The Island of the Colour-blind: Medical mysteries and other stories

Book review: The Island of the Colour-blind by Oliver Sacks

I’ve always found Oliver Sacks’ books fascinating. Sacks was a neurologist, but in this book he gives us a glimpse of his childhood interests. In his early years he was fascinated by the natural world. He had a particular interest in cycad trees and islands, and he explores these passions in this book. And so the reader is not only entertained, but also learns a good deal about many aspects of Science without really trying.

The book is a collection of reminiscences from Sacks’ travels in the Pacific islands. But it’s interwoven with scientific anecdotes that bring many topics in Biology, Geology and Anthropology to life. And there’s a medical mystery or two.

The people of the title, who make up a tenth of the population of the island of Pingelap, cannot see colour at all. Their eyes have no cones, and so we learn a bit about how colour vision works, the genetics of it, and in evolutionary terms how this extremely rare condition became common because of a population bottleneck when only 20 islanders survived a catastrophic event.

The Island of the Colour-blind

Other examples are given to illustrate aspects of evolution, including the rapid changes to finches and cichlid fish when challenged by changes in their habitat.

Another fascinating example of evolution AND symbiosis, thrown in for good measure, is the golden jellyfish in Palau. Due to the lack of prey in the lake where their ancestors were trapped, their stingers have all but disappeared. The jellyfish survive on the food made by the photosynthesising algae that live in them.

On the island of Guam, Sacks meets many local wildlife experts and a doctor who is trying to get to the bottom of a mysterious neurological illness. And we learn a lot about cycads, one of the prime suspects.

There’s plenty to entertain and educate in these stories. I think the anecdotes and explanations are a great resource to help flesh out any student’s understanding of the various topics in the book.  If you’re studying Science or just like a good nature story, you will get a lot out of The Island of the Colour-blind.

 

In case you’re interested…

Shortly before his death, Oliver Sacks wrote this reflection on the periodic table.

This sticky end is a clue to cancer’s causes

How do healthy cells turn cancerous? Their  DNA gradually accumulates errors. Most of these errors aren’t important, but occasionally they stop the cell from working properly. They might cause a cell to grow out of control – and this can lead to cancer.

Myelodysplastic syndromes, or MDS, are a range of blood disorders caused by such errors in the genes. Some types of MDS are relatively mild, but about a third go on to become acute myeloid leukaemia (AML). Thanks to research on MDS we understand its causes a lot better than we did ten or fifteen years ago.

My lab recently published a paper describing three cases of poor prognosis MDS and one case of AML with unusual but remarkably similar changes to the DNA. This complicated structure could not have been predicted by the standard methods of analysing cancer DNA or chromosomes. These features showed us the likely steps that led to these diseases.

Each long string of DNA is folded up neatly to make a chromosome. This is a Claymation that shows how Barbara McClintock’s classic breakage-fusion-bridge cycle causes chromosome abnormalities. The video shows one way that chromosomes (packages of DNA) can become disorganised.

The  telomeres (that cap and protect the ends of the chromosomes) are shown falling off, making sticky chromosome ends which join together (see NOTE 2). It’s well accepted that these changes greatly increase the chance of cancerous gene changes. This process has reproduced many, many times in the lab. The problem is that it’s not often been demonstrated in actual cancers. But we did that.

Sometimes only part of the telomere erodes away – enough is lost that it no longer protects the chromosomes from sticking together. But there can be enough telomere DNA left to be a molecular signature of the telomere.

The arrow points to green dots in the middle of a chromosome. This is the left-over telomere signature that tells us that this abnormal chromosome was made by the joining together of sticky chromosome ends that had their telomeres eroded away. The other green dots are at the chromosome ends. The left and right photos show the same cell but in the right one the abnormal chromosome is identified by its red and blue label.

The arrow points to green dots in the middle of a chromosome. This is the left-over telomere signature that tells us that this abnormal chromosome was made by the joining together of sticky chromosome ends that had their telomeres eroded away. The other green dots are at the chromosome ends. The left and right photos show the same cell but in the right one the abnormal chromosome is identified by its red and blue label.

In our four cases we found that there was a small but non-functional piece of telomere DNA left behind where the two chromosomes joined. Because the telomeres didn’t function, the two chromosome ends could stick together. These caused breakage-fusion-bridge events that caused a protective tumour suppressor gene to be lost, and may have also caused cancer-causing genes to multiply.

MDS and AML have similar genetic causes, so if we learn about the causes of one of them it can help us understand the other. This is often the case with cancer research in a broader sense – if we understand the basic mechanisms in one cancer it can help us understand the mechanisms at work in other cancers better. Telomere fusion could potentially play a role in any cancer, so our MDS research is relevant to cancer research in general.

