as Neil Shubin further explains: “It's cold; it's about freezing every day over the summer. Winds are high; they can get up to 50 miles per hour. There are polar bears there. We have to prepare ourselves by carrying guns. It's a beautiful place. You've got to love it. It's my summer home.” Wednesday nights in my house are science nights on TV. Between shows like Nature, Nova and NovaNow, my TV never leaves the PBS network on a Wednesday night. Yet on this occasion I thought, have I already seen this show? The scientist seemed so familiar. That is when I realized that the author of the book I had just started to read is the same scientist appearing on Nova, Neil Shubin .
Neil Shubin’s Your Inner Fish had been given to me by my daughter, who thought that I would really like it. She was indeed correct. Shubin explains that the book is developed from his University course on anatomy. He puts together a package that goes far beyond the comparative anatomy course I had as an undergrad. I have developed a mental picture that Shubin has the ideal science job. It is apparent that he combines the skill set of a geoscientist to the science of paleontology, taking field trips near and far in search of elusive fossils. But then in his laboratory, he applies the biochemical skills of a CSI researcher in pursuit of the genomics of embryology and body development. He then weaves the information together to explain how we can find evidence of evolution in every feature in our bodies. Without explicitly arguing against irreducible complexity, in one chapter he helps us to understand that the complexity of the modern eye can be traced back to light gathering molecules found in simple bacteria. The history of the eye is shown as it improves from a simple light gathering organ to the complexity of an eye sending an image to the brain. The eye is not at all irreducibly complex.
One of Neil Shubin’s claims to fame is his work on the first organisms to come out of the water. His Canadian field studies led to the discovery of the organism called Tiktaalik which he describes with deserved pride. He interweaves Tiktaalik throughout the book as he describes such features as teeth, nose, ears, eyes and body plans. The Vintage Books edition I read has a new afterword added to the book since its first publication in 2008. In the afterword, Shubin emphasises that Tiktaalik is not as some would suggest, a missing link. No indeed, it is a found link.
I highly recommend this book to anyone interested to see how big idea science comes from combining information gained through many separate reductionist studies to produce our modern view of life on earth.
It is Science Fair season in Alberta, and once again, Genome Alberta is helping Regional Science Fairs in this province through a sponsorship and awards program. We are pleased to recognize the achievements of our young student scientists doing outstanding projects in the life sciences, and especially in genetics and genomics.
It is extremely rewarding to interact with these young scientists as they showcase their scientific work. Here are our recommendations on how you can participate:
Parents of school-aged children: get your children involved by taking them to see a regional fair or by encouraging them to participate in the process.
Interested adults: take the time to volunteer as a judge or on a committee which puts on the fair.
Teachers: inspire your students to pursue science fair projects. These projects build skills and confidence in cross-curricular areas including language arts, oral presenting, artwork, mathematics and science.
I have listed below the locations and dates of the fairs in your region of the province. Please take this opportunity to become involved or just take in the excitement of your local Science Fair.
It was impressive to see so many students file in quickly from their buses to their seats in the Epcor Centre. I learned that Cenovus Energy is a major sponsor, helping reduce the cost to the schools bringing students to the event. The Epcor Centre provides links to educational resources on their website. Before the program started, students were kept engaged with the Geo Bee Challenge, an on-screen quiz with some fun geography questions. I could tell that many students were participating as I heard little cheers in various sections of the crowd as the answers came up confirming their choices.
It was hard finding a place to park in Inglewood, but I was confident there would be plenty of spaces to sit. Was I wrong! I should have known better. The Science Café has been going on for six years now and has grown in popularity with each event. Add the star power of a Jay Ingram and you have the Ironwood so full that people are even sitting on chairs ringing the sides of stage.
Dr. Sim asked us to think back to high school and compare the science nerds with the drama geeks. She pointed out that while there were exceptions, the two groups did not often overlap. Fast forward to adult careers, and you have the white-coated scientist, perhaps using a lot of jargon, having their story greatly shortened and retold with a potentially misinterpreted message which does not relay the passion for which the original science was done.
