F6- excellent post- this article expresses my sentiments about the science of evolution exactly. maybe now we can be in agreement about the science of evolution?
the article stared out like this (which is funny given the attached link):
this was the point i thought i have been making for the last 3 days- obviously i'm not very articulate:
However, Darwin’s 1859 classic, On the Origin of Species, somewhat ironically doesn't answer that very question – how species actually originated. And to this day, how that first tiny pool of chemicals twitched to life remains a puzzle.
then it ended with this:
“Indeed, the quest for the origin of life seems a futile endeavor because life in its entirety is a natural process that has, according to the second law of thermodynamics, no definite beginning,” he said. “To ask how life started would be the same as to ask when and where did the first wind blow that quivered the surface of a warm pond.”
A Yale University zoologist has used a laser vibrometer and high speed videos from a wind tunnel to work out [ http://www.nsf.gov/news/news_summ.jsp?cntn_id=121361&org=NSF&from=news ] how the hummingbird makes its famous hum, and found that the males of each species have their own signature sound.
The male hummingbird [ http://www.wired.co.uk/news/archive/2009-06/10/the-hummingbird-thats-faster-than-a-fighter-jet ] produces a high-pitched fluttering sound during its elaborate courtship ritual. The bird will fly five to 40 meters into the air, before quickly dive-bombing past a perched female. At the lowest point, he rapidly spreads and closes his tail feathers to produce the hum.
Clark used a Scanning Laser Doppler Vibrometer [ http://en.wikipedia.org/wiki/Laser_Doppler_vibrometer ] — an instrument that is used to measure the vibrations of a surface — to measure the fluttering feathers, and studied the different feathers shapes and movements by viewing high speed videos of the tail feathers in a wind tunnel.
The data reveals that the feather spreading causes the features of the tail to be exposed to air, which causes them to flutter and generate noise. This also causes neighboring feathers [ http://www.wired.co.uk/news/archive/2011-07/01/ancient-bird-feathers ] to flutter, amplifying the sound — two feathers fluttering in unison can produce a sound about 12 decibels louder than two fluttering independently.
These different frequencies, volumes and sounds give the males of each hummingbird species their own signature noise. Other factors, such as the size, shape, mass and stiffness of the feathers also help determine the tone of each species’ sound. “The sounds that hummingbird feathers can make are more varied than I expected,” said Yale University’s Christopher Clark in a press release [ http://www.eurekalert.org/pub_releases/2011-09/nsf-haa090111.php ].
Clark hypothesizes that the volume of the sound made by the male hummingbird is impressive to females, who see the noise as an indicator of the male’s flying prowess. The loudest males would thereby gain a selective advantage and be favored by evolution [ http://www.wired.co.uk/news/archive/2011-09/08/cavefish-circadian-cycles ] — leading to the sounds we hear today.
The playful calf, aged between two and five months, thrilled hundreds of whale watchers at Bondi Beach yesterday, as it passed Sydney with its mother on its migration south about 11am yesterday.
Lapping up the attention of one group of tourists aboard a Whale Watching Sydney vessel as it passed by, the youngster joyfully jumped out of the water several times as if to pose for the cameras.
While it would take a DNA test to remove any doubt, National Parks whale expert Geoff Ross said it was "highly likely" the calf was the offspring of the famous Migaloo - the world's only all-white humpback whale.
Migaloo, spotted last Sunday off Cape Byron on the state's northern coast, is now swimming past Eden, about a week ahead of Migaloo Junior and the mother.
"It's a beautiful, very healthy calf," Mr Ross said. "The chances of it being Migaloo's are high. I'm very surprised to see two albinos so close together in distance.
"Even if you have one albino, it is very rare for the melanistic gene to be passed."
He said it would be Migaloo junior's first visit to Sydney.
NOBELIST Jack Szostak shifted his focus from telomeres to the origins of life. Bryce Vickmark for The New York Times
By CLAUDIA DREIFUS Published: October 17, 2011
BOSTON — The October night before he learned he had won the 2009 Nobel Prize in medicine, the biochemical researcher Jack W. Szostak says he slept like a log.
“I wasn’t going to lose a night’s sleep because of work I’d done in the 1980s,” Dr. Szostak, 58, said with a laugh during a recent two-hour interview at his laboratory at Massachusetts General Hospital. “It was old work.”
That “old work,” for which he had already won the Lasker Prize, was to help identify the nature and biochemistry of telomeres, the tips at the ends of chromosomes. Understanding them may be the key to unlocking the mysteries of cancer and cell aging. An edited version of our conversation follows.
Was telomere research your life’s work?
It was somewhat of a side project. Before I began working on telomeres, I’d been studying DNA recombination. What do cells do when they see a broken piece of DNA? Cells don’t like such breaks. They’ll do pretty much anything they can to fix things up. If a chromosome is broken, the cells will repair the break using an intact chromosome. That process is called recombination. And that’s what I was looking at.
Now, telomeres: They are the ends of chromosomes, the caps, and they don’t recombine. One day in 1980, I heard Liz [his colleague Elizabeth H. Blackburn] at a conference talking about how telomeres behaved. It was the contrast between the DNA she was working with and the material I was studying that caught my attention. I wanted to understand what was going on. So I wrote Liz right afterward.
What did you discover together?
We figured out what was going on at normal chromosome ends. We figured out the underlying biochemistry and showed that lots of different organisms use that biochemistry. We figured out that there was an enzyme, telomerase, that adds DNA to the ends of chromosomes to balance out the DNA that is naturally lost as cells grow.
Afterward, as people in the field began to see how important it was, telomere research just took off. It became clear that the loss of DNA from telomeres might have something to do with aging. Subsequently, it’s turned out that in almost all cancers, telomerase is turned on so those cells grow indefinitely. Of course, it’s very nice that work we did so long ago turned out to be important! But the truth is my work has gone off in several different directions.
What do you study now?
The origins of life. In my lab, we’re interested in the transition from chemistry to early biology on the early earth. Let’s go back to the early earth — let’s say probably some time within the first 500 million years. And let’s say the right chemistry that would make the building blocks of life has happened and you have the right molecules with which you can spark life. How did those chemicals get together and act something like a cell? You want something that can grow and divide and, most importantly, exhibit Darwinian evolution. The way that we study that is by trying to make it happen in the lab. We take simple chemicals and put them together in the right way. And we’re trying to build a very, very simple cell that might look like something that might have developed spontaneously on the early earth.
How far have you gotten?
Maybe I can say we’re halfway there.
We think that a primitive cell has to have two parts. First, it has to have a cell membrane that can be a boundary between itself and the rest of the earth. And then there has to be some genetic material, which has to perform some function that’s useful for the cell and get replicated to be inherited. The part we’ve come to understand reasonably well is the membrane part. The genetic material is the harder problem; the chemistry is just more complicated. The puzzle has been understanding how a molecule like RNA can get replicated before there were enzymes and all this fancy biological stuff, protein machinery, that we have now in our cells.
It’s very unusual for a researcher who’s made big breakthroughs in one scientific area to move into a completely different one. Why shift fields?
Because by the mid-1980s, it became clear what the questions with telomeres were and that they were going to be addressed perfectly well by others. I’m not the sort of person who likes a lot of competition. I particularly don’t like the feeling that if I wasn’t around doing certain work, it wouldn’t make any difference. If it’s going to be done anyway, what’s the point, right?
For about a year, I actually took courses here at Harvard, looking for something else to work on. I looked at cognitive neuroscience, which is incredibly fascinating, but seemed way too hard. RNA structure appealed because it could be key to understanding the beginning of life on earth.
You’ve now been working on this problem for a quarter of a century. Do you ever grow weary of it?
No. No. Because this isn’t a monolithic question where there’s nothing interesting until you get to the end. In fact, the question breaks down into maybe a dozen smaller questions. Each has interesting parts. Eventually it will all fit together.
For instance, we’ve made progress on the question of how you make a primitive cell membrane. Others had showed how a common clay mineral, montmorillonite, might have played a role in helping to make RNA. Our lab showed how it could help membranes to form and bring the RNA into the membrane.
You try to actually make life in your lab. In essence, you’re trying to prove evolutionary theory in a petri dish. How do religious fundamentalists feel about your work?
After that work on clay was published, we got a lot of e-mail from fundamentalists: “Oh, this is so wonderful. We are so happy that you’ve shown that it’s just like it’s written in the Bible or the Koran.” In Genesis, it begins with clay.
Growing up in Canada, were you one of those children who did chemistry experiments in the kitchen?
We did things that were ridiculously dangerous. But they were exciting, too. I remember in 1967, when there was that terrible fire on NASA’s Apollo 1 rocket that killed three astronauts, my father made pure oxygen and we lit this tiny cup and burned it. Suddenly, we had an unbelievable jet and a fire. You just could see exactly what had happened.
There’s no way that you could do that at home today. I guess a lot of kids lost eyes and limbs with the older stuff. The concern is understandable. Still, a kid needs to see something happening to get excited. My younger son, who is 11, likes chemistry. It’s a challenge to find anything exciting for him to try out.
Did the Nobel Prize change your life?
Nothing significant is any different. More people come up to me at conferences and want to have their picture taken with me. I wouldn’t say it’s any easier for us to get our papers accepted or to get grants.
The thing about the Nobel ceremony is that for a whole week, you get treated like a superstar. You get driven everywhere. You have minders who always make sure you get where you’re going. And you always get into the back seat of the limo. So we were told this story about one Nobel laureate who flies home, and he goes to get his car and he gets into the back seat and he just waits.
The world's earliest known evidence for animals may be these 570-million-year-old fossils from China. Shuhai Xiao
Microscopic 570-million-year-old fossils from China may represent the earliest evidence of animal life on Earth.
By Jennifer Viegas Tue Dec 6, 2011 07:00 PM ET
THE GIST
- The world's earliest known evidence for animals may be 570-million-year-old fossils from China.
- A new study negates that the fossils represent bacteria, strengthening the theory that the fossils are either animals or some type of protist.
- Animal life on Earth may have begun in South China -- the site of these fossils -- but it's also just possible that ocean conditions there helped to preserve the remains.
Microscopic 570-million-year-old fossils from China may represent the earliest evidence for animal life on Earth, suggests a new study in the Proceedings of the Royal Society B.
Previous theories have said that the fossils represented giant bacteria.
"One of the proponents of the bacteria theory was a co-author of this paper (Jake Bailey of the University of Minnesota) and he now agrees that the fossils do not represent a giant sulfur bacteria," co-author Philip Donoghue, a professor of palaeobiology at the University of Bristol, told Discovery News.
Images previously taken by Shuhai Xiao, a professor of geobiology at Virginia Tech, reveal that many of the fossils from the Dousantuo Formation in South China look like mini baseballs and soccer balls.
With the bacteria hypothesis negated, that leaves a few possibilities as to what these unusual fossils represent. One, argued by Xiao and others, is that the fossils are of metazoan embryos. If so, they would present one of the oldest records of the animal evolutionary lineage.
Another theory is that the fossils are protists, which are unicellular organisms lacking a definite cellular arrangement. Protists include bacteria, algae, diatoms and fungi. Although not animals, early protists may have given rise to the world’s first animals and plants.