 

 

NOTES
The paper: The dicentric chromosome dic(20;22) is a recurrent abnormality in myelodysplastic syndromes and is a product of telomere fusion. Ruth MacKinnon, Hendrika Duivenvoorden, Lynda Campbell and Meaghan Wall, 2016. Cytogenetic and Genome Research 150(3-4):262-272
The gene errors discussed here usually occur in the body cells rather than the reproductive cells, so they’re not inherited.
For simplicity the Claymation shows telomere fusion in chromosomes that are dividing.  In fact it probably occurs when the DNA is unravelled in the interphase nucleus.

This is cross-posted from ChromosomesandCancer.com.

Bedtime Science: Why do seeds travel?

A lot of plants have seeds that are made to travel to new places. Why is this?

Plants get their energy from the sun. They need this energy to grow. What happens if a seed falls from a lovely leafy tree? The new plant is in the shade. The sunlight falls on the leaves above it and the seedling won’t get as much.

Not only that, but it’s trying to grow in space that’s taken up by the big tree’s roots. It’s not going to grow big very fast.

To have a better chance at life this seed needs to get away from its parent. That’s why nature has come up with all sorts of different ways for seeds to travel. We’ve looked at helicopters, hooks and darts (prickles). Can you think of any more? Go and have a look outside. Maybe you can discover more some for yourself.

Blown dandelions (Viggo Venneløs løvetann)

Do you know what these are?

EXTRAS

Image attribution: By Erlend Schei (http://www.flickr.com/photos/nerdegutt/3585220976/) [CC BY 2.0 (http://creativecommons.org/licenses/by/2.0)], via Wikimedia Commons

Hint: Taraxacum

Bedtime Science: How do seeds travel?

If animals run out of food they can can move to where there’s more. Plants can’t get up and move to find a better place to grow. But they have found ways to send their “children” to new places where they might have a better chance of surviving. Different plants have a lot of different tricks for doing this.

Some seeds travel in a helicopter. Others can stick to animals that will carry them somewhere.

Where are the seeds on these plants? What’s about to happen to them? How do they get their seeds to new places?

By FoeNyx, France (Self-published work by FoeNyx) [GFDL (http://www.gnu.org/copyleft/fdl.html), CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0/) or CC BY-SA 1.0 (http://creativecommons.org/licenses/by-sa/1.0)], via Wikimedia CommonsBy Taken byfir0002 | flagstaffotos.com.auCanon 20D + Sigma 150mm f/2.8 - Own work, GFDL 1.2, https://commons.wikimedia.org/w/index.php?curid=2038646

 

If these seeds are eaten how does the plant produce new plants? (Ancient versions of these plants were around and getting eaten long before humans grew them.)

When strawberries and tomatoes are eaten that’s not the end of their seeds. A lot of fruit seeds can pass through the animal that ate them without getting damaged, and get pooped out somewhere.

Then what?!

If the seeds are undamaged they can grow. To cap it off, they’re sitting in a nice pile of dung, which makes a good fertiliser. These seeds could travel a long way while the animal that ate them digests the fruit.

Fruits are meant to be eaten.

Can you think of other ways plants can send their seeds away from home? How about putting your ideas in the comments?

PHOTO ATTRIBUTIONS

Strawberry: By FoeNyx, France (Self-published work by FoeNyx) [GFDL (http://www.gnu.org/copyleft/fdl.html), CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0/) or CC BY-SA 1.0 (http://creativecommons.org/licenses/by-sa/1.0)], via Wikimedia Commons

Tomato: By Taken byfir0002 | flagstaffotos.com.auCanon 20D + Sigma 150mm f/2.8 – Own work, GFDL 1.2, https://commons.wikimedia.org/w/index.php?curid=2038646

What’s the point of prickles?

Have you ever stood on a prickle? Going barefoot in summer often meant a foot full of bindii prickles where I grew up.

These prickles that are even more painful to stand on.

5376444-PPT

Three-corner jacks are very painful if you stand on them.

What good are prickles anyway?

A prickle is attached to a seed which is catching a ride somewhere. The sharp (ouch) pointy bit attaches it to something, usually an animal. If you take a dog for a walk through long grass you might discover a few prickles and other seeds that stick well to dogs and socks.

I found all these different seeds sticking to my socks after a walk in long grass. They’re  full of hooks, darts and bristles.

burr

This is a burr magnified ten times. It’s about the size of a little fingernail. Look at all those tiny hooks. Did you know that velcro was invented by copying the little hooks on burrs? I never knew that before!

