Donald Rasmussen: Coal miners’ physician, humble man [The Pump Handle]

During the holiday season, Kim, Liz and I are taking a short break from blogging.  We are posting some of our favorite posts from the past year. Here’s one of them, originally posted on July 27, 2015:

by Celeste Monforton, DrPH, MPH

The occupational health community, coal miners, their families and labor advocates are mourning the loss of physician Donald Rasmussen, 87.

For more than 50 years, he diagnosed and treated coal miners with work-related lung disease, first at the then Miners Memorial Hospital in Beckley, WV and later at his own black lung clinic. A lengthy story by John Blankenship in Beckley’s Register-Herald written two years ago profiledDr. Rasmussen’s career.

“ In 1962, a young doctor from Manassa, Colorado, saw a help wanted advertisement in a medical journal needing doctors in Beckley at the then Miners Memorial Hospital. ‘I was looking for a place to set up practice after getting out of the Army,’ Rasmussen recalled. ‘I had never been to West Virginia and was a little skeptical about the move.’ But when the doctor arrived in Beckley he was impressed with what he saw. ‘The scenic beauty of the area, the wonderful people who lived here and the staff and the work going on at the Miners hospital were simply amazing.’”

“Rasmussen began working with coal miners, which would become his life’s mission. ‘Before I came here, I really had no exposure or knowledge about coal miner’s lung disease, known today as black lung,’ he said. Rasmussen says he began to see many miners who experienced shortness of breath and other trouble with their lungs and breathing. ‘I was asked to evaluate some of the miners.’”

“…For coal miners and their families, Rasmussen became known as the ‘doctor with a heart.’ But Rasmussen said he was just doing his job. “I wasn’t trying to take one side over another,” he explained. ‘But I saw a lot of injustice being done to coal miners and their families.’”

Evan Smith with the Appalachian Citizens’ Law Center writes:

“There is no single source that can catch the breadth of his work, but any account of the black lung movement and the current state of the disease must include his name. In the early days of the black lung movement, Dr. Rasmussen was one of the key players in the group called Physicians for the Miners’ Health and Safety that provided medical support for miners’ experiences with black lung—a disease that most of the medical community refused to acknowledge at the time.

Dr. Rasmussen’s evidence-based approach and detailed research helped to prove that coal-mine dust causes breathing problems that may not show up on x-ray and may not show up without quality exercise testing. Dr. Rasmussen’s advocacy contributed to the passage of the landmark 1969 Coal Act which set the first federal limits on miners’ exposure to coal-mine dust and created the federal black lung benefits system for miners disabled by the disease.

The Charleston (WV) Gazette’s Paul J. Nyden explains Rasmussen’s role in the larger fight for worker health and safety:

“Rasmussen, Dr. Isadore E. Buff and Dr. Hawey Wells helped spark growing concerns about black lung disease throughout the coalfields, when they spoke in union halls, schools and churches. The black lung issue came to statewide and national attention after a Nov. 20, 1968, methane and coal dust explosion killed 78 miners in Consolidation Coal’s No. 9 Mine between Mannington and Fairmont in Marion County. “

“In the wake of that tragedy, miners at the East Gulf Mine near Rhodell walked out on strike on Feb. 18, 1969, protesting the failure of the state Legislature to pass black lung legislation. By March 5, when the state Senate began debating the bill, more than 40,000 of the state’s 43,000 miners were on strike. Rasmussen, Buff and Wells played a central role in backing the strike and pressuring the state Legislature to pass its first black lung law. They helped counter many medical professionals who continued to deny that black lung was a serious health threat. After then-Gov. Arch Moore signed the bill on March 11, miners returned to work the next morning. “

Rasmussen’s early papers include “Pulmonary impairment in southern West Virginia coal miners” (Am Rev Respir Dis (1968)), “Respiratory function in southern Appalachian coal miners (Am Rev Respir Dis (1971)), “Patterns of physiological impairment in coal workers’ pneumoconiosis” (Ann N Y Acad Sci (1972)), and “Impairment of oxygen transfer in dyspneic, nonsmoking soft coal miners (J Occup Med (1971)).

Physicians who worked with Dr. Rasmussen are offering their own tributes. Karen Mulloy, an occupational medicine physician at Case Western Reserve University told me:

“He was an exceptional human being. I had the privilege of working for him for 5 years from 1970 to
1975. It was my first job in the medical field, as a cardio-pulmonary technician, testing the miners in his lab for Black Lung. His compassion for the miners and his righteous anger over the inequities that faced them and the coal companies refusal to make the coal mines safe was more than inspiring. His example of how a doctor of the people could be was the reason I went to medical school and has been the guiding principle of my life.”

Robert Cohen, MD, an expert in pulmonary medicine at Northwestern University Feinberg School of Medicine, told me:

“I first met Don in 1994 at a Black Lung clinics conference and have been in touch with him, advised by him, and mentored by him ever since. He was a gentle, soft spoken man with a huge heart, who worked tirelessly to merge science and clinical medicine with his passion for social justice, and in this case, to give coal miners a fair shake in the battle to be compensated for their occupational illness.”

“His early work on the exercise physiology of black lung disease lead to the inclusion of exercise testing with arterial blood gases in the black lung disability evaluation regulations. “

J. Davitt McAteer, one of the nation’s leading experts on miners’ health and safety, added this:

“When the definitive history of the black lung issue is written, Dr. Donald Rasmussen will be recognized as the central figure. By bringing scientific evidence to the debate, he created the momentum which resulted in the passage of state and federal laws to protect miners’ health.”

McAteer attended Dr. Rasmussen’s memorial service and sent along a copy of a eulogy. It was offered by Craig Robinson who was a VISTA volunteer in the 1960’s when he first met Dr. Rasmussen. Robinson remarks on a recent meeting of Rasmussen and former ABC anchor Ted Koppel.