When it was Jay Ingram’s time to talk, he pointed out that shows like Discovery.Ca are for profit and they must understand and cater to the viewers to keep getting the numbers required by the sponsors. Furthermore, with the show’s success and the need to continue growing audiences, there is less appetite for risk taking. This actually shrinks the types of stories that will be told.
Ingram and Sim next conducted hilarious mock interviews illustrating three types of dysfunctional communication between a scientist and a media person. This demonstration had the audience in stitches of laughter, as we all recognized that we have witnessed each of these interview styles over the years.
There is a buzz coming from the audience, comprised of a significant percentage of excited young children. Then, near silence as the lights dim and Marion Hutchins steps into the spotlight and asks if we like dinosaurs. The children roar their approval. After explaining the Science in the Cinema program, she introduces today’s speaker, Dr. Derrick Rancourt, PhD, professor in the department of medical genetics at University of Calgary's Faculty of Medicine.
Dr. Rancourt explains that he studies the genetic manipulation of mice. He also tells us that he is a big fan of author Michael Crichton. Jurassic Park, published in 1990, was written by Crichton to help the public understand the societal issues that arise from cloning. Crichton also wrote the screenplay of the movie, which was released in 1993. Mice had already been cloned by 1987; Dolly the sheep was not cloned until 1996, three years after the movie’s premiere.
To get us ready to watch the movie, Dr. Rancourt explains that cloning in the 1990s required an intact nucleus from the organism to be placed into a de-nucleated cell. He notes that finding an intact dinosaur nucleus is not very probable. Dr. Rancourt asks us to think about the feasibility of two things during the course of the movie for discussion afterwards:
1.The process of putting the dinosaur DNA into the cell; and
2.The procedures used for biocontainment.*
Don’t worry about the Mayan calendar. The important day this year is April 20 which has been declared DNA Day in Alberta. In a previous blog, I reminded you to keep a spot on your calendar; now, as I learn additional details, I am keeping you posted.
I had a lot of fun last year on DNA Day, and I learned a lot when I was able to simultaneously participate in four moderated chatrooms dedicated to discussion with some of Canada’s foremost scientists in the field of genomics. Again this year, this is an excellent opportunity for teachers to showcase social media opportunities to their students through communication with scientists who are the innovative leaders in both research and communication technologies.
Recently, Alana DeLong (MLA for Calgary-Bow) released a YouTube video of her speech in the Alberta Legislature regarding last year’s DNA Day. It is nice to see such support for our endeavor.
Sarthak Sinha was a silver medalist at the Canada-Wide Science Fair 2011. He was also the winner of both the Bachelor of Health Science Award and the Calgary Medical Society Award at the Calgary Youth Science Fair this past year. As he prepares for the 2012 Science Fair season, he took the time out to send me a small video sharing his excitement for his latest project which examines Retinoic Acid signalling on skin derived precursors.
Sarthak is a Grade 10 International Baccalaureate student at Henry Wise Wood High School. He joined the Biernaskie Lab at the University of Calgary to gain a hands-on understanding of how human bodies function and how to better administer clinical treatments. He has done research in the field of stem cells since ninth grade.
What are the chances that, immediately after I finish reading a book, I end up noticing two announcements about issues talked about in the final chapters of the book? Well, if it is a book about mathematics, the chances are pretty good.
Yesterday, two apparently unrelated announcements were made. In the first, the genome of the so-called arsenic bacterium was sequenced. There has been a year-long debate over whether extra-terrestrial life implications were found in this bacterium, which purportedly uses arsenic in place of phosphorus in its DNA backbone. The other announcement proclaimed that a Super-Earth is only 600 light years away. This is exciting news indeed, though with this Goldilocks exoplanet being in such a far-off solar system, it will take the equivalent of the Starship Enterprise to visit it. I’m not packing my bags for this trip yet.