To test out the theories, Donoghue and his colleagues focused on the possibility that the sports equipment-looking fossils were bacteria. Living and decayed Thiomargarita, a modern bacteria, were compared with modern embryos.
The researchers used a big particle accelerator in Switzerland to study the fossils down to their most minute details -- just one quarter of a micron. The extreme up-close look revealed that the bacteria and the Doushantuo fossils are indeed very different.
Negation of the bacteria theory now strengthens the argument that the fossils, be they embryos or some kind of protist, sit at the base of the animal tree of life.
Donoghue doesn't think all animal life on Earth emerged from this particular site. The location was "just chance," in terms of preservation.
"It is the most awesome fossil deposit," he said. "Every single grain is a fossil, and the deposit is 8 meters (over 26 feet) thick."
Donoghue explained that there was a lot of dissolved phosphate in the ocean at this now-China location during the Ediacaran Period. The phosphate helped to preserve the fossils over the many millions of years.
He said at least two animals have already been identified at the site, but the finds are very controversial at present. One has been called Vernanimalcula, meaning "small spring animal,” referring to its appearance in the fossil record at the end of what is known as the “Snowball Earth” freeze period.
Jun-Yuan Chen of the Nanjing Institute of Geology and Paleontology at the Chinese Academy of Sciences and his colleagues believe Vernanimalcula is the first known bilateral animal, meaning the first with body symmetry. Donoghue and others, however, dispute that claim.
Unfortunately, the jury is still out on what exactly the baseball and soccer ball-shaped fossils represent.
Yet another rival for "world's oldest known animals" are fossils from the Flinders Ranges of South Australia. They may also be animals and date to nearly the same time period of around 570 million years ago.
Although China and Australia seem very disconnected today, that may not always have been the case.
"According to paleogeographic reconstructions, South China and South Australia were close to each other at the time, belonging to a supercontinent called Gondwana," Maoyan Zhu, a scientist at the Nanjing Institute, told Discovery News.
Findings concerning additional research on the Doushantuo fossils are expected to be released soon, however, so the mystery over what the fossils are may at last be resolved.
At left, an original strain of brewer’s yeast. At right, the multicellular form. (Ratcliff et al./PNAS)
By Brandon Keim January 17, 2012 | 4:49 pm
An evolutionary transition that took several billion years to occur in nature has happened in a laboratory, and it needed just 60 days.
Under artificial pressure to become larger, single-celled yeast became multicellular creatures. That crucial step is responsible for life’s progression beyond algae and bacteria, and while the latest work doesn’t duplicate prehistoric transitions, it could help reveal the principles guiding them.
“This is actually simple. It doesn’t need mystical complexity or a lot of the things that people have hypothesized — special genes, a huge genome, very unnatural conditions,” said evolutionary biologist Michael Travisano of the University of Minnesota, co-author of a study Jan. 17 in the Proceedings of the National Academy of Sciences.
In the new study, researchers led by Travisano and William Ratcliff grew brewer’s yeast, a common single-celled organism, in flasks of nutrient-rich broth.
Once per day they shook the flasks, removed yeast that most rapidly settled to the bottom, and used it to start new cultures. Free-floating yeast were left behind, while yeast that gathered in heavy, fast-falling clumps survived to reproduce.
Within just a few weeks, individual yeast cells still retained their singular identities, but clumped together easily. At the end of two months, the clumps were a permanent arrangement. Each strain had evolved to be truly multicellular, displaying all the tendencies associated with “higher” forms of life: a division of labor between specialized cells, juvenile and adult life stages, and multicellular offspring.
Multicellular yeast reproduces itself; the offspring will not reproduce until it has grown. (Ratcliff et al./PNAS)
“Multicellularity is the ultimate in cooperation,” said Travisano, who wants to understand how cooperation emerges in selfishly competing organisms. “Multiple cells make make up an individual that cooperates for the benefit of the whole. Sometimes cells give up their ability to reproduce for the benefit of close kin.”
According to Travisano, too much emphasis was placed on identifying some genetic essence of complexity. The new study suggests that environmental conditions are paramount: Give single-celled organisms reason to go multicellular, and they will.
Apart from insights into complexity’s origins, the findings could have implications for researchers in other fields. While multicellularity would have a hard time emerging now in nature, where existing animals have a competitive advantage, the underlying lesson of rapid, radical evolution is universal.
“That idea of easy transformability changes your perspective,” said Travisano. “I’m certain that rapid evolution occurs. We just don’t know to look for it.”
Targeted breeding of single-celled organisms into complex, multicellular forms could also become a biotechnological production technique.
“If you want to have some organism that makes ethanol or a novel compound, then — apart from using genetic engineering — you could do selection experiments” to shape their evolution, Travisano said. “What we’re doing right here, engineering via artificial selection, is something we’ve done for centuries with animals and agriculture.”
Researchers evolve a multicellular yeast in the lab in 2 months
By John Timmer | Published January 18, 2012
When we think of life on Earth, most of us think of multicellular organisms, like large mammals or massive trees. But we're only aware of three groups of complex, multicellular organisms, which suggested it might be a major hurdle. Now, a new study describes how researchers evolved a multicellular form of yeast (the same species that contributes to bread and beer), and were able to see specialized cell behaviors and reproduction in as little as 60 days.
The authors lay out the problem very simply in their introduction, stating that, "Multicellularity was one of the most significant innovations in the history of life, but its initial evolution remains poorly understood." There is some evidence that it can be a favorable trait—research shows that clusters of cells evolve when a single-celled organism is kept in culture with a predator that can only swallow one cell at a time.
But that's about as far as these experiments went. It wasn't clear how these clusters of cells formed, whether they were genetically related, or whether they engaged in any sort of specialized behavior. More significantly, it wasn't obvious whether these clusters took a sort of "every cell for itself" approach to reproduction. So, although this work showed a multicellular lifestyle could be selected for, the researchers didn't look into how far down the road towards specialization those cells would go.
The new study attempts to follow more the behavior of simple multicellular groups more closely. It uses baker's yeast (Saccharomyces cerevisiae), an organism that normally grows as single cells. The authors grew these in culture and, once a day, transferred them in a way that favored multicellular growth.
Their method was pretty simple. Normally, yeast are grown in a culture that's shaken, and the single cells will only slowly settle to the bottom when that's stopped. The authors only transferred the cells at the bottom of the culture to fresh food, so that they selected for those cells that settled to the bottom quickly. This favors large clusters of cells, instead of single ones.
With only 60 daily transfers, all of their experimental populations were dominated by yeast cells that grew as clusters, which the authors describe as "roughly spherical snowflake-like." These were formed because, instead of separating after they divided, cells would remain attached, expanding the cluster with each division. Although this comes at a cost compared to individual cells—the authors calculate that individual cells in the cluster are 10 percent less fit than their single-celled relatives when they're not selecting for things on the bottom. But, with the selection in place, the clusters had a huge advantage.
But the clusters didn't simply keep growing indefinitely. Instead, the yeast quickly evolved a form of reproduction by splitting off what the authors call "propagules," or smaller clusters that break off and go on to develop on their own.
With more generations, this form of reproduction began to include specialized cell behavior. A small percentage of cells in the cluster would start committing suicide through a process called apoptosis. This death would allow the propagule to split off cleanly at the site of the dead cell, improving the efficiency of reproduction. Normally, there's no evolutionary advantage to a cell ending up dead but, since the cells in the propagule are genetically identical, this behavior can be selected for.
This new form of growth and reproduction is still a long way off from the complex, specialized tissues found in most multicellular organisms. But the ease with which this behavior evolved suggests that the foundations of multicellularity may evolve very easily, and don't present the barrier to complexity that many people have assumed it was.
Yeast Experiment Hints at a Faster Evolution From Single Cells
Video [embedded] Evolving Yeast Cells
By CARL ZIMMER Published: January 16, 2012
Our ancestors were single-celled microbes for about three billion years before they evolved bodies. But in a laboratory at the University of Minnesota, brewer’s yeast cells can evolve primitive bodies in about two weeks.
The transition to multicellular life has long intrigued evolutionary biologists. The cells in our bodies have evolved to cooperate with exquisite precision. The human body has more than 200 types of cells, each dedicated to a different job. And a vast majority of the 100 trillion cells in our bodies sacrifice their own long-term legacy: Only eggs and sperm have a chance to survive our own death.
These demands for cooperation and sacrifice ought to make it hard for single-celled life to become multicellular. Yet animals, plants and other life forms have evolved bodies. “We know that multicellularity has evolved in different lineages at least 25 times in the history of life,” said William Ratcliff, a postdoctoral researcher at the University of Minnesota.
Dr. Ratcliff and his adviser, Michael Travisano, are experts in experimental evolution. They design experiments in which microbes can evolve interesting new traits within weeks.
“We were sitting in his office drinking coffee, talking about what would be the coolest thing you could do in the lab,” Dr. Ratcliff said. “O.K., the origin of life would be too hard. But other than the origin of life, what would be the coolest thing?” They decided it would be observing single-celled microbes evolving a primitive form of multicellularity.
The scientists designed an experiment with brewer’s yeast, which normally lives as single cells, feeding on sugar and budding off daughter cells to reproduce.
Dr. Ratcliff and his colleagues set up an experiment that might favor multicellularity in yeast. They reared lines of yeast, starting from a single cell, in 10 flasks of broth. They kept the flasks shaking for a day and then let the yeast settle. The scientists then took out a drop of the settled yeast cells and transferred it to a fresh flask, where the yeast could continue to grow. In this experiment, natural selection favored any new mutation that would let the yeast fall quickly. Yeast cells that were still floating high in the broth would not have a chance to be delivered to the next flask.
In a matter of weeks, Dr. Ratcliff noticed, the yeast was sinking fast, forming a cloudy layer at the bottom of the flasks. He put the yeast under a microscope and discovered that most of it was no longer growing as single cells. Instead, the broth was dominated by snowflake-shaped clusters of hundreds of cells stuck together.
These were not clumps of unrelated cells, he found. When he isolated individual cells and let them grow, they formed new snowflakes. Instead of drifting away, newly budded yeast cells remained stuck to their parents. By staying stuck together, these yeast clusters fell faster than individual cells.
A single cell needs a few hours to grow to “adult” size, Dr. Ratcliff found. After it matures, its growing branches start to press against one another until they snap apart. These broken branches are yeast versions of plant cuttings: Each one grows into a snowflake of its own, which then snaps apart in turn.
Dr. Ratcliff also found that this new form of reproduction is possible only because some of the yeast cells make the ultimate sacrifice. Once a snowflake reaches adult size, a fraction of the cells commit suicide. “The cells that kill themselves act as weak links,” he said.
“This is a really interesting and important study,” said Richard Lenski, a biologist at Michigan State University and the editor of the paper. “It shows that a major transition in evolution — going from unicellular to multicellular life forms — might not be as hard to achieve as most biologists have long thought.”
Dr. Ratcliff suspects that the transformation of the yeast in his lab may offer hints about how animals and other lineages became multicellular hundreds of millions of years ago. “Forming clusters isn’t a freaky yeast thing,” he said. The closest single-celled relatives of animals, called choanoflagellates [ http://www.nytimes.com/2010/12/14/science/14creatures.html ], also sometimes grow as clusters of cells.
