There’s an ongoing debate about where and when dogs originated. The when part might be closer to an answer now. Genetic drift is used by evolutionary biologist to try to recreate the lineage of species. The discovery of a 35,000-year-old wolf rib bone in the Taimyr peninsula in northern Siberia was the key to this story. The DNA from that bone suggests that it diverged from a common ancestor of present-day wolves and dogs near the beginning of the domestic dog lineage. Their technique uses genetic drift of ‘regular’ DNA and mitochondrial DNA.
► Genetic Drift
There are non-lethal random mutations in DNA that survive to the next generation due to natural selection and sometimes due to ‘luck’. Surviving by natural selection makes sense, a mutation affords an advantage so that offspring should excel and survive. Genetic drift is when a mutation doesn’t necessarily result in an advantage but is nevertheless passed on ‘by chance’. Tracing these mutations help create a lineage for evolutionary biologists.
► Mitochondrial DNA vs. Nuclear DNA
Mitochondria are the energy power plants inside cells. They have a few genes necessary for oxidative phosphorylation, which is a fancy term for making energy. The nucleus of the cell is where the chromosomes are. Nuclear DNA is the DNA that you hear about in the news, for example in forensic science. In the figure below, you can see that mitochondrial DNA is passed on only by the mother while nuclear DNA is passed along by both parents. Genetic drift in mitochondrial DNA is much slower and helps refine the lineage of a species. It is slower because it is only inherited by half of the genetic source, i.e., the mother.
You can read a summary of the article in layman’s terms here:
With a moose population around 1,200, we need to relocate some wolves to Isle Royale National Park. As the article mentions, too many herbivores without a top predator is not sustainable. Climate change has reduced the number and frequency of ice bridges. That limits the introduction of new wolves to the gene pool. So inbreeding has limited the ability of wolves to maintain their population on the island. #ThanksClimateChange
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You can read more about the wolf repopulation program at Yellowstone National Park here:
The retired Japanese engineer Akira Haraguchi (1946–) claims to hold the world record for reciting the most memorized digits of the number pi. He set the record starting at 9am on October 3, 2006, and reached digit number 100,000 at 1.28am on October 4, 2006.
The event was filmed in a public hall near Tokyo. Haraguchi took 5-minute breaks to eat every two hours, and even his trips to the toilet were filmed to prove that the feat was genuine. This broke Haraguchi’s previous record of 83,431 digits, which he performed from July 1–2, 2005.
The reason I say that Haraguchi claims to hold the record is that, for some reason, the Guinness World Records organization has failed to recognize this achievement, despite the existence of witnesses and detailed documentation. The Guinness-recognized record for reciting pi is 67,890 digits by Lu Chao, a 24-year-old graduate student from China, who recited the digits, without error, in 24 hours and 4 minutes.
Haraguchi’s technique for memorizing long lists of numbers is quite interesting. He assigns kana characters to each number, each of which represents a Japanese syllable. In his system, the digit 0 can be read as o, ra, ri, ru, re, ro, wo, on or oh; the digit 1 can be read as a, i, u, e, hi, bi, pi, an, ah, hy, hyan, bya, or byan; and there are analogous rules for the other digits.
Using this system, Haraguchi has created many stories and poems, including a story about the 12th century hero Minamoto no Yoshitsune. The first 15 digits of pi, which are 3.14159265358979, are rendered in Haraguchi’s system as the words saishi ikokuni mukosan kowakunaku, whose approximate meaning is “the wife and children have gone abroad; the husband is not scared.”
Given all this, it may be surprising to learn that as a child, Haraguchi was neither a prodigy nor a mathematical genius. On the contrary, one of his teachers once made him stand to attention in the hallway as a punishment for badly failing to memorize multiplication tables of one-digit numbers.
It looks as if the article’s URL may change at some point, so you may want to Google the article’s title instead: How can anyone remember 100,000 numbers?
The web site http://pi-world-ranking-list.com/ maintains a list of records of reciting from memory digits of the irrational numbers pi, e, and the square root of 2.
Thanks Brian Koberlein for explaining this way better than I could. Once again, the media takes some interesting science news and runs with a few misconceptions.
