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by Meredith HanelPeaches and nectarines are the same fruit minus a small genetic variation that makes nectarines hairless. When I first learned this little trivia tidbit I wondered about the difference in flavour. I prefer nectarines to peaches, but wondered if the taste difference was all in my head. Well, it’s not.
The genetic variation affects flavour, aroma, size, shape and texture. While the rough location of the genetic change has been known for some time, the exact gene and the exact change in the DNA sequenceof “nectarineness” has been a mystery. In March, scientists from Italy finally identified a disruption in a “fuzz” gene that is absent in peaches.
Agriculturists in China gifted fruit lovers with the peach about 4000 to 5000 years ago. At least 2000 years ago, again in China, nectarines burst on to the scene. Charles Darwin pondered about how nectarines popped up on peach trees and vice versa and described the odd finding of one fruit that was half and half. Would we call that a “peacharine?”
Darwin, and others, deduced that the nectarine was a peach variety. In 1933, scientists determined a recessive gene variant was responsible for the inheritance pattern of the nectarine’s hairless (glabrous) skin. The glabrous trait was given the designation G, with big G for the normal fuzzy peach character and little g for the glabrous nectarine character. Each fruit has two copies of this gene. Each parent gives one to the offspring fruit, which can be either GG, Gg, or gg, and only the gg fruits are nectarines.
The chromosomal location of the G trait was already roughly landmarked but the Italian research team zoomed in on the spot, sort of like how you zoom in to street view with Google maps. Many DNA sequence differences exist between nectarines and peaches that are not located in genes but are useful as landmarks along the chromosomes. These are called genetic markers. To zoom in on the G trait, the researchers crossed peach and nectarine trees and followed the offspring through two generations. The offspring had a mixture of peach and nectarine markers along their chromosomes but certain genetic markers, the ones closest to the G trait location, always went along with the nectarineness. These genetic markers landmarked the region to search for genes with mutations that could explain a nectarine’s fuzz-less-ness.
Within the landmarked region, the researchers identified a disrupted gene. The peach to nectarine gene disruption is a genetic modification by the hand of Mother Nature, an insertion of a transposable element. This type of DNA element can move because it contains its own code for the production of an enzyme that can “cut”and “paste”the transposable element to other locations in the genome. Transposable elements can get pasted right in the middle of genes, disrupting the DNA sequence. They are a known cause of genetic variation in plants. If you like chardonnay wine, you can thank a transposable element for disrupting the cabernet grape genome long ago.
In nectarines the transposable element stuck itself right in the middle of a gene called PpeMYB25. Genes with similarities to PpeMYB25 in other plants are important for making plant hair, called trichome, which can occur on the stem, leaves, flowers and fruit of plants. The PpeMYB25 gene is the recipe for making a protein that is a transcription factor, a type of protein that controls when and how much other genes are turned on, so a mutation in this one gene could explain not just baldness in nectarines but other nectarine characteristics as well, depending on what these other genes are that it controls. In this report the researchers focused on the peach fuzz characteristic. When they looked at flower buds during the period when fuzz or trichome first develops, they found PpeMYB25 to be active in the peach but not the nectarine buds.
This is the first description of a specific genetic modification that can explain the difference between peaches and nectarines, something that has long been a mystery.
This research makes a strong case that nectarine lack of fuzz is due to the inability of nectarines to produce the PpeMYB25 protein. How lack of PpeMYB25might lead to the other nectarine characteristics — flavour, for instance — still needs to be worked out.
Vendramin, E. et al. (2014) A Unique Mutation in a MYB Gene Cosegregates with the Nectarine Phenotype in Peach. PLOS ONE. 9: e90574 Get paper
Meredith Hanel earned her PhD in medical genetics and spent many years in the lab doing research in molecular and developmental biology related to medicine. Meredith works in science outreach with Scientists in School. She enjoys writing about science and loves to find out the biology behind just about anything in nature.
Open up any science magazine today and you’re likely to find at least one story having to do with the microbiome – all the bacteria that live in you and on you – and its impact on health. Although this field of science is in its early stages, researchers are linking disruptions in the microbiome to many big health problems we deal with today, including obesity, type 1 and 2 diabetes, celiac disease, as well as allergies and some forms of cancer.