Joe Main, the assistant secretary of labor for mine safety and health, and former H&S director for the United Mine Workers issued a statement saying:

“The coal mining community has lost one of its most passionate advocates. …Dr. Rasmussen was a humble man, and he would say he was merely a physician performing his duty to his patients. But for so many of us who shared his vision, he was a hero. He will be greatly missed by miners and their families across the country whose lives he touched.”

Dr. Rasmussen passed away on July 23. He continued to see patients in his clinic until May 2015 when he suffered a fall. His family says “he’s now moved his offices upstairs.”

[Update (8/3/15): The New York Times’ published on 8/2/15 an obituary about Dr. Rasmussenentitled “Crusader for Coal Miners’ Health.”]

from ScienceBlogs http://ift.tt/1Ts3qpm

During the holiday season, Kim, Liz and I are taking a short break from blogging.  We are posting some of our favorite posts from the past year. Here’s one of them, originally posted on July 27, 2015:

by Celeste Monforton, DrPH, MPH

The occupational health community, coal miners, their families and labor advocates are mourning the loss of physician Donald Rasmussen, 87.

For more than 50 years, he diagnosed and treated coal miners with work-related lung disease, first at the then Miners Memorial Hospital in Beckley, WV and later at his own black lung clinic. A lengthy story by John Blankenship in Beckley’s Register-Herald written two years ago profiledDr. Rasmussen’s career.

“ In 1962, a young doctor from Manassa, Colorado, saw a help wanted advertisement in a medical journal needing doctors in Beckley at the then Miners Memorial Hospital. ‘I was looking for a place to set up practice after getting out of the Army,’ Rasmussen recalled. ‘I had never been to West Virginia and was a little skeptical about the move.’ But when the doctor arrived in Beckley he was impressed with what he saw. ‘The scenic beauty of the area, the wonderful people who lived here and the staff and the work going on at the Miners hospital were simply amazing.’”

“Rasmussen began working with coal miners, which would become his life’s mission. ‘Before I came here, I really had no exposure or knowledge about coal miner’s lung disease, known today as black lung,’ he said. Rasmussen says he began to see many miners who experienced shortness of breath and other trouble with their lungs and breathing. ‘I was asked to evaluate some of the miners.’”

“…For coal miners and their families, Rasmussen became known as the ‘doctor with a heart.’ But Rasmussen said he was just doing his job. “I wasn’t trying to take one side over another,” he explained. ‘But I saw a lot of injustice being done to coal miners and their families.’”

Evan Smith with the Appalachian Citizens’ Law Center writes:

“There is no single source that can catch the breadth of his work, but any account of the black lung movement and the current state of the disease must include his name. In the early days of the black lung movement, Dr. Rasmussen was one of the key players in the group called Physicians for the Miners’ Health and Safety that provided medical support for miners’ experiences with black lung—a disease that most of the medical community refused to acknowledge at the time.

Dr. Rasmussen’s evidence-based approach and detailed research helped to prove that coal-mine dust causes breathing problems that may not show up on x-ray and may not show up without quality exercise testing. Dr. Rasmussen’s advocacy contributed to the passage of the landmark 1969 Coal Act which set the first federal limits on miners’ exposure to coal-mine dust and created the federal black lung benefits system for miners disabled by the disease.

The Charleston (WV) Gazette’s Paul J. Nyden explains Rasmussen’s role in the larger fight for worker health and safety:

“Rasmussen, Dr. Isadore E. Buff and Dr. Hawey Wells helped spark growing concerns about black lung disease throughout the coalfields, when they spoke in union halls, schools and churches. The black lung issue came to statewide and national attention after a Nov. 20, 1968, methane and coal dust explosion killed 78 miners in Consolidation Coal’s No. 9 Mine between Mannington and Fairmont in Marion County. “

“In the wake of that tragedy, miners at the East Gulf Mine near Rhodell walked out on strike on Feb. 18, 1969, protesting the failure of the state Legislature to pass black lung legislation. By March 5, when the state Senate began debating the bill, more than 40,000 of the state’s 43,000 miners were on strike. Rasmussen, Buff and Wells played a central role in backing the strike and pressuring the state Legislature to pass its first black lung law. They helped counter many medical professionals who continued to deny that black lung was a serious health threat. After then-Gov. Arch Moore signed the bill on March 11, miners returned to work the next morning. “

Rasmussen’s early papers include “Pulmonary impairment in southern West Virginia coal miners” (Am Rev Respir Dis (1968)), “Respiratory function in southern Appalachian coal miners (Am Rev Respir Dis (1971)), “Patterns of physiological impairment in coal workers’ pneumoconiosis” (Ann N Y Acad Sci (1972)), and “Impairment of oxygen transfer in dyspneic, nonsmoking soft coal miners (J Occup Med (1971)).

Physicians who worked with Dr. Rasmussen are offering their own tributes. Karen Mulloy, an occupational medicine physician at Case Western Reserve University told me:

“He was an exceptional human being. I had the privilege of working for him for 5 years from 1970 to
1975. It was my first job in the medical field, as a cardio-pulmonary technician, testing the miners in his lab for Black Lung. His compassion for the miners and his righteous anger over the inequities that faced them and the coal companies refusal to make the coal mines safe was more than inspiring. His example of how a doctor of the people could be was the reason I went to medical school and has been the guiding principle of my life.”

Robert Cohen, MD, an expert in pulmonary medicine at Northwestern University Feinberg School of Medicine, told me:

“I first met Don in 1994 at a Black Lung clinics conference and have been in touch with him, advised by him, and mentored by him ever since. He was a gentle, soft spoken man with a huge heart, who worked tirelessly to merge science and clinical medicine with his passion for social justice, and in this case, to give coal miners a fair shake in the battle to be compensated for their occupational illness.”

“His early work on the exercise physiology of black lung disease lead to the inclusion of exercise testing with arterial blood gases in the black lung disability evaluation regulations. “

J. Davitt McAteer, one of the nation’s leading experts on miners’ health and safety, added this:

“When the definitive history of the black lung issue is written, Dr. Donald Rasmussen will be recognized as the central figure. By bringing scientific evidence to the debate, he created the momentum which resulted in the passage of state and federal laws to protect miners’ health.”