Animals and plants did not evolve inside flasks, of course. But natural conditions could have favored clusters of cells. They might have been harder for predators to eat, for example. A cluster of cells might also be able to feed more efficiently in some cases.
Dr. Ratcliff and his colleagues are now examining 25 genomes of the evolved yeast, looking for the mutations that gave them snowflake bodies. Meanwhile, their yeast continues to evolve. Once the cells gain the ability to form snowflakes, they become better adapted to multicellular life. They snap off smaller branches, allowing them to reproduce faster.
Dr. Ratcliff would not go into detail about where the yeast evolution was going until he published the latest results. “We’re getting really interesting things happening now” was all he would say.
Berkeley Lab researchers at the Advanced Light Source have discovered a nucleotide-sensing loop that synchronizes conformational changes in the three domains of group II chaperonin for the proper folding of other proteins. (Photo Credit: Image courtesy of Berkeley Lab)
(From left) Paul Adams, Corie Ralston, Jose Henrique Pereira and Ryan McAndrew at the Advanced Light Source where they used the facilities of the Berkeley Center for Structural Biology to reveal important new information on protein folding. (Photo Credit: Photo by Roy Kaltschmidt, Berkeley Lab)
Overlooking the San Francisco Bay, Berkeley Lab's Advanced Light Source is a DOE Office of Science national user facility providing premier beams of X-ray and ultraviolet light for scientific research. (Photo Credit: Photo by Roy Kaltschmidt, Berkeley Lab)
Posted On: February 24, 2012 - 6:30pm
The gold standard for nanotechnology is nature's own proteins. These biomolecular nanomachines – macromolecules forged from peptide chains of amino acids - are able to fold themselves into a dazzling multitude of shapes and forms that enable them to carry out an equally dazzling multitude of functions fundamental to life. As important as protein folding is to virtually all biological systems, the mechanisms behind this process have remained a mystery. The fog, however, is being lifted.
A team of researchers with the U.S. Department of Energy (DOE)'s Lawrence Berkeley National Laboratory (Berkeley Lab), using the exceptionally bright and powerful x-ray beams of the Advanced Light Source, have determined the crystal structure of a critical control element within chaperonin, the protein complex responsible for the correct folding of other proteins. The incorrect or "misfolding" of proteins has been linked to many diseases, including Alzheimer's, Parkinson's and some forms of cancer.
"We identified, for the first time, a region within group II chaperonins we call the nucleotide-sensing loop, which detects the presence of the ATP molecules that fuel the chaperonin folding motion," says Paul Adams, a bioengineer with Berkeley Lab's Physical Biosciences Division and leading authority on x-ray crystallography who led this work. ""We knew that ATP hydrolysis is important for promoting protein folding, but we did not know how ATP activity was sensed and communicated."
Adams is the corresponding author of a paper in The EMBO Journal that describes this study, which was performed in collaboration with colleagues at MIT and Stanford. The paper is titled "Mechanism of nucleotide sensing in group II Chaperonins." Co-authoring this paper were Jose Pereira, Corie Ralston, Nicholai Douglas, Ramya Kumar, Tom Lopez, Ryan McAndrew, Kelly Knee, Jonathan King and Judith Frydman.
Chaperonins promote the proper folding of newly translated proteins and proteins that have been stress-denatured – meaning they've lost their structure - by encapsulating them inside a protective chamber formed from two rings of molecular complexes stacked back-to-back. There are two classes of chaperonins, group I found in prokaryotes; and group II found in eukaryotes. Much of the basic architecture has been evolutionarily preserved across these two classes but they do differ in how the protective chamber is opened to accept proteins and closed to fold them. Whereas group I chaperonins require a detachable ring-shaped molecular lid to open and close the chamber, group II chaperonins have a built-in lid.
"We obtained crystal structures at sufficient resolution to allow us to examine, in detail, the effects that changes in nucleotides states have on ATP binding and hydrolysis in group II chaperonins," Adams says. "From these structures we see that the nucleotide-sensing loop monitors ATP binding sites for changes and communicates this information throughout the chaperonin. Functional analysis further suggests that the nucleotide-sensing loop region uses this information to control the rate of ATP binding and hydrolysis, which in turn controls the timing of the protein folding reaction."
The double-ring chaperonin complex features multiple subunits that are grouped into three domains - apical, intermediate and equatorial. For group II chaperonins, the closing of the lid for protein-folding causes all three domains to rotate as a single rigid body, resulting in conformational changes to the chamber that enable the proteins within to be folded. The synchronized rotation of the chaperonin domains is dependent upon the communication to all the subunits that is provided by the nucleotide-sensing loop. In identifying the nucleotide-sensing loop and its controlling role in group II chaperonin protein-folding, Adams and his colleagues may have opened a new avenue by which modified protein-folding activities could engineered.
"The strong relationship between incorrectly folded proteins and pathological states is well documented," Adams says. "Since ATP hydrolysis is required for protein folding, it could be possible to engineer a nucleotide-sensing loop that promotes slower or faster protein folding activity in a given chaperonin. This could, for example, be used to increase the protein folding activity of human chaperonin, or perhaps reduce the cellular accumulation of misfolded proteins that can cause disease and other problems."
A key factor that enabled Adams and his colleagues to solve the three-dimensional crystal structure of the nucleotide sensing loop and determine its pivotal role in the protein folding of group II chaperonins was the unique protein crystallography capabilities of the Berkeley Center for Structural Biology. The BCSB operates five protein crystallography beamlines for Berkeley Lab's Advanced Light Source (ALS), a DOE Office of Science national user facility for synchrotron radiation, and the first of the world's third generation light sources. For this particular study, Adams and his colleagues used ALS beamlines 8.2.1 and 8.2.2, which are powered by a superconducting bending magnetic to yield higher energy x-rays that are optimized for the study of single crystals of biological molecules.
In this study, Adams and his colleagues studied an archaeon chaperonin. In their followup research, they will apply what they have learned to study the chaperonin known as TRiC, which is the human chaperonin.
"We believe that chaperonins have evolved to work on specific substrates and that the rates of protein folding may vary greatly between chaperonins in different organisms," Adams says. "The structural and biochemical identification of the changes related to ATP hydrolysis provides important insights into the complex puzzle of protein folding for each type of chaperonin."
The bizarre rules of quantum mechanics may in fact enable many of life's fundamental processes, scientists say. CREDIT: agsandrew | Shutterstock
Clara Moskowitz, LiveScience Senior Writer Date: 05 June 2012 Time: 11:33 AM ET
NEW YORK — The bizarre rules of quantum physics are often thought to be restricted to the microworld, but scientists now suspect they may play an important role in the biology of life.
Evidence is growing for the involvement of quantum mechanics in a wide range of biological processes, including photosynthesis, bird migration, the sense of smell, and possibly even the origin of life.
"Quantum mechanics is weird, that's its defining characteristic. It's funky and strange," said MIT mechanical engineer Seth Lloyd.
These oddities generally don't affect everyday macroscopic objects, which are thought to be too hot and wet for delicate quantum states to withstand. But it seems nature may have found ways to harness quantum mechanics to power some of its most complex and vital systems.
"Life is made out of atoms and atoms behave quantum mechanically," said cosmologist Paul Davies of Arizona State University. "Life has been around for a long time — 3.5 billion years on this planet at least — and there's plenty of time to learn some quantum trickery if it confers an advantage."
Bird brains
One area where clues are implicating quantum mechanics is the internal compasses of birds [ http://www.livescience.com/4641-birds-earth-magnetic-fields.html ] and other migratory animals. Many bird species migrate thousands of miles every year to return not just to the same region, but to the exact same breeding spot.
For ages, scientists have puzzled how birds could achieve such a feat of navigation, assuming they possess some ability to sense direction based on Earth's magnetic field.
"We see clearly they can detect the magnetic field," said University of California, Irvine, biophysicist Thorsten Ritz. "What we cannot do is say, 'This is the magnetic organ.'"
Mounting evidence now suggests birds may be relying on quantum entanglement [ http://www.livescience.com/19975-spooky-quantum-entanglement.html ] — the strange ability of particles to share properties even when separated, so that if an action is performed on one, the other feels its consequences.
Scientists think the process is made possible by a protein inside birds' eye cells called cryptochrome.
When green light passes into the bird's eye, it hits cryptochrome, which gives an energy boost to one of the electrons of an entangled pair, separating it from its partner. In its new location, the electron experiences a slightly different magnitude of Earth's magnetic field, and this alters the electron's spin. Birds can use this information to build an internal map of Earth's magnetic field to figure out their position and direction.
"It's certainly very plausible," Lloyd said. "It sounded kind of crazy when I first heard it. We don't have direct experimental evidence, but it does make sense."
The theory gained support from a recent experiment with fruit flies, which also contain cryptochrome. When this light-detecting protein was extracted from the fruit flies, they lost their magnetic sensitivity and became discombobulated.
Sniffing scents
Another case where quantum mechanics may come to the rescue is the sense of smell [ http://www.lifeslittlemysteries.com/36-how-does-scent-travel.html ]. At first, biologists thought they understood smell through a simple model: Odor molecules waft into the nose, and receptor molecules there bind to these molecules and identify them based on their particular shape.
But scientists realized that some odor molecules that have identical shapes have completely different smells, due to a minute chemical change, such as a single hydrogen atom in the molecule being replaced by a heavier version of hydrogen called deuterium. While this affects the weight of the molecule, it doesn't change its shape, so it still fits into the receptor molecule in exactly the same way.
"The theory is that even if the shape of the molecule is the same, because it's got this slight difference, it vibrates in a different fashion," Lloyd said. "And this kind of wavelike nature, which is a purely quantum kind of effect, somehow this receptor is able to sense this vibrational difference."
Missing pieces
Physicists are probing more and more unsolved mysteries of biology, hoping that quantum mechanics may provide the missing piece of the puzzle. They even have hope that it could shed light on one of the most intractable questions in all of biology: How did life get started? [7 Theories on the Origin of Life [ http://www.livescience.com/13363-7-theories-origin-life.html ]]
"We want to know 'How did non-life turn into life?'" Davies said. "Life is clearly a distinctive state of matter. What we would like to know is if that distinctiveness is fundamentally quantum mechanical."
But in their excitement to try the quantum key in the locks of biology, some scientists are wary of overreaching.
"Quantum mechanics is strange and mysterious," Lloyd said. "The origins of life are strange and mysterious. That doesn’t mean that they're all the same thing. I think one should be careful saying that all strange and mysterious things have the same origin."
For years, bacteria have had a bad name. They are the cause of infections, of diseases. They are something to be scrubbed away, things to be avoided.
But now researchers have taken a detailed look at another set of bacteria that may play even bigger roles in health and disease: the 100 trillion good bacteria that live in or on the human body.
No one really knew much about them. They are essential for human life, needed to digest food, to synthesize certain vitamins, to form a barricade against disease-causing bacteria. But what do they look like in healthy people, and how much do they vary from person to person?
They discovered more strains than they had ever imagined — as many as a thousand bacterial strains on each person. And each person’s collection of microbes, the microbiome, was different from the next person’s [ http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html ]. To the scientists’ surprise, they also found genetic signatures of disease-causing bacteria lurking in everyone’s microbiome. But instead of making people ill, or even infectious, these disease-causing microbes simply live peacefully among their neighbors.