Every article has its own way of framing the microbiome, whether the writer does it consciously or not. Take this line from a 2012 article in the Economist, which implies that a body and its bacteria live in a sort of mutualistic symbiosis – the two species live in a mutually beneficial relationship, and may in fact need each other to exist: “In exchange for raw materials and shelter the microbes that live in and on people feed and protect their hosts, and are thus integral to that host’s well-being.”
Yet I Contain Multitudes, the title of an upcoming book on microbes and their influence on the lives of animals by science writer Ed Yong, suggests a certain separateness between microbe and man. Similarly, this text from a recent article by Bryn Nelson of Gizmodo connotes a microbiome that is segregated from us, despite its constant ability to change in response to us: “This microscopic jungle is constantly adapting in response to our diet, antibiotic use and other environmental influences.”
As microbiome-related treatments take shape in the years ahead, regulators are struggling with how to conceptualize the microbiome. Should the microbiome be defined as an entity completely separate from us or should it be thought of as an integral part of what it means to be human – like the brain? Or perhaps it would be more appropriate to define it somewhere in between, as an organ that is part of us but which we could theoretically live without – like the spleen.
It’s not just semantic whimsy: it has implications for how we will one day access microbiome-related treatments for our own health.
One example where this concept hangs in the balance is the issue of fecal microbiota transplantation, or FMT. This is a medical treatment in which a fecal sample from a healthy donor is administered to a sick patient in order to ‘re-colonize’ the digestive tract with a better-functioning population of bacteria. The evidence that it works for C. difficile infection is irrefutable; no other treatment comes close.
Regulation of FMT has been a tricky issue, and it’s far from being resolved. Doctors have been quietly carrying out the procedure for years, but as FMT gets more widespread and the scientific literature grows, the United States’ FDA and equivalent agencies all around the world need to figure out how to regulate it. In doing so, the agency is trying to decide on your relationship status with your stool.
Dr. Alexander Khoruts, a FMT researcher and a leading clinical expert on the procedure, disagrees with the FDA’s current decision to regulate FMT as a drug, which implies the view that the bacterial population is completely separate from the human body.
“I think it is an organ transplant. I’m willing to [call] it a tissue transplant,” says Khoruts. “The reason why the FDA did not accept the notion of a transplant is because it considers this material not human. And the law is written that human transplants are distinct from drugs.”
He argues, however, that the bacteria inside us, which happen to come out in fecal form, are part of what makes the human species. “[There is] good evidence that these microorganisms have co-evolved with their human hosts,” he explains. “It’s true they’re open to the environment and they are changing; however, it may be they’re still part of humans. There are no germ-free people running around. So to me, it is an organ transplant.”
The FMT discussion continues to broil, but other examples are going to emerge. What if we take a bacterial species found in most humans and give it to an obese patient who doesn’t have it? What if we make a ‘functional food’ by adding to cheese three species of bacteria that are commonly found in Western, but not Eastern, populations? Regulators of all kinds will have to consider our relationship with the microbiome in the coming years. We’d best lead the way by watching our language.
by Lillianne Cadieux-ShawA giant shadow slices through the water, effortlessly, gracefully almost, as if in a ballet’s glissade. An eye glints in the darkness. A row of carnassial teeth appears and grows wider, darker, deeper in the depths. Then, panicked bubbles, flailing limbs, a desperate attempt to swim up towards the surface. But it’s too late. The poor floral-swimsuited victim knows it. The ancient poikilothermic beast with jaws the size of a fridge knows it. Everyone at home, white-knuckle gripping their popcorn bowl as they watch, knows it. There will be blood. This is Shark Week after all.
In 1988, a bunch of Discovery Channel executives were out at a bar, shooting the breeze, talking about what kinds of shows would be fun to produce, and one guy said: “You know what would be awesome? A week where we just have shows about sharks.” And they laughed. Because how preposterous that would be! A week of sharks! But they did agree it was a good idea. It would definitely be fun. One of them scribbled it down on a napkin. They brought the idea into the studio with them and gave it fins, airing 10 episodes that July. The first show was called Caged in Fear, about the testing process for motorized shark cages. To their surprise, ratings that week doubled. Discovery had stumbled on to something big, a key formula of entertainment that Discovery Channel founder John Hendricks articulated best when he said, “If an animal can eat you, ratings go through the roof.”