McAteer attended Dr. Rasmussen’s memorial service and sent along a copy of a eulogy. It was offered by Craig Robinson who was a VISTA volunteer in the 1960’s when he first met Dr. Rasmussen. Robinson remarks on a recent meeting of Rasmussen and former ABC anchor Ted Koppel.

Joe Main, the assistant secretary of labor for mine safety and health, and former H&S director for the United Mine Workers issued a statement saying:

“The coal mining community has lost one of its most passionate advocates. …Dr. Rasmussen was a humble man, and he would say he was merely a physician performing his duty to his patients. But for so many of us who shared his vision, he was a hero. He will be greatly missed by miners and their families across the country whose lives he touched.”

Dr. Rasmussen passed away on July 23. He continued to see patients in his clinic until May 2015 when he suffered a fall. His family says “he’s now moved his offices upstairs.”

[Update (8/3/15): The New York Times’ published on 8/2/15 an obituary about Dr. Rasmussenentitled “Crusader for Coal Miners’ Health.”]

from ScienceBlogs http://ift.tt/1Ts3qpm

Protecting waterways, one lasagna pan at a time

by Jennie Saxe

How can a mundane task, like washing dishes, protect local waterways like the Delaware River? It’s simple! When you roll up your sleeves to scrub that lasagna pan, reach for a dish soap with EPA’s Safer Choice label. Formerly known as EPA’s Design for the Environment (DfE) program, the Safer Choice label indicates products that have safer chemical ingredients and meet quality and performance standards.

Products with the Safer Choice label have been reviewed to make sure they use chemicals from EPA’s Safer Chemicals Ingredients List that do their specific job (for example, as solvents – needed to dissolve substances – or antimicrobials that limit or prevent bacterial growth) and are safer for aquatic life after they go down the drain. Safer Choice labeled products, like laundry detergent and dish soap, are reviewed to make sure that their ingredients and the break-down products (or “degradates” for the chemists out there) are not carcinogens, toxics, or persistent in the environment.

If the products are “greener” when they go down the drain, they’ll have less of an impact on aquatic life if they do happen to make their way through the wastewater treatment process. There is even a subset of Safer Choice products that are labeled for use in situations, such as cleaning your boat, where they could be directly released to the environment.

Check out the list of products that have received the Safer Choice label, and look for them at a store near you!

 

About the author: Dr. Jennie Saxe joined EPA’s Mid-Atlantic Region in 2003 and works in the Water Protection Division on sustainability programs.

 

from The EPA Blog http://ift.tt/1TrVjJw

by Jennie Saxe

How can a mundane task, like washing dishes, protect local waterways like the Delaware River? It’s simple! When you roll up your sleeves to scrub that lasagna pan, reach for a dish soap with EPA’s Safer Choice label. Formerly known as EPA’s Design for the Environment (DfE) program, the Safer Choice label indicates products that have safer chemical ingredients and meet quality and performance standards.

Products with the Safer Choice label have been reviewed to make sure they use chemicals from EPA’s Safer Chemicals Ingredients List that do their specific job (for example, as solvents – needed to dissolve substances – or antimicrobials that limit or prevent bacterial growth) and are safer for aquatic life after they go down the drain. Safer Choice labeled products, like laundry detergent and dish soap, are reviewed to make sure that their ingredients and the break-down products (or “degradates” for the chemists out there) are not carcinogens, toxics, or persistent in the environment.

If the products are “greener” when they go down the drain, they’ll have less of an impact on aquatic life if they do happen to make their way through the wastewater treatment process. There is even a subset of Safer Choice products that are labeled for use in situations, such as cleaning your boat, where they could be directly released to the environment.

Check out the list of products that have received the Safer Choice label, and look for them at a store near you!

 

About the author: Dr. Jennie Saxe joined EPA’s Mid-Atlantic Region in 2003 and works in the Water Protection Division on sustainability programs.

 

from The EPA Blog http://ift.tt/1TrVjJw

Are the December solstice and January perihelion related?

Earth comes closest to the sun on January 2, 2016 at around 23 UTC. This event is called Earth’s perihelion. Meanwhile, the December solstice took place on December 22. At perihelion in January, Earth is about 147 million kilometers from the sun, in contrast to about 152 million kilometers in July. At the solstice, Earth’s Southern Hemisphere is tilted most toward the sun; it’s the height of summer in that hemisphere. Are the December solstice and January perihelion related? No. It’s just a coincidence that they come so close together.

The date of Earth’s perihelion drifts as the centuries pass. These two astronomical events are separated by about two weeks for us. But they were closer a few centuries ago – and in fact happened at the same time in 1246 AD.

As the centuries continue to pass, these events will drift even farther apart. On the average, one revolution of the Earth relative to perihelion is about 25 minutes longer than one revolution relative to the December solstice. Perihelion advances one full calendar date every 60 or so years.

Earth’s perihelion – or closest point to the sun – will happen at the same time as the March equinox in about 6000 AD.

Earth and sun via ISS Expedition 13 / NASA.

Bottom line: December solstice 2015 was December 22. Earth is closest to the sun in 2016 on January 2. Despite their nearness in time, these two events are not related.

Earth closest to the sun on January 2, 2016

Everything you need to know: December solstice

Why does the New Year begin on January 1?

from EarthSky http://ift.tt/1BsSUVq

Earth comes closest to the sun on January 2, 2016 at around 23 UTC. This event is called Earth’s perihelion. Meanwhile, the December solstice took place on December 22. At perihelion in January, Earth is about 147 million kilometers from the sun, in contrast to about 152 million kilometers in July. At the solstice, Earth’s Southern Hemisphere is tilted most toward the sun; it’s the height of summer in that hemisphere. Are the December solstice and January perihelion related? No. It’s just a coincidence that they come so close together.

The date of Earth’s perihelion drifts as the centuries pass. These two astronomical events are separated by about two weeks for us. But they were closer a few centuries ago – and in fact happened at the same time in 1246 AD.

