Monthly Archives: July 2015

On this day in Science History: The First Iron Lung was Installed

In 1927, the first iron lung (electric respirator) was
installed at Bellevue hospital in New York for the post war polio epidemic. The
first iron lung was developed at Harvard University by Phillip Drinker and
Louis Agassiz Shaw built with two vacuum cleaners.

The iron lung is a negative pressure machine which
surrounds the patient’s body except for the head, and alternates a negative
atmospheric pressure with the ambient one, resulting in rhythmic expansion of
the chest cage (and thus inhalation) in response to the negative extra thoracic
pressure. During periods of ambient extrathoracic pressure, the lungs deflate.

Humans, like most animals, breathe by negative pressure
breathing: the rib cage expands and the diaphragm contracts, expanding the
chest cavity. This causes the pressure in the chest cavity to decrease, and the
lungs expand to fill the space. This, in turn, causes the pressure of the air
inside the lungs to decrease (it becomes negative, relative to the atmosphere),
and air flows into the lungs from the atmosphere: inhalation. When the
diaphragm relaxes, the reverse happens and the person exhales. If a person
loses part or all of the ability to control the muscles involved, breathing
becomes difficult or impossible.

The person using the iron lung is placed into the central
chamber, a cylindrical steel drum. A door allowing the head and neck to remain
free is then closed, forming a sealed, air-tight compartment enclosing the rest
of the person’s body. Pumps that control airflow periodically decrease and
increase the air pressure within the chamber, and particularly, on the chest.
When the pressure is below that within the lungs, the lungs expand and
atmospheric pressure pushes air from outside the chamber in via the person’s
nose and airways to keep the lungs filled; when the pressure goes above that
within the lungs, the reverse occurs, and air is expelled. In this manner, the
iron lung mimics the physiological action of breathing: by periodically
altering intrathoracic pressure, it causes air to flow in and out of the lungs.
The iron lung is a form of non-invasive therapy.

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On this day in Science History: The Last Fragments of Comet Shoemaker-Levy Struck Jupiter

In 1994, the last of the large fragments of the comet
Shoemaker-Levy struck Jupiter (Fragment W).

This was a comet that broke apart, colliding with Jupiter
and providing the first direct observation of an extraterrestrial collision of
Solar System objects. This generated a large amount of coverage in the popular
media, and the comet was closely observed by astronomers worldwide. The
collision provided new information about Jupiter and highlighted its role in
reducing space debris in the inner Solar System.

“Shoemaker-Levy 9 on 1994-05-17” by NASA, ESA, and H. Weaver and E. Smith (STScI) – (direct link). Licensed under Public Domain via Wikimedia Commons 

The comet was discovered by astronomers Carolyn and Eugene
M. Shoemaker and David Levy.  Shoemaker–Levy 9, at the time captured by and
orbiting Jupiter, was located on the night of March 24, 1993, in a photograph
taken with the 40 cm (16 in) Schmidt telescope at the Palomar Observatory in
California. It was the first comet observed to be orbiting a planet, and had
probably been captured by the planet around 20 – 30 years earlier. 

Calculations showed that its unusual fragmented form was
due to a previous closer approach to Jupiter in July 1992. At that time, the
orbit of Shoemaker–Levy 9 passed within Jupiter’s Roche limit, and Jupiter’s
tidal forces had acted to pull apart the comet. The comet was later observed as
a series of fragments ranging up to 2 km (1.2 mi) in diameter. These fragments
collided with Jupiter’s southern hemisphere between July 16 and July 22, 1994,
at a speed of approximately 60 km/s (37 mi/s) or 216,000 km/h (134,000 mph).
The prominent scars from the impacts were more easily visible than the Great
Red Spot and persisted for many months.

Observers hoped that the impacts would give them a first
glimpse of Jupiter beneath the cloud tops, as lower material was exposed by the
comet fragments punching through the upper atmosphere. Spectroscopic studies
revealed absorption lines in the Jovian spectrum due to diatomic sulfur (S2)
and carbon disulfide (CS2), the first detection of either in Jupiter, and only
the second detection of S2 in any astronomical object. Other molecules detected
included ammonia (NH3) and hydrogen sulfide (H2S). The amount of sulfur implied
by the quantities of these compounds was much greater than the amount that
would be expected in a small cometary nucleus, showing that material from within
Jupiter was being revealed. Oxygen-bearing molecules such as sulfur dioxide
were not detected, to the surprise of astronomers.

As well as these molecules, emission from heavy atoms such
as iron, magnesium and silicon was detected, with abundances consistent with
what would be found in a cometary nucleus. While substantial water was detected
spectroscopically, it was not as much as predicted beforehand, meaning that
either the water layer thought to exist below the clouds was thinner than
predicted, or that the cometary fragments did not penetrate deeply enough. The relatively low levels of water were later confirmed by Galileo’s
atmospheric probe, which explored Jupiter’s atmosphere directly.