And these…

arrowhead seed

These little arrowheads aren’t so sharp, but look at all those little bristles that can get stuck on socks and fur. This is taken with a 10x microscope – the arrowhead is about 7 mm or 5/12 inch long.

And this…

photo (88)

…this photo is life-size.

I’ll bet where you live there are different types of prickles and other things that can stick to your clothes.

PHOTO ATTRIBUTIONS

Three corner jack (Emex australis): Julia Scher, Federal Noxious Weeds Disseminules, USDA APHIS ITP, Bugwood.org
Creative Commons License   licensed under a Creative Commons Attribution-Noncommercial 3.0 License.

Helicopter trees

Did you know that helicopters grew on trees long before people invented them?

The helicopters I played with growing up in Queensland were from a hiptage bush. This plant is originally from Southeast Asia.

hiptage-jpg

These seed pods make beautiful little helicopters. With three blades they spin quickly as they fall. A breeze can lift them up and carry them along. We would drop them from the highest window, or have races to see whose would land first.

 

If you live in North America or Europe you might have seen or played with a different type of helicopter seed – from a maple tree (in Europe it’s called sycamore tree).

 

A seed pod from a sugar maple tree.

These two types of plant aren’t related but they’ve both come up with the same solution to a problem.

If trees drop their seeds on the ground below, the tall older trees block the energy-giving sunlight from the short young trees. And it gets a bit crowded. If the seeds are planted somewhere else the young trees will have more space, sunlight, and other things they need. They have a better chance of surviving and in turn making their own seeds.

Both of these have trees solved this problem by making helicopter seedpods that fly their seeds away.

 

MORE READING

Some clever people have worked out the science behind how the maple seed spins. http://www.livescience.com/3672-secret-flight-helicopter-seeds.html

IMAGES

Hiptage benghalensis: Creative Commons license by Siddarth Jude Machado. Creative Commons license. From http://indiabiodiversity.org/observation/show/378471?species%3DHiptage%20benghalensis%20(L.)%20Kurz

Sugar maple: Creative Commons license. Acer Saccharum Marsh – Steve Hurst @ USDA-NRCS PLANTS Database. https://commons.wikimedia.org/wiki/File:Acer_saccharum_seeds.jpg

Putting poison in the pantry: Plastic microfibres

All sorts of plastic get into waterways, pollute the ocean and poison sealife. There is growing awareness about the damage caused by plastic bag pollution and microbead pollution, but scientists have shown that much of the plastic in the ocean is actually plastic microfibres. In some waterways they make up close to three quarters of the plastic pollution.

Plastic “is like a little sponge for … chemicals”. Poisons stick to the outside of plastic. The smaller the pieces of plastic the more chemicals can stick to them. This is because the more bits a piece of plastic is broken into, the more outside surface there is for chemicals to stick to. Dr Chelsea Rochman found a chemical that was banned in the USA in the 1970s (DDT) on every piece of plastic she took out of the ocean. (DDT is still used in certain circumstances, but much less than before its hazards were known.)

Shellfish eats plastic, little fish eats shellfish and big fish eats little fish. The toxins of concern that stick to plastic don’t break down easily. Each time these poisons go up the food chain they get more concentrated.

Where do these microfibres in the ocean come from? They come from washing synthetic clothes. Addressing this problem will be a mammoth task, because synthetic clothes are so common.

About 0.7 grams of plastic microfibre end up in rivers, lakes and oceans when a polar fleece jacket is washed (there are about 30 grams in an ounce). People eat seafood that has eaten microfibres. These and other research findings are summarised in Microfiber Pollution and the Apparel Industry from the University of California Santa Barbera.

What can be done? Natural fibres were used for thousands of years before synthetic fibres were invented, but according to the Catalyst video, around 2/3 of our clothes are now synthetic. Plastic microfibres would be much harder to phase out than microbeads. Some solutions have been suggested, such as adding filters to washing machines, waterless washing machines, gadgets that catch the fibres in the wash, and new types of synthetic fibre.

Governments and industry have started to phase out microbeads, but they will have to become more aware of microfibre pollution if the plastic pollution problem is going to be solved. Consumers can play a role too, in the choices they make and in spreading awareness. Two advocacy groups, Plastic Soup Foundation and Parley for the Oceans, have started a campaign to raise awareness. In the clothing industry, Patagonia is supporting research by scientists at University of California Santa Barbera into the problem.

It’s not just seafood. Microfibres are also found on land. What’s in your food?