As the centuries continue to pass, these events will drift even farther apart. On the average, one revolution of the Earth relative to perihelion is about 25 minutes longer than one revolution relative to the December solstice. Perihelion advances one full calendar date every 60 or so years.

Earth’s perihelion – or closest point to the sun – will happen at the same time as the March equinox in about 6000 AD.

Earth and sun via ISS Expedition 13 / NASA.

Bottom line: December solstice 2015 was December 22. Earth is closest to the sun in 2016 on January 2. Despite their nearness in time, these two events are not related.

Earth closest to the sun on January 2, 2016

Everything you need to know: December solstice

Why does the New Year begin on January 1?

from EarthSky http://ift.tt/1BsSUVq

Why does the new year begin on January 1?

Photo credit: Daniel Moile

The date of New Year’s Day seems so fundamental that it’s almost as though nature ordained it. But New Year’s Day is a civil event. Its date isn’t precisely fixed by any natural seasonal marker.

Our modern celebration of New Year’s Day stems from an ancient Roman custom, the feast of the Roman god Janus – god of doorways and beginnings. The name for the month of January also comes from Janus, who was depicted as having two faces. One face of Janus looked back into the past, and the other peered forward to the future.

For us in the Northern Hemisphere, early January is a logical time for new beginnings. At the December solstice in the Northern Hemisphere, we had the shortest day of the year. By early January, our days are obviously lengthening again. This return of longer hours of daylight had a profound effect on cultures that were tied to agricultural cycles. It has an emotional effect on people even in cities today.

Everything you need to know: December solstice

The early calendar-makers didn’t know it, but today we know there is another bit of astronomical logic behind beginning the year on January 1. Earth is always closest to the sun in its yearly orbit around this time. This event is called Earth’s perihelion.

People didn’t always celebrate the new year on January 1. The earliest recording of a new year celebration is believed to have been in Mesopotamia, circa 2000 B.C. That celebration – and many other ancient celebrations of the new year following it – were celebrated around the time of the vernal equinox, around March 20. Meanwhile, the ancient Egyptians, Phoenicians, and Persians began their new year with the autumnal equinox around September 20. And the ancient Greeks celebrated on the winter solstice, around December 20.

By the Middle Ages, though, in many places the new year began in March. Around the 16th century, a movement developed to restore January 1 as New Year’s Day. In the New Style or Gregorian calendar, the New Year begins on the first of January.

Enjoying EarthSky? Sign up for our free daily newsletter today!

Bottom line: There’s no astronomical reason to celebrate New Year’s Day on January 1. Instead, our modern New Year’s celebration stems from the ancient, two-faced, Roman god Janus – for whom the month of January is also named. One face of Janus looked back into the past, and the other peered forward to the future.

from EarthSky http://ift.tt/1vdAyn3

Photo credit: Daniel Moile

The date of New Year’s Day seems so fundamental that it’s almost as though nature ordained it. But New Year’s Day is a civil event. Its date isn’t precisely fixed by any natural seasonal marker.

Our modern celebration of New Year’s Day stems from an ancient Roman custom, the feast of the Roman god Janus – god of doorways and beginnings. The name for the month of January also comes from Janus, who was depicted as having two faces. One face of Janus looked back into the past, and the other peered forward to the future.

For us in the Northern Hemisphere, early January is a logical time for new beginnings. At the December solstice in the Northern Hemisphere, we had the shortest day of the year. By early January, our days are obviously lengthening again. This return of longer hours of daylight had a profound effect on cultures that were tied to agricultural cycles. It has an emotional effect on people even in cities today.

Everything you need to know: December solstice

The early calendar-makers didn’t know it, but today we know there is another bit of astronomical logic behind beginning the year on January 1. Earth is always closest to the sun in its yearly orbit around this time. This event is called Earth’s perihelion.

People didn’t always celebrate the new year on January 1. The earliest recording of a new year celebration is believed to have been in Mesopotamia, circa 2000 B.C. That celebration – and many other ancient celebrations of the new year following it – were celebrated around the time of the vernal equinox, around March 20. Meanwhile, the ancient Egyptians, Phoenicians, and Persians began their new year with the autumnal equinox around September 20. And the ancient Greeks celebrated on the winter solstice, around December 20.

By the Middle Ages, though, in many places the new year began in March. Around the 16th century, a movement developed to restore January 1 as New Year’s Day. In the New Style or Gregorian calendar, the New Year begins on the first of January.

Enjoying EarthSky? Sign up for our free daily newsletter today!

Bottom line: There’s no astronomical reason to celebrate New Year’s Day on January 1. Instead, our modern New Year’s celebration stems from the ancient, two-faced, Roman god Janus – for whom the month of January is also named. One face of Janus looked back into the past, and the other peered forward to the future.

from EarthSky http://ift.tt/1vdAyn3

Sirius midnight culmination New Years Eve

Tonight – December 31, 2015 – look up for the brightest star in the sky, Sirius, in the constellation Canis Major. This star is up in the evening every year at this time, and – from all parts of Earth (except those far-southern realms in continuous daylight now) – Sirius is easy to identify. December 31 is a special night, the end of a calendar year. And it’s a special night for Sirius, too. This star’s official midnight culmination – when it’s highest in the sky at midnight – comes only once every year. And tonight’s the night.

The New Year always begins with Sirius’ culmination at the midnight hour. It’s a fun sky event to watch for, if you happen to be outside at midnight on this night.

From the Northern Hemisphere … look toward the south, and you’ll easily notice Sirius shining there.

From the Southern Hemisphere … look overhead or high in the north.

This star is so bright that you might notice it twinkling fiercely, especially from northerly latitudes, where the star stays closer to the horizon.

You might even see it flashing different colors – just hints of colors from red to blue – like the celestial counterpart to an earthly diamond.

The three stars of Orion’s Belt always point to the sky’s brightest star, Sirius. This photo comes from EarthSky Facebook friend Susan Jensen in Odessa, Washington. Thank you, Susan!

