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October 5, 2008

Milestones on the Voyage to the Bottom of the Sea

Dive! Dive! Dive!

0 FEET: EPIPELAGIC ZONE
Ample sunlight penetrates down to 650 feet, making photosynthesis possible. With abundant plant life (read: food), this zone is the most densely populated with fish.

656 FEET: MESOPELAGIC ZONE
Too deep to support photosynthesis: The fish that survive here are sit-and-wait predators that tend to have large mouths and specialized retinas to increase light reception.

1,640 feet: Maximum diving depth of the blue whale.
1,969 feet: The Deep Sound Channel, a layer in which acoustic signals travel far and fast.
1,969 feet: Maximum diving depth of nuclear-powered attack subs.

3281 FEET: BATHYPELAGIC ZONE
The ocean is dark at this level; the only glow is from bioluminescent animals. There are no living plants, and creatures subsist by eating the debris that falls from the levels above, including dead or dying fish and plankton.

3,281 feet: Maximum diving depth of the sperm whale. To navigate in the darkness, these whales emit high pitched sounds and use echoes to determine the location of prey.
3,937 feet: Maximum diving depth of the leatherback sea turtle.
4,000 feet: The domain of the Pacific sleeper shark, the largest toothed shark ever photographed. It can reach lengths of 28 feet.

5,187 feet: Maximum diving depth of the elephant seal.

13,123 FEET: ABYSSOPELAGIC ZONE
In the pitch-dark of the abyss, there is no light at all, the water temperature is near freezing. Of the few creatures found at these crushing depths, most are blind and have long tentacles - tiny invertebrates such as shrimp, basket stars, and small squids.

19,685 FEET: HADOLPELAGIC ZONE
Despite the intense pressure and frigid temperature in the deepwater trenches and canyons, life still exists here, especially near hydrothermal vents on the ocean floor. Invertebrates such as starfish actually thrive.

Related: Ocean Life - Giant Star Fish and More in Antarctica - ocean related posts - Female Sharks Can Reproduce Alone

September 4, 2008

Do Dolphins Sleep?

Do dolphins sleep?, MIT:

Dolphins do sleep, but not quite in the same way that people do. They sleep with one half of the brain at a time and with one eye closed. Dolphins rest this way on and off throughout the day, switching which side of the brain they shut down. During these periods, everything inside the dolphin slows down, and the mammal moves very little.

Related: Why do We Sleep? - Energy Efficiency of Digestion - interesting science facts - Why is the Sky Blue?

September 2, 2008

8 Percent of the Human Genome is Old Virus Genes

In Our Genes, Old Fossils Take On New Roles

It turns out that about 8 percent of the human genome is made up of viruses that once attacked our ancestors. The viruses lost. What remains are the molecular equivalents of mounted trophies, insects preserved in genomic amber, DNA fossils.

The thousands of human endogenous retroviruses, or HERVs, sketch a history of rough times during the 550 million years of vertebrate evolution. The best-preserved one, HERV-K113, probably arrived less than 200,000 years ago, long after human beings and chimpanzees diverged from a common ancestor.

But these retroviruses are more than just curiosities. They are some of the most important enemies we ever had. They helped mold the immune system that is one of the evolutionary marvels of life on Earth.

I must say there is tons of amazing stuff I learn about but I still find retroviruses amazing.

Related: Amazing Science: Retroviruses - Old Viruses Resurrected Through DNA - One Species’ Genome Discovered Inside Another’s - Our Genome Changes as We Age - posts on genes and genome

August 28, 2008

A Journey Into the Human Eye


Zoom into a human eye

The webcast goes into the human eye while describing the microscopic details of the human eye. See more such videos: The Eyes of a Fly - Zoom Into a Fish - Zoom Into a Butterfly

Related: Non-Newtonian Fluid Demo - posts on biology - science webcasts

July 26, 2008

Life After the Chernobyl Nuclear Accident

Silent Spring by Lauren Monaghan, Cosmos

Ever since, a 30 km ‘exclusion zone’ has existed around the contaminated site, accessible to those with special clearance only. It’s quite easy, then, to conjure an apocalyptic vision of the area; to imagine an eerily deserted wasteland, utterly devoid of life.