The results, published on Wednesday in Nature and three PLoS journals, are expected to change the research landscape.
The work is “fantastic,” said Bonnie Bassler, a Princeton University microbiologist who was not involved with the project. “These papers represent significant steps in our understanding of bacteria in human health.”
Until recently, Dr. Bassler added, the bacteria in the microbiome were thought to be just “passive riders.” They were barely studied, microbiologists explained, because it was hard to know much about them. They are so adapted to living on body surfaces and in body cavities, surrounded by other bacteria, that many could not be cultured and grown in the lab. Even if they did survive in the lab, they often behaved differently in this alien environment. It was only with the advent of relatively cheap and fast gene sequencing methods that investigators were able to ask what bacteria were present.
Examinations of DNA sequences served as the equivalent of an old-time microscope, said Curtis Huttenhower of the Harvard School of Public Health, an investigator for the microbiome project. They allowed investigators to see — through their unique DNA sequences — footprints of otherwise elusive bacteria.
The work also helps establish criteria for a healthy microbiome, which can help in studies of how antibiotics perturb a person’s microbiome and how long it takes the microbiome to recover.
In recent years, as investigators began to probe the microbiome in small studies, they began to appreciate its importance. Not only do the bacteria help keep people healthy, but they also are thought to help explain why individuals react differently to various drugs and why some are susceptible to certain infectious diseases while others are impervious. When they go awry they are thought to contribute to chronic diseases and conditions like irritable bowel syndrome, asthma, even, possibly, obesity.
Humans, said Dr. David Relman, a Stanford microbiologist, are like coral, “an assemblage of life-forms living together.”
Dr. Barnett Kramer, director of the division of cancer prevention at the National Cancer Institute, who was not involved with the research project, had another image. Humans, he said, in some sense are made mostly of microbes. From the standpoint of our microbiome, he added, “we may just serve as packaging.”
The microbiome starts to grow at birth, said Lita Proctor, program director for the Human Microbiome Project. As babies pass through the birth canal, they pick up bacteria from the mother’s vaginal microbiome.
“Babies are microbe magnets,” Dr. Proctor said. Over the next two to three years, the babies’ microbiomes mature and grow while their immune systems develop in concert, learning not to attack the bacteria, recognizing them as friendly.
Babies born by Caesarean section, Dr. Proctor added, start out with different microbiomes, but it is not yet known whether their microbiomes remain different after they mature. In adults, the body carries two to five pounds of bacteria, even though these cells are minuscule — one-tenth to one-hundredth the size of a human cell. The gut, in particular, is stuffed with them.
“The gut is not jam-packed with food; it is jam-packed with microbes,” Dr. Proctor said. “Half of your stool is not leftover food. It is microbial biomass.” But bacteria multiply so quickly that they replenish their numbers as fast as they are excreted.
The bacteria also help the immune system, Dr. Huttenhower said. The best example is in the vagina, where they secrete chemicals that can kill other bacteria and make the environment slightly acidic, which is unappealing to other microbes.
Including the microbiome as part of an individual is, some researchers said, a new way to look at human beings.
It was a daunting task, though, to investigate the normal human microbiome. Previous studies of human microbiomes had been small and had looked mostly at fecal bacteria or bacteria in saliva in healthy people, or had examined things like fecal bacteria in individuals with certain diseases, like inflammatory bowel disease, in which bacteria are thought to play a role.
But, said Barbara B. Methé, an investigator for the microbiome study and a microbiologist at the J. Craig Venter Institute, it was hard to know what to make of those studies.
“We were stepping back and saying, ‘We don’t really have a population study. What does a normal microbiome look like?’ ” she said.
The first problem was finding completely healthy people for the study. The investigators recruited 600 subjects, ages 18 to 40, poking and prodding them. They brought in dentists to probe their gums, looking for gum disease, and pick at their teeth, looking for cavities. They brought in gynecologists to examine the women to see if they had yeast infections. They examined skin and tonsils and nasal cavities. They made sure the subjects were not too fat and not too thin. Even though those who volunteered thought they filled the bill, half were rejected because they were not completely healthy. And 80 percent of those who were eventually accepted first had to have gum disease or cavities treated by a dentist.
When they had their subjects — 242 men and women deemed free of disease in the nose, skin, mouth, gastrointestinal tract and, for the women, vagina — the investigators collected stool samples and saliva, and scraped the subjects’ gums and teeth and nostrils and their palates and tonsils and throats. They took samples from the crook of the elbow and the folds of the ear. In all, women were sampled in 18 places, including three sites in the vagina, and men in 15. The investigators resampled subjects three times during the course of the study to see if the bacterial composition of their bodies was stable, generating 11,174 samples.
To catalog the body’s bacteria, researchers searched for DNA with a specific gene, 16S rRNA, that is a marker for bacteria and whose slight sequence variations can reveal different bacterial species. They sequenced the bacterial DNA to find the unique genes in the microbiome. They ended up with a deluge of data, much too much to study with any one computer, Dr. Huttenhower said, creating “a huge computational challenge.”
The next step, he said, is to better understand how the microbiome affects health and disease and to try to improve health by deliberately altering the microbiome.
But, Dr. Relman said, “we are scratching at the surface now.”
The healthy adult body hosts ten times as many microbial cells as human cells, including bacteria, archaea, viruses, and eukaryotic microbes resident on nearly every body surface. The metagenome carried collectively by these microbial communities dwarfs the human genome in size, and their influences on normal development, diet and obesity, immunity, and disease are under active research.
Funded by the National Institutes of Health Common Fund, the Human Microbiome Project (HMP) was established to provide a comprehensive baseline of the microbial diversity at 18 different human body sites. This includes reference genomes of host-associated microbial isolates, 16S rRNA marker gene sequencing for thousands of healthy microbiomes, 3.5Tb of metagenomic sequences, assemblies, and metabolic reconstructions, and a catalogue of over 5M microbial genes. These data join resources generated by computational tool development for analysis of the microbiome, research on the ethical, legal, and social implications of the microbiota, technology development for investigating these microbial communities, and a range of disease-focused microbiome demonstration projects. All resources generated by the Human Microbiome Project are publicly available at: http://hmpdacc.org.
The Human Microbiome Project Collection encompasses publications from consortium members generating, leveraging, and exploring these resources. Articles are presented in order of publication date and new articles will be added to the Collection as they are published. For more information on the Human Microbiome Project, please contact HMPinformation@mail.nih.gov.
Research Articles
Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome Sahar Abubucker, Nicola Segata, Johannes Goll, Alyxandria M. Schubert, Jacques Izard, Brandi L. Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat, Owen White, Scott T. Kelley, Barbara Methé, Patrick D. Schloss, Dirk Gevers, Makedonka Mitreva, Curtis Huttenhower PLoS Computational Biology: Published 13 Jun 2012 | info:doi/10.1371/journal.pcbi.1002358 http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358
Inflammatory Bowel Diseases Phenotype, C. difficile and NOD2 Genotype Are Associated with Shifts in Human Ileum Associated Microbial Composition Ellen Li, Christina M. Hamm, Ajay S. Gulati, R. Balfour Sartor, Hongyan Chen, Xiao Wu, Tianyi Zhang, F. James Rohlf, Wei Zhu, Chi Gu, Charles E. Robertson, Norman R. Pace, Edgar C. Boedeker, Noam Harpaz, Jeffrey Yuan, George M. Weinstock, Erica Sodergren, Daniel N. Frank PLoS ONE: Published 13 Jun 2012 | info:doi/10.1371/journal.pone.0026284 http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0026284
Sequence Analysis of the Human Virome in Febrile and Afebrile Children Kristine M. Wylie, Kathie A. Mihindukulasuriya, Erica Sodergren, George M. Weinstock, Gregory A. Storch PLoS ONE: Published 13 Jun 2012 | info:doi/10.1371/journal.pone.0027735 http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0027735
A Case Study for Large-Scale Human Microbiome Analysis Using JCVI’s Metagenomics Reports (METAREP) Johannes Goll, Mathangi Thiagarajan, Sahar Abubucker, Curtis Huttenhower, Shibu Yooseph, Barbara A. Methé PLoS ONE: Published 13 Jun 2012 | info:doi/10.1371/journal.pone.0029044 http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0029044
Host Genes Related to Paneth Cells and Xenobiotic Metabolism Are Associated with Shifts in Human Ileum-Associated Microbial Composition Tianyi Zhang, Robert A. DeSimone, Xiangmin Jiao, F. James Rohlf, Wei Zhu, Qing Qing Gong, Steven R. Hunt, Themistocles Dassopoulos, Rodney D. Newberry, Erica Sodergren, George Weinstock, Charles E. Robertson, Daniel N. Frank, Ellen Li PLoS ONE: Published 13 Jun 2012 | info:doi/10.1371/journal.pone.0030044 http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030044
Novel Bacterial Taxa in the Human Microbiome Kristine M. Wylie, Rebecca M. Truty, Thomas J. Sharpton, Kathie A. Mihindukulasuriya, Yanjiao Zhou, Hongyu Gao, Erica Sodergren, George M. Weinstock, Katherine S. Pollard PLoS ONE: Published 13 Jun 2012 | info:doi/10.1371/journal.pone.0035294 http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0035294
Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities John Martin, Sean Sykes, Sarah Young, Karthik Kota, Ravi Sanka, Nihar Sheth, Joshua Orvis, Erica Sodergren, Zhengyuan Wang, George M. Weinstock, Makedonka Mitreva PLoS ONE: Published 13 Jun 2012 | info:doi/10.1371/journal.pone.0036427 http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0036427
A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy Kjersti Aagaard, Kevin Riehle, Jun Ma, Nicola Segata, Toni-Ann Mistretta, Cristian Coarfa, Sabeen Raza, Sean Rosenbaum, Ignatia Van den Veyver, Aleksandar Milosavljevic, Dirk Gevers, Curtis Huttenhower, Joseph Petrosino, James Versalovic PLoS ONE: Published 13 Jun 2012 | info:doi/10.1371/journal.pone.0036466 http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0036466
After more than 4,000 years — almost since the dawn of recorded time, when Utnapishtim told Gilgamesh that the secret to immortality lay in a coral found on the ocean floor — man finally discovered eternal life in 1988. He found it, in fact, on the ocean floor. The discovery was made unwittingly by Christian Sommer, a German marine-biology student in his early 20s. He was spending the summer in Rapallo, a small city on the Italian Riviera, where exactly one century earlier Friedrich Nietzsche conceived “Thus Spoke Zarathustra”: “Everything goes, everything comes back; eternally rolls the wheel of being. Everything dies, everything blossoms again. . . .”
Sommer was conducting research on hydrozoans, small invertebrates that, depending on their stage in the life cycle, resemble either a jellyfish or a soft coral. Every morning, Sommer went snorkeling in the turquoise water off the cliffs of Portofino. He scanned the ocean floor for hydrozoans, gathering them with plankton nets. Among the hundreds of organisms he collected was a tiny, relatively obscure species known to biologists as Turritopsis dohrnii. Today it is more commonly known as the immortal jellyfish.