By the way, by midnight, we mean the middle of the night, midway between sunset and sunrise.

The midnight culmination of Sirius by the clock may be off by as much as one-half hour or so, depending on how far east or west you live from the meridian that governs your time zone.

Transit (midnight culmination) times for Sirius in your sky

Bottom line: If you’re celebrating the New Year tonight, and you happen to gaze up at the sky, look for Sirius – and take a moment to celebrate the sky’s brightest star.

Donate: Your support means the world to us

from EarthSky http://ift.tt/1B0cJDP

Tonight – December 31, 2015 – look up for the brightest star in the sky, Sirius, in the constellation Canis Major. This star is up in the evening every year at this time, and – from all parts of Earth (except those far-southern realms in continuous daylight now) – Sirius is easy to identify. December 31 is a special night, the end of a calendar year. And it’s a special night for Sirius, too. This star’s official midnight culmination – when it’s highest in the sky at midnight – comes only once every year. And tonight’s the night.

The New Year always begins with Sirius’ culmination at the midnight hour. It’s a fun sky event to watch for, if you happen to be outside at midnight on this night.

From the Northern Hemisphere … look toward the south, and you’ll easily notice Sirius shining there.

From the Southern Hemisphere … look overhead or high in the north.

This star is so bright that you might notice it twinkling fiercely, especially from northerly latitudes, where the star stays closer to the horizon.

You might even see it flashing different colors – just hints of colors from red to blue – like the celestial counterpart to an earthly diamond.

The three stars of Orion’s Belt always point to the sky’s brightest star, Sirius. This photo comes from EarthSky Facebook friend Susan Jensen in Odessa, Washington. Thank you, Susan!

By the way, by midnight, we mean the middle of the night, midway between sunset and sunrise.

The midnight culmination of Sirius by the clock may be off by as much as one-half hour or so, depending on how far east or west you live from the meridian that governs your time zone.

Transit (midnight culmination) times for Sirius in your sky

Bottom line: If you’re celebrating the New Year tonight, and you happen to gaze up at the sky, look for Sirius – and take a moment to celebrate the sky’s brightest star.

Donate: Your support means the world to us

from EarthSky http://ift.tt/1B0cJDP

Protein modeling and the Siamese cat [Discovering Biology in a Digital World]

“By night all cats are gray”  – Miguel Cervantes in Don Quixote

 

I’ve always liked Siamese cats.   Students do, too.  “Why Siamese cats wear masks” is always a favorite story in genetics class.  So, when I opened my January copy of The Science Teacher, I was thrilled to see an article on Siamese cat colors and proteins AND molecular genetics (1).

In the article, the authors (Todd and Kenyon) provide some background information on the enzymatic activity of tyrosinase and compare it to the catechol oxidase that causes fruit to brown, especially apples.  Tyrosinase catalyzes the first step of a biochemical pathway where tyrosine is converted to dopaquinone and then to the dark colored substance, melanin.  Melanin is responsible for the brown color in the ears, paws, tail, and face of Siamese cats.

Melanin in Molecule World

 

 

 

 

 

 

 

 

 

 

 

The fun part of the story is that some versions of the tyrosinase gene have a mutation that makes this enzyme less stable at warmer temperatures.  In warmer areas of the cat’s body, less melanin is produced, giving the cat a lighter colored body.

I love the story of the coat coloring  and I think this activity has the potential to interest students.

I also like the approach that the authors take with discussing proteins and the associated phenotypes first before getting into DNA and the central dogma.  I use this same order in my bioinformatics class.

There are, however, a few things that I would change with this activity.

Too many hydroxyl groups

First, the article and the teacher guide have the structure of tyrosine wrong.  Tyrosine only has one hydroxyl group attached to the six-carbon ring, as shown below, not two hydroxyl groups as shown in the article and the teachers’ guide.

Tyrosinase reaction from Teachers’ Guide. The extra hydroxyl group is marked.

 

 

 

 

 

 

 

Space-filling models of Tyrosine and Dopaquinone downloaded from the NCBI’s PubChem database are shown below.

Tyrosine and dopaquinone

 

 

 

 

 

 

 

Too many proteins in too short a time

Second, I think the authors include way too many different protein stories and different explanations for why a protein might be inactivated.  Todd and Kenyon have done quite a bit of work creating activities with several different proteins. But I think the plan to have students cover all eight proteins in six days would be too confusing for many students.  The activity has students read about or work with:  lactase, cellulase, tyrosinase, catechol oxidase, proteases, kinesin, galactosyl transferase, and tyrosine kinase, not to mention Gleevec and the way it interacts with the BCR-ABL fusion protein.  I teach a college bioinformatics course and even the best of my students would get confused by looking at eight different proteins without some kind of common thread.  The take home lesson that denaturation negatively impacts tyrosinase activity is easy to lose among all the unrelated activities.

Where are the 3D models?

My greatest disappointment though was that the article talked about having students look at 3D models and how students could look at molecules and see how they changed when they were denatured by heat or pH. I completely misinterpreted that description. If I were teaching this class, I would rather have students work first-hand with structure models instead the authors provide a link where students can watch a video on denaturation.

This is my bias, but I think an active learning approach, where students actually look at 3D protein and chemical models and identify chemical interactions, would be better in long run and better equip students for future learning. I think the common practice of hiding the biochemistry makes genetics much harder to understand and far less straightforward than it should be.

And, as it turns out there are 3D models of tyrosinase that students could use.  They’re from Bacillus megatherium, but that’s how biology works.  If an enzyme activity is beneficial, evolutionary processes tend to keep it around.

Using 3D Models to look at albino cats

No models exist from the Siamese cat protein with the brown ear point mutation, but it is possible to make 3D protein models that show the affect of a different mutation, in tyrosinase, that leads to albino cats. This mutation occurs when a cytosine is deleted at nucleotide 975, creating a frameshift (2).  To simulate the mutation’s effect, we can hide the amino acids that would be lost.  This model isn’t perfect because the shorter protein might fold somewhat differently, but this does provide a satisfying explanation for an inactive enzyme.

