19 Jan 2018

Getting the Science Right

By Joan Marie Galat

How far will an author go to get her facts straight? In my case, it was a nearly-4000-kilometre round trip from my home in Alberta to Laramie, Wyoming. The program, called Launch Pad Astronomy, is a week-long workshop designed specifically for science-writing authors. It was established to make sure writers present science accurately when creating stories or writing nonfiction.

Whether you are reading a book or watching a movie, television show, or other media, it is not hard to get caught up in the story and assume it reflects genuine scientific principles. Launch Pad helps writers avoid presenting or creating misconceptions. Here are a few examples of how science can crop up in creative writing, followed by an explanation of why the scientific reference just won’t work. You will see how easy it is for even a well-intentioned writer to misstep.
  • It was 6 am, too early for the courier to arrive with the first copies of Joan’s new middle-grade (and up) book: Dark Matters-Nature’s Reaction to Light Pollution. She took one last glance at the rising Full Moon and turned inside.
    SCIENCE FAIL: The Full Moon only rises at sunset.

  • It had been dark for several hours. The courier was lost. His GPS battery was dead and his charger not working since it fell into a milkshake. Pulling over, he looked for the brightest star in the sky, certain the North Star would guide him home.
    SCIENCE FAIL: The North Star is not the brightest star in the sky.

  • The courier remembered he needed to call his mother for her birthday. His cell phone was dead and the charger — well, you don’t want to know. Not wanting to admit his shortcomings, he decided upon an excuse. He would say he burned his hand when picking up a meteorite that had landed when he was searching for the North Star.
    Photo credit: NASA/SETI/P. Jenniskens

    SCIENCE FAIL: It’s not common to find meteorites within seconds of them landing on the ground. Little is known about the immediate temperature of new meteorites, however scientists generally believe small rocks from space will be cool or only slightly warm upon striking the Earth.
Other common misconceptions abound about why seasons occur, the strength of gravity on the Moon, the direction a comet's tail will face, and other topics. The Smithsonian’s “Science Done Wrong” offers additional compelling examples.

Next time you read a book or watch a movie, consider whether the science is accurate and conduct a bit of research of your own to find out what is fact and what is fiction. If you’re a fellow author, consider applying to attend Launch Pad Astronomy. It is an experience you won’t want to miss.

Joan Marie Galat is the author of more than a dozen books, including the Dot to Dot in the Sky astronomy and mythology series. Science talks have taken her from the Arctic Circle to South Korea. Check out her book trailers and speaker demo.

13 Jan 2018

Family Tree for All Living Things

By Paula Johanson

When I want to relax this winter, I've been going to a science website called OneZoom. If you like biology, you might like it too! They've made an interactive image called the Open Tree of Life, that shows on your computer screen a family tree for all living things on Earth. You can zoom in to look at a branch of the family tree. The shape of the family tree is curved like a spiral, and the branches of the tree are curved too. As you zoom in, the shape of a branch is like a smaller version of the entire tree. This kind of design is called a fractal.

I zoomed in today and a circle on the tree grew large enough for me to read: "650 million years ago, during the Cryogenian Period, lived the most recent common ancestor to today's Animals."

OneZoom is a registered charity in the UK. They want to provide easy access to scientific knowledge about biodiversity and evolution. “This NSF-funded project will produce the first online, comprehensive first-draft tree of all named species, accessible to both scientists and the public,” reads their profile on Twitter for Open Tree of Life.

Are you looking for information, and maybe images, to use in your own project such as a school assignment? OneZoom says on their page of Frequently Asked Questions:
Please feel free to use our fractal visualizations as you wish for non-commercial purposes, as long as you credit us. The images themselves have been gathered from a large number of sources (Wikipedia, Flickr, etc.), mostly via the Encyclopedia of Life, and each will have their own licence (either public domain, or cc-by, or cc-by-sa). You can look this up by zooming into the small copyright symbol at the bottom left of every image on the tree: the symbol also serves as a link that will take you to the image page on the Encyclopedia of Life, from where you can find the original source. For more details please see our terms of use. Note that if you wish to use a screenshot without having to provide a list of sources, then we recommend that you use our public domain only visualization (Menu→Settings→Image Sources→Public Domain). We can also produce higher resolution SVG images on request.

