Bad Timing

Got to the Intelligent Design thread on the St. Louis Post-Dispatch blog a little late in the game. The thread died after several comments of mine. Darn it!

20,000,000 Million Year Old Spider

The above is a picture of a 20,000,000 year old spider trapped in amber. Sciectists recently created an interesting method for studying the creature - shades of Jurassic Park.

According to BBC News:

Palaeontologist Dr David Penney, of the University of Manchester, found the 4cm long by 2cm wide fossil during a visit to a museum in the Dominican Republic.

Since the discovery two years ago, he has used droplets of blood in the amber to reveal the age of the specimen.

It is thought to be the first time spider blood has been found in amber and scientists hope to extract its DNA.

Even more interesting:

Dr Penney believes it was climbing up a tree 20 million years ago when it was hit on the head by fast flowing resin, became engulfed in the resin and died.

He claims the shape and position of the blood droplets revealed which direction the spider was travelling in and which of its legs broke first.

You can see more images of spiders trapped in amber atMesozoic Arachnids along with other interesting info about Mesozoic spiders.

Gorillas Discovered Using Tools

In a study to be published in the November issue of PLOS Biology scientist announce they have discovered gorillas using tools. It has been known for quite some time that chimps use tools but no one had ever witnessed gorillas using tools in the wild. What makes this study so important, though, isn't the fact that gorillas were using tools. It's how they used them that made the study so important.
From New Scientist:

They saw a female gorilla nicknamed Leah attempting to wade through a pool of water created by elephants. After quickly sinking waist deep, she got out of the water and picked up a metre-long stick, says Breuer. She then re-entered the water and repeatedly prodded the stick ahead of her as if to test for depth. She advanced about 10 metres before returning to her wailing infant on the edge of the pool.

“It was exactly how you or I might have tested the depth of the water,” Breuer told New Scientist, by satellite phone from a forest clearing in Nouabalé-Ndoki.

A second example was also captured on film, when Efi, a gorilla from another group, used a stick to lean on for support while she foraged for food with her free hand. She then used the same stick as a bridge to help her cross a patch of swampy ground, says Breuer.

*snip*

“Both cases seem related to the problems of locomotion in this swampy forest clearing,” says Breuer. This suggests that the tool use stems from an ecological need.

“Most great ape tool use is based around the retrieval of food,” notes Gillian Sebestyen-Forrester who studies gorilla communication at the University of Sussex, UK. But the “incredibly intuitive” behaviour of using a stick to test water depth is something quite different, she says.

“The gorillas have understood in some capacity that they can extend their sensory experience and find out more about their environment by physically extending their bodies with an inanimate object,” she says. "This suggests that the gorilla is capable of some mental calculation and abstract thought."

Footprints of gorillas were found on branches in nearby clearings suggesting their use as bridges could be widespread, says Breuer.

From National Geographic News:

"The most fascinating thing about this observation is the similarity [to humans] with which the gorillas solve the problems in this particular habitat," he said. "If you or me want to cross a swamp, we use the same solutions as gorillas."

Like humans, the gorillas in the swampy clearing jump from one dry patch to another, walk over branches, swing from trees, and—as the observations and photographs now show—use tools.

Totally cool research!

Added Later: Abnormal Interests has a post on the gorillas as well.

Darwin and the Quagga

If you have read any of Darwin's works you will recognize the Quagga. It is related to zebra. Darwin mentioned it in several of his works - at least once in connection with atavism (the idea that some organisms revert to some or all of their ancestral traits).



The two animals in the bottom row are quagga. They became extinct around a hundred years ago. Recently researchers, using hides and a skeleton in museum collections were able to unravel phylogeny and evolutionary history of the quagga:

The quagga, Equus quagga, a South African relative of horses and zebras, having a front half with zebra-like stripes and a back section like a horse with no marking, became extinct about 100 years ago. The pelt from a quagga museum specimen was the subject of tissue sampling that launched the field of ancient DNA analysis.