In The Mathematics of Life, author Ian Stewart proclaims that there have been five major revolutions in Biology, with a sixth on the way:
•Invention of the microscope
•Systematic classification of living things
•Development of the theory of evolution
•Discovery of the gene
•Discovery of the structure of DNA
•Broader incorporation of biomathematics
I picked the book up hoping that I might gain a better understanding of the relatively new science of bioinformatics. Bioinformatics only recently entered the scientific lexicon as the mathematical analogy to biochemistry and biophysics. I personally have become more aware of bioinformatics as it makes an important contribution to interpreting genomic data. Stewart points out that bioinformatics is the science of big computing used to sort through billions of data points related to genomics. His book is primarily about the application of mathematics to biological problems. I learned about the mathematics of virus shapes, and nodes in nerves, movement, and hallucinations. Stewart tells about calculations needed to determine if DNA forms knots. He looks at patterns of spots and stripes. I enjoyed the way he formed a mathematical relationship between predicting the outcome of a game of rock/paper/scissors and evolution. He devotes entire chapters to each of the math of networks and populations. I was slightly disappointed in his treatment of chaos. Although he defines the concept, I was left bewildered when he says it is possible to tell the difference between random and chaos results. I am not sure he told us how.
In the end, I was fascinated with the mathematics of life on other planets. Stewart talks about both exoplanets and DNA with arsenic in place of phosphorus in the backbone. Stewart shows how we might not ever be able to prove life exists on other planets, but he suggests that we can certainly use mathematical modelling to explore the possibility that there is anybody out there.
The Mathematics of Life by Ian Stewart is a book I recommend to anyone with an interest in the interplay of mathematics and biological sciences. Teachers should mention this as a great read to the type of students who are very strong in mathematics and just taking biology because it is a necessary credit course. They will gain an appreciation of the application of pure mathematics to everything from molecules to exoplanets.
In 2007, Canadians adopted Movember as a major awareness and fund raising activity during the month of November in support of prostate cancer. I am constantly reminded of the competitive element through the jovial jousting of the various male newscasters and professional athletes I see on television. I am told that I can donate or that I can watch celebrities shave their moustaches on November 30. But what else am I aware of?
Besides funding prostate cancer research, Movember Canada includes building awareness of additional men`s health issues. They strongly advise men to maintain a healthy diet and appropriate weight. They promote smart lifestyle choices such as staying physically active, not smoking, consuming alcohol in moderation, and getting regular medical examinations.
In a paper released today* (September 1, 2011) researchers M.J. Dougherty, C. Pleasants, L. Solow, A. Wong, and H. Zhang pose the question, “Are States Keeping Pace with Modern Genetics?” This study comes from the American Society of Human Genetics (ASHG) which is America’s leading genetics scientific society.
Dougherty et al. are well aware that science education in the United States is driven by testing and accountability. They make no judgement with regard to the value of this except to note that since learning outcomes (standards) drive testing, these standards ultimately influence curriculum and instruction. Dougherty’s group cites previous research which documented misconceptions that frequently appear in essays submitted to the National DNA Day Essay Contest. This suggests the need to assess the quality of the high school genetics education standards. Furthermore, they assert that there have been few comprehensive evaluations of specific science content in state standards, and none by a professional scientific society. For the current research, ASHG used the following methodology:
I’ve been aware of the Royal Botanical Gardens, Kew for a long time. My interest in visiting Kew Gardens spiked when I read Age of Wonder and learned more of the long history and importance of this place. Now a UNESCO World Heritage Site, Kew maintains one of the world’s most complete seed banks, and its Jodrell Laboratory has been doing research in the field of plant physiology since 1877.
As a visitor to the gardens, I was in awe at just about every step. I would have difficulty coming up with just one favourite part, so let me tell you about three:
“Let nothing which can be treated by diet be treated by other means.” Maimonides.
Yesterday, this quote was almost trending on Twitter. It is difficult to know who first tweeted it as many people seemed to be claiming it as their own. I wouldn’t have paid much attention except that I just recently visited Cordoba, Spain. While there, I saw a bronze statue celebrating the early scientist and philosopher Maimonides.
I didn’t know about Maimonides prior to this visit. My daughter, who took some history of science courses at the University of Calgary, was very excited that we were visiting the statues of both Maimonides and Averroes. They are described in the Rick Steves Guidebook as Cordoba’s “deepest thinking homeboys”. I probably would not have remembered either except for the Maimonides quote making the rounds on Twitter within a day of my return home.