Published research:

Chelsea Rochman et al., University of California Davis 2015. Anthropogenic debris in seafood: Plastic debris and fibers from textiles in fish and bivalves sold for human consumption. Nature Scientific Reports 5, Article number 14340. http://www.nature.com/articles/srep14340 

Mark Browne et al., University of New South Wales 2011. Accumulation of Microplastic on Shorelines Woldwide: Sources and Sinks. Environ. Sci. Technol., 2011, 45 (21), pp 9175–9179 http://pubs.acs.org/doi/abs/10.1021/es201811s

Niko Hartline et al., University of California Santa Barbera 2016. Microfiber Masses Recovered from Conventional Machine Washing of New or Aged Garments. Environ. Sci. Technol., 2016, 5021 pp 11532–11538 http://pubs.acs.org/doi/abs/10.1021/acs.est.6b03045

Other links:

Microfiber pollution and the apparel industryresearch summary (research. http://brenmicroplastics.weebly.com/project-findings.html) and a literature review (http://brenmicroplastics.weebly.com/microplastics-pollution.html) of other

 

The man who discovered a new world in a drop of water

Science for Kids

This is a true story about a man who lived in the Netherlands more than 300 years ago.

Antoni van Leeuwenhoek was born in 1632, and lived in a city called Delft. He was married and had one child, a girl called Maria. He was quite a well-known person around town and he made a living selling woollen cloth and other fabric.

Antonius van Leeuwenhoek. Coloured stipple engraving by J. Chapman, 1813, after J. Verkolje. [CC BY 4.0 (http://creativecommons.org/licenses/by/4.0)], via Wikimedia Commons

Antonius van Leeuwenhoek. Coloured stipple engraving by J. Chapman, 1813, after J. Verkolje. [CC BY 4.0 (http://creativecommons.org/licenses/by/4.0)], via Wikimedia Commons

Cloth sellers liked to look at their cloth up close with a magnifying glass. A magnifying glass is a lens, which is piece of glass in a special shape that can make things look bigger than they are.

Antoni taught himself how to make much better lenses. He made these into microscopes. These could make things look at least 200 times bigger than they really are! These microscopes don’t look anything like the big microscopes we have today. They were quite small and you had to hold them up very close to the eye.

Using these home-made microscopes Antoni could see things that were smaller than anyone had ever seen before.

Antoni was curious, and he loved to explore things with his microscopes. So he explored a lot of the things that he found around him. When he looked in a drop of water he saw tiny living things that people had never imagined before. He called them “animalcules”.

Antoni wrote about these tiny creatures to a club for important scientists called the Royal Society. These scientists thought well of him as a scientist until they read his letter about a tiny world inside a drop of water. They laughed and thought he was being silly. But when they saw these creatures for themselves they were convinced and soon made him a member of their club.

Many people were amazed, and kings and queens wanted him to show them these little creatures. Today we call these tiny creatures Protists.

Antoni didn’t work as a scientist, but in fact he was doing real science with his home-made microscopes. He made a lot of very important discoveries.

 

For the grown-ups

Google has marked Antoni van Leeuwenhoek’s 384th birthday. Who was he? He wasn’t a scientist, but he was. He wasn’t a professional scientist, but he was a true, groundbreaking scientist. He’s been praised* for having an open mind: he knew the difference between fact and speculation, and he wasn’t held back by incorrect beliefs of the time, such as scientists often find it hard to break away from. As he himself said, his discoveries were driven by his exceptional curiosity.

He discovered bacteria, protists, sperm, microscopic nematode worms, the crystals that cause gout, and much more. He worked out that fly eyes are made of many small eyes. This idea was also ridiculed by scientists of the day.

Children are naturally curious. I hope the story of Van Leeuwenhoek will inspire young children to treasure and nurture their curiosity.

Links

A replica of a van Leeuwenhoek microscope http://physicsmuseum.uq.edu.au/van-leeuwenhoek-microscope-replica

Check this page for a photo of one of the microscopes being used properly – held right up to the eye. http://www.vanleeuwenhoek.com/#hiswork

http://www.vanleeuwenhoek.com/

Includes extracts from letters to and from the Royal Society. The members said they giggled at van Leeuwenhoek’s description of animalcules. http://lacelula.udl.es/documents/leeuwen.pdf

http://www.bbc.co.uk/history/historic_figures/van_leeuwenhoek_antonie.shtml

How the lenses and microscopes were made http://www.famousscientists.org/antonie-van-leeuwenhoek/

http://www.history-of-the-microscope.org/anton-van-leeuwenhoek-microscope-history.php

About van Leeuwenhoek as a scientist, and his own descriptions of some of his discoveries: http://www.ucmp.berkeley.edu/history/leeuwenhoek.html

https://en.wikipedia.org/wiki/Antonie_van_Leeuwenhoek

* http://www.vanleeuwenhoek.com/ Reference to Dobell’s quote in Antonj van Leeuwenhoek “Father of Microbiology” by Dobell C. (ed.) 1992, 1960. Antony van Leeuwenhoel and His Little Animals. Dover Publications, New York

 

A closer look at microbeads

Plastic microbeads in cosmetics are getting into oceans and waterways. They soak up poison and get into the food chain. Many organisations are pushing for awareness and banning the microbead (there are links at the end of this post). This is a serious enough problem that governments are starting to ban them.