#ScienceEveryday
Originally shared by Brian Koberlein
Two for One
There’s been much buzz about a new paper claiming that it’s observed light acting as both a particle and a wave at the same time. Is this legitimate research? Yes, absolutely. Did they actually observe particles and waves at the same time? Well…
Much of the hype around this paper is driven by some basic misconceptions regarding quantum objects. The popular view of quantum theory is that things like photons are sometimes particles and sometimes waves, and which one they become depends upon how you observe them. But in fact quantum objects are neither particles nor waves. They are quanta, which is a separate thing altogether. Under the right conditions quanta can demonstrate wave-like and particle-like behaviors, and there is complementarity between them so that quanta tend to lean toward one or the other in an experiment. But within the formalism of quantum theory, particle-wave duality is a property of the quanta as a whole. Thinking of quanta as particles or waves is far to simplistic when dealing with quantum theory. This is important to keep in mind when popular articles such as this hit the web.
As research areas such as quantum optics and quantum computing developed, we’ve gained tools to really start looking at sophisticated quantum interactions. It’s how we’ve been able to study things like the connection between the uncertainty principle and entropy, or study phase velocity in a quantum system. But since this kind of work isn’t easy to describe in simple terms, it gets hyped as “quantum mechanics gets simpler!” or “speed of light not absolute!” The same is the case here.
So what’s really going on in this work? The team pulsed laser light at a tiny wire of conductive material (a nanowire). The light induced what is known as surface plasmon polaritons in the nanowire, which is basically an electromagnetic wave pattern within the electrons of material. Because of the size of the nanowire, the plasmon polaritons form a standing wave within the wire, which is where the “wave” aspect comes into the experiment. They also radiate light, which in a quantum sense means that photons are emanating from this standing wave. The team then aimed a beam of electrons at the set up. Some of the electrons collided with the emanating photons, and thus gained some energy. Since these collisions are particle-like, they gain specific (quantized) energy amounts from the induced photons. Basically the team found a way to induce particle-like interactions while maintaining the overall wave aspect of the system at the same time.
Does this mean the team caused a specific photon or electron to behave as a particle and wave at the same time? No. The particle interactions with the electrons and the induced wave pattern in the wire are two separate aspects of the system. But their result is useful because it could allow us to study quantum interactions directly. This type of work is really useful for photonics and quantum computing, and it’s a clever way to interact with quantum systems.
But this is not an experiment that somehow violates quantum theory. We’ve known for a while that we should be able to do this kind of thing in theory. The achievement here is that they actually pulled it off.
Paper: L Piazza, et al. Simultaneous observation of the quantization and the interference pattern of a plasmonic near-field. Nature Communications 6:6407 DOI: 10.1038/ncomms7407 (2015)
These twelve items have two important things in common:
(1) They’re important and valuable things, and
(2) They have absolutely nothing to do with autism.
Lead is a heavy metal which melts at low temperatures. It’s used in large batteries like the ones in your car, as well as as a stabilization weight and radiation shield. It can be poisonous if you ingest it, though, so be careful! (The #1 safety risks in most radiation labs is actually accidental lead poisoning from the shielding equipment)
Fluoride is an ion of the Fluorine molecule. It’s critical for human health: without it, your teeth will decay and fall out. In some places, it’s found naturally in local foods and water, but in other places, it gets added to reservoirs or table salt instead. Water fluoridation is considered one of the ten greatest public health achievements of the 20th century, and is a major reason why people today have healthy teeth. It was also believed by some to be part of a Communist plot to corrupt the Purity of Essence of our Precious Bodily Fluids. (And yes, people describing the plot Liked to Capitalize Things)
Antibiotics are probably the single greatest public health improvement of the twentieth century: they’re drugs which can give our immune system the capability to fight off bacterial infections. Without them, common diseases like strep and TB will simply kill you. However, antibiotics do nothing against viruses. In fact, if you don’t have a bacterial disease, or take only part of a course, antibiotics are dangerous: they’ll kill just the bacteria which were most vulnerable to them, leaving behind the strongest and most resistant ones to breed! Overuse of antibiotics has resulted in the development of many strains of bacteria which are resistant to even very powerful antibiotics, leading to the fear that we may soon be vulnerable to these diseases again. The most important things you can do are (a) don’t ever pressure a doctor to prescribe them when they aren’t appropriate, and (b) fight their overuse in ranching, where they’re given as prophylactics to otherwise healthy animals — thus breeding deadly resistances.