Sommer kept his hydrozoans in petri dishes and observed their reproduction habits. After several days he noticed that his Turritopsis dohrnii was behaving in a very peculiar manner, for which he could hypothesize no earthly explanation. Plainly speaking, it refused to die. It appeared to age in reverse, growing younger and younger until it reached its earliest stage of development, at which point it began its life cycle anew.
Sommer was baffled by this development but didn’t immediately grasp its significance. (It was nearly a decade before the word “immortal” was first used to describe the species.) But several biologists in Genoa, fascinated by Sommer’s finding, continued to study the species, and in 1996 they published a paper called “Reversing the Life Cycle.” The scientists described how the species — at any stage of its development — could transform itself back to a polyp, the organism’s earliest stage of life, “thus escaping death and achieving potential immortality.” This finding appeared to debunk the most fundamental law of the natural world — you are born, and then you die.
One of the paper’s authors, Ferdinando Boero, likened the Turritopsis to a butterfly that, instead of dying, turns back into a caterpillar. Another metaphor is a chicken that transforms into an egg, which gives birth to another chicken. The anthropomorphic analogy is that of an old man who grows younger and younger until he is again a fetus. For this reason Turritopsis dohrnii is often referred to as the Benjamin Button jellyfish.
Yet the publication of “Reversing the Life Cycle” barely registered outside the academic world. You might expect that, having learned of the existence of immortal life, man would dedicate colossal resources to learning how the immortal jellyfish performs its trick. You might expect that biotech multinationals would vie to copyright its genome; that a vast coalition of research scientists would seek to determine the mechanisms by which its cells aged in reverse; that pharmaceutical firms would try to appropriate its lessons for the purposes of human medicine; that governments would broker international accords to govern the future use of rejuvenating technology. But none of this happened.
Some progress has been made, however, in the quarter-century since Christian Sommer’s discovery. We now know, for instance, that the rejuvenation of Turritopsis dohrnii and some other members of the genus is caused by environmental stress or physical assault. We know that, during rejuvenation, it undergoes cellular transdifferentiation, an unusual process by which one type of cell is converted into another — a skin cell into a nerve cell, for instance. (The same process occurs in human stem cells [ http://topics.nytimes.com/top/news/health/diseasesconditionsandhealthtopics/stemcells/index.html ].) We also know that, in recent decades, the immortal jellyfish has rapidly spread throughout the world’s oceans in what Maria Pia Miglietta, a biology professor at Notre Dame, calls “a silent invasion.” The jellyfish has been “hitchhiking” on cargo ships that use seawater for ballast. Turritopsis has now been observed not only in the Mediterranean but also off the coasts of Panama, Spain, Florida and Japan. The jellyfish seems able to survive, and proliferate, in every ocean in the world. It is possible to imagine a distant future in which most other species of life are extinct but the ocean will consist overwhelmingly of immortal jellyfish, a great gelatin consciousness everlasting.
But we still don’t understand how it ages in reverse. There are several reasons for our ignorance, all of them maddeningly unsatisfying. There are, to begin with, very few specialists in the world committed to conducting the necessary experiments. “Finding really good hydroid experts is very difficult,” says James Carlton, a professor of marine sciences at Williams College and the director of the Williams-Mystic Maritime Studies Program. “You’re lucky to have one or two people in a country.” He cited this as an example of a phenomenon he calls the Small’s Rule: small-bodied organisms are poorly studied relative to larger-bodied organisms. There are significantly more crab experts, for instance, than hydroid experts.
But the most frustrating explanation for our dearth of knowledge about the immortal jellyfish is of a more technical nature. The genus, it turns out, is extraordinarily difficult to culture in a laboratory. It requires close attention and an enormous amount of repetitive, tedious labor; even then, it is under only certain favorable conditions, most of which are still unknown to biologists, that a Turritopsis will produce offspring.
In fact there is just one scientist who has been culturing Turritopsis polyps in his lab consistently. He works alone, without major financing or a staff, in a cramped office in Shirahama, a sleepy beach town in Wakayama Prefecture, Japan, four hours south of Kyoto. The scientist’s name is Shin Kubota, and he is, for the time being, our best chance for understanding this unique strand of biological immortality.
Many marine biologists are reluctant to make such grand claims about Turritopsis’ promise for human medicine. “That’s a question for journalists,” Boero said (to a journalist) in 2009. “I prefer to focus on a slightly more rational form of science.”
Kubota, however, has no such compunction. “Turritopsis application for human beings is the most wonderful dream of mankind,” he told me the first time I called him. “Once we determine how the jellyfish rejuvenates itself, we should achieve very great things. My opinion is that we will evolve and become immortal ourselves.”
I decided I better book a ticket to Japan.
One of Shirahama’s main attractions is its crescent-shaped white-sand beach; “Shirahama” means “white beach.” But in recent decades, the beach has been disappearing. In the 1960s, when Shirahama was connected by rail to Osaka, the city became a popular tourist destination, and blocky white hotel towers were erected along the coastal road. The increased development accelerated erosion, and the famous sand began to wash into the sea. Worried that the town of White Beach would lose its white beach, according to a city official, Wakayama Prefecture began in 1989 to import sand from Perth, Australia, 4,700 miles away. Over 15 years, Shirahama dumped 745,000 cubic meters of Aussie sand on its beach, preserving its eternal whiteness — at least for now.
Shirahama is full of timeless natural wonders that are failing the test of time. Visible just off the coast is Engetsu island, a sublime arched sandstone formation that looks like a doughnut dunked halfway into a glass of milk. At dusk, tourists gather at a point on the coastal road where, on certain days, the arch perfectly frames the setting sun. Arches are temporary geological phenomena; they are created by erosion, and erosion ultimately causes them to collapse. Fearing the loss of Engetsu, the local government is trying to restrain it from deteriorating any further by reinforcing the arch with a harness of mortar and grout. A large scaffold now extends beneath the arch and, from the shore, construction workers can be seen, tiny flyspecks against the sparkling sea, paving the rock.
Engetsu is nearly matched in beauty by Sandanbeki, a series of striated cliffs farther down the coast that drop 165 feet into turbulent surf. Beneath Sandanbeki lies a cavern that local pirates used as a secret lair more than a thousand years ago. Today the cliffs are one of the world’s most famous suicide spots. A sign on the edge serves as a warning to those contemplating their own mortality: “Wait a minute. A dead flower will never bloom.”
But Shirahama is best known for its onsen, saltwater hot springs that are believed to increase longevity. There are larger, well-appointed ones inside resort hotels, smaller tubs that are free to the public and ancient bathhouses in cramped huts along the curving coastal road. You can tell from a block away that you are approaching an onsen, because you can smell the sulfur.
Each morning, Shin Kubota, who is 60, visits Muronoyu, a simple onsen popular with the city’s oldest citizens that traces its history back 1,350 years. “Onsen activates your metabolism and cleans away the dead skin,” Kubota says. “It strongly contributes to longevity.” At 8:30 a.m., he drives 15 minutes up the coast, past the white beach, where the land narrows to a promontory that extends like a pointing, arthritic finger, separating Kanayama Bay from the larger Tanabe Bay. At the end of this promontory stands Kyoto University’s Seto Marine Biological Laboratory, a damp, two-story concrete block. Though it has several classrooms, dozens of offices and long hallways, the building often has the appearance of being completely empty. The few scientists on staff spend much of their time diving in the bay, collecting samples. Kubota, however, visits his office every single day. He must, or his immortal jellyfish will starve.
The world’s only captive population of immortal jellyfish lives in petri dishes arrayed haphazardly on several shelves of a small refrigerator in Kubota’s office. Like most hydrozoans, Turritopsis passes through two main stages of life, polyp and medusa. A polyp resembles a sprig of dill, with spindly stalks that branch and fork and terminate in buds. When these buds swell, they sprout not flowers but medusas. A medusa has a bell-shaped dome and dangling tentacles. Any layperson would identify it as a jellyfish, though it is not the kind you see at the beach. Those belong to a different taxonomic group, Scyphozoa, and tend to spend most of their lives as jellyfish; hydrozoans have briefer medusa phases. An adult medusa produces eggs or sperm, which combine to create larvae that form new polyps. In other hydroid species, the medusa dies after it spawns. A Turritopsis medusa, however, sinks to the bottom of the ocean floor, where its body folds in on itself — assuming the jellyfish equivalent of the fetal position. The bell reabsorbs the tentacles, and then it degenerates further until it becomes a gelatinous blob. Over the course of several days, this blob forms an outer shell. Next it shoots out stolons, which resemble roots. The stolons lengthen and become a polyp. The new polyp produces new medusas, and the process begins again.
Kubota estimates that his menagerie contains at least 100 specimens, about 3 to a petri dish. “They are very tiny,” Kubota, the proud papa, said. “Very cute.” It is cute, the immortal jellyfish. An adult medusa is about the size of a trimmed pinkie fingernail. It trails scores of hairlike tentacles. Medusas found in cooler waters have a bright scarlet bell, but more commonly the medusa is translucent white, its contours so fine that under a microscope it looks like a line drawing. It spends most of its time floating languidly in the water. It’s in no rush.
For the last 15 years, Kubota has spent at least three hours a day caring for his brood. Having observed him over the course of a week, I can confirm that it is grueling, tedious work. When he arrives at his office, he removes each petri dish from the refrigerator, one at a time, and changes the water. Then he examines his specimens under a microscope. He wants to make sure that the medusas look healthy: that they are swimming gracefully; that their bells are unclouded; and that they are digesting their food. He feeds them artemia cysts — dried brine shrimp eggs harvested from the Great Salt Lake in Utah. Though the cysts are tiny, barely visible to the naked eye, they are often too large for a medusa to digest. In these cases Kubota, squinting through the microscope, must slice the egg into pieces with two fine-point needles, the way a father might slice his toddler’s hamburger into bite-size chunks. The work causes Kubota to growl and cluck his tongue.
“Eat by yourself!” he yells at one medusa. “You are not a baby!” Then he laughs heartily. It’s an infectious, ratcheting laugh that makes his round face even rounder, the wrinkles describing circles around his eyes and mouth.
It is a full-time job, caring for the immortal jellyfish. When traveling abroad for academic conferences, Kubota has had to carry the medusas with him in a portable cooler. (In recent years he has been invited to deliver lectures in Cape Town; Xiamen, China; Lawrence, Kan.; and Plymouth, England.) He also travels to Kyoto, when he is obligated to attend administrative meetings at the university, but he returns the same night, an eight-hour round trip, in order not to miss a feeding.
Turritopsis is not the only focus of his research. He is a prolific author of scientific papers and articles, having published 52 in 2011 alone, many based on observations he makes on a private beach fronting the Seto Lab and in a small harbor on the coastal road. Every afternoon, after Kubota has finished caring for his jellyfish, he walks down the beach with a notebook, noting every organism that has washed ashore. It is a remarkable sight, the solitary figure in flip-flops, tramping pigeon-toed across the 400-yard length of the beach, hunched over, his floppy hair jogging in the breeze, as he intently scrutinizes the sand. He collates his data and publishes it in papers with titles like “Stranding Records of Fishes on Kitahama Beach” and “The First Occurrence of Bythotiara Species in Tanabe Bay.” He is an active member of a dozen scientific societies and writes a jellyfish-of-the-week column in the local newspaper. Kubota says he has introduced his readers to more than 100 jellyfish so far.