My first thought when I saw the quote was ‘is this Maimonides the original nutrigenomist’? Now I know that we have to be exceedingly careful when reading stuff about nutrigenomics on the web. I learned the hard way that it is a science that has been hijacked by a variety of pseudoscientists. I once retweeted a nutrigenomics link that many of my colleagues immediately recognized as junk science. Let me tell you, they sure let me know about it! Very embarrassing.
Well, getting back to Maimonides, I wanted to find the context of this quote. Since I don’t read ancient Persian, I found a translation of his work.
This past week, there has been a great deal of excitement over NASA’s announcement of finding a life-form that does not follow the usual pattern of life on earth. Almost immediately there was additional blogosphere buzz viewing this research with a critical eye indicating that perhaps much more careful work needs to be done. To me, this discussion is clearly evidence of the process of science. How did we get to the stage where a science discovery is peer reviewed, published and critiqued then verified, modified or rejected?
To answer the question, I’m going to suggest reading the book The Age of Wonder by Richard Holmes. Although the book was published in 2009, I just recently received the paperback version. The book has more than 500 pages with a small font. However, once I got going on it, I could hardly put it down. This book begins with a comprehensive account of the adventures of Joseph Banks who, as a young man, accompanied Captain James Cook on his first exploratory voyage to the south Pacific. The narrative continues through the years until we find a young Charles Darwin meeting and being influenced by John Herschel in South Africa.
This is the time of year that school teachers in Alberta are back in schools starting to plan for the arrival of students early next week. I know the teachers will be attending important meetings. I hope there will also be time for the important planning of the year ahead. News over the summer indicates that some Calgary area schools are gearing up to make a lot more use of computers in their classrooms. University of Calgary research just announced that tech-savvy students have an advantage, but only if their teachers are tech-savvy too. The Genome Alberta website is a major landing site for tech-savvy science teachers. Let me tell you why it should be for you as well.
It's an age-old joke, or perhaps an old-age joke, that when asked the question, “Who wants to live to be 100?”, the answer is “anyone who is 99!”
In my family we celebrated two 90th birthdays over the past two months. Friends have asked me if I am lucky enough to have the good genes. I could only smile and hope. This week however, research from the New England Centenarian Study (NECS) published in Science, revealed that there are in fact 19 genetic clusters of extreme longevity (EL). Perhaps soon I will be able to answer the question.
April 25 is DNA Day because on this date in 1953, Watson and Crick published their paper Molecular Structure of Nucleic Acids. The 57 years that followed have led to remarkable advances in our knowledge of genetics and genomics.
Scientific method taught in schools and judged at science fairs is a series of steps that guides the student to design an experiment including listing the problem, hypothesis, variables, and procedure. After the experiment is designed, there is the collection and interpretation of data. I know that some people champion the need to emphasize and reinforce the scientific method among science fair participants. At a recent science fair, I overheard some judges debating the value of “study” projects compared to “experimental” projects. One went as far as suggesting that by eliminating all but “experimental” the quality of projects would improve (additional descriptions)
While I generally support the concept, I had to ask myself, would Watson and Crick have got past the first round judges with their model?
Max is a 3-year old bunny, Ruby is his 7-year old sister, and they star in their own cartoon show. Little children watch their show and learn life’s lessons. And the children ask questions. One question sent to me recently was “Can white rabbits produce black rabbits and visa versa? Or do white rabbits make white rabbits only and black rabbits make black rabbits?” It was signed Confused Family.
My immediate response was that I did not think bunny colour genetics was Mendelian and I told them I would get back to them after I learned more. Well, this took me a little longer than I thought. Rabbit genetics are not simple.
Maybe Prince Charles should look again at Malthus. Malthus looked a population (P). Was Malthus wrong? In the early 1800’s, Malthus worried that the human population would soon outstrip the ability of humans to feed themselves. By the mid 1940’s agricultural methods were not keeping up with the human population and widespread famine seemed possible. Then, improved agricultural methods increased food production. Each time as the human population increases, scientific research translated into modern agricultural methods move the line. Which line am I talking about?