Vaccines are antibiotics’ competitor for greatest public health victories. They’re small doses of dead or weakened viruses which are injected into you, letting your immune system learn to recognize and destroy the real ones when they come. They’re the reason that so many of the deadliest diseases of the past — smallpox, measles, pertussis, and the like — are things of the past. However, unscrupulous folks have tried at times to convince the public that these are dangerous (generally as part of a scheme involving lawsuits), and as a result, some people are avoiding them! This can cause many other people to die, because of what’s called herd immunity. You can learn more about vaccines from this great comic:
Pesticides are chemicals which kill pests which destroy crops. These are a dangerous, but important, tradeoff: their residues can be poisonous, especially if they accumulate in groundwater; they can kill insects which are not just beneficial, but critical, like bees; and their misuse can lead to monoculture, which we’ll talk about in a moment. On the upside, they greatly increase crop production, and have been a major factor in ending starvation. They can also kill insects like the tsetse fly and malaria mosquito which are major vectors of disease. Together, this makes them a powerful lifesaving tool which has to be carefully managed.
GMOs are any sorts of organisms whose genes have been modified. This is a blanket term for a wide range of things, from corn that produces additional nutrients, to wheat that can grow in a wide range of climates, to goats which can produce antibiotics in their milk (!), to crops which are immune to certain pesticides and herbicides. “GMO” is a term for the technique which produces all of these. Some of these are huge benefits, but some of them are dangerous: for example, herbicide-resistant crops can be doused with huge doses of powerful weed-killers. In addition to their normal risks, this creates what’s called a “monoculture,” where only one species of plant can survive. This can make an entire crop vulnerable to a single blight, so it’s extremely dangerous for food security. Also, many companies who make such products are known for unethical business practices, so many people hear “GMO” and think of them. But don’t be led astray! GM is a technique which saves lives, too.
Balloons may make you think of things at birthday parties, but they’re also the best way to get high into the stratosphere. Weather balloons, made of modern materials like mylar and kevlar and filled with Helium, can fly over 100,000’ above the ground fairly cheaply, making it possible to understand weather patterns in places where satellites can’t be. They were also the way the recent record-breaking skydivers got up: you can watch Alan Eustace’s record-breaking jump at https://www.youtube.com/watch?v=AsftfzBrVko. In the process of doing this, he and his team invented several new technologies which should make flight safer, balloons cheaper, and more.
Tubesocks are long socks which can protect your shins. More important than protection, they wick moisture away from your feet, which are some of the heaviest sweat-producers in your body: they can produce as much as a quarter-pint of sweat each day. By moving the moisture away, they can protect you from frostbite in the cold, and fungi like athlete’s foot in the heat.
Testicles are the organs in which sperm is produced in male animals. They’re also important glands, producing hormones such as testosterone which help regulate bodily function. They hang outside the body in most land mammals in a sac called the scrotum, because sperm production works best when the testes are kept below body temperature. Because your body considers them pretty important, they’re therefore covered with nerves to quickly tell if something’s wrong. That means that you don’t want to hit them, but that they often enjoy gentle touch.
Bunnies, also known as rabbits, are small mammals with big ears. They’re shy herbivores, depending for their survival upon their ability to hear and quickly run away from prey – but also on their ability to reproduce quickly, so that their groups can sustain losses and keep going. Most species of rabbit live in burrows, often networked together to form a warren. People’s opinions of them are split: some people raise them for food or fur, while others love them as pets. They can also turn into a plague, as happened when they were introduced into Australia: feral rabbits caused tremendous damage to agriculture and local species. You can see many pictures of bunnies at http://goo.gl/FVlVJD.