Check out OneZoom on their website. Their home page explains a little about this website. To see the family tree, you can either click on their link for the tree of life explorer, or type this link http://www.onezoom.org/life into your browser. You can read tweets posted by OneZoom on Twitter at https://twitter.com/OneZoomTree

5 Jan 2018

Crayola’s New Blue and Other Hidden Opportunities

By Larry Verstraete

Months ago, Crayola, the crayon giant announced the removal of Dandelion from its palette of yellows and oranges. In March, the company issued a news release saying that Dandelion’s replacement would be in the blue family. Not long after, it added another tidbit of information. The replacement would be a newly invented, never seen before, hue of blue with a backstory as unique as its name, “YInMn Blue”.

In 2009, Mas Subramanian, an Oregon State University (OSU) chemist, discovered the colour with his grad student, Andrew Smith. The two were heating batches of manganese to 1200 °C (~2000 °F), hoping to produce a high-efficiency electronic material. After one attempt, Smith pulled a striking, brilliant-blue compound out of the furnace. Subramanian knew right off it was a research breakthrough. Unwittingly, they had created a shade of blue unlike any other from a combination of yttrium, indium, manganese, and oxygen.

Recognizing opportunity, Subramanian and his team shifted gears. They expanded their research. To date, they have created a range of new pigments, everything from bright oranges to vibrant hues of purple, turquoise, and green.

Discoveries of this sort are not uncommon in science. X-rays, penicillin, and Kevlar are a few items that owe their existence to usual circumstances where scientists were looking for one thing and happily found something else. The nicotine patch is another.

In 1986, as Frank Etscorn, a behavioural psychologist, walked across the floor of his basement laboratory in the New Mexico Institute of Mining and Technology carrying an open vial, he stumbled. He had been studying sugar dependency in rats and the vial contained a nausea-inducing substance found in tobacco that he thought might reduce the rats’ cravings for sweets. When he stumbled, the brown liquid sloshed on to his arm. “I wiped it off and didn’t pay attention,” he told a reporter for People Magazine later. “But after about 15 minutes I felt nauseated.”

The experience sidetracked Etscorn, steering him into a new area of research. “Almost immediately, I realized this could be a way for people to stop smoking.”

It took years to produce a workable nicotine patch, but the accident was the start of the process. Just as in Subramanian’s case, Etscorn saw something others might have missed.

What does it take to recognize hidden opportunities when they arise? Brain research provides some clues. The corpus callosum, a thick band of more than 200 million nerve fibres, connects the left and right hemisphere. Think of it as a busy freeway where impulses fire back and forth, facilitating communication between the two sides of the brain.

In brain studies, neuroscientists discovered that the corpus callosum of creative individuals was thicker than normal. In such brains, there appears to be more communication between the two hemispheres and greater potential of connecting seeming disconnected ideas.

Not every brain hardwired with a thick callosum connects the dots and capitalizes on unexpected circumstances, however. And it doesn’t mean that a brain with a thin callosum cannot be a member of the discovery club either. There’s more at play in taking advantage of serendipitous events than simple brain mechanics.

Over a century ago, Louis Pasteur made a major discovery after his lab assistants neglected a batch of petri dishes. Wondering how this would affect his results, Pasteur opted to carry on the experiment.  His decision led to a breakthrough in the development of vaccines.

Luck played a role in the discovery. The lab assistants messed up, providing Pasteur with opportunity. But Pasteur recognized that more than luck was involved, too. Knowledge and experience combined with curiosity seem to be another part of the formula. Or, to quote Pasteur’s famous line, ‘Chance favours the prepared mind’.

There you go, crayon lovers. Colour on with Crayola’s new blue knowing that you are holding a bit of chance between your fingers.

Images from Pixabay

29 Dec 2017

Naming Weather Highs and Lows

By Adrienne Montgomerie

When the weather forecast calls for a Colorado low or a Texas low, what does that mean?

satellite view of North American continentThe name is actually pretty easy to figure out: The low or high refers to the air pressure. The place name tells you where it is coming from. Weather generally moves across the North American continent from west to east, and more often from south to north.

Low pressure tends to bring clouds and warmer temperatures.
High pressure is associated with clear skies and cold.