But the truth is quite the opposite. The exclusion zone is teeming with wildlife of all shapes and sizes, flourishing unhindered by human interference and seemingly unfazed by the ever-present radiation. Most remarkable, however, is not the life buzzing around the site, but what’s blooming inside the perilous depths of the reactor.

Sitting at the centre of the exclusion zone, the damaged reactor unit is encased in a steel and cement sarcophagus. It’s a deathly tomb that plays host to about 200 tonnes of melted radioactive fuel, and is swarming with radioactive dust.

But it’s also the abode of some very hardy fungi which researchers believe aren’t just tolerating the severe radiation, but actually harnessing its energy to thrive.

“Our findings suggest that [the fungi] can capture the energy from radiation and transform it into other forms of energy that can be used for growth,” said microbiologist Arturo Casadevall from the Albert Einstein College of Medicine at Yeshiva University in New York, USA.

Taken together, the researchers think their results do indeed hint that fungi can live off ionising radiation, harnessing its energy through melanin to somehow generate a new form of biologically usable growing power.

If they’re right, then this is powerful stuff, said fungal biologist Dee Carter from the University of Sydney. The results will challenge fundamental assumptions we have about the very nature of fungi, she said.

It also raises the possibility that fungi might be using melanin to secretly harvest visible and ultraviolet light for growth, adds Casadevall. If confirmed, this will further complicate our understanding of these sneaky organisms and their role in ecosystems.

Pretty amazing stuff. It really is great all that nature gives us to study and learn about using science.

Related: Radiation Tolerant Bacteria - Not Too Toxic for Life - Bacterium Living with High Level Radiation - What is an Extremophile?

June 24, 2008

Bees, Hornets and Wasps

Photo of a bee by Justin Hunter

Bee vs. Hornet vs. Wasp

A bee can generally only sting you once, while hornets and wasps can sting multiple times.

Bees are fuzzy pollen collectors that almost always die shortly after stinging people (because the stinger becomes embedded in the skin, which prevents multiple stings). Bees don’t die each time they sting, though; the primary purpose of the stinger is to sting other bees, which doesn’t result in the loss of the stinger.

Wasps are members of the family Vespidae, which includes yellow jackets and hornets. Wasps generally have two pairs of wings and are definitely not fuzzy. Only the females have stingers, but they can sting people repeatedly.

Hornets are a small subset of wasps not native to North America (the yellow jacket is not truly a hornet). Somewhat fatter around the middle than your average wasp, the European hornet is now widespread on the East Coast of the U.S. Like other wasps, hornets can sting over and over again and can be extremely aggressive.

Photo by Justin Hunter

Related: Bye Bye British Bees - Wasps Used to Detect Explosives - Colony Collapse Disorder Continues - Bye Bye Bees - Vanishing Giant Nests of Yellow-jackets

May 13, 2008

Cosmology Questions Answered

A great list of Cosmology Questions Answered, including: Why do we think that the expansion of the Universe is accelerating? What is quintessence? What is the Universe expanding into?

Everything that we measure is within the Universe, and we see no edge or boundary or center of expansion. Thus the Universe is not expanding into anything that we can see, and this is not a profitable thing to think about. Just as Dali’s Corpus Hypercubicus is just a 2-D picture of a 3-D object that represents the surface of a 4-D cube, remember that the balloon analogy is just a 2-D picture of a 3-D situation that is supposed to help you think about a curved 3-D space, but it does not mean that there is really a 4-D space that the Universe is expanding into.
May 4, 2008

Backyard Wildlife: Birds

photo of a bird

The last few days a bird like this one has been chasing a crow in my yard (unfortunately I have not been able to get an action picture of that). If you know what type of bird this is please add a comment.

When I see robins pecking away in the grass sometimes I see them get worms but my guess is they often are eating other stuff. I also see starlings feeding on my lawn. I found some online links that I quote below on what robins and starlings eat.