It worked. By 2006, Shark Week had been immortalized as a pop-culture phenomenon when Tracy Morgan’s character in 30 Rock gave advice to a colleague to “Live every week like it’s Shark Week.” Now, it is in its 27th season, with around 30 million viewers. Colbert declared it the second holiest annual holiday after Christmas. It has its own drinking game (rules can be found here) and the amount of adorable Shark Week related baked goods on Pinterest is just absurd. There’s no doubt that through its rowdy approach to wildlife, many people got excited about marine biology.
There’s just one problem, though — Shark Week is a fraud. Though it has always been about entertainment, at least Discovery based it on real science. Now, it’s hard to separate the science from the science-fiction.The highest rated program in Shark Week history, which aired last year, was called Megalodon: The Monster Shark That Lives. It depicted a terrifying prehistoric shark with teeth six inches long and jaws that could crush a Volkswagen. After the show aired, an online poll on Discovery’s website (which was quickly taken down) showed that three quarters of respondents believed the Megalodon was still alive, roaming the seas. This was presumably even after reading the brief disclaimer at the end of the program that vaguely said, “though certain events and characters in this film have been dramatized, sightings of [the giant creature] continue to this day. Megalodon was a real shark. Legends of giant sharks persist all over the world. There is still debate about what they might be.” The Megalodon did exist, and was surely terrifying. But, according to all archaeological and biological sources, the Megalodon went extinct two million years ago. It also turned out that some of the ‘scientists’ on the show were paid actors, images were doctored, and real scientists were misled and their quotes distorted. Discovery received quite the backlash for their scientifically misleading program. So it was a bit of a surprise that one of the high-billed programs this year was….you guessed it! Megalodon: New Evidence, sequel to the Monster Shark That Lives.
When asked about the scandal, and why they continue to insist that an extinct mega-predator may still be skulking around, the general atmosphere has been one of wishy-washying executives waggling their fingers and saying things like, “Well, who really knows?” in mysterious voices.
And unfortunately, it isn’t just the Megalodon episodes which are misleading. Shark of Darkness: Wrath of Submarine had the same flawed conceit – that there’s a big shark out there for which there is no scientific evidence. Lair of the Mega Shark? Also about a big imaginary shark.
Perhaps these problems seem silly — Shark Week has never been anything but entertainment, right? Cooked up by Discovery execs at a bar as a silly idea to boost ratings, Shark Week has always been about getting more viewers. In fact, the descent into parody should have been obvious from the repeated showings of Sharknado, the B movie satire about literally a tornado of sharks, over the course of this year’s Shark Week (or equally apparent even by glancing at the titles of their actual shows – Sharkaggedon, Zombie Sharks, Lair of the Mega Shark). Shark Week is marketed like any other form of mass entertainment, with the average viewer in mind, who is tuning in for escapism, or even just mild diversion. So isn’t all this brouhaha really a criticism of the decline of public programming in general? Unfortunately, Discovery must be held to a different standard, one with if not real science, then at least transparent motives.
The first problem is with the channel’s consistent breach of basic journalistic ethics. Shark Week not only hired actors to play scientists, but also got real scientists to contribute and then took their words out of context, making it seem like they agreed with some preposterous claim. One scientist who appeared on Voodoo Shark last year was interviewed about bull sharks, and asked if there might be any in the area. He said it was entirely likely. According to the scientist in an interview with io9, the show spliced out the question and put his answer to a question about whether there was a local-legend ‘voodoo’ shark nearby. Kristine Stump, a research associate at Shedd Aquarium, felt equally misled when she saw how her team’s research was portrayed on Monster Hammerhead.
