Category Archives: Life Science

Bacteria Frozen for 8 Million Years In Polar Ice Resuscitated

Eight-million-year-old bug is alive and growing

Kay Bidle of Rutgers University in New Jersey, US, and his colleagues extracted DNA and bacteria from ice found between 3 and 5 metres beneath the surface of a glacier in the Beacon and Mullins valleys of Antarctica. The ice gets older as it flows down the valleys and the researchers took five samples that were between 100,000 and 8 million years old.

They then attempted to resuscitate the organisms in the oldest and the youngest samples. “We tried to grow them in media, and the young stuff grew really fast. We could plate them and isolate colonies,” says Bidle. The cultures grown from organisms found in the 100,000-year-old ice doubled in size every 7 days on average.

Whereas the young ice contained a variety of microorganisms, the researchers found only one type of bacterium in the 8-million-year-old sample. It also grew in the laboratory but much more slowly, doubling only every 70 days.

Related: What is an Extremophile?

Where is “Everybody”

The Fermi Paradox: Back with a vengeance

The Fermi Paradox is the contradictory and counter-intuitive observation that we have yet to see any evidence for the existence of ETI’s. The size and age of the Universe suggests that many technologically advanced ETI’s ought to exist. However, this hypothesis seems inconsistent with the lack of observational evidence to support it.i”The Fermi Paradox is the contradictory and counter-intuitive observation that we have yet to see any evidence for the existence of ETI’s. The size and age of the Universe suggests that many technologically advanced ETI’s ought to exist. However, this hypothesis seems inconsistent with the lack of observational evidence to support it.
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There are more stars in the Universe than we can possibly fathom. Any conception of ‘rare’ ‘not enough time’ or ‘far away’ has to be set against the inability of human psychology to grasp such vast cosmological scales and quantities. The Universe and the Milky Way are extremely old, our galaxy has been able to produce rocky planets for quite some time now, and our earth is a relative new-comer to the galaxy.
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The fact that our Galaxy appears unperturbed is hard to explain. We should be living in a Galaxy that is saturated with intelligence and highly organized. Thus, it may be assumed that intelligent life is rare, or, given our seemingly biophilic Universe, our assumptions about the general behaviour of intelligent civilizations are flawed.

A paradox is a paradox for a reason: it means there’s something wrong in our thinking.

I agree. I am going with the it is hard for life to start and it what has started is really far away (so we can’t detect what life there is). Another option I could believe is once you reach a certain level of technological sophistication you often wipe out your civilization – leaving relatively short periods where civilizations produce signals we can detect (included in this is creating something that wipes themselves out, and a nasty thing [virus, bacteria, whatever…] that spreads everywhere because of instant transportation and wipes everybody out). Or maybe civilizations quickly go through a technology phase producing signals we can detect and move onto something else (though I can’t really understand why or what that would mean really). Or, similar to that one, for some reason we are really really odd in our move to technology – maybe most of the time things just stay in a natural state and nothing evolves that wants to do more than eat and sleep (if they sleep). That seems really unlikely but…

Contradictory Medical Studies

I have written before about false research findings. This is an important topic – we need to remember that the interpritation of one study (or many studies) in not necessarily conclusive. Another article – When Medical Studies Collide:

Two years ago, the headlines blared that echinacea was a bust. Millions of people who believed the best-selling herbal remedy was warding off colds were probably deluding themselves, according to The New England Journal of Medicine. Now echinacea is back in the news. This time, it works! So says a study in The Lancet Infectious Diseases.

How could two studies come to such different conclusions—especially when there have been no new trials of the herb? While the New England Journal reported on one clinical trial, authors of the latest report combined data from previous studies, a controversial approach called a meta-analysis. Its conclusion is dramatically different—not just from that of the New England Journal paper, but also from a review last year of the same studies.
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The problem is, the world of medical and health research is messier than most people realize. Black-and-white answers are rare, even when it comes to a single drug trial.

Just remember those last two sentences. Very simple. And most people would agree if you showed them those two sentences and asked if they agreed. But then they see a headline and away they go… Just force yourself to repeat that idea every time you see a health report. Don’t believe the headline without strong support.

An interesting tidbit from the article. The coneflower is the source of echinacea. I tried to find photos that I am pretty sure I have on my hard drive of the flowers in my back yard, but I couldn’t.