From the Yardener:

Next to beneficial insects, songbirds consume the most pest insects in your yard. Robins, blackbirds, flickers and starlings will eat a lot of webworms if they are in your lawn. Many seed-eating birds prey on caterpillars while raising their young. Encourage birds to settle in or near your yard and prey on fleas by offering them food, water, and shelter.

Related: Backyard Wildlife: Sharpshinned Hawk - Cool Crow Research - Backyard Wildlife: Fox - Backyard Wildlife: Turtle

Cornell University: American Robin

The American Robin eats both fruit and invertebrates. Earthworms are important during the breeding season, but fruit is the main diet during winter. Robins eat different types of food depending on the time of day; they eat earthworms early in the day and more fruit later in the day.

History And Biology Of European Starlings In North America
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April 24, 2008

Bacteriophages: The Most Common Life-Like Form on Earth

photo of bacteriophage

Bacteriophages: The Most Common Life-Like Form on Earth

There are more bacteriophages on Earth than any other life-like form. These small viruses are not clearly a form of life, since when not attached to bacteria they are completely dormant. Bacteriophages attack and eat bacteria and have likely been doing so for over 3 billion years ago. Although initially discovered early last century, the tremendous abundance of phages was realized more recently when it was found that a single drop of common seawater typically contains millions of them. Extrapolating, phages are likely to be at least a billion billion times more numerous than humans. Pictured above is an electron micrograph of over a dozen bacteriophages attached to a single bacterium. Phages are very small — it would take about a million of them laid end-to-end to span even one millimeter. The ability to kill bacteria makes phages a potential ally against bacteria that cause human disease, although bacteriophages are not yet well enough understood to be in wide spread medical use.

Photo credit: Wikipedia Electron micrograph of bacteriophages attached to a bacterial cell. These viruses have the size and shape of coliphage T1.; Insert: Mike Jones

Related: webcast of Bacteriophage T4 - types of microbes - What are Viruses? - Amazing Science: Retroviruses - Using Bacteria to Carry Nanoparticles Into Cells

February 25, 2008

Your Inner Fish

photo of Neil Shubin

Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body by Neil Shubin. A great piece from the University of Chicago, Fish out of Water, provides a good preview to the book:

What are the leading causes of death in humans? Four of the top ten causes—heart disease, diabetes, obesity, and stroke - have some sort of genetic basis and, likely, a historical one. Much of the difficulty is almost certainly due to our having a body built for an active animal but the lifestyle of a spud.

The problem is that the brain stem originally controlled breathing in fish; it has been jerry-rigged to work in mammals… This works well in fish, but it is a lousy arrangement for mammals.

The example from microbes is not unique. Judging by the Nobel Prizes awarded in medicine and physiology in the past 13 years, I should have called this book Your Inner Fly, Your Inner Worm, or Your Inner Yeast. Pioneering research on flies won the 1995 Nobel Prize in medicine for uncovering a set of genes that builds bodies in humans and other animals. Nobels in medicine in 2002 and 2006 went to people who made significant advances in human genetics and health by studying an insignificant-looking little worm (C. elegans). Similarly, in 2001, elegant analyses of yeast (including baker’s yeast) and sea urchins won the Nobel in medicine for increasing our understanding of some of the basic biology of all cells. These are not esoteric discoveries made on obscure and unimportant creatures. These discoveries on yeast, flies, worms, and, yes, fish tell us about how our own bodies work, the causes of many of the diseases we suffer, and ways we can develop tools to make our lives longer and healthier.

Two of my more controversial posts have been: Evolution is Fundamental to Science and Understanding the Evolution of Human Beings by Country. Evolution is not controversial scientifically. Just as gravity is not. Obviously this understanding is far from universal however.

But it is just a matter of time: similar to Galileo Galilei and heliocentric cosmology. See: Galileo’s Battle for the Heavens - Copernican System - Galileo). We now sit maybe 100 years after Galileo’s death (based on the evidence available in support of each scientific theory). At some point the evidence is accepted and life continues. Though I must admit it, I find it a bit disappointing how long it is taking for some people to accept the evidence of evolution. But I probably need to learn to be more patient - I have been told that more than once. All I can do is try to help present some small amount of the great work so many scientists have done to advance our knowledge. And here I am talking about evolution - for the 28% of those in the USA that couldn’t provide the answer that earth revolves around the sun, in 1998, well, they need much more help than I can provide.