Strippers are a kind of sex worker. Most famously, they perform erotic dances (often using a fixed pole as a prop) for an audience. But most of their work takes the form of one-on-one interaction with patrons, performing individually for them in settings from the public (such as table dances) to private rooms. Strippers will create one or more personas for this, working to create a fantasy environment for the patron in which they feel aroused, appreciated, and at the center of attention. Many strippers travel from city to city around the year, as the best business is often found in different places at different times. The most important thing to remember about strippers is that, while they may be playing any number of roles that seem different, they are professional entertainers and should be treated with respect.
Dromedaries are the famous “one-humped camels” of the Sahara and Arabian deserts. Their two-humped Bactrian cousins live further east. Dromedaries are known for their incredible ability to store water in their bodies, allowing them to travel across the entire desert. Unlike horses, they have paws rather than hooves, which gives them excellent traction on difficult terrain. As a result, they are highly valued as pack and riding animals, and camel racing is a major sport. Dromedaries were what made the Spice Road and the western part of the Silk Road possible, and they continue to be an important way to transport people and goods across the desert to this day.
So next time someone shows you a list like this, think through all of the various items in them and realize all of the ways in which they’ve made our world a better place. Some of them, like pesticides and bunnies, involve tradeoffs which you need to manage carefully; others, like antibiotics and vaccines, simply need to be used correctly to make the world a better place.
I really enjoy Compound Interest’s post and this one follows my Christkindlmarket post nicely. Glühwein anyone? Make sure you click on the link and not just the infographic or you’ll miss these gems:
Eugenol also has a mild anaesthetic effect, which is one of the reasons that clove oil is occasionally used as a traditional remedy for toothache.
Myristicin actually lends nutmeg hallucinogenic qualities, but only in doses larger than those commonly used in cooking and mulled wine making. Allegedly, the effects of ingesting the nutmeg required are none-too-pleasant, so it isn’t an experience that comes recommended!
Cinnamaldehyde, which makes up around 90% of the essential oil of cinnamon bark, is the main contributor to this flavour, and to the aroma of cinnamon. It has also previously been added to chewing gums, and research has shown it to have some antimicrobial effects.
#ScienceEveryday
Originally shared by Compound Interest
Not much beats a mug of mulled wine on a cold winter’s evening. Here’s a breakdown of some selected chemical ingredients: http://wp.me/p4aPLT-QJ
In the infographic below, they bust the myth about chloroform being used for nefarious activity. Chloroform takes about 5 minutes to have an effect. That’s not what’s portrayed in the movies.
Maybe Compound Chemistry will inspire posts by our resident chemist, Siromi Samarasinghe.
Clearly #Sacks4Science needs to be a thing to support testicular cancer research and fight sexism in science. Since I don’t have a post about testicular cancer, I’m re-sharing this post about prostate cancer. Let me explain where the #Sacks4Science hashtag is coming from.
There’s a post about a group in Italy that want to promote science by showing pictures of breasts with a sign about science.
That is almost as bad as the #HUGS4JUGS “campaign”. The only time that breasts should be mentioned in a conversation about science, is if the science is about breasts.
Some pedantic arguing ensued on that thread, so I turned my attention back to science. I’m working on data to see if a new imaging agent can detect if a tissue is positive for the progesterone receptor, which would guide therapy choices without invasive biopsies.
In a conversation about the boobs for science post, Rachel Blum said
Clearly: ask for guys to do a shot of their penis untying at an important section in a scientific paper. Share a few shopped ones with the MOAR BOOBS crowd.
“Oh, that makes you uncomfortable? But it’s FOR SCIENCE”.
I mention it should be for prostate cancer awareness or show your balls for testicular cancer awareness. I bet a lot of bros will jump on that bandwagon.
Then Buddhini Samarasinghe said, we should call the campaign “Sacks for Science”. We all agreed that #Sacks4Science needs to be a thing. So support #Movember and prostate cancer awareness. Support science, without sensationalizing it. And if you’re ready to jump on the bandwagon, help us support #Sacks4Science to support testicular cancer research and fight sexism in STEM.
#ScienceEveryday
Originally shared by Chad Haney
The real #Movember for #ScienceSunday .