Given Kubota’s obsessive focus on his work, it is not surprising that he has been forced to neglect other areas of his life. He never cooks and tends to bring takeout to his office. At the lab, he wears T-shirts — bearing images of jellyfish — and sweat pants. He is overdue for a haircut. And his office is a mess. It does not appear to have been organized since he began nurturing his Turritopsis. The door opens just widely enough to admit a man of Kubota’s stature. It is blocked from opening farther by a chest-high cabinet, on the surface of which are balanced several hundred objects Kubota has retrieved from beaches — seashells, bird feathers, crab claws and desiccated coral. The desk is invisible beneath a stack of opened books. Fifty toothbrushes are crammed into a cup on the rusting aluminum sink. There are framed pictures on the wall, most of them depicting jellyfish, including one childish drawing done in crayons. I asked Kubota, who has two adult sons, whether one of his children had made it. He laughed, shaking his head.
“I’m not a very good artist,” he said. I followed his glance to his desk, where there was a box of crayons.
The bookshelves that lined the walls were jammed to overflowing with textbooks, journals and science books, as well as a number of titles in English: Frank Herbert’s “Dune,” “The Works of Aristotle,” “The Life and Death of Charles Darwin.” Kubota first read Darwin’s “On the Origin of the Species” in high school. It was one of the formative experiences of his life; before that, he thought he would grow up to be an archaeologist. He was then already fascinated with what he calls the “mystery of human life” — where did we come from and why? — and hoped that in the ancient civilizations, he might discover the answers he sought. But after reading Darwin he realized that he would have to look deeper into the past, beyond the dawn of human existence.
Kubota grew up in Matsuyama, on the southern island of Shikoku. Though his father was a teacher, Kubota didn’t get excellent marks at his high school, where he was a generation behind Kenzaburo Oe. “I didn’t study,” he said. “I only read science fiction.” But when he was admitted to college, his grandfather bought him a biological encyclopedia. It sits on one of his office shelves, beside a sepia-toned portrait of his grandfather.
“I learned a lot from that book,” Kubota said. “I read every page.” He was especially impressed by the phylogenetic tree, the taxonomic diagram that Darwin called the Tree of Life. Darwin included one of the earliest examples of a Tree of Life in “On the Origin of Species” — it is the book’s only illustration. Today the outermost twigs and buds of the Tree of Life are occupied by mammals and birds, while at the base of the trunk lie the most primitive phyla — Porifera (sponges), Platyhelminthes (flatworms), Cnidaria (jellyfish).
“The mystery of life is not concealed in the higher animals,” Kubota told me. “It is concealed in the root. And at the root of the Tree of Life is the jellyfish.”
Until recently, the notion that human beings might have anything of value to learn from a jellyfish would have been considered absurd. Your typical cnidarian does not, after all, appear to have much in common with a human being. It has no brains, for instance, nor a heart. It has a single orifice through which its food and waste pass — it eats, in other words, out of its own anus. But the Human Genome Project, completed in 2003, suggested otherwise. Though it had been estimated that our genome contained more than 100,000 protein-coding genes, it turned out that the number was closer to 21,000. This meant we had about the same number of genes as chickens, roundworms and fruit flies. In a separate study, published in 2005, cnidarians were found to have a much more complex genome than previously imagined.
“There’s a shocking amount of genetic similarity between jellyfish and human beings,” said Kevin J. Peterson, a molecular paleobiologist who contributed to that study, when I visited him at his Dartmouth office. From a genetic perspective, apart from the fact that we have two genome duplications, “we look like a damn jellyfish.”
This may have implications for medicine, particularly the fields of cancer research and longevity. Peterson is now studying microRNAs (commonly denoted as miRNA), tiny strands of genetic material that regulate gene expression. MiRNA act as an on-off switch for genes. When the switch is off, the cell remains in its primitive, undifferentiated state. When the switch turns on, a cell assumes its mature form: it can become a skin cell, for instance, or a tentacle cell. MiRNA also serve a crucial role in stem-cell research — they are the mechanism by which stem cells differentiate. Most cancers, we have recently learned, are marked by alterations in miRNA. Researchers even suspect that alterations in miRNA may be a cause of cancer. If you turn a cell’s miRNA “off,” the cell loses its identity and begins acting chaotically — it becomes, in other words, cancerous.
Hydrozoans provide an ideal opportunity to study the behavior of miRNA for two reasons. They are extremely simple organisms, and miRNA are crucial to their biological development. But because there are so few hydroid experts, our understanding of these species is staggeringly incomplete.
“Immortality might be much more common than we think,” Peterson said. “There are sponges out there that we know have been there for decades. Sea-urchin larvae are able to regenerate and continuously give rise to new adults.” He continued: “This might be a general feature of these animals. They never really die.”
Peterson is closely following the work of Daniel Martínez, a biologist at Pomona College and one of the world’s leading hydroid scholars. The National Institutes of Health has awarded Martínez a five-year, $1.26 million research grant to study the hydra — a species that resembles a polyp but never yields medusas. Its body is almost entirely composed of stem cells that allow it to regenerate itself continuously. As a Ph.D. candidate, Martínez set out to prove that hydra were mortal. But his research of the last 15 years has convinced him that hydra can, in fact, survive forever and are “truly immortal.”
“It’s important to keep in mind that we’re not dealing with something that’s completely different from us,” Martínez told me. “Genetically hydra are the same as human beings. We’re variations of the same theme.”
As Peterson told me: “If I studied cancer, the last thing I would study is cancer, if you take my point. I would not be studying thyroid tumors in mice. I’d be working on hydra.”
Hydrozoans, he suggests, may have made a devil’s bargain. In exchange for simplicity — no head or tail, no vision, eating out of its own anus — they gained immortality. These peculiar, simple species may represent an opportunity to learn how to fight cancer, old age and death.
But most hydroid experts find it nearly impossible to secure financing. “Who’s going to take a chance on a scientist who doesn’t work on mammals, let alone a jellyfish?” Peterson said. “The granting agencies are always talking about trying to be imaginative and reinvigorate themselves, but of course you’re stuck in a lot of bureaucracy. … The pie is only so big.”
Even some of Kubota’s peers are cautious when speaking about potential medical applications in Turritopsis research. “It is difficult to foresee how much and how fast . . . Turritopsis dohrnii can be useful to fight diseases,” Stefano Piraino, a colleague of Ferdinando Boero’s, told me in an e-mail. “Increasing human longevity has no meaning, it is ecological nonsense. What we may expect and work on is to improve the quality of life in our final stages.”
Martínez says that hydra, the species he studies, is more promising. “Turritopsis is cool,” he told me. “Don’t get me wrong. It’s interesting that it does this weird, peculiar thing, and I support researching it further, but I don’t think it’s going to teach us a lot about human beings.”
Kubota sees it differently. “The immortal medusa is the most miraculous species in the entire animal kingdom,” he said. “I believe it will be easy to solve the mystery of immortality and apply ultimate life to human beings.” ?
Kubota can be encouraged by the fact that many of the greatest advancements in human medicine came from observations made about animals that, at the time, seemed to have little or no resemblance to man. In 18th-century England, dairymaids exposed to cowpox helped establish that the disease inoculated them against smallpox; the bacteriologist Alexander Fleming accidentally discovered penicillin when one of his petri dishes grew a mold; and, most recently, scientists in Wyoming studying nematode worms found genes similar to those inactivated by cancer in humans, leading them to believe that they could be a target for new cancer drugs. One of the Wyoming researchers said in a news release that they hoped they could “contribute to the arsenal of diverse therapeutic approaches used to treat and cure many types of cancer.”
And so Kubota continues to accumulate data on his own simple organism, every day of his life.
There was a second photograph on Shin Kubota’s office shelf, beside the portrait of his grandfather. It showed a class of young university students posing on the campus of Ehime University, in Matsuyama. The photograph is 40 years old, but the 20-year-old Kubota was immediately recognizable — the round face, the smiling eyes, the floppy black hair. He sighed when I asked him about it.
“So young then,” he said. “So old now.”
I told him that he didn’t look very different from the young man in the picture. He’s perhaps a few pounds heavier, and though his features are not quite as boyish, he retains the exuberant energy of a middle-schooler, and his hair is naturally jet black. Yes, he said, but his hair hasn’t always been black. He explained that five years ago, when he turned 55, he experienced what he called a scare.
It was a stressful time for Kubota. He had separated from his wife, his children had moved out of the house, his eyesight was fading and he had begun to lose his hair. It was particularly noticeable around his temples. He blames his glasses, which he wore on a band around his head. He needed them to write but not for the microscope, so every time he raised or lowered his glasses, the band wore away at the hair at his temples. When the hair grew back, it came in white. He felt as if he had aged a lifetime in one year. “It was very astonishing for me,” he said. “I had become old.”
I told him that he looked much better now — significantly younger than his age.
“Too old,” he said, scowling. “I want to be young again. I want to become miracle immortal man.”
As if to distract himself from this trajectory of thought, he removed a petri cup from his refrigerator unit. He held it under the light so I could see the ghostly Turritopsis suspended within. It was still, waiting.
“Watch,” he said. “I will make this medusa rejuvenate.”
The most reliable way to make the immortal jellyfish age in reverse, Kubota explained to me, is to mutilate it. With two fine metal picks, he began to perforate the medusa’s mesoglea, the gelatinous tissue that composes the bell. After Kubota poked it six times, the medusa behaved like any stabbing victim — it lay on its side and began twitching spasmodically. Its tentacles stopped undulating, and its bell slightly puckered. But Kubota, in what appeared a misdirected act of sadism, didn’t stop there. He stabbed it 50 times in all. The medusa had long since stopped moving. It lay limp, crippled, its mesoglea torn, the bell deflated. Kubota looked satisfied.
“You rejuvenate!” he yelled at the jellyfish. Then he started laughing.
We checked on the stab victim every day that week to watch its transformation. On the second day, the depleted, gelatinous mess had attached itself to the floor of the petri dish; its tentacles were bent in on themselves. “It’s transdifferentiating,” Kubota said. “Dynamic changes are occurring.” By the fourth day the tentacles were gone, and the organism ceased to resemble a medusa entirely; it looked instead like an amoeba. Kubota called this a “meatball.” By the end of the week, stolons had begun to shoot out of the meatball.
This method is, in a certain sense, cheating, as physical distress induces rejuvenation. But the process also occurs naturally when the medusa grows old or sick. In Kubota’s most recent paper on Turritopsis, he documented the natural rejuvenation of a single colony in his lab between 2009 and 2011. The idea was to see how quickly the species would regenerate itself when left to its own devices. During the two-year period, the colony rebirthed itself 10 times, in intervals as brief as one month. In his paper’s conclusion, published in the journal Biogeography, Kubota wrote, “Turritopsis will be kept forever by the present method and will . . . contribute to any study for everyone in the future.”