"Twenty years ago this exact species opened the field of ancient DNA studies on extinct animals," said one of the authors, Gisella Caccone, senior research scientist in the Department of Ecology and Evolutionary Biology at Yale. "Now, thanks to technological advances in the field, we revisited the story and used a population level approach to this question by analyzing a larger fragment of DNA and multiple specimens."

In the past, the quagga has alternatively been described as a species and a subspecies of the Plains zebra.These researchers asked how and when the quagga diverged from all the remaining related horses, zebras, and asses. They compared the genetics, coat color and habitats of existing zebras with related extinct species.

Results indicate that the quagga descended from the plain's zebra some 120,000-290,000 years ago:

These results suggest that the quagga descended from a population of plains zebras that became isolated and the distinct quagga body type and coloring evolved rapidly.

This study reveals that the Ice Age was important not just in Europe and North America, but also in Africa.

"The rapid evolution of coat color in the quagga could be explained by disrupted gene flow because of geographical isolation, an adaptive response to a drier habitat, or a combination of both of the two forces," said Caccone.

Sounds like a punctuational kind of event to me, but I haven't read the original study.

The Best Laid Plans....

Originally in this post I was going to mention that the afarensis family was moving about five miles west in about a week and that I was busy packing. I was going to mention that blonging would be light, except on Sunday when I had a special post planned. Except, I was going to say, if I found any really interesting to blog about...

Intelligent Design on the St. Louis Post-Dispatch Blog

I don't know how I missed this but the St. Louis Post-Dispatch blog has a thread on Intelligent Design. Some are against teaching it in schools. Others are for it. Some of the arguments in favor are pretty idiotic. For example, one person makes an argument about the speed of light slowing down (even the ICR stopped using that one), others trot out Behe, flagella and Mt. Rushmore. I've put my two cents in. There is still plenty enough silliness to go around if anyone wants to join the fun.

Circus of the Spinless

will be Friday. It is hosted by Tony at milkriverblog (whom I need to add to my blog roll - along with several others). Watch for it!

Bone Eating Sea Worms

Below is a picture of a type of polychaeta belonging to the genus Osedax. They were recently discovered feasting on the skeleton of a juvenile grey whale. This ability of Osadax species to feed on skeletal material is quite interesting and - heretofore - unknown.

According to a recent article in Environmental Microbiology this is how it works. Like a some other sea worms (such as red tube worms)Osedax lack a mouth and functional gut. They also, unlike other sea worms, lack a trophosome (an internal organ that houses endosymbionts - sea worms with trophosomes derive nutrition from the endosymbionts).
Instead, Osedax species have a highly vascularized root system (r in the righthand picture above) that invades the bone marrow. The root system is connected to a large eggsac (o in the righthand picture above). Both eggsac and root system are filled with bacteriocytes. This is where the story gets even more interesting. Normally, the bacteria found in most sea worms are autotrophic, that is, they produce their own food. Osedax bacteria, on the otherhand, are hetertrophic. The way the symbiotic relatonship was established makes for fascinating reading and I strongly recommend you follow the link and read for yourself (you should probably reread my posts on stable isotope analysis first).

Austrian Twins Update

The above is a picture of the 27,000 year old infant skeletons discovered in Austria. New Scientisist has a story on them as well:

The remains have yet to be carbon-dated but are thought to be at least 27,000 years old, because other artefacts from the area have been dated to between 40,000 and 27,000 years old. During this period, which falls within the Upper Palaeolithic, Neanderthals were superseded by modern humans, who were developing increasingly sophisticated hunting abilities and forms of culture.

The babes were placed side by side in their grave and protected beneath a woolly mammoth's shoulder blade, which was propped up by pieces of mammoth tusk. The bodies were wrapped in a material such as animal hide that has since deteriorated and were covered with ochre.