Here’s what to do:

1. Open Molecule World on the iPad (*).
2. Download 4P6R.
3. Color the protein chains by molecule.
4. Open the sequence viewer and touch the name of the last row to select it.  This row contains tyrosine, the substrate for the enzyme, and for each chain, two atoms of zinc.
5. Change the coloring style to element.

Now, you can see the substrate bound in the active site.  Notice this protein has two identical subunits.  Each one is bound to tyrosine and zinc.

Tyrosinase with tyrosine and zinc in the active site.

 

 

 

 

 

 

 

 

 

 

You may want to change the atom visibility to show all the atoms or just the core backbone, like I have here, to see how the tyrosine is positioned.

*Many of the things I describe here can be done in Cn3D, but it’s a bit more complicated.

 

Modeling the mutation’s affect

This next part is a little more complicated because I had to split the protein sequence into three parts to avoid introducing spaces.

1. Carry out the following process in three steps. First, copy the sequence below.KYRVRKNVLHLTDTEKRDFVRTVLIKEKGIYDRYIAWHGAAGKFHTPPGSDRNA
2. Touch the Selection button and paste the sequence below in the Select pattern window.
3. Start the search.  The pasted sequence will be highlighted in the protein sequence.
4. Copy the next part of the sequence (below).  Touch the Selection button again and search for this pattern as before.
   AHMSSAFLPWHREYLLRFERDQSINPEVTLPYWEWETDAQMQDPSQSQIWSADFMGGN
5. Copy the next part of the sequence (below).  Touch the Selection button again and search for this pattern as before.

   GNPIKDFIVDTGPFAAGRWTTIDEQGNPSGGLKRNFGATKAPTLPTRDDVL

6. When you’re done highlighting sequences, you’ll see each subunit has a region that appears brighter and a region in the center that appears more dim. The bright colored residues are incorporated into the protein before ribosomes encounter the frame shift mutation and a stop codon shortly afterwards. This portion of the protein can be produced in the albino cat.
7. Look at the dim areas of each subunit.  These amino acids would be lost when the frameshift mutation is present.  Notice where the tyrosine is located.

Residues that would be lost because of the frameshift mutant are shown in gray.

 

 

 

 

 

 

 

 

 

 

 

8.  To make the mutations affect on the protein even more clear, open the Show/Hide button and choose “Hide unselected.”  The amino acid residues that would be lost because of the mutation disappear.

Residues that would be lost because of the frame shift mutation are hidden.

 

 

 

 

 

 

 

 

 

 

Now, it’s really clear.  If the residues that bind tyrosine and modify it’s structure are gone, the enzyme is unable to function.  If we don’t have tyrosinase working to help make melanin, we get white cats.

 

References:

1. Amber Todd and Lisa Kenyon, How do Siamese cats get their color? The Science Teacher. 2016;83(1):29-36
2. Imes D, Geary L, Grahn R, Lyons L. Albinism in the domestic cat (Felis catus) is associated with a tyrosinase (TYR) mutation. Animal Genetics. 2006;37(2):175-178. doi:10.1111/j.1365-2052.2005.01409.x.

from ScienceBlogs http://ift.tt/1mr5yCU

“By night all cats are gray”  – Miguel Cervantes in Don Quixote

 

I’ve always liked Siamese cats.   Students do, too.  “Why Siamese cats wear masks” is always a favorite story in genetics class.  So, when I opened my January copy of The Science Teacher, I was thrilled to see an article on Siamese cat colors and proteins AND molecular genetics (1).

In the article, the authors (Todd and Kenyon) provide some background information on the enzymatic activity of tyrosinase and compare it to the catechol oxidase that causes fruit to brown, especially apples.  Tyrosinase catalyzes the first step of a biochemical pathway where tyrosine is converted to dopaquinone and then to the dark colored substance, melanin.  Melanin is responsible for the brown color in the ears, paws, tail, and face of Siamese cats.

Melanin in Molecule World

 

 

 

 

 

 

 

 

 

 

 

The fun part of the story is that some versions of the tyrosinase gene have a mutation that makes this enzyme less stable at warmer temperatures.  In warmer areas of the cat’s body, less melanin is produced, giving the cat a lighter colored body.

I love the story of the coat coloring  and I think this activity has the potential to interest students.

I also like the approach that the authors take with discussing proteins and the associated phenotypes first before getting into DNA and the central dogma.  I use this same order in my bioinformatics class.

There are, however, a few things that I would change with this activity.

Too many hydroxyl groups

First, the article and the teacher guide have the structure of tyrosine wrong.  Tyrosine only has one hydroxyl group attached to the six-carbon ring, as shown below, not two hydroxyl groups as shown in the article and the teachers’ guide.

Tyrosinase reaction from Teachers’ Guide. The extra hydroxyl group is marked.

 

 

 

 

 

 

 

Space-filling models of Tyrosine and Dopaquinone downloaded from the NCBI’s PubChem database are shown below.

Tyrosine and dopaquinone

 

 

 

 

 

 

 

Too many proteins in too short a time

Second, I think the authors include way too many different protein stories and different explanations for why a protein might be inactivated.  Todd and Kenyon have done quite a bit of work creating activities with several different proteins. But I think the plan to have students cover all eight proteins in six days would be too confusing for many students.  The activity has students read about or work with:  lactase, cellulase, tyrosinase, catechol oxidase, proteases, kinesin, galactosyl transferase, and tyrosine kinase, not to mention Gleevec and the way it interacts with the BCR-ABL fusion protein.  I teach a college bioinformatics course and even the best of my students would get confused by looking at eight different proteins without some kind of common thread.  The take home lesson that denaturation negatively impacts tyrosinase activity is easy to lose among all the unrelated activities.

Where are the 3D models?