Bacteria Can Transfer Genes to Other Bacteria

From page 115 of Good Gems, Bad Germs:

Microbiologists of the 1950’s did not appreciate the stunning extent to which bacteria swap genes… In 1959 Japanese hospitals experience outbreaks of multidrug-resistant bacterial dysentery. The shigella bacteria, which caused the outbreaks, were shrugging off four different classes of previously effective antibiotics: sulfonamides, streptomycins, chloramphenicols, and tetracyclines… In fact, the Japanese researches found it quite easy to transfer multidrug resistance from E. coli to shingella and back again simply by mixing resistant and susceptible strains together in a test tube.

Related: Blocking Bacteria From Passing Genes to Other Bacteria - Bacteria generous with their genes - Disrupting the Replication of Bacteria - articles on the overuse of anti-biotics - Raised Without Antibiotics

February 4, 2008

Water: Supercool and Strange

Supercool, and Strange

As liquids go, water is a radical nonconformist—differing from other liquids in dozens of ways (see the latest count at www.lsbu.ac.uk/water/anmlies). Most famous among water’s peculiarities is its density at low temperatures. While other liquids contract and get denser as they cool toward their freezing points, water stops contracting and starts to expand. That’s why ice floats and frozen pipes burst.

Water gets even weirder at colder temperatures, where it can exist as a liquid in a supercooled state well below its ordinary freezing point. Recent evidence suggests that supercooled water splits its personality into two distinct phases—another oddity unseen in other liquids. And last year, water surprised scientists yet again, when they found that at –63 degrees Celsius, supercooled water’s weird behavior returns to “normal.”

Related: Try to Answer 6 Basic Science Questions - Bdelloid Rotifers Abandoned Sex 100 Million Years Ago - Non-Newtonian video

February 2, 2008

Rainforests

John Hunter in Costa Rica

Facts about Rainforests by The Nature Conservancy

  • Covering less than 2 percent of the Earth’s total surface area, the world’s rainforests are home to 50 percent of the Earth’s plants and animals.
  • Seventy percent of the plants identified by the U.S. National Cancer Institute as useful in the treatment of cancer are found only in rainforests.
  • Less than one percent of the tropical rainforest species have been analyzed for their medicinal value.
  • Originally, 6 million square miles of tropical rainforest existed worldwide. But as a result of deforestation, only 2.6 million square miles remain.
  • At the current rate of tropical forest loss, 5-10 percent of tropical rainforest species will be lost per decade.
  • Every second, a slice of rainforest the size of a football field is mowed down. That’s 86,400 football fields of rainforest per day, or over 31 million football fields of rainforest each year.

Photo of John Hunter in Costa Rican rain forest, by Justin Hunter.

Related: Incredible Insects - 10 Science Facts You Should Know - Curious Cat Hoh Rain Forest Photo Essay

December 3, 2007

People Have More Bacterial Cells than Human Cells

Humans Carry More Bacterial Cells than Human Ones

All the bacteria living inside you would fill a half-gallon jug; there are 10 times more bacterial cells in your body than human cells

The infestation begins at birth: Babies ingest mouthfuls of bacteria during birthing and pick up plenty more from their mother’s skin and milk—during breast-feeding, the mammary glands become colonized with bacteria. “Our interaction with our mother is the biggest burst of microbes that we get,”

there are estimated to be more than 500 species living at any one time in an adult intestine, the majority belong to two phyla, the Firmicutes (which include Streptococcus, Clostridium and Staphylococcus), and the Bacteroidetes (which include Flavobacterium).

probiotics - dietary supplements containing potentially beneficial microbes - have been shown to boost immunity. Not only do gut bacteria “help protect against other disease-causing bacteria that might come from your food and water,” Huffnagle says, “they truly represent another arm of the immune system.”