*snip*

The pair has been moved to Vienna's Natural History Museum, where they will be examined further and carbon-dated by Maria Teschler-Nicole. She will place the remains within a chamber with controlled humidity in order to limit further deterioration.

Mexican Footprints: An Update

Readers may remember the footprints found in Mexico that have been dated to about 40,000 years BP. Geotimes has an interesting story on the subject:

In summer 2003, researchers Matthew Bennett of Bournemouth University and Silvia Gonzalez and David Huddart of Liverpool John Moores University in the United Kingdom were dating and mapping the geology of the Valsequillo Basin in Mexico, about 130 kilometers south of Mexico City, when they came across what appeared to be footprints on the floor of an abandoned quarry. Examining the site further, they found the site littered with footprints, Bennett says — 269 individual prints of humans and animals intermingled.

Sixty percent of the footprints appear to be human, with telltale arches and impressions of the heels, balls and toes, and 36 percent of those appear to be child-sized, according to the researchers, whose work is in press in Quaternary Science Reviews. The remaining 40 percent of the prints were from a variety of animals, Bennett says, including dogs, big cats and animals with cloven hooves, such as deer and camels. The researchers also found mastodon and mammoth teeth.

Previously, in the 1960s and 1970s, archaeologists found megafaunal remains, including bones that had been “worked” with tools, scattered throughout the basin. Those remains had been unreliably dated to be between 20,000 and 40,000 years old, Bennett says, so the sites have been somewhat ignored since then.

The footprints are preserved in a layer of volcanic ash from the eruption of Cerro Toluquilla beneath a shallow lake in the Valsequillo Basin just over 40,000 years ago. “Volcanic ash lithifies quickly, like cement,” Bennett says, so when the inhabitants of the lake shores wandered across the mucky ash, their footprints were captured. When lake levels later rose, water washed over the footprints, burying them in lake sediments, he says. “So we have this great stratigraphic sequence” of lake sediments, topped by ash, which is then topped again by lake sediments, Bennett says, that can be dated.

The dissenting opinion:

But Michael Waters, a geoarchaeologist at Texas A&M University in College Station, is not convinced. He says that the ash layer is likely much older than 40,000 years, and should be retested using different methods. Furthermore, says Waters, who has visited the site, “I have serious reservations as to whether or not these are even footprints, human or animal.” The site has been so extensively quarried over the years, being chopped with axes and picks, that these imprints could just be tool marks that have weathered.

The team, Waters says, needs to find tracks in outcrops or areas that have not been quarried — “look for them like you would look for dinosaur or other trackways.” Bennett says that he and his colleagues are planning to begin just such excavations soon.

Even more interesting, there is a link to the Mexican Footprints Website Which contains a wide variety of information on the geology, dating methods, etc. Based on what I saw at the site I am a little less skeptical - although I still have some reservations.

Two 27,000 Year Old Baby Skeltons Found in Austria

News 24 is reporting that two 27,000 year old skeletons - believed to be from twins - have been found in Austria:

The 27 000 year old skeletons of two ice age infants have been found near Krems in northern Austria, the first discovery of its kind in Europe, the Austrian press reported on Saturday.

The perfectly preserved skeletons measuring 40cm had been protected by a mammoth's shoulder-blade bone, under which they had been buried on a sheltered hillside on the banks of the Danube river.

The grave, discovered 5.5m below ground, also contained a necklace of 31 pearls made from mammoth ivory and was located next to an area inhabited by ancient "homo sapiens fossilis", newspapers reported.

"It is the first discovery of a child's grave dating from this period," confirmed the excavation manager, Christine Neugebauer-Maresch, to the daily newspaper Kurier. "They may have been twins, but we have not yet been able to establish that," she told Die Presse.

The age of the skeletons will be analysed by the Institute of Natural Sciences in Vienna, which will also determine the cause of death.

"Homo sapiens fossilis" came out of Asia during the ice age as Neanderthal Man was dying out, and mastered stone and wood, but did not discover metal.