He has made other significant findings in recent years. He has learned, for instance, that certain conditions inhibit rejuvenation: starvation, large bell size and water colder than 72 degrees. And he has made progress in solving the largest mystery of all. The secret of the species’s immortality, Kubota now believes, is hidden in the tentacles. But he will need more financing for experiments, as well as assistance from a geneticist or a molecular biologist, to figure out how the immortal jellyfish pulls it off. Even so, he thinks we’re close to solving the species’s mystery — that it’s a matter of years, perhaps a decade or two. “Human beings are so intelligent,” he told me, as if to reassure me. But then he added a caveat. “Before we achieve immortality,” he said, “we must evolve first. The heart is not good.”
I assumed that he was making a biological argument — that the organ is not biologically capable of infinite life, that we needed to design new, artificial hearts for longer, artificial lives. But then I realized that he wasn’t speaking literally. By heart, he meant the human spirit.
“Human beings must learn to love nature,” he said. “Today the countryside is obsolete. In Japan, it has disappeared. Big metropolitan places have appeared everywhere. We are in the garbage. If this continues, nature will die.”
Man, he explained, is intelligent enough to achieve biological immortality. But we don’t deserve it. This sentiment surprised me coming from a man who has dedicated his life to pursuing immortality.
“Self-control is very difficult for humans,” he continued. “In order to solve this problem, spiritual change is needed.”
This is why, in the years since his “scare,” Kubota has begun a second career. In addition to being a researcher, professor and guest speaker, he is now a songwriter. Kubota’s songs have been featured on national television, are available on karaoke machines across Japan and have made him a minor Japanese celebrity — the Japanese equivalent of Bill Nye the Science Guy.
It helps that in Japan, the nation with the world’s oldest population, the immortal jellyfish has a relatively exalted status in popular culture. Its reputation was boosted in 2003 by a television drama, “14 Months,” in which the heroine takes a potion, extracted from the immortal jellyfish, that causes her to age in reverse. Since then Kubota has appeared regularly on television and radio shows. He showed me recent clips from his television reel and translated them for me. In March, “Morning No. 1,” a Japanese morning show devoted an episode to Shirahama. After a segment on the onsen, the hosts visited Kubota at the Seto Aquarium, where he talked about Turritopsis. “I want to become young, too!” one host shrieked. On “Love Laboratory,” a science show, Kubota discussed his recent experiments while collecting samples on the Shirahama wharf. “I envy the immortal medusa!” gushed the hostess. On “Feeding Our Bodies,” a similar program, Kubota addressed the camera: “Among the animals, the immortal jellyfish is the most splendid.” There followed an interview with 100-year-old twins.
But no television appearance is complete without a song. For his performances, he transforms himself from Dr. Shin Kubota, erudite marine biologist in jacket and tie, into Mr. Immortal Jellyfish Man. His superhero alter ego has its own costume: a white lab jacket, scarlet red gloves, red sunglasses and a red rubber hat, designed to resemble a medusa, with dangling rubber tentacles. With help from one of his sons, an aspiring musician, Kubota has written dozens of songs in the last five years and released six albums. Many of his songs are odes to Turritopsis. These include “I Am Scarlet Medusa,” “Life Forever,” “Scarlet Medusa — an Eternal Witness,” “Die-Hard Medusa” and his catchiest number, “Scarlet Medusa Chorus.”
My name is Scarlet Medusa, A teeny tiny jellyfish But I have a special secret that no others may possess I can — yes, I can! — rejuvenate
Other songs apotheosize different forms of marine life: “We Are the Sponges — A Song of the Porifera,” “Viva! Variety Cnidaria” and “Poking Diving Horsehair Worm Mambo.” There is also “I Am Shin Kubota.”
My name is Shin Kubota Associate professor of Kyoto University At Shirahama, Wakayama Prefecture I live next to an aquarium Enjoying marine-biology research Every day, I walk on the beach Scooping up with a plankton net Searching for wondrous creatures Searching for unknown jellyfish. Dedicate my life to small creatures Patrolling the beaches every day Hot spring sandals are always on Necessary item to get in the sea Scarlet medusa rejuvenates Scarlet medusa is immortal
“He is important for the aquarium,” Akira Asakura, the Seto lab director told me. “People come because they see him on television and become interested in the immortal medusa and marine life in general. He is a very good speaker, with a very wide range of knowledge.”
Science classes regularly make field trips to meet Mr. Immortal Jellyfish Man. During my week in Shirahama, he was visited by a group of 150 10- and 11-year-olds who had prepared speeches and slide shows about Turritopsis. The group was too large to visit Seto, so they sat on the floor of a ballroom in a local hotel. After the children made their presentations (“I have jellyfish mania!” one girl exclaimed), Kubota took the stage. He spoke loudly, with great animation, calling on the children and peppering them with questions. How many species of animals are there on earth? How many phyla are there? The karaoke video for “Scarlet Medusa Chorus” was projected on a large screen, and the giggling children sang along.
Kubota does not go to these lengths simply for his own amusement — though it is clear that he enjoys himself immensely. Nor does he consider his public educational work as secondary to his research. It is instead, he believes, the crux of his life’s work.
“We must love plants — without plants we cannot live. We must love bacteria — without decomposition our bodies can’t go back to the earth. If everyone learns to love living organisms, there will be no crime. No murder. No suicide. Spiritual change is needed. And the most simple way to achieve this is through song.
“Biology is specialized,” he said, bringing his palms within inches of each other. “But songs?”
He spread his hands far apart, as if to indicate the size of the world.
Every night, once Kubota is finished with work, he grabs a bite to eat and heads to a karaoke bar. He sings karaoke for at least two hours a day. He owns a karaoke book that is 1,611 pages long, with dimensions somewhat larger than a phone book and even denser type. His goal is to sing at least one song from every page. Every time he sings a song, he underlines it in the book. Flipping through the volume, I saw that he had easily surpassed his goal.
“When I perform karaoke,” he said, “another part of the brain is used. It’s good to relax, to sing a heartfelt song. It’s good to be loud.”
His favorite karaoke bar is called Kibarashi, which translates loosely to “recreation” but literally means “fresh air.” Kibarashi stands at the end of a residential street, away from the coastal road and the city’s other main commercial stretches. He’d given me clear directions, but I struggled to find it. The street was silent and dark. I was ready to turn back, assuming I’d made a wrong turn, when I saw a small sign decorated with an illuminated microphone. When I opened the door, I found myself in what resembled a living room — couches, coffee tables, pots with plastic flowers, goldfish in small tanks. A low, narrow bar ran along one wall. A karaoke video of a tender Japanese ballad was playing on two televisions that hung from the ceiling. Kubota stood facing one of them, microphone in hand, swaying side to side, singing full-throatedly in his elegant mezzo-baritone. The bartender, a woman in her 70s, was seated behind the bar, tapping on her iPhone. Nobody else was there.
We sang for the next two hours — Elvis Presley, the Beatles, the Beastie Boys and countless Japanese ballads and children’s songs. At my request, Kubota sang his own songs, seven of which are listed in his karaoke book. Kibarashi’s karaoke machine is part of an international network of karaoke machines, and the computer displays statistics for each song, including how many people in Japan have selected it in the past month. It seemed as if no one had selected Kubota’s songs.
“Unfortunately they are not sung by many people,” he told me. “They’re not popular, because it’s very difficult to love nature, to love animals.”
On my last morning in Shirahama, Kubota called to cancel our final meeting. He had a bacterial infection in his eye and couldn’t see clearly enough to look through his microscope. He was going to a specialist. He apologized repeatedly.
“Human beings very weak,” he said. “Bacteria very strong. I want to be immortal!” He laughed his hearty laugh.
Turritopsis, it turns out, is also very weak. Despite being immortal, it is easily killed. Turritopsis polyps are largely defenseless against their predators, chief among them sea slugs. They can easily be suffocated by organic matter. “They’re miracles of nature, but they’re not complete,” Kubota acknowledged. “They’re still organisms. They’re not holy. They’re not God.”
And their immortality is, to a certain degree, a question of semantics. “That word ‘immortal’ is distracting,” says James Carlton, the professor of marine sciences at Williams. “If by ‘immortal’ you mean passing on your genes, then yes, it’s immortal. But those are not the same cells anymore. The cells are immortal, but not necessarily the organism itself.” To complete the Benjamin Button analogy, imagine the man, after returning to a fetus, being born again. The cells would be recycled, but the old Benjamin would be gone; in his place would be a different man with a new brain, a new heart, a new body. He would be a clone.
But we won’t know for certain what this means for human beings until more research is done. That is the scientific method, after all: lost in the labyrinth, you must pursue every path, no matter how unlikely, or risk being devoured by the Minotaur. Kubota, for his part, fears that the lessons of the immortal jellyfish will be absorbed too soon, before man is ready to harness the science of immortality in an ethical manner. “We’re very strange animals,” he said. “We’re so clever and civilized, but our hearts are very primitive. If our hearts weren’t primitive, there wouldn’t be wars. I’m worried that we will apply the science too early, like we did with the atomic bomb.”
I remembered something he said earlier in the week, when we were watching a music video for his song “Living Planet — Connections Between Forest, Sea and Rural Area.” He described the song as an ode to the beauty of nature. The video was shot by his 88-year-old neighbor, a retired employee of Osaka Gas Company. Kubota’s lyrics were superimposed over a sequence of images. There was Engetsu, its arch covered with moss and jutting oak and pine trees; craggy Mount Seppiko and gentle Mount Takane; the striated cliffs of Sandanbeki; the private beach at the Seto Laboratory; a waterfall; a brook; a pond; and the cliffside forests that abut the city, so dense and black that the trees seem to be secreting darkness.
“Nature is so beautiful,” Kubota said, smiling wistfully. “If human beings disappeared, how peaceful it would be.”
Nathaniel Rich is an author whose second novel, ‘‘Odds Against Tomorrow,’’ will be published in April.
Giant Sequoia Tree 'The President' Tops 'General Grant'
By TRACIE CONE 12/01/12 02:03 PM ET EST
FRESNO, Calif. -- Deep in the Sierra Nevada, the famous General Grant giant sequoia tree is suffering its loss of stature in silence. What once was the world's No. 2 biggest tree has been supplanted thanks to the most comprehensive measurements taken of the largest living things on Earth.
The new No. 2 is The President, a 54,000-cubic-foot gargantuan not far from the Grant in Sequoia National Park. After 3,240 years, the giant sequoia still is growing wider at a consistent rate, which may be what most surprised the scientists examining how the sequoias and coastal redwoods will be affected by climate change and whether these trees have a role to play in combatting it.
"I consider it to be the greatest tree in all of the mountains of the world," said Stephen Sillett, a redwood researcher whose team from Humboldt State University is seeking to mathematically assess the potential of California's iconic trees to absorb planet-warming carbon dioxide.
The researchers are a part of the 10-year Redwoods and Climate Change Initiative funded by the Save the Redwoods League in San Francisco. The measurements of The President, reported in the current National Geographic, dispelled the previous notion that the big trees grow more slowly in old age.
It means, the experts say, the amount of carbon dioxide they absorb during photosynthesis continues to increase over their lifetimes.
In addition to painstaking measurements of every branch and twig, the team took 15 half-centimeter-wide core samples of The President to determine its growth rate, which they learned was stunted in the abnormally cold year of 1580 when temperatures in the Sierra hovered near freezing even in the summer and the trees remained dormant.