Evolutionary Design

Evolutionary algorithms now surpass human designers by Paul Marks:

Evolutionary Algorithms take two parent designs – for a boat hull, say – and blend components of each, perhaps taking the surface area of one and the curvature of another, to produce multiple hull offspring that combine the features of the parents in different ways. Then the algorithm selects those offspring it considers are worth re-breeding – in this case those with the right combination of parameters to make a better hull. The EA then repeats the process. Although many offspring will be discarded, after thousands of generations or more, useful features accumulate in the same design, and get combined in ways that likely would not have occurred to a human designer. This is because a human does not have the time to combine all the possibilities for each feature and evaluate them, but an EA does.

Evolving new designs is very cool. One point I would like to make (I am biased since my father did a great deal of work in this area) is the power of design of experiments to allow experimenting on multiple factors at once. This is a methodology that is still used far too little. Regardless, evolutionary design is very cool. The Human-Competitive awards highlight some examples.

Light-harvesting Bacterium Discovered in Yellowstone

photo of Mammoth Hot Springs, Yellowstone National Park, by John Hunter

Surprising new species of light-harvesting bacterium discovered in Yellowstone

In the hot springs of Yellowstone National Park, a team of researchers has discovered a novel bacterium that transforms light into chemical energy.
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Remarkably, the new genus and species Cab. thermophilum also belongs to a new phylum, Acidobacteria. The discovery marks only the third time in the past 100 years that a new bacterial phylum has been added to the list of those with chlorophyll-producing members. Although chlorophyll-producing bacteria are so abundant that they perform half the photosynthesis on Earth, only five of the 25 major groups, or phyla, of bacteria previously were known to contain members with this ability.

“The microbial mats give the hot springs in Yellowstone their remarkable yellow, orange, red, brown and green colors,” explained Bryant. “Microbiologists are intrigued by Octopus and Mushroom Springs because their unusual habitats house a diversity of microorganisms, but many are difficult or impossible to grow in the lab. Metagenomics has given us a powerful new tool for finding these hidden organisms and exploring their physiology, metabolism and ecology.”
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Unexpectedly, the new bacterium has special light-harvesting antennae known as chlorosomes, which contain about 250,000 chlorophylls each. No member of this phylum nor any aerobic microbe was known to make chlorosomes before this discovery. The team found that Cab. thermophilum makes two types of chlorophyll that allow these bacteria to thrive in microbial mats and to compete for light with cyanobacteria.

This discovery is particularly important because members of the Acidobacteria have proven very hard to grow in laboratory cultures, which means their ecology and physiology are very poorly understood. Most species of Acidobacteria have been found in poor or polluted soils that are acidic, with a pH below 3. However, the Yellowstone environments are more alkaline, about pH 8.5 (on a scale of 1 to 14). Bryant noted, “Judging from their 16S rRNA sequences, the closest relatives of Cab. thermophilum are found around Mammoth Hot Springs in Yellowstone and hot springs in Tibet and Thailand. As we look more closely, we may find relatives of Cab. thermophilum in the microbial mats of thermal sites worldwide.”

Photo of Mammoth Hot Springs, Yellowstone National Park by John Hunter.

Lifestyle Drugs and Risk

I see taking drugs as risky. Certain drug have long histories and seem safe and even seem to have positive side effect like Aspirin (though even it is not without risks – see below). Even if a drug has a good chance of a positive result in treating some medical condition – assuming it is otherwise safe is not wise. I believe you have have a significant positive known benefit to consider taking drugs given the unknown problems that are likely to be lurking. I find the pop a pill culture for anything that might be a minor annoyance to be foolish – taking risks without consideration. Taking drugs entails taking a risk and the more you take the risks of interactions and cumulative effects increase the risks to you. Business Week (somewhat surprising given the huge amount drug makers pay to advertise lifestyle drugs) has a decent article pointing out some of the foolishness involved in the Lifestyle Drug Binge:

The renewed excitement is most evident in four treatment areas that account for the bulk of lifestyle-drug sales: weight loss, hair loss, sleep, and sexual dysfunction.

This trend is surprising because such treatments can expose patients to risks, sparking criticism of drug companies at a time when patient safety is already under a spotlight. Lifestyle drugs are defined loosely as products used to treat conditions that are not life-threatening. Because people take them over long periods of time, sometimes on a daily basis, they may be more dangerous than they first appear.