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Leaving on a biofueled jet plane

The problem is simple to understand. Molecules of carbon and
other greenhouse gases absorb heat. The more greenhouse gases emitted into the
atmosphere, the warmer the atmosphere becomes, exacerbating global climate
change. Solving the problem is not so simple, especially with regards to
aviation — the source of two-percent of the annual greenhouse gas emissions
from human activity. While biofuels have proven to be an effective, renewable,
low-carbon alternative to gasoline and diesel, jet fuels pose unique
challenges. These challenges have now been met with a new technique developed
by researchers at the Energy Biosciences Institute (EBI), a partnership led by
the University of California (UC) Berkeley that includes Lawrence Berkeley
National Laboratory (Berkeley Lab) and the University of Illinois at
Urbana-Champaign, and the BP energy company.

“We’ve combined chemical catalysis with life-cycle
greenhouse gas modeling to create a new process for producing bio-based
aviation fuel as well as automotive lubricant base oils,” says Alexis
Bell, a chemical engineer with joint appointments at Berkeley Lab and UC
Berkeley. “The recyclable catalysts we developed are capable of converting
sugarcane biomass into a new class of aviation fuel and lubricants with
superior cold-flow properties, density and viscosity that could achieve net
life-cycle greenhouse gas savings of up to 80-percent.” These challenges
have now been met with a new technique developed by researchers at the Energy
Biosciences Institute (EBI), a partnership led by the University of California
(UC) Berkeley that includes Lawrence Berkeley National Laboratory (Berkeley
Lab) and the University of Illinois at Urbana-Champaign, and the BP energy

Alex Bell, a leading authority on catalysis in biofuels. Credit:Image courtesy of DOE/Lawrence Berkeley National Laboratory

Bell is one of three corresponding authors of a paper
describing this research in the Proceedings of the National Academy of Sciences
(PNAS). The paper is titled “Novel pathways for fuels and lubricants from
biomass optimized using life-cycle greenhouse gas assessment.” Corinne
Scown, a research scientist with Berkeley Lab’s Energy Analysis and Environmental
Impacts Division, and Dean Toste, a chemist with joint appointments at Berkeley
Lab and UC Berkeley, are the other two corresponding authors. Additional
authors are are Madhesan Balakrishnan, Eric Sacia, Sanil Sreekumar, Gorkem
Gunbas and Amit Gokhale.

The concentrations of carbon and other greenhouse gases in
Earth’s atmosphere are now at their highest levels in the past three million
years, primarily as a result of the burning of petroleum and other fossil
fuels. Biofuels synthesized from the sugars in plant biomass help mitigate
climate change. However, jet fuels have stringent requirements that must be

“Jet fuels must be oxygen-free, have the right boiling
point distribution and lubricity, and a very low pour point, meaning the fuel
can’t become gelatinous in the cold temperatures of the stratosphere,”
Bell says. “Biofuel solutions, such as farnesane, mixed directly with
petroleum jet fuel have been tested, but offer only modest greenhouse gas
reduction benefits. Ours is the first process to generate true drop-in aviation

Scown cites the Intergovernmental Panel on Climate Change
(IPCC) on the importance of drop-in aviation biofuels.

“In a 2014 report, the IPCC pointed out that drop-in
biofuels are the only viable alternative to conventional jet fuels,” she
says. “If we want to reduce our dependence on petroleum, air travel is
going to require renewable liquid fuels because batteries and fuel cells simply
aren’t practical.”

The process developed at EBI can be used to selectively
upgrade alkyl methyl ketones derived from sugarcane biomass into trimer
condensates with better than 95-percent yields. These condensates are then
hydro-deoxygenated into a new class of cycloalkane compounds that contain a
cyclohexane ring and a quaternary carbon atom. These cycloalkane compounds can
be tailored for the production of either jet fuel, or automotive lubricant base
oils. Lubricant base oils can produce even more greenhouse gas emissions on a
per-mass basis than petroleum-derived fuels if even a fraction of the lubricant
is repurposed as fuel. The ability of the EBI process to yield jet fuel or
lubricants should be a significant advantage for biorefineries.

“Sugarcane biorefineries today produce ethanol, sugar
and electricity,” says PNAS paper co-author Gokhale, a chemical engineer,
who is managing the research project from BP’s side. “Expanding the
product slate to include aviation fuels and lubricant base oils could allow for
operators to manage their market risks better, which is exactly how
petrochemical refinery complexes operate today. Rather than optimize for one
product, they try to optimize the overall product slate.”