Other news sources have reported it as well but all contain about the same amount of info as the above. For example this from Live Science:

Archaeologists have uncovered the remains of two newborns dating back 27,000 years while excavating a hillside in northern Austria, the scientist in charge of the project said Monday.

Last week's find near the Danube River city of Krems is important because the newborns were buried beneath mammoth bones and with a string of 31 beads _ suggesting that the internment involved some sort of ritual, said Christine Neugebauer-Maresch, the project's leader at the Austrian Academy of Sciences.

"They could be twins,'' she said. "They have the same (length) limbs and were buried together.''

The burial _ one of the oldest in the region _ is also significant in that the children were not simply disposed of after their deaths, Neugebauer-Maresch said. The burial suggests "they were members of society,'' she said.

Archaeologists are combing the area to see if the infants' mother is nearby, as giving birth to twins in that era would have been extremely difficult and potentially fatal.

Interesting, because the burial was intentional and because of the age of the find.

My Politics

You are a Social Liberal (71% permissive) and an... Economic Liberal (11% permissive) You are best described as a: Socialist Link: The Politics Test on Ok Cupid

Cute Animal Quiz

Via An Ethereal Girl's Adventures in Cyberland

You Are A: Turtle!

These reptiles, famous for their hard outer shells, spent their days roaming for food and relaxing in the water. As a turtle you are not very speedy, nor are you soft and cuddly. You tend to hide in your shell and you aren't much of a sprinter, but you are quite tough. You also happen to be as cute as you are fascinating.

You were almost a: Bear Cub or a Frog
You are least like a: Puppy or a SquirrelCute Animal Quiz!

Word! Although being a bear cub would have been cool.

A Cool Idea

Henry's Webiocosm has a cool idea (which I am shamelessly pilfering)! Learn something new about a random organism.

I learned about: Cambarus (Glareocola) brachydactylus a plant that inhabits tributaries of the Cumberland River in Tennessee.

What did you learn about?

Noodles in Spaaaaceee

Truely, the Flying Spaghetti Monster works in mysterious ways:

Nissin Food Products announced Monday it will collaborate with Japan's Space Agency, NASDA, to make instant noodles that can be eaten on space missions.

``Space Ram'' _ that's short for ramen, the name for Japan's favorite slurpable snack _ will be made especially for astronauts flying on the Kibo research module, Japan's contribution to the International Space Station, Nissin said in a press release.

Brothers and Sisters in his infinite wisdom he is making sure we have adequate provender as we go to Mars:

Nissin said its top researchers will be devoting their noodles to making a product that tastes good and doesn't fall apart in zero gravity. The goal? ``To create the ultimate light snack.''

``This is also in response to a strong wish by our chairman Momofuku Ando, who invented the instant noodle, to create food for outer space,'' the company said.

NASDA's Kibo research module will be launched by the U.S. space shuttle to the space station in three separate shots beginning in 2004. Nissin plans to have its extraterrestrial noodles ready by then.

Ando, affectionately known in Japan as the ``noodle king,'' is credited with revolutionizing the eating habits of his nation and turning instant ramen into a multi-billion dollar business here.

Noodle fanatics can visit a faithful recreation of the wooden shack where Ando created instant ramen 44 years ago at the Instant Noodle Museum in western Japan.

I suggest we send FSM evangelists to Japan immediately as the ground seems fertile for converting many:

In Japan, instant ramen ingenuity is not just limited to dreams of outer space. At convenience stores around the nation, entire shelves are devoted to noodles that come in tastes that range from Korean ``kimchi'' cabbage to spicy cod roe spaghetti.

The snack, voted in a recent Japanese poll as ``the food of the century,'' is such big business that instant noodle makers from around the world converge on Tokyo every other year for the summit of the Instant Ramen Manufacturers' Association. Ando is chairman.

Truely, the Japanese have been touched by his noodley appendage!