We have found amazingly helpful and useful drugs. This is great. But people need to remember these drugs are not without potential negative consequences. Take advantage of them when appropriate but don’t forget the risks each instance has for negative side effects. Related: health care improvement articles – health care blog posts
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Evolution at Work – Blue Moon Butterfly

Butterfly shows evolution at work

The tropical Blue Moon butterfly has developed a way of fighting back against parasitic bacteria. Six years ago, males accounted for just 1% of the Blue Moon population on two islands in the South Pacific. But by last year, the butterflies had developed a gene to keep the bacteria in check and male numbers were up to about 40% of the population.

Scientists believe the comeback is due to “suppressor” genes that control the Wolbachia bacteria that is passed down from the mother and kills the male embryos before they hatch. “To my knowledge, this is the fastest evolutionary change that has ever been observed,” said Sylvain Charlat, of University College London, whose study appears in the journal Science.
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“We’re witnessing an evolutionary arms race between the parasite and the host. This strengthens the view that parasites can be major drivers in evolution,” Mr Charlat said.

It makes a great deal of sense that evolution would have such bursts under the right conditions. This seems an nearly perfect example of such conditions – if males can be produced they are going to have a large opening to reproduce and rapidly pass on a new tool to fight the bacteria. The University of California – Berkeley has a good site on understanding evolution (with lesson plans for k-16 and information for anyone interested in science).

Relates: Two Butterfly Species Evolved Into Third – Evolution in Darwin’s Finches – Evolution In Action – Evo-Devo

Well Preserved Baby Mammoth Discovered in Permafrost

Baby mammoth discovery unveiled

The six-month-old female calf was discovered on the Yamal peninsula of Russia and is thought to have died 10,000 years ago. The animal’s trunk and eyes are still intact and some of its fur remains on the body.
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Mammoths first appeared in the Pliocene Epoch, 4.8 million years ago. What caused their widespread disappearance at the end of the last Ice Age remains unclear; but climate change, overkill by human hunters, or a combination of both could have been to blame. One population of mammoths lived on in isolation on Russia’s remote Wrangel Island until about 5,000 years ago.

Interesting Lobsters

Is there a 400 pound lobster out there?

Lobsters sometimes bury their food and eat it over several days. They use teeth located in their stomachs, eat their molted shells (full of calcium) and can shed appendages if attacked, wounded or surprised, only to regenerate them later. Finally, lobsters live in a hierarchy and it’s the females who do the courting.

But there’s one lobster fact that trumps them all: lobsters show no apparent signs of aging. They don’t slow down or become weaker or more susceptible to disease. They don’t get infertile — older lobsters are actually more fertile than younger ones. Most lobsters seem to die because of something inflicted upon them and not because a body part failed or broke down. They’re such hardy creatures that scientists aren’t even sure how old lobsters can get. Add in that lobsters grow throughout their lives, and one has to ask: Is possible that a lobster born before Napoleon and as heavy as an NFL lineman is chowing down on the seafloor?

Obesity Epidemic Explained – Kind Of

Graphic: percentage of population over 15 with a body-mass index greater than 30, for more see Wellington Grey

Obesity Epidemic Explained – Kind Of

So maybe everyone else already knew this and I am like, bumpkin girl, but I just have to take a moment and point everyone to this USDA research site on the massive inflationary trend in daily caloric consumption over the past three decades.

1970 – Americans ate an average of 2170 calories per day
2000 – Americans ate an average of 2700 calories per day

I don’t think most people know that. It does seem odd to me that so much effort is put into trying to come up with explanations that are much more complicated. Most of the complicated suggestions (usually some explanation that indicates it is some biology issue and not eating to much or exercising too little) don’t explain why there is an increase in the incidence of obesity over time – at least I don’t see how they do. It seems to me the base requirement for improving the health issue of increasing obesity is to have an explanation of what has caused the incredible increase.

I can certainly believe biological issues impact how easy it is to become obese or how difficult it is to maintain a healthy weight. But it seems to me the proportion of the population that is obese has drastically increased over time (or different regions of the globe with a similar genetic makeup) and the logical place to look for an explanation is behavior differences that created this change (not some biological issue that has changed). If 5% of the population was predisposed obesity in 1950 to obesity I can’t see any rational reason to think that has increased to 30% today.