Another larger journalistic issue is with how their programming exploits shark-as-vicious-predator rather than shark-as-endangered-species. They focus on the thriller appeal of great whites and not enough attention on the five hundred other species of shark. They spend inordinate amounts of time detailing sharks attacking humans, though you are more likely to die from digging holes on the beach than from a shark attack, statistically speaking. This emphasis on shark aggression rather than shark conservation is akin to finding one scientist who denies climate change and then claiming that the entire scientific community is divided on the subject. With a quarter of all shark species threatened by extinction, they have much more to fear from us than we ever will from them—portraying them as human-eating beasts only increases a disassociation from them as living creatures deserving of our respect and protection.
The second problem with Shark Week is about the standard of science they are expected to uphold. Misleading viewers into believing there is a shark splashing around that all scientists agree went extinct in the early Stone Age is not even bad science, which can be dismissed as an isolated breach of the scientific method, but is pseudoscience, the “promotion of teachings different from those that have scientific legitimacy,” according to the Stanford Encyclopedia of Philosophy. Discovery’s Shark Week used to be a reliable and trustworthy source for popular science. It is this prior reputation which makes their scientific breaches such a disappointment — they are relying on their once-upheld educational values to convince otherwise rational people of fiction. They are mongering fear, exploiting a human need for drama, and peddling penny dreadful pasquinades masquerading as real science, all under the guise of the popular science they used to do so well.
The democratization of science has made it easier for everyone to have access to scientific news, journals and educational material. But because there’s so much information out there, we must somehow separate the words from the static, which can seem like an overwhelming, Sisyphean task. That’s why Discovery was so exciting, because they dug for diamonds in field upon field of coal, and made it fun in the process. But when they start turning up coal, painting it in cheap, sparkly glitter and trying to pass it off as diamonds, that’s when people feel betrayed. The one promising streak out of this hullabaloo, is that it mattered. People wanted real science.
The comment section obloquies and adversative media afterclap, the scientists coming out warning other scientists to think twice before talking to Shark Week producers, the thousands of Facebook vows to never trust Discovery again, it all shows a deep caring, an upset that viewers were being treated as if they didn’t care about scientific and journalistic integrity. It is this optimistic reaction which should make Discovery rethink before airing a Megalodon: Revisited trilogy.
Lillianne Cadieux-Shaw is a freelance journalist and writer passionate about science journalism, wildlife, space exploration and finding photos of pugs on the Internet. You can find her on Twitter: @lilcadieuxshaw
by Robert Aboukhalil
It is often said that data science is 80 percent data preparation and 20 percent science. This was demonstrated in the previous installment of my Data-Driven Journalism series, where I used basic command line tools to find the coldest and warmest days in Montreal over the last decade. In this post, I introduce a few more command line tools and demonstrate their use for analyzing a dataset about the passengers aboard the Titanic.
Using this data, we will answer the following questions:
- What is the percentage of passengers who survived?
- Were first-class passengers more likely to survive?
- Was the “women first” code applied?
Setup your workspace
Let’s get started! [To refresh your memory, click on here.] Open up a Terminal and create a folder on your desktop to store today’s analysis using the ‘make directory’, or ‘mkdir’, command:
Remember that the tilde character (~) is just a shortcut to the current user’s home directory.
Next, navigate to the folder you just created using the ‘change directory’, or ‘cd’, command:
To download the Titanic dataset, use the curlcommand:
curl -o titanic.txt http://lib.stat.cmu.edu/S/Harrell/data/ascii/titanic.txt
To understand how curl works, let’s unpack this command (read the graph below from right to left):
To catch a glimpse of what the dataset holds, use the head command:
You should see the first 10 lines of the file:
Note that there are 11 columns in this dataset, each separated by a comma. Luckily, the first line tells us what each column refers to:
|2||Passenger class (1st, 2nd, 3rd)|
|3||Survival status (1 if survived; 0 otherwise)|
|6||Port where they embarked|
Although there were over 2,200 passengers on the Titanic, keep in mind that this dataset only has information about 1,314 of them.