But the bacterial body has made another contribution to our humanity - genes. Soon after the Human Genome Project published its preliminary results in 2001, a group of scientists announced that a handful of human genes - the consensus today is around 40 - appear to be bacterial in origin.

How cool is science? Very, I think :-)

Related: Tracking the Ecosystem Within Us - Beneficial Bacteria - Energy Efficiency of Digestion - Large Number of Bacteria on our Skin - Where Bacteria Get Their Genes - Amazing Science: Retroviruses

November 28, 2007

Amazing Science: Retroviruses

One of the great things about writing this blog is I find myself more focused on reading about interesting science. Retroviruses are very interesting and frankly amazing. Darwin’s Surprise by Michael Specter, The New Yorker:

A retrovirus stores its genetic information in a single-stranded molecule of RNA, instead of the more common double-stranded DNA. When it infects a cell, the virus deploys a special enzyme, called reverse transcriptase, that enables it to copy itself and then paste its own genes into the new cell’s DNA. It then becomes part of that cell forever; when the cell divides, the virus goes with it. Scientists have long suspected that if a retrovirus happens to infect a human sperm cell or egg, which is rare, and if that embryo survives - which is rarer still - the retrovirus could take its place in the blueprint of our species, passed from mother to child, and from one generation to the next, much like a gene for eye color or asthma.

When the sequence of the human genome was fully mapped, in 2003, researchers also discovered something they had not anticipated: our bodies are littered with the shards of such retroviruses, fragments of the chemical code from which all genetic material is made. It takes less than two per cent of our genome to create all the proteins necessary for us to live. Eight per cent, however, is composed of broken and disabled retroviruses, which, millions of years ago, managed to embed themselves in the DNA of our ancestors. They are called endogenous retroviruses, because once they infect the DNA of a species they become part of that species. One by one, though, after molecular battles that raged for thousands of generations, they have been defeated by evolution. Like dinosaur bones, these viral fragments are fossils. Instead of having been buried in sand, they reside within each of us, carrying a record that goes back millions of years. Because they no longer seem to serve a purpose or cause harm, these remnants have often been referred to as “junk DNA.” Many still manage to generate proteins, but scientists have never found one that functions properly in humans or that could make us sick.

How amazing is that? I mean really think about it: it is incredible. The whole article is great. Related: Old Viruses Resurrected Through DNA - DNA for once species found in another species’ Genes - New Understanding of Human DNA - Retrovirus overview (Tulane) - Cancer-Killing Virus
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August 30, 2007

One Species’ Genome Discovered Inside Another’s

Video describing genome inside genome Watch video of Professor Werren describing the genome-in-a-genome at the University of Rochester.

More incredible gene research. Scientists at the University of Rochester and the J. Craig Venter Institute have discovered a copy of the genome of a bacterial parasite residing inside the genome of its host species. The research, reported in today’s Science, also shows that lateral gene transfer—the movement of genes between unrelated species—may happen much more frequently between bacteria and multicellular organisms than scientists previously believed, posing dramatic implications for evolution.

Such large-scale heritable gene transfers may allow species to acquire new genes and functions extremely quickly, says Jack Werren, a principle investigator of the study. If such genes provide new abilities in species that cause or transmit disease, they could provide new targets for fighting these diseases.

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The results also have serious repercussions for genome-sequencing projects. Bacterial DNA is routinely discarded when scientists are assembling invertebrate genomes, yet these genes may very well be part of the organism’s genome, and might even be responsible for functioning traits.

“This study establishes the widespread occurrence and high frequency of a process that we would have dismissed as science fiction until just a few years ago,” says W. Ford Doolittle, Canada Research Chair in Comparative Microbial Genomics at Dalhousie University, who is not connected to the study. “This is stunning evidence for increased frequency of gene transfer.”

Related: Opossum Genome Shows ‘Junk’ DNA is Not Junk - Bdelloid Rotifers Abandoned Sex 100 Million Years Ago - Scientists discover new class of RNA - Where Bacteria Get Their Genes - New Understanding of Human DNA - Old Viruses Resurrected Through DNA

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