But that was an anomaly, Sillett said. The President adds about one cubic meter of wood a year during its short six-month growing season, making it one of the fastest-growing trees in the world. Its 2 billion leaves are thought to be the most of any tree on the planet, which would also make it one of the most efficient at transforming carbon dioxide into nourishing sugars during photosynthesis.
"We're not going to save the world with any one strategy, but part of the value of these great trees is this contribution and we're trying to get a handle on the math behind that," Sillett said.
After the equivalent of 32 working days dangling from ropes in The President, Sillett's team is closer to having a mathematical equation to determine its carbon conversion potential, as it has done with some less famous coastal redwoods. The team has analyzed a representative sample that can be used to model the capacity of the state's signature trees.
More immediately, however, the new measurements could lead to a changing of the guard in the land of giant sequoias. The park would have to update signs and brochures – and someone is going to have to correct the Wikipedia entry for "List of largest giant sequoias," which still has The President at No. 3.
Now at 93 feet in diameter and with 45,000 cubic feet of trunk volume and another 9,000 cubic feet in its branches, the tree named for President Warren G. Harding is about 15 percent larger than Grant, also known as America's Christmas Tree. Sliced into one-foot by one-foot cubes, The President would cover a football field.
Giant sequoias grow so big and for so long because their wood is resistant to the pests and disease that dwarf the lifespan of other trees, and their thick bark makes them impervious to fast-moving fire.
It's that resiliency that makes sequoias and their taller coastal redwood cousin worthy of intensive protections – and even candidates for cultivation to pull carbon from an increasingly warming atmosphere, Sillett said. Unlike white firs, which easily die and decay to send decomposing carbon back into the air, rot-resistant redwoods stay solid for hundreds of years after they fall.
Though sequoias are native to California, early settlers traveled with seedlings back to the British Isles and New Zealand, where a 15-foot diameter sequoia that is the world's biggest planted tree took root in 1850. Part of Sillett's studies involves modeling the potential growth rate of cultivated sequoia forests to determine over time how much carbon sequestering might increase.
All of that led him to a spot 7,000 feet high in the Sierra and to The President, which he calls "the ultimate example of a giant sequoia." Compared to the other giants whose silhouettes are bedraggled by lightning strikes, The President's crown is large with burly branches that are themselves as large as tree trunks.
The world's biggest tree is still the nearby General Sherman with about 2,000 cubic feet more volume than the President, but to Sillett it's not a contest.
"They're all superlative in their own way," Sillett said.
Scientists snap a picture of DNA’s double helix for the very first time
George Dvorsky Nov 29, 2012 9:45 AM
Though they've never actually seen it with their own eyes, scientists know that DNA's structure is composed of a spiraling corkscrew. They know this thanks to molecular theory and and an old-time technique called X-ray crystallography, where patterns of dots are converted into an overarching image using mathematics. But now, for the first time ever, scientists have actually snapped a real image of DNA using an electron microscope — spiraling corkscrew and all.
The image was taken by Enzo di Fabrizio from the University of Genoa, Italy. He choreographed the scene by pulling a small strand of DNA from a diluted solution and then propping it up like a clothesline between two nanoscopic silicon pillars.
The trick to the technique was in acquiring a discrete strand of DNA that could be stretched out and ready to view with an electron microscope. Di Fabrizio managed this by creating a pattern of pillars that repelled water — which resulted in quick moisture evaporation and a residual strand of DNA all ready to go.
Then, in order to create a high-resolution image, di Fabrizio drilled tiny holes in the base of the nanopillar bed and shone beams of electrons.
Aside from creating a cool image, the technique will allow the researchers to investigate DNA in greater detail, as well as seeing how it interacts with proteins and RNA.
Scientists believe they have discovered the origin of copulation.
An international team of researchers says a fish called Microbrachius dicki is the first-known animal to stop reproducing by spawning and instead mate by having sex.
The primitive bony fish, which was about 8cm long, lived in ancient lakes about 385 million years ago in what is now Scotland.
--- "They couldn't have done it in a 'missionary position'"
Prof John Long Flinders University ---
Lead author Prof John Long, from Flinders University in Australia, said: "We have defined the very point in evolution where the origin of internal fertilisation in all animals began.
"That is a really big step."
Prof Long added that the discovery was made as he was looking through a box of ancient fish fossils.
He noticed that one of the M. dicki specimens had an odd L-shaped appendage. Further investigation revealed that this was the male fish's genitals.
"The male has large bony claspers. These are the grooves that they use to transfer sperm into the female," explained Prof Long.
Microbrachius dicki fossils are common - but nobody noticed the sexual organs until now
The female fish, on the other hand, had a small bony structure at their rear that locked the male organ into place.
Constrained by their anatomy, the fish probably had to mate side by side.
"They couldn't have done it in a 'missionary position'," said Prof Long. "The very first act of copulation was done sideways, square-dance style."
He added that the fish were able to stay in position with the help of their small arm-like fins.
"The little arms are very useful to link the male and female together, so the male can get this large L-shaped sexual organ into position to dock with the female's genital plates, which are very rough like cheese graters.
"They act like Velcro, locking the male organ into position to transfer sperm."
Copulation using this method did not stay around for long - fish reverted to spawning
Surprisingly, the researchers think this first attempt to reproduce internally was not around for long.
As fish evolved, they reverted back to spawning, in which eggs and sperm to fertilise them are released into the water by female and male creatures respectively. It took another few million years for copulation to make a come-back, reappearing in ancestors of sharks and rays.
Commenting on the research, Dr Matt Friedman, from the University of Oxford, UK, said: "The placoderm group (which includes Microbrachius dicki) is a well known group - the fossils are pretty common, and it's not as if this one was found in some far-off, exotic part of the world. It was found in Scotland.
"It is very remarkable that we haven't noticed this before."
Using computer models and statistical methods, biochemist Douglas Theobald .. http://www.bio.brandeis.edu/faculty/theobald.html .. calculated the odds that all species from the three main groups, or "domains," of life evolved from a common ancestor—versus, say, descending from several different life-forms or arising in their present form, Adam and Eve style.
The domains are bacteria, bacteria-like microbes called Archaea, and eukaryotes, the group that includes plants and other multicellular species, such as humans.
The "best competing multiple ancestry hypothesis" has one species giving rise to bacteria and one giving rise to Archaea and eukaryotes, said Theobald, a biochemist at Brandeis University in Waltham, Massachusetts.
But, based on the new analysis, the odds of that are "just astronomically enormous," he said. "The number's so big, it's kind of silly to say it"—1 in 10 to the 2, 680th power, or 1 followed by 2,680 zeros.
Theobald also tested the creationist idea that humans arose in their current form and have no evolutionary ancestors.
The statistical analysis showed that the independent origin of humans is "an absolutely horrible hypothesis," Theobald said, adding that the probability that humans were created separately from everything else is 1 in 10 to the 6,000th power.
(As of publication time, requests for interviews with several creationist scientists had been either declined or unanswered.)
All species in all three domains share 23 universal proteins, though the proteins' DNA sequences—instructions written in the As, Cs, Gs, and Ts of DNA bases—differ slightly among the three domains (quick genetics overview .. https://genographic.nationalgeographic.com/genographic/lan/en/overview.html ).
The 23 universal proteins perform fundamental cellular activities, such as DNA replication and the translation of DNA into proteins, and are crucial to the survival of all known life-forms—from the smallest microbes to blue whales .. http://animals.nationalgeographic.com/animals/mammals/blue-whale/ .
A universal common ancestor is generally assumed to be the reason the 23 proteins are as similar as they are, Theobald said.
That's because, if the original protein set was the same for all creatures, a relatively small number of mutations would have been needed to arrive at the modern proteins, he said. If life arose from multiple species—each with a different set of proteins—many more mutations would have been required.
But Theobald hoped to go beyond conventional wisdom.
"What I wanted to do was not make the assumption that similar traits imply a shared ancestry ... because we know that's not always true," Theobald said.
"For instance, you could get similarities that are not due to common ancestry but that are due to natural selection"—that is, when environmental forces, such as predators or climate, result in certain mutations taking hold, such as claws or thicker fur.
Biologists call the independent development of similar traits in different lineages "convergent evolution." The wings of bats, birds, and insects are prime examples: They perform similar functions but evolved independently of one another.
But it's highly unlikely that the protein groups would have independently evolved into such similar DNA sequences, according to the new study, to be published tomorrow in the journal Nature .. http://www.nature.com/nature/index.html .
"I asked, What's the probability that I would see a human DNA polymerase [protein] sequence and another protein with an E. coli DNA polymerase sequence?" he explained.
"It turns out that probability is much higher if you use the hypothesis that [humans and E. coli] are actually related."
Penny had been part of a similar, but more narrowly focused, study in the 1980s. His team had looked at shared proteins in mammals and concluded that different mammalian species are likely descended from a common ancestor.
Testing the theory of universal common ancestry is important, because biologists should question their major tenets just as scientists in other fields do, said Penny, who wasn't part of the new study.
"Evolution," he said, "should not be given any special status."
Editor's note: Two corrections have been made to this article. In the first sentence "million" has been changed to "billion." In the seventh paragraph, "10 followed by 2,680 zeros" has been changed to "1 followed by 2,680 zeros." Many thanks to readers for pointing out these typos.
Comet contains glycine, key part of recipe for life
"Why Life Originated (And Why it Continues) "
May 27, 2016
An important amino acid called glycine has been detected in a comet for the first time, supporting the theory that these cosmic bodies delivered the ingredients for life on Earth, researchers said Friday.
Glycine, an organic compound contained in proteins, was found in the cloud around Comet 67P/Churyumov-Gerasimenko by the European Space Agency's probe, Rosetta, said the study in the journal Science Advances.
The discovery was made using an instrument on the probe, called the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) mass spectrometer.
"This is the first unambiguous detection of glycine .. http://phys.org/tags/glycine/ .. in the thin atmosphere of a comet," said lead author Kathrin Altwegg, principal investigator of the ROSINA instrument at the Center of Space and Habitability of the University of Bern.
In addition to the simple amino acid glycine .. http://phys.org/tags/amino+acid+glycine/ , the instrument also found phosphorus. The two are key components of DNA and cell membranes.
Glycine has been detected in the clouds around comets before, but in previous cases scientists could not rule out the possibility of Earthly contamination.
This time, however, they could, because the mass spectrometer directly detected the glycine, and there was no need for a chemical sample preparation that could have introduced contamination.
"The multitude of organic molecules already identified by ROSINA, now joined by the exciting confirmation of fundamental ingredients like glycine and phosphorus, confirms our idea that comets have the potential to deliver key molecules for prebiotic chemistry," said Matt Taylor, Rosetta project scientist of the European Space Agency ESA.
"Demonstrating that comets are reservoirs of primitive material in the Solar System, and vessels that could have transported these vital ingredients to Earth, is one of the key goals of the Rosetta mission, and we are delighted with this result."
Scientists have long debated the question of whether comets and asteroids brought the components of life to Earth by smashing into oceans on our planet.
More than one hundred molecules have been detected on comets and in their dust and gas clouds, including many amino acids.
Previous data from Rosetta has shown that water on Comet 67P/C-G is significantly different from water on Earth, suggesting that comets did not play as big a role in delivering water as once thought.
However, the latest finding shows "they certainly had the potential to deliver life's ingredients," said a statement by the University of Bern.
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