Most of you probably know that the pink ribbon in October means, breast cancer awareness month. I disagree with the commercialization of the pink ribbon and attempts to trademark it, but that’s another story. I want to talk about Movember. You’ve seen the mustaches and the hashtag. How many of you know it is for men’s health awareness? Specifically prostate and testicular cancer. I’m going to focus on prostate cancer.
PSA about PSA
Public service announcement about prostate-specific antigen screening: For many years, PSA testing was suggested to start at age 40. The current recommendation:
The American Cancer Society recommends that men discuss the possible risks and benefits of prostate cancer screening with their doctor before deciding whether to be screened. The discussion about screening should take place starting at age 50 for men who are at average risk of prostate cancer and expect to live at least 10 more years. It should take place at age 45 for men who are at higher risk, including African-American men and men who have a father or brother diagnosed with prostate cancer, and at age 40 for men at even higher risk.
For many years researchers in the trenches were finding that PSA screening often led to false positives. There’s too much variability in the PSA screening method.
Ex vivo MRI
The purpose of the study that I’m presenting was to take advantage of higher resolution MRI, using ex vivo samples in a pre-clinical high field MRI scanner (9.4T vs. 1.5T clinical MRI). Histology is orders of magnitude higher resolution even compared to the pre-clinical scanner. The idea was that better MRI images could be correlated with histology. Ultimately decisions are made based on histology, typically via biopsy. Identifying which features in MRI correlate with histology could set up a feed back loop to improve the in vivo MRI images. What’s shown below is an early proof of concept study.
I don’t know the PSA scores for the patients in the study below, but I’m sure they were high enough to justify biopsies. We were blinded to patient names and a lot of their health records for both privacy reasons and to remove bias. There are risks and side effects associated with getting a prostate biopsy. That’s part of the reason for changing the PSA screening recommendations. If you are curious what a human prostate looks like, there’s one pictured below. It’s about the size of the palm of your hand (at least my hand).
The other two figures show what the prostate looks like using MRI (panel A, C, and D) and histology (panel B). Panel A is a T2-weighted spin echo image. Panel C is a T2 map, i.e. a display of the actual T2 values. Panel D is an apparent diffusion coefficient (ADC) map. You can review the MRI terminology in the link below.
The first figure, which outlines the cancer with a dotted line in the histology image is from a 71-year-old patient. The second is from a 63-year-old patient without malignant cancer. In the examples below it isn’t obvious which MRI parameter best correlates with cancer. In the 71-year-old patient, the low T2 values along with low ADC values appears to correlate well with the tumor outlined in the histology slide. However, the 63-year-old patient also displays low ADC values, whereas the T2 values are higher. Overall, with 9 patients, the T2 values were about 10 msec longer (P < 0.03) and the average ADC values were about 1.4 times larger (P < 0.002) when comparing normal peripheral zones vs. cancerous peripheral zones. With a larger sample size we hope to improve the correlation between both the in vivo and ex vivo MRI with histology.
References:
Medical Imaging 101 pt 3: MRI from my #CHMedicalImagingSeries
Science Friday host Ira Flatow joins Sound Opinions hosts Jim DeRogatis and Greg Kot to discuss music and science. Then Jim and Greg dissect The Wall by Pink Floyd. The Wall (album) was released on 30 November 1979 almost 35 years ago. The movie followed in 1982. I have to agree with Jim and Greg’s statement that Waters had the creative genius that Gilmour lacked and Waters was nothing without Gilmour’s unique musical talent. In other words, they needed each other and Pink Floyd wasn’t as good after the split. They also discuss Wright and Mason’s contributions, just so you don’t think it’s all Waters and Gilmour. So have a listen. You might want to download the podcast.
References:
Your Brain on Jazz
Dr. Charles Limb from Johns Hopkins University discusses how jazz improvisation is like wordless communication, i.e., it uses the part of the brain for language. (see the PLoS One link within).
Ira Flatow mentioned a study where twins were used to determine how much practice plays a role in learning to play an instrument vs. the genetic influence.
Snow leopards have declined in population by 20 percent over the past two decades—primarily due to human activity—but in one community, the cat lives on.