Adds Scown, “Another important advantage offered by our
process is that it enables refineries to convert a portion of the bagasse, the
fibrous residue that remains after juice is extracted from sugarcane stalk,
into fuels and other products. The rest of the waste biomass can be combusted
to produce process heat and electricity to operate the refinery.” This new
EBI process for making jet fuel and lubricants could also be used to make
diesel and additives for gasoline as Gokhale explains.

“With some minimal modifications to both the catalysts
and the reaction schemes we can produce drop-in diesel as well,” he says.
“We’re planning further studies on this.”

Although the goal of this study was to develop a strategy
for the flexible production of jet fuels and lubricant base oils in a Brazilian
sugarcane refinery, the strategy behind the process could also be applied to
biomass from other non-food plants and agricultural waste that are fermented by
genetically engineered microbes.

“Although there are some additional technical challenges
associated with using sugars derived entirely from biomass feedstocks like
Miscanthus and switchgrass, there is no fundamental reason why we could not
produce similar outputs, albeit in different proportions,” Scown says.
“We expect that further research will make this option increasingly

In their PNAS paper the authors acknowledge that the
commercial implementation of their proposed process would include financial
implications that extend beyond greenhouse gas emission reductions but hold
that there still important incentives to encourage investments.

“We’ve shown in this study that biorefineries can use
inexpensive catalysts to produce a suite of hydrocarbon fuels and
lubricants,” Scown says. “By strategically piecing together biological
and thermochemical processes, biorefineries can also operate without any
fossil-derived inputs.”

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The Event that Transformed Earth

Up until 2.4 billion years ago, there was no oxygen in the air. It took something big to change that – perhaps the biggest evolutionary leap of all.

If you could build a time machine and go back to Earth’s distant past, you’d get a nasty surprise. You wouldn’t be able to breathe the air. Unless you had some breathing apparatus, you would asphyxiate within minutes.

The Great Oxidisation Event (Credit: APIX / Alamy)

For the first half of our planet’s history, there was no oxygen in the atmosphere. This life-giving gas only started to appear about 2.4 billion years ago.

This “Great Oxidation Event” was one of the most important things to ever happen on this planet. 

Without it, there could never have been any animals that breathe oxygen: no insects, no fish, and certainly no humans.

For decades, scientists have worked to understand how and why the first oxygen was pumped into the air. They have long suspected that life itself was responsible for creating the air that we breathe.

But not just any life. If the latest findings are to be believed, life itself was undergoing a tremendous transformation just before the Great Oxidation Event. This evolutionary leap forward may be the key to understanding what happened.

Earth was already 2 billion years old at the time of the Great Oxidation Event, having formed 4.5 billion years ago. It was inhabited, but only by single-celled organisms.

It’s not clear exactly when life began, but the oldest known fossils of these microorganisms date back 3.5 billion years, so it must have been before that. That means life had been around for at least a billion years before the Great Oxidation Event.

Those simple life-forms are the prime suspects for the Great Oxidation Event. One group in particular stands out: cyanobacteria. Today, these microscopic organisms sometimes form bright blue-green layers on ponds and oceans.

Their ancestors invented a trick that has since spread like wildlife. They evolved a way to take energy from sunlight, and use it to make sugars out of water and carbon dioxide.

This is called photosynthesis, and today it’s how all green plants get their food. That tree down your street is pretty much using the same chemical process that the first cyanobacteria used billions of years ago.

It was the cyanobacteria, pumping out unwanted oxygen, that transformed Earth’s atmosphere

From the bacteria’s point of view, photosynthesis has one irritating downside. It produces oxygen as a waste product. Oxygen is of no use to them, so they release it into the air.

So there’s a simple explanation for the Great Oxidation Event. It was the cyanobacteria, pumping out unwanted oxygen, that transformed Earth’s atmosphere.

But while this explains how it happened, it doesn’t explain why, and it certainly doesn’t explain when it happened.

The problem is that cyanobacteria seem to have been around long before the Great Oxidation Event. 

“They’re probably among the first organisms we have on this planet,” says Bettina Schirrmeister of the University of Bristol in the UK.

We can be confident that there were cyanobacteria by 2.9 billion years ago, because there is evidence of isolated “oxygen oases” at that time. They might date as far back as 3.5 billion years, but it’s hard to tell because the fossil record is so patchy.

That means the cyanobacteria were busy pumping out oxygen for at least half a billion years before oxygen started appearing in the air. That doesn’t make a lot of sense.

One explanation is that there were a lot of chemicals around – perhaps volcanic gases – that reacted with the oxygen, effectively “mopping it up”.

But there’s another possibility, says Schirrmeister. Maybe the cyanobacteria changed. “Some evolutionary innovation in cyanobacteria helped them to become more successful and more important,” she says.

Some modern cyanobacteria have done something that, by bacterial standards, is remarkable. While the vast majority of bacteria are single cells, they are multicellular.