My greatest disappointment though was that the article talked about having students look at 3D models and how students could look at molecules and see how they changed when they were denatured by heat or pH. I completely misinterpreted that description. If I were teaching this class, I would rather have students work first-hand with structure models instead the authors provide a link where students can watch a video on denaturation.

This is my bias, but I think an active learning approach, where students actually look at 3D protein and chemical models and identify chemical interactions, would be better in long run and better equip students for future learning. I think the common practice of hiding the biochemistry makes genetics much harder to understand and far less straightforward than it should be.

And, as it turns out there are 3D models of tyrosinase that students could use.  They’re from Bacillus megatherium, but that’s how biology works.  If an enzyme activity is beneficial, evolutionary processes tend to keep it around.

Using 3D Models to look at albino cats

No models exist from the Siamese cat protein with the brown ear point mutation, but it is possible to make 3D protein models that show the affect of a different mutation, in tyrosinase, that leads to albino cats. This mutation occurs when a cytosine is deleted at nucleotide 975, creating a frameshift (2).  To simulate the mutation’s effect, we can hide the amino acids that would be lost.  This model isn’t perfect because the shorter protein might fold somewhat differently, but this does provide a satisfying explanation for an inactive enzyme.

Here’s what to do:

1. Open Molecule World on the iPad (*).
2. Download 4P6R.
3. Color the protein chains by molecule.
4. Open the sequence viewer and touch the name of the last row to select it.  This row contains tyrosine, the substrate for the enzyme, and for each chain, two atoms of zinc.
5. Change the coloring style to element.

Now, you can see the substrate bound in the active site.  Notice this protein has two identical subunits.  Each one is bound to tyrosine and zinc.

Tyrosinase with tyrosine and zinc in the active site.

 

 

 

 

 

 

 

 

 

 

You may want to change the atom visibility to show all the atoms or just the core backbone, like I have here, to see how the tyrosine is positioned.

*Many of the things I describe here can be done in Cn3D, but it’s a bit more complicated.

 

Modeling the mutation’s affect

This next part is a little more complicated because I had to split the protein sequence into three parts to avoid introducing spaces.

1. Carry out the following process in three steps. First, copy the sequence below.KYRVRKNVLHLTDTEKRDFVRTVLIKEKGIYDRYIAWHGAAGKFHTPPGSDRNA
2. Touch the Selection button and paste the sequence below in the Select pattern window.
3. Start the search.  The pasted sequence will be highlighted in the protein sequence.
4. Copy the next part of the sequence (below).  Touch the Selection button again and search for this pattern as before.
   AHMSSAFLPWHREYLLRFERDQSINPEVTLPYWEWETDAQMQDPSQSQIWSADFMGGN
5. Copy the next part of the sequence (below).  Touch the Selection button again and search for this pattern as before.

   GNPIKDFIVDTGPFAAGRWTTIDEQGNPSGGLKRNFGATKAPTLPTRDDVL

6. When you’re done highlighting sequences, you’ll see each subunit has a region that appears brighter and a region in the center that appears more dim. The bright colored residues are incorporated into the protein before ribosomes encounter the frame shift mutation and a stop codon shortly afterwards. This portion of the protein can be produced in the albino cat.
7. Look at the dim areas of each subunit.  These amino acids would be lost when the frameshift mutation is present.  Notice where the tyrosine is located.

Residues that would be lost because of the frameshift mutant are shown in gray.

 

 

 

 

 

 

 

 

 

 

 

8.  To make the mutations affect on the protein even more clear, open the Show/Hide button and choose “Hide unselected.”  The amino acid residues that would be lost because of the mutation disappear.

Residues that would be lost because of the frame shift mutation are hidden.

 

 

 

 

 

 

 

 

 

 

Now, it’s really clear.  If the residues that bind tyrosine and modify it’s structure are gone, the enzyme is unable to function.  If we don’t have tyrosinase working to help make melanin, we get white cats.

 

References:

1. Amber Todd and Lisa Kenyon, How do Siamese cats get their color? The Science Teacher. 2016;83(1):29-36
2. Imes D, Geary L, Grahn R, Lyons L. Albinism in the domestic cat (Felis catus) is associated with a tyrosinase (TYR) mutation. Animal Genetics. 2006;37(2):175-178. doi:10.1111/j.1365-2052.2005.01409.x.

from ScienceBlogs http://ift.tt/1mr5yCU

Our Engineering Stories of 2015

From $1 microscopes to shape-shifting robots, we covered some pretty awesome engineering stories in 2015. Here’s a look back at those stories.

Engineering Is Bringing Fish Up from the Deep
We began the year diving deep into the ocean and showing how scientists at the California Academy of Sciences engineered a device that safely brings fish up from the twilight zone, a region of the ocean so deep that light barely reaches it. Fish living at these depths are accustomed to life at a higher pressure, and because many fish have a gas-filled organ called a swim bladder, they are super sensitive to fast changes in pressure. If scientists want to bring the fish up to study them at sea level, their swim bladders can expand and crush other vital organs– killing the fish. So scientists at the California Academy of Sciences engineered a portable device that maintains high ocean pressures, so they can collect the fish and bring them safely to the surface.

For an even deeper learning experience check out our collection of associated resources about this project, including science and career spotlight videos, a hands-on activity, a Do Now activity and an e-book.

Engineering Is Diagnosing Diseases with Origami Microscopes
Next, we got an up-close look at how Manu Prakash, a bioengineer at Stanford University created the Foldscope, a $1 paper microscope. This nifty invention could one day help diagnose diseases in remote or resource-poor areas throughout the world. In fact, these microscopes are currently in validation studies and clinical trials to be used as diagnostic tools for malaria, African sleeping sickness and schistosomiasis. In addition to diagnosing diseases, he hopes these microscopes will be used by students, teachers and life-long learners to explore their own world. Through the Ten Thousand Microscope Project, Prakash has shipped approximately 50,000 Foldscopes to students and lifelong learners in more than 130 countries who submitted ideas for experiments or questions that they would like to answer using the Foldscopes.

