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!

1 Dec 2017

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

by L. E. Carmichael

Welcome to Part 2 of my series on gene therapy! If you haven't already, I recommend that you read Part 1, Introduction to Gene Therapy: It Sounds Simple, But It's Sure Not Easy, before continuing with this post.

Ready? Here we go.

Viruses: FedEx For Genes

Gene therapy involves repairing or replacing a faulty gene that has led to disease. In order to do that, one major hurdle must be overcome: getting new DNA into the patient's cells. Cells, however, are designed to keep things out. That's why they have wrappers, called cell membranes. Scientists needed vectors: gene delivery systems capable of crossing the membrane.

In the early days of gene therapy research (by which I mean the 80s), the obvious way to cross the membrane was to use a virus. Viruses are highly efficient invaders - they have to be, because they are not capable of copying their own DNA. In other words, the only way a virus can reproduce and spread is to invade a host cell, hijack its equipment, and force the cell to package new viruses that can carry on the cycle of infection.

But what if scientists could replace some of the virus's DNA with a therapy gene? The virus would invade a patient's cells as per usual, but instead of causing infection, deliver some healthy human DNA. Sort of like molecular FedEx. Some viruses even contain DNA sequences that match sequences found in human DNA. These complementary sequences would prompt the host cell to incorporate the therapy gene into its own genome. Not only would the patient be cured, but the cure would be permanent.

What's that line about how it seemed like a good idea at the time?

The Problem With Viruses

For starters, they are viruses. The human immune system is designed to find and destroy viruses, before they invade the body's cells. This happens all the time, without our even realizing it. But sometimes, the immune system gets a little carried away.

That's exactly what happened to Jesse Gelsinger in 1999. The 18-year-old was part of a clinical trial of a gene therapy for a genetic disease known as OTC. When he received the treatment, his immune system had a massive over-reaction to the viral vector and began attacking his own cells. He died just a few days later.

The Other Problem With Viruses

Remember I said that some viruses can insert their own DNA - or therapy DNA - into the human genome, making a therapy permanent? Early gene therapy research occurred before we sequenced the entire human genome. Scientists didn't realize that complementary DNA sequences could occur in more than one location in a person's DNA... or that some of those locations were inside other genes. No good providing DNA to cure one genetic disease if your cure is going to knock out another gene. Especially if that gene helps to controls cell division... because uncontrolled cell division leads to cancer.

That's what happened to a number of young patients during an early clinical trial for the immune system deficiency SCID. And since those kids had compromised immune systems, they had no natural defences against the cancer their cure had created.

A Light at the End of the Tunnel

After these tragedies, scientists spent a lot of time searching for viral vectors that would NOT cause such horrific side effects. One type belongs to a family of viruses known as AAV. A gene therapy for Leber congenital amaurosis is built around AAV. It replaces a faulty gene in retina cells that causes children to go blind. And after decades of research, it looks as though this therapy will soon be available to the public. Developed by Spark Therapeutics, the treatment just received a unanimous endorsement from an FDA review panel, meaning approval for the therapy could be just around the corner - a literal light at the end of the tunnel for these patients.

So What is CRISPR, and Why Is Everyone So Excited About It?

A major downside of AAV viruses is that they do not incorporate their genetic package into the patient's existing genome. Which means they don't cause cancer, but also that the therapy gene can't be reliably passed on to daughter cells. That's OK for retinal cells, which don't divide. It's a lot less useful for treating diseases in other parts of the body.

CRISPR, on the other hand, works in all types of cells. It allows scientists to edit a patient's existing genes - correcting the typos that cause disease - and the changes are permanent. Here's how it works and why it's such a big deal.

Here's another really great video explaining CRISPR and its applications that unfortunately I was not able to embed.

And yes. You still have to get the components for CRISPR into the cell in the first place. One group of scientists has just found a way to do this without using viruses. They used gold particles instead.

As you can see, CRISPR could lead to incredible breakthroughs, and not just in gene therapy. But there are concerns as well. Stay tuned for Part 3, where I will explore what's perhaps the biggest one.