RAmen

Interesting News on RNA, DNA and the Evolution of Protein

Regular readers of this blog know that I that I get a lot of science news from Science Daily and frequently turn that news into a post. This post is no exception. I have come across several interesting articles on RNA, DNA, protein evolution and lifes origins (one of which I have blogged about before).

The first concerns the RNA world:

In the primordial soup that produced life on earth, there were organic molecules that combined to produce the first nucleic acid chains, which were the first elements able to self-replicate. According to one of the more accepted theories, these molecules were ribonucleic acid (RNA) chains, a molecule that is practically identical to DNA and that today has the secondary role in cells of copying information stored in DNA and translating it into proteins. These proteins have a direct active role in the chemical reactions of the cell. In the early stages of life, it seems that the first RNA chains would have had the dual role of self-replicating (as is today the case with DNA) and participating actively in the chemical reactions of the cell activity. Because of their dual role, these cells are called ribozymes (a contraction of the words ribosome and enzyme). But there is an important obstacle to the theory of ribozymes as the origin of life: they could not be very large in length as they would not be able to correct the replication errors (mutations). Therefore they were unable to contain enough genes even to develop the most simple organisms.

Recent research has indicated a likely way around the limiting factor of length mainly because the replication error rate is higher than previously thought:

In practice, this means that the first riboorganisms (protocells in which RNA is responsible for genetic information and metabolic reactions) could have a much bigger genome than was previously thought: they could contain more than 100 different genes, each measuring 70 bases in length (bases are the units that constitute the genes and codify the information), or more than 70 genes, each measuring 100 bases. It is worth remembering that tRNAs (essential molecules for the synthesis of proteins) are approximately 70 bases long.

This is important because previous research indicates that the minimum number of DNA genes needed for simple organisms is about 200 but:

But in riboorganisms there can be much fewer genes, since DNA genomes include a number of genes that have the role of making the RNA translation system (which enables proteins to be produced) work, which would not be required in RNA-based organism.

Which brings us to the second article (published in 2002). Two scientists at the Scripps Research Center created an enzyme based on a binary genetic code - that is a genetic code having only two different subunits (which I assume means bases). The research demonstrated that evolution can occur in a genetic system composed of two bases and shows that an early life form could exist with only two bases:

Where protein enzymes are polymer strings made up of 20 building blocks (the amino acids), and RNA or DNA enzymes are made up of four different building blocks (the nucleotides), the world's first binary enzyme has but two different building blocks, based on the nucleotides A and U.

This enzyme is functionally equivalent to a "polymerase" molecule. Polymerases are ubiquitous in nature as the enzymes tasked with taking a "template" string of DNA or RNA bits and making copies of it.

Reader and Joyce's binary enzyme is able to join pieces of RNA that are composed of the same two nucleotide symbols. In the test tube, the binary string folds into an active three-dimensional structure and uses a portion of this string as a template. On the template, it "ligates," or joins subunits together, copying the template.

*snip*

One of the great advances in the last few decades has been the notion that at one time life was ruled by RNA-based life--an "RNA world" in which RNA enzymes were the chief catalytic molecules and RNA nucleotides were the building blocks that stored genetic information.

"It's pretty clear that there was a time when life was based on RNA," says Joyce, "not just because it's feasible that RNA can be a gene and an enzyme and can evolve, but because we really think it happened historically."

However, RNA is probably not the initial molecule of life, because one of the four RNA bases--"C"--is chemically unstable. It readily degrades into U, and may not have been abundant enough on early Earth for a four-base genetic system to have been feasible.

Which brings us to the third article (published in April of 05). Scientists at Scripps Research Center successfully created a third base pair. There are basically only two in DNA guanine-cytosin and adenine-thymine:

Scripps Research scientists’ DNA has a third pairing: “3FB-3FB” between two unnatural bases called 3-fluorobenzene (or 3FB). Unlike other unnatural base pairs, DNA polymerases are able to replicate this base pair, albeit with reduced fidelity. To improve replication, the scientists also reported the development of a system capable of evolving polymerases to better recognize 3FB in DNA. Using a selection system some liken to evolution in the test tube, they are creating their own “polymerase” enzyme able to replicate the unnatural DNA.