Analysis 1: Percentage of survivors
To calculate how many passengers died and how many survived, we need to extract the third column and count the number of passengers with either a 1 or a 0. There’s a very important command called cut that will allow you to extract columns from a file:
cut -f3 -d, titanic.txt
This will extract the third column and will define columns as being delimited by commas as shown below:
When you run the command above, you should see many lines of 1s and 0s. To only show the lines with 1s in them, we can use the grep command, another very important command, which we use here to only keep lines with ‘1’ in them:
cut -f3 -d, titanic.txt | grep 1
Note that the pipe symbol | allows you to chain commands by executing a command on the result of another one. In the example above, we execute grep on the output of cut. This is convenient because it allows us to perform complex operations without saving results from intermediary steps.
If you run this command, only the lines with 1s in them will show. Now let’s use another command, wc(word count), to count the number of lines with 1s. Although you can use wc to count the number of words, wc -l will tell you how many lines are in a file:
cut -f3 -d, titanic.txt | grep 1 | wc -l
This should return 449 passengers.
Likewise, we can count the number of passengers in this dataset that did not survive (864):
cut -f3 -d, titanic.txt | grep 0 | wc -l
From this analysis, we would conclude that ~66 percent of passengers did not survive. This is very similar to what other sources have reported.
Analysis 2: Survival by passenger class
Next, we’d like to know the percentage of passengers who died from each passenger class (1st class, 2nd class, 3rd class). First, we use grep to extract 1st class passengers, and then wc to count how many of them there were:
grep 1st titanic.txt | wc -l
Note the difference between this grep command and the previous. Since the grep command does not come after the pipe symbol |, we must specify the source that we’re “grepping” on, in this case the titanic.txt file.
From the output of this command, we conclude there were 323 first class passengers. To calculate how many of them did not survive, we extract the third column and count the number of 0s:
grep 1st titanic.txt | cut -f3 -d, | grep 0 | wc -l
There were 130 first class passengers who died (40 percent).
Repeating the same analysis for the two other classes yields the interesting result that a much greater proportion of 3rd class passengers died, compared to first and second class passengers:
1st class 40% of passengers survived
2nd class 58% of passengers survived
3rd class 81% of passengers survived
Analysis 3: the “women first” code
With such a dataset, we can even attempt to guess whether the ‘women first’ code was applied on the Titanic.
Using everything we learned so far, we can make the following command to count the number of female passengers who survived:
grep female titanic.txt | cut -f3 -d, | grep 1 | wc -l
Here, grep will only select lines from titanic.txt that contain “female” in them, cut will select the 3rd column from the remaining lines, and the second grep will only show lines with 1s in them. Finally wc -l is used to count the number of 1s.
This should output 307. Next, we obtain the total number of female passengers:
grep female titanic.txt | cut -f3 -d, | wc -l
That should give 463 (66 percent survived). Doing the same for men yields 142 survivors out of 850 (17 percent).
Clearly, a much greater proportion of women survived the Titanic accident, but the staggering discrepancy between survival rates suggests some other effect could be at play. In fact, it seems there was confusion on the ship: when Captain Smith ordered his officers that women and children should go first, some of them understood that only women and children could go and therefore prevented men from boarding the life boats.
Looking further, scientists have recently combined survival data from many shipwrecks and concluded that “in contrast to the Titanic, […] the survival rate for men is basically double that for women.”
The last word
In my last post about data science for journalists, we learned the basics of using the command line with commands such as cd, mkdir, ls, head and sort.
In this post, I covered a few more of the key commands such as curl, cut and grep. With all this knowledge in hand, you should now be well equipped to do some data analysis of your own! To get you started, here is a link where you will find a long list of publicly available datasets to play with: http://www.quora.com/Where-can-I-find-large-datasets-open-to-the-public.
By day, Robert Aboukhalil is a computational biologist; by night, he is an entrepreneur and science communicator. He is currently pursuing a Ph.D. in computational biology at Cold Spring Harbor Laboratory and is the Editor-in-Chief of Technophilic Magazine.
by Kimberly Moynahan
Well here we are, finally in the dog days of summer. We’ve earned this after a long record-breaking winter and a much delayed spring here in southern Ontario.
The dog days are named for the binary Dog Star, Sirius, also known as Alpha Canis Majoris, the brightest star in the night sky and the largest star in the constellation Canis Major. Among ancient Romans, the hottest days of the year were associated with the first heliacal rising of Sirius –the day when Sirius first becomes visible on the eastern horizon just before sunrise. This year that occurred on August 7th.