The individual cyanobacterial cells have joined up into stringy filaments, like the carriages of a train. 

That in itself is unusual for bacteria, but some have gone further.

“Many cyanobacteria are able to produce specialised cells that lose their ability to divide,” says Schirrmeister. “This is the first form of specialisation we see.” It’s a simple version of the many specialised cells that animals have, such as muscle, nerve and blood cells.

Schirrmeister thinks multicellularity could have been a game-changer for Earth’s early cyanobacteria. It offers several possible advantages.

On the early Earth, single-celled organisms often lived together in flat layers of gunk called “mats”. 

Within each mat there would have been many different species of cyanobacteria, and a host of other things to boot.

A multicellular cyanobacterium would have one clear advantage compared to its single-celled rivals. 

It would find it easier to spread, because its larger surface area would mean it was better at attaching itself to slippery rocks. Such an organism would be “less likely to wash away in the current”, says Schirrmeister.

Many modern multicellular cyanobacteria can move around within their mats. “They’re not extremely fast but they can move,” says Schirrmeister. That suggests the primordial ones could as well.

Moving could have helped them survive. At the time the Earth was being bombarded with harmful ultraviolet radiation from the Sun, and there was no ozone layer to keep it out.

“In modern mats, cyanobacteria will turn around and appear vertical instead of horizontal to protect themselves from excess sunlight,” says Schirrmeister. “You have also movement between layers. It might be these multicellular cyanobacteria had the ability to position themselves optimally within the mat.”

It’s a neat idea. But for it to be true, cyanobacteria must have evolved multicellularity before the Great Oxidation Event.

Schirrmeister has spent the last few years trying to figure out when cyanobacteria first evolved multicellularity.

The clues lie in their genes. By examining genes that all cyanobacteria share, and identifying tiny differences between them, Schirrmeister could figure out how they are all related – essentially drawing up a family tree of cyanobacteria.

With that tree in place, Schirrmeister could then home in on the multicellular cyanobacteria, and estimate roughly when they first became multicellular.

Her first attempt, published in 2011, suggested that most modern cyanobacteria are descended from multicellular ancestors. That suggested multicellularity was ancient, but it was difficult to put a firm date on it.

Schirrmeister refined her methods for a second paper, published in 2013. This suggested that multicellularity evolved not long before the Great Oxidation Event, at a time when cyanobacteria were diversifying rapidly.

But that didn’t clinch the argument. Her family tree was only based on one gene, albeit a gene shared by every single species of cyanobacterium. That meant the tree was suspect.

So Schirrmeister has now gone one better.

“This time I worked with 756 genes,” says Schirrmeister. “The genes I took are present in all cyanobacteria.”

Her estimate of the origin of multicellularity is still rough, but it seems to be around 2.5 billion years ago – before the Great Oxidation Event.

There are several different ways to calculate these family trees, and they all gave the same answer. “No matter how we calibrate our phylogeny, it seems more likely we have multicellularity evolving before the Great Oxidation Event,” says Schirrmeister.

The results are published in Palaeontology.

This may not be the end of the story. Even if Schirrmeister’s results are confirmed, and cyanobacteria did become multicellular just before the Great Oxidation Event, there are two big questions.

The first is, did multicellularity really offer them the advantages she thinks it did? We don’t know, but we could find out: by testing how modern single-celled and multicellular cyanobacteria cope with different situations.

The second question is harder: why did it take so long for cyanobacteria to become multicellular? If it is so advantageous, why did they not evolve it sooner, and trigger an earlier Great Oxidation Event?

“The next step is to find out which genes are responsible for multicellularity in cyanobacteria,” says Schirrmeister. “Then I could say why did it take that long, why didn’t it evolve earlier.” If lots of new genes were required, it becomes understandable that it took the cyanobacteria a long time to evolve it.

Whatever caused the Great Oxidation Event, it’s clear that it is one of the most important things to ever happen on this planet.

In the short term, it was probably rather bad news for life.

“Oxygen would have been lethal for many bacteria,” says Schirrmeister. “It’s hard to prove, because from the fossil record we don’t have a lot of deposits from that time… [but] we can assume we had a lot of bacteria dying at that point.”

But in the longer term, it allowed a whole new kind of life to evolve. Oxygen is a reactive gas – that’s why it starts fires – so when some organisms figured out how to harness it, they suddenly had access to a major new source of energy.

By breathing oxygen, organisms could become much more active, and much larger. Moving beyond the simple multicellularity developed by cyanobacteria, some organisms became far more intricate. 

They became plants and animals, from sponges and worms to fish and, ultimately, humans.

If Schirrmeister is right, those first multicellular cyanobacteria triggered the evolution of complex life, including us, by producing oxygen on a global scale. “It made complex life possible,” she says.
Not bad for a bunch of tiny blue-green bacteria.

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