So a Colorado low is an area of low pressure that formed in the US state of Colorado. It usually forms in winter and brings a lot more precipitation than usual for several days. From Colorado in the centre-west of the USA, that weather can travel up to Winnipeg and right over to the Atlantic ocean. Because it's winter, that precipitation is usually snow, which we can have a lot of fun with!

Another system that usually brings a lot of snowfall is a Texas low. As it moves across the continent, it picks up a lot of moisture from the Gulf of Mexico. When it reaches the colder temperatures of the Great Lakes, it drops that moisture as heaps and heaps of snow. It is said that most snowstorms in Ontario come from a Texas low.

An Alberta clipper is a little harder to figure out. Like the names for highs and lows, the place name tells you where it is coming from; but what does "clipper" mean? It's a system of low pressure too. Unlike the general way that weather systems move, the Alberta clipper heads southeast, toward the Great Lakes into the US. It carries precipitation and a quick drop in temperature plus strong wind. The winds are why this weather system is called a clipper: clippers were the fastest ships in the 19th century.

Sometimes there is more than one of these weather systems happening at once. Then, they can collide or clash, resulting in an even bigger storm.

Keep your ears open. What other storm names do you hear? Can you use what you know about lows and highs now to predict what kind of weather they will bring your way? If you live on the west coast, where do your weather systems come from?

22 Dec 2017

Star Wars: The Last Jedi, and 3D

The Last Jedi is a fun movie, packed with science fiction, lots of it more fiction than science. (I kept wondering how people were able to open hatches into deep space with no oxygen tanks and no protective gear, and still survive). Suspend belief and enjoy the story.

And also enjoy the 3D picture. It's very cool. It's also only the tip of the iceberg for 3D perception.

How do 3D movies work? 

One way of perceiving depth is using our stereoscopic vision. Our eyes are about five centimeters apart, so the view from each is slightly different. Our brains are smart enough to integrate those two views and figure out, using triangulation, how far away objects are.

Our brilliant brains automatically do the math to figure out that the orange is closer than the apple

So to get stereoscopic vision in a movie, the movie has to be shot using two cameras, side by side. Because our eyes are about 6 cm (2.5 inches) apart, that's the optimal distance that the two camera lenses should be apart, to make the movie look realistic for humans. If the lenses are too far apart, the world will look very small; if the lenses are too close, objects will look gigantic. Some more subtlety about the cameras: they won't normally be parallel to each other, but will be turned slightly towards each other. The "plane of convergence" is where the two cameras are focused to meet. Objects closer to that plane will "pop" off the screen.
Now the trick is to get the left hand camera image to the viewer's left eye and the right hand image to the viewer's right eye. Both movies are projected onto the screen, one with a vertical and one with a horizontal polarizing filter. You can think of these polarizing filters as only allowing horizontally or vertically vibrating light to pass through. The movie goer wears glasses with lenses which are also polarized - one horizontal and one vertical. So each lens only admits light from one of the two projectors. And Bingo! The left eye only sees the images from the left hand camera and the right eye only the images from the right hand camera.

Earlier versions of the technology used red and green filters to do the job, but that messed up the colours a little, so the polarizing filters work much better.

Now what if you want to watch The Last Jedi with your pet squirrel? Will he be able to enjoy the movie if you make him a very small pair of polarized glasses. Sadly, it turns out not.
Eastern Grey Squirrel. Photo by BirdPhotos.com via Wikimedia Commons.
Not all animals have the gift of stereoscopic vision. If your eyes don't both face front, you have to make other arrangements for depth perception. So 3D movies work for us apes, and probably for wookiees and porgs, but not for squirrels, chameleons or most birds. One strategy that birds and squirrels use is to bob their heads up and down. By moving your eye, objects close to your eye seem to move and objects far away seem to be static. (Think of looking sideways out of a car or train window). So based on how much objects seem to move, a bobbing bird brain will perceive depth.

There are other cues for human distance perception, beyond stereoscopic vision. Moving objects coming toward you appear bigger. This may not seem like a hugely accurate way to measure distance, but it can be, with some practice. Mansoor Ali Khan (also known as the Nawab of Pataudi) was a brilliant cricket batsman. At the age of 20, when he was already a star player, he had a car accident which essentially destroyed the vision in his right eye. Six months later he had learned to play with only one eye and represented India in international matches against England. To understand the depth perception problem faced by a cricketer, you should know that the size of ball, the speed and distance to the bat is almost exactly the same as for baseball. That means less than half a second from ball release to bat. You need awfully good depth perception to make contact! Khan could only have been using the apparent size of the ball to figure out the distance.