Most people, unaware of the astral connection, associate the dog days of summer with their own earthbound canines, sprawled belly down on cool kitchen tiles or retreating to damp excavations under the porch. For humans, the dog days are a time to shelter from the heat in air conditioned interiors or to take to the water – be it the local pool, the lake or the ocean.
But, while our urge is to siesta away the steamy days, one small creature is working diligently, recovering from last winter and preparing for the next.
This is the season of summer honey.
By the time the dog days hit us, honeybees have long-since used up last year’s store of honey and have been working ceaselessly since the first blooms of early spring – those of maples, pussy willows and bugloss, to name a few — to feed their young and grow their ranks.
Recently, they made the decision of whether or not to divide the colony and swarm. Some hives did and some did not, depending on how crowded the colony had become. Now settled into their permanent digs until next summer, they are making honey from the nectar sources in their range.
If you are only familiar with the mass-produced product in squeezable plastic bears, you may think that there is just one honey and that it is of uniform golden colour and singular mild flavour. That’s what I used to believe until I started frequenting farmers’ markets and talking to beekeepers – and most importantly, tasting the honey. As it turns out, in nature, no two honeys are alike.
The uniform colour and flavour of commercial honey is a result of raising bees near single crops such as clover or canola, feeding bees cane sugar or corn syrup, mixing many sources of honey to an “average” flavour and sweetness, and, in some cases, ultra-filtering it to remove all traces of pollen – a practice that removes some of the distinct flavours and also helps prevent the honey from crystalizing, leading to the misguided belief that “good” honey should remain liquid forever.
But like wine, coffee and tea, real honey is variable, taking on the characteristics of its environment or “terroir” – that is, the collection of elements that affect plants and the make-up of their nectar, such as season, climate, soil, weather, geology and human activity.
The taste of honey has several components. The most obvious is its perceived sweetness. This largely depends on the ratio of fructose to glucose; the more fructose, the sweeter the honey. Most mono-flower honeys – or varietals, as they are called – are similar in sweetness, but some, such as orange-blossom honey, have a much stronger sweet-factor.
In addition to sweetness, different varietals have unique identifiable flavours and aromas, the subtleties of each dependent on the chemical makeup of the nectar and the final product as made by the bees.
For instance, two major components responsible for the odor of Linden [also known as Basswood] honey are, terpenes linden ether (3,9-epoxy-1,4(8)-p-menthadiene) that has a flowery, mint-like odor, and cis-rose oxide that has a powerful, green, geranium type odor. (The Honey Traveler)
Eighty percent of Canada’s honey crop comes from the vast prairies of Alberta, Saskatchewan and Manitoba. Much of this is a mono-floral by-product of the canola industry, where more than 300,000 colonies of honeybees pollinate the world’s largest crop of canola seed. Smaller commercial operations in the east focus their efforts on apple orchards and blueberry crops. These are the sources of plastic bear honey.
However, twenty percent of Canada’s honeybee colonies are owned by hobbyists and small producers and this is where you begin to see the delectable array of honey that’s possible to produce in this country.
Most people are probably unaware that every temperate Canadian region offers a dazzling range of luminous, astonishing honeys. (The National Post )
When bees are surrounded by an abundance of summer wildflowers, berries, and a variety of agricultural and cover crops, the flavour and aroma of summer honey can be delightful and complex.
“Harvested from mid-July to August, the honey is made from the nectar of white clover, raspberry bush, alfalfa, mint and wild flowers. There is nothing cloying or rich about it. Though delicate, it is full-flavoured. It trickles down the throat softly without a blast of sweetness hitting my molars, or any trace of bitterness catching in my throat. Divine.” (Montreal Gazette)
So, if you have never tried real summer honey, take a trip to your nearest farmers’ market and buy yourself a bit of that succulent sunlight. I promise, if you do, you’ll never go back to the bear.
Kimberly Moynahan writes on the natural sciences and reflects on that uneasy space in the Venn diagram where humans and wildlife overlap, both physically and emotionally. Her work can be found on her blog, Endless Forms Most Beautiful.