While the polymerase does not replicate the unnatural DNA with the same fidelity observed in nature, (roughly one mistake for every 10 million bases of DNA copied), its fidelity is reasonable (typically making only one mistake for every 1000 base pairs). This is the first time anyone has been able to replicate unnatural DNA with fidelity against every possible mispair.

Which demonstrates that it is possible for things to have evolved from a system with just say g-c or a-t to a system with both.

Which brings us to the fourth article (which I have blogged about previously):

As the DNA ‘alphabet’ contains four letters - called bases - there are as many as 64 three-letter words available in the DNA dictionary. This is because it is mathematically possible to produce 64 three-letter words from any combination of four letters.

But why there should be 64 words in the DNA dictionary which translate into just 20 amino acids, and why a process that is more complex than it needs to be should have evolved in the first place, has puzzled scientists for the last 40 years.

*snip*

One of quirks of the genetic code is that there are groups of codons which all translate to the same amino acid. For example, the amino acid leucine can be translated from six different codons whilst some amino acids, which have equally important functions and are translated in the same amount, have just one.

The new theory builds on an original idea suggested by Francis Crick - one of the discoverers of the structure of DNA - that the three-letter code evolved from a simpler two-letter code, although Crick thought the difference in number was simply an accident “frozen in time”.

The University of Bath researchers suggest that the primordial ‘doublet’ code was read in threes - but with only either the first two ‘prefix’ or last two ‘suffix’ pairs of bases being actively read.

By combining arrangements of these doublet codes together, the scientists can replicate the table of amino acids - explaining why some amino acids can be translated from groups of 2, 4 or 6 codons. They can also show how the groups of water loving (hydrophilic) and water-hating (hydrophobic) amino acids emerge naturally in the table, evolving from overlapping ‘prefix’ and ‘suffix’ codons.

“When you evolve our theory for a doublet system into a triplet system, you get an exact match up with the number and range of amino acids we see today,” said Dr van den Elsen, who has worked with Dr Stefan Babgy and Huan-Lin Wu on the theory.

*snip*

The theory also explains how the structure of the genetic code maximises error tolerance. For instance, ‘slippage’ in the translation process tends to produce another amino acid with the same characteristics, and explains why the DNA code is so good at maintaining its integrity.

“This is important because these kinds of mistakes can be fatal for an organism,” said Dr van den Elsen. “None of the older theories can explain how this error tolerant structure might have arisen.”

The new theory also highlights two amino acids that can be excluded from the doublet system and are likely to be relatively recent ‘acquisitions’ by the genetic code. As these amino acids - glutamine and asparagine - are unable to hold their shape in high temperatures, this suggests that heat prevented them from being acquired by the code at some point in the past.

One possible reason for this is that the Last Universal Common Ancestor (LUCA), which evolved into all life on earth, lived in a hot sulphurous pool or thermal vent. As it moved into cooler conditions, it was able to take up these two additional amino acids and evolve into more complex organisms. This provides further evidence for the debate on whether life emerged from a hot or cold primordial soup.

Which brings us to the fifth article which discusses the evolution of proteins:

By examining how proteins have evolved, UT Southwestern Medical Center researchers have discovered a set of simple "rules" that nature appears to use to design proteins, rules the scientists have now employed to create artificial proteins that look and function just like their natural counterparts.

*snip*

"The goal of our research was not to find another way to make artificial proteins in the lab, but to discover the rules that nature and evolution have used to design proteins," Dr. Ranganathan said. "The rules we have extracted from the evolutionary record of proteins contain a substantial fraction of the information required to rebuild modern-day proteins. We're building solutions so close that, at least in a test tube, we can't tell them apart from natural proteins."

Here is how it works:

"How did nature devise the right sequences that resulted in functioning