Not useful for baseball or cricket, but another depth perception clue is "distance haze". Because light from distant objects has to travel through a lot of atmosphere, it gets scattered and less light reaches the eye. So distant objects appear less sharp than close objects. Photographers sometimes sharpen their pictures by increasing the contrast of distant objects.

The future of 3D movies

Scientists are working on systems to show 3D movies without glasses. The technique is to project two pictures in slices, so that the viewer can position themselves to see an appropriate picture in each eye. This is a huge challenge for practical viewing, when you have hundreds of viewers, each in a different position in the theatre. But teams are working with systems of lenses and mirrors in front of the screen, and have already had some limited success with low resolution pictures and a small number of viewers.

Will they be successful? Perhaps. If the tiny Resistance led by Leia and Rey can survive against the powerful First Order, anything's possible.

15 Dec 2017

Read It and Weep: Fungal Guttation

by Jan Thornhill
Guttation on Fomitopsis pinicola bracket fungus
Young Red-Belted Polypore (Fomitopsis pinicola) with guttation drops
Some fungi are prone to exhibiting a curious phenomenon—they exude beads of moisture, called guttation. In several polypores, such as Fomitopsis pinicola, the liquid produced can look so much like tears that you'd swear the fungus was weeping. Or maybe sweating. Other species produce pigmented drops that can look like milk, or tar, or even blood.

Guttation is more well-known in some vascular plants. During the night, when the plant's transpiration system is shut down, pressure from excess moisture in the roots can force beads of sap out of special structures on leaf edges. 

strawberry leaf guttation noah erhardt
Guttation droplets on strawberry leaves (Noah Erhardt/Wikipedia)
In fungi, the guttation mechanism is not so well understood. In many species, however, it's so often observed, particularly during times of rapid growth when temperature and humidity are favourable, that these beads of liquid can be a reliable macroscopic characteristic. Hydnellum peckii, for instance, so frequently "bleeds" pigmented drops in its early stages of growth that it's been given gruesome nicknames, including "Bleeding Tooth Fungus" and "Devil's Tooth." Coincidentally, a 1965 study found a compound in the fruiting body of  H. peckii that has anticoagulant properties similar to those of heparin, too much of which can make one bleed to death internally.   

bleeding mushroom guttation lisa neighbour
Bleeding Tooth Fungus (Hydnellum peckiiproduces red-pigmented 
guttation droplets during periods of rapid growth(Lisa Neighbour)
A couple of years ago, I came across a crop of Inonotus glomeratus on a maple log. I'd found this amazing polypore a few times, once right after it had showered itself, and everything else around it, with millions of sulphur-yellow spores. The one I'd found, though, was very young, and instead of spewing spores, it was weeping globules of "tar" in copious enough amounts that shiny black pools were accumulating on the forest floor. Unlike most guttation drops, which are watery, these exudations were thick and sticky and stained my finger and thumb a deep auburn brown. And kind of glued them together. Oddly, though this unusual guttation has been noted by others, there seems to be no mention of it in the literature. I. glomeratus is so unusual in so many ways, I ended up writing a whole post about it.

Inonotus glomeratus fungus dripping black tar guttation
Fast-growing Inonotus glomeratus produces tarry guttation.
yellow spores of polypore Inonotus glomeratus
This Inonotus glomeratus continued to drip its viscous black exudate
even after it began releasing its yellow spores.
holes made guttation Inonotus glomeratus
The guttation drops on this Inonotus glomeratus were so thick that the fungus grew
around them, producing a pitted appearance after rain washed them away.
Polypores and Hydnoids are not the only fungi to produce guttation. In moist conditions, young Suillus americanus stipes can be heavy with yellow-tinted drops. Guttation is also common enough in the uncommon Rhodotus palmatus that this characteristic is often included in descriptions. 

Suillus americanus liquid drops stem
Chicken Fat Suillus (Suillus americanus) 
guttation of young Rhodotus palmatus
Wrinkled peach (Rhodotus palmatus) 

Guttation can happen in incredibly small ways, too. During the Toronto Bioblitz a few years ago, we found some Lachnum subvirgineum that, despite what seemed like dry conditions, were covered in minute guttation droplets, as were most other Lachnum I've since come across. 