To get a closer look at this project, check out our collection of associated resources including a science and career spotlight video, a Do Now activity and an e-book.

Engineering Is Cleaning Poop from Drinking Water
In this story, we travel to Dhaka, Bangladesh, the tenth largest city in the world where travel by boat and Rickshaw is a common way to get around town. While the waterways are an inviting lure to this populated city, water is also the source of many diseases, particularly in Dhaka’s crowded slums. Here, sewage can seep into low-pressure, old, leaky pipes that transport the town’s drinking water, exposing residents to harmful bacteria and viruses. But, researchers at Stanford University have engineered a cheap device that can clean drinking water where it is collected, at communal hand-pumps.

For more resources about this project, check out our collection, which includes a science and career spotlight video and an e-book.

Engineering Is Exploring Space with Shape-Shifting Robots
A fan favorite of 2015, this engineering story is out of this world, (or, it might be one day). Researchers at NASA Ames Research Center in Mountain View, CA have teamed up with researchers at University of California, Berkeley to design and engineer what might be the next generation of space-exploring robots. These robots are wildly different than traditional rovers, which are super expensive, really heavy and hard to land. The new robots are based on a type of structure known as a “tensegrity” structure.

For more resources about this project check out our collection, which includes a science and career spotlight video, classroom activities and an e-book.

Engineering Is 3-D Mapping Your World with a Backpack
For this next story we got the inside scoop from Avideh Zakhor, a UC Berkeley professor of electrical engineering, about her 3-D mapping backpack which can be used to map the interior of buildings. This technology has a lot of potential applications including aiding with search and rescue, commercial real estate, building construction and energy audits. Some companies are even putting consumer grade versions of this technology in smartphones, so users can create their own 3-D maps of interior buildings.

Check out our collection of resources for this engineering story which includes a science and career spotlight video and classroom activities.

Engineering Is Converting Buses into Mobile Showers
Our most recent engineering story, this one describes how Lava Mae, a non-profit organization recycles retired public transportation buses and converts them into mobile showers for San Francisco’s homeless population. Check out how these shower buses work, and the thoughtful design that went into them.

More resources about this project coming soon.

from QUEST http://ift.tt/1NSEw0L

From $1 microscopes to shape-shifting robots, we covered some pretty awesome engineering stories in 2015. Here’s a look back at those stories.

Engineering Is Bringing Fish Up from the Deep
We began the year diving deep into the ocean and showing how scientists at the California Academy of Sciences engineered a device that safely brings fish up from the twilight zone, a region of the ocean so deep that light barely reaches it. Fish living at these depths are accustomed to life at a higher pressure, and because many fish have a gas-filled organ called a swim bladder, they are super sensitive to fast changes in pressure. If scientists want to bring the fish up to study them at sea level, their swim bladders can expand and crush other vital organs– killing the fish. So scientists at the California Academy of Sciences engineered a portable device that maintains high ocean pressures, so they can collect the fish and bring them safely to the surface.

For an even deeper learning experience check out our collection of associated resources about this project, including science and career spotlight videos, a hands-on activity, a Do Now activity and an e-book.

Engineering Is Diagnosing Diseases with Origami Microscopes
Next, we got an up-close look at how Manu Prakash, a bioengineer at Stanford University created the Foldscope, a $1 paper microscope. This nifty invention could one day help diagnose diseases in remote or resource-poor areas throughout the world. In fact, these microscopes are currently in validation studies and clinical trials to be used as diagnostic tools for malaria, African sleeping sickness and schistosomiasis. In addition to diagnosing diseases, he hopes these microscopes will be used by students, teachers and life-long learners to explore their own world. Through the Ten Thousand Microscope Project, Prakash has shipped approximately 50,000 Foldscopes to students and lifelong learners in more than 130 countries who submitted ideas for experiments or questions that they would like to answer using the Foldscopes.

To get a closer look at this project, check out our collection of associated resources including a science and career spotlight video, a Do Now activity and an e-book.

Engineering Is Cleaning Poop from Drinking Water
In this story, we travel to Dhaka, Bangladesh, the tenth largest city in the world where travel by boat and Rickshaw is a common way to get around town. While the waterways are an inviting lure to this populated city, water is also the source of many diseases, particularly in Dhaka’s crowded slums. Here, sewage can seep into low-pressure, old, leaky pipes that transport the town’s drinking water, exposing residents to harmful bacteria and viruses. But, researchers at Stanford University have engineered a cheap device that can clean drinking water where it is collected, at communal hand-pumps.

For more resources about this project, check out our collection, which includes a science and career spotlight video and an e-book.

Engineering Is Exploring Space with Shape-Shifting Robots
A fan favorite of 2015, this engineering story is out of this world, (or, it might be one day). Researchers at NASA Ames Research Center in Mountain View, CA have teamed up with researchers at University of California, Berkeley to design and engineer what might be the next generation of space-exploring robots. These robots are wildly different than traditional rovers, which are super expensive, really heavy and hard to land. The new robots are based on a type of structure known as a “tensegrity” structure.

For more resources about this project check out our collection, which includes a science and career spotlight video, classroom activities and an e-book.

Engineering Is 3-D Mapping Your World with a Backpack
For this next story we got the inside scoop from Avideh Zakhor, a UC Berkeley professor of electrical engineering, about her 3-D mapping backpack which can be used to map the interior of buildings. This technology has a lot of potential applications including aiding with search and rescue, commercial real estate, building construction and energy audits. Some companies are even putting consumer grade versions of this technology in smartphones, so users can create their own 3-D maps of interior buildings.

Check out our collection of resources for this engineering story which includes a science and career spotlight video and classroom activities.

Engineering Is Converting Buses into Mobile Showers
Our most recent engineering story, this one describes how Lava Mae, a non-profit organization recycles retired public transportation buses and converts them into mobile showers for San Francisco’s homeless population. Check out how these shower buses work, and the thoughtful design that went into them.

More resources about this project coming soon.

from QUEST http://ift.tt/1NSEw0L