I took a closer look at some facial scrubs for myself. I have a fairly basic USB microscope so I examined three products with microbeads in them. Last time I looked at a “natural” product:

kiwi2

This one with the natural goodness of kiwifruit and aloe vera

kiwi3

and microbeads.

 

 

This one lets you know it contains “powerful microbeads”:

It's got some jagged blue bits (plastic again I'm guessing) and some clear round beads.

It’s got some jagged blue bits of plastic and some clear round beads.

Here’s one of those beautifully round beads next to a 2 millimeter grid (each square is about 1/12 inch wide). The bead is less than a millimeter wide.

g__ier5

 

In the third product, “tiny spherical beads gently buff, refine and smooth”.

n__io3

 

These bits of plastic aren’t so spherical.

This product felt very gritty. I diluted it with water to get a clearer look at the beads, then let the bits of plastic settle. Then I put the settled sediment on a glass microscope slide.

Besides the bigger bits, at 20x you could just make out some very small dots – here they are with the 2 mm grid:

At 20 times magnification next to a 2 millimeter (about 1/12 inch) grid.

At 20 times magnification next to a 2 millimeter (about 1/12 inch) grid.

All the images above are at 20 times magnification. Lets take a closer look at these tiny dots.

Here they are at 200 times magnification. The largest ones are about 1/10 of a millimeter wide and the smallest (arrowed) less than 1/100 of a millimeter, or ten micrometers.

Here they are at 200 times magnification. The largest ones are about 1/10 of a millimeter wide and the smallest (arrowed) less than 1/100 of a millimeter, or ten micrometers.

So these must be the “tiny spherical beads”. According the the United Nations Environment Program (UNEP) microbeads can be as small as one micrometer.

Links

Microbeads and microplastics in cosmetic and personal care products. Oliver Bennett. House of Commons Briefing Paper May 2016. http://webcache.googleusercontent.com/search?q=cache:LjCahOMK214J:researchbriefings.files.parliament.uk/documents/CBP-7510/CBP-7510.pdf+&cd=12&hl=en&ct=clnk&gl=au

Plastic in Cosmetics. UNEP Fact Sheet. Are we polluting the environment through our personal care? http://unep.org/gpa/documents/publications/PlasticinCosmetics2015Factsheet.pdf

Microbeads – A Science Summary. July 2015. Where the Canadian Government recommends listing microbeads as a toxic product. http://www.ec.gc.ca/ese-ees/ADDA4C5F-F397-48D5-AD17-63F989EBD0E5/Microbeads_Science%20Summary_EN.pdf

For more links see Putting Poison in the Pantry (Fireside Science).

Can you tell if that product contains microbeads?

Maybe cosmetics with microbeads are easy to spot because it’s proudly written on the label. Like this one:

g--r_blurb

Why would you want to know? Microbeads are tiny plastics that are polluting the oceans and waterways. Once they’re in the ocean they don’t go away. Poisons stick to them, and these poisons get into the wildlife that eats them. There’s more detail in a previous post.

But they’re not always the company’s selling point.  On the face of it this one is all natural and wholesome.

Hmmm - its green and you can see little black bits of exfoliating kiwi fruit seed, right? Wrong.

back-kiwi-2

Hmmm – it’s green and you can see little black bits of exfoliating kiwi fruit seed, right? Wrong!

Check the ingredients list.

kiwi_ing

Polyethylene is plastic (i.e. microbeads) and it’s there, near the top of the ingredients list, and kiwifruit extract is much further down, a few before the chromium oxide greens. And where’s the aloe? (Ingredients are listed in order, from what it contains the largest amount of, to what is present in the smallest amount.)

What about those seedy bits?  I took a closer look with a simple low-powered microscope.

kiwi-black-microbeads-png

These were big dark microbeads and there lots more smaller clear ones.

Look out for polyethylene in your cosmetics. You can find out about other plastics that are used for microbeads in my last post or The Story of Stuff.

Putting poison in the pantry