Lachnum subvirgineum with guttation water droplets
The largest of these Lachnum subvirgineum was less than .5 mm. in 
diameter, which makes the guttation droplets impressively small.

Another minute character is so characteristically bejewelled in guttation droplets, it's named for it: Pilobolus crystallinus, which is one of the "Cannon" or "Hat Thrower" fungi found on herbivore dung.

Dung-loving Pilobilus crystallinus, is named for its sparkling
guttation droplets. (See my post about this remarkable,
tiny fungus, also called Hat Thrower, or Cannon Fungus)
Though little is known about guttation in wild fruiting bodies of fungi, it's a common phenomenon of fungal mycelia and hyphae in the lab, and a number of studies have been done to determine what the exudates contain. Penicillin has been found in the guttation droplets produced by Penicillium species in similar concentrations to that found in the culture broth, while gliotoxin, which has immunosuppressive qualities, has been found in guttation droplets of Aspergillus fumigatusDo these fungi use guttation droplets as reservoirs for metabolic byproducts, or do they simply use them for water storage

Or have different species evolved to produce guttation droplets for different purposes? The edible bolete, Suillus bovinus, for instance, has been shown in the lab to reabsorb nutrients from its guttation droplets, while leaving behind less useful byproducts, such as oxalic acid. So perhaps guttation has evolved as an efficient method of expelling waste for some fungi. 

Is that what's going on with Inonotus glomeratus? Is that viscous, black ooze just a collection of rejected metabolic byproducts? If anyone would like to analyze it and has the means, I have some dehydrated exudate that I'd love to send you!  

slime mold Stemonitis flavogenita guttation drops
Even some slime moulds, like this immature Stemonitis 
flavogenita, produce guttation droplets. (Ulrike Kullik) 
pink polypore Fomitopsis rose
Pink-pored Fomitopsis rosea are even prettier when 
decorated with shimmering beads of moisture. I think the 
pattern on rim was made by the "teeth" of a grazing slug.

young Punctularia strigosozonata bleeding
Tree Bacon (Punctularia strigosozonata) "bleeds" rust-tinted droplets.
Early nubbins of an unidentified polypore exude milky drops.
teardrop shaped indentations left by guttation on bracket fungus
This Red-belted Polypore (Fomitopsis pinicola) produced guttation 
droplets for three months one summer. When it finally stopped, 
trompe l'oeil teardrop-shaped indentations were left behind.
Wet weather makes Xylaria hypoxylon produce beads of moisture.
Weeping Pleurotus dryinus
This large Pleurotus dryinus was weeping copiously
despite there having been no rain  for a week.
Many parasitic Hypomyces, such as this H. chrysospermus, are prolific weepers. 
Inonotus dryadeus is a lumpy polypore known for its ample
 production of amber guttation droplets. (Wikipedia)
Jack-o-lantern Mushroom (Omphalotus illudens) guttation
The Jack-o-lantern Mushroom (Omphalotus illudens) not only
glows in the dark, it also produces orange-staining guttation.
Resinous Polypore, (Ischnoderma resinosum) guttation droplets
The Resinous Polypore, (Ischnoderma resinosum), is also named
for the droplets it produces when very young.
Mycena  leianna produced tiny white droplets
The reddish-rimmed gills of this group of Mycena
produced tiny white droplets. 
hairy asexual form of Postia ptychogaster produces guttation
Even the hairy asexual form of Postia ptychogaster produces guttation.

Selected References:

Erast Parmasto, Andrus Voitk, (2010). Why Do Mushrooms Weep? Fungi, Vol. 3:4

Hutwimmer, S., Wang, H., Strasser, H., Burgstaller, W. (2010) Formation of exudate droplets by Metarhizium anisopliae and the presence of destruxins.Mycologia, Vol. 102 no. 1, 1-10

Gerhard Saueracker. On the Exudates of Polypore Fungi. Fungimap Newsletter 48, Jan. 2013

(NB: This is a slightly edited repost from my other blog: Weird & Wonderful Wild Mushrooms

8 Dec 2017

Gene Therapy: Embryonic Engineering and the Future of Human Evolution

by L. E. Carmichael

Welcome to Part 3 of my series on gene therapy and genetic engineering. If you haven't already, I'd suggest reading Parts 1 and 2 before you continue:

Introduction to Gene Therapy: It Sounds Simple, But It's Sure Not Easy

Gene Therapy: Vectors, Viruses, and Why CRISPR Will Change Everything

Today, we're talking about the second major challenge with gene therapy - getting replacement DNA into EVERY affected cell in a patient's body - and why that problem leads to the central ethical debate in this field.

Who Are the Patients?

Gene therapy is designed for patients with genetic diseases. The word "patient" implies a couple of things. First of all, a child or adult that has multiple cells... hence the crux of the gene delivery problem we discussed earlier.

The second critical implication is that patients are autonomous human beings who are capable of understanding the treatment, including its risks and benefits, and are also capable giving their informed consent. Many genetic diseases strike during childhood, and in those cases, parents or guardians are legally permitted to give consent for their children's care.

Carry that thought to its logical extension, and it implies that parents could also have the right to consent to gene therapy on behalf of unborn babies - and specifically, single-celled embryos.

Embryonic Gene Therapy

In September, Chinese scientists announced that they had used CRISPR technology to edit a disease gene in human embryos. If those embryos had been implanted and allowed to develop, they would have been born as disease-free humans. It was an incredible breakthrough... and it opens up a lot of questions.

From a technological standpoint, embryonic gene therapy is absolutely the way to go:
  1. If you're doing gene therapy on a fertilized egg - by definition a single cell - the whole problem of delivering functional genes to every affected cell just goes away. Because "every" is now "one."
  2. Every cell in the eventual human body descends from that fertilized egg. So every cell in the human being that egg becomes carries the therapy gene. The cure is permanent.
  3. That human being's own eggs or sperm will also carry the functional gene. In other words, the cure is not just permanent, but heritable. It will be passed down to the person's own children, meaning one treatment could wipe out the disease from an entire future family tree.
Now We Know We Can... Does That Mean We Should?

The heritability of embryonic gene therapy is the reason that the vast majority of scientists have long considered such procedures unethical - or at the very least, warranting serious discussion. It is one thing to permanently alter the health of an existing human being - we've been doing that for centuries, using medical treatments as diverse as vaccines and surgeries. And indeed, if we have the power to improve someone's life and relieve their suffering, don't we have a moral obligation to at least try?

Altering the genomes of theoretical future humans is another thing entirely. First, because it's much harder to predict the consequences of actions on that scale, and second, because theoretical humans cannot consent to the alteration of their DNA when they do not yet exist. What right do we have to take those choices away? And while it's hard to imagine why someone would want to live with a disease when they didn't have to, our potential to impact the human genome, and therefore the course of human evolution, doesn't stop there.

After all, DNA is DNA. And CRISPR works on ALL the genes, not just the ones that can cause disease.

Embryonic Engineering and "Designer Babies"

Thanks to the Human Genome Project, we have a better understanding of our DNA than ever before. We're finding genes linked to all kinds of interesting traits, like eye colour and height and muscle development and intelligence...

Chinese scientists have genetically engineering dogs with over-developed musculature. Want your kid to be an Olympic power lifter, a soldier, a firefighter? Why bother building the necessary physique with diet and exercise when you could hard-wire their DNA? Ditto if you want your kid to get into Harvard or win a Nobel Prize.There have already been stories about parents undergoing IVF treatments who choose traits like the sex of their unborn child. With genetic engineering, the possibilities are truly becoming limitless.

The Ethics of Gene Therapy and Genomic Engineering

Just because a technology is potentially limitless, doesn't mean it has to be used to its full potential. We have an obligation to decide what uses of gene editing techniques are acceptable and what uses are not, and a further obligation to enforce whatever standards we agree upon.

The ethics of genetic engineering have been debated since the 1970s, when it became possible to manipulate DNA directly for the first time (before that, we had to do it the old fashioned way, using selective breeding). The debates will continue, and in light of these recent Chinese studies, likely intensify. And that's as it should be. Like so many technologies before them, gene therapy and genetic engineering have enormous potential for good, and enormous potential to be abused.

The choice will be up to us.

I hope you've enjoyed learning more about these topics, and I hope you'll continue following news reports about CRISPR and genetic engineering in the news. In the meantime, I'd love to know your thoughts on these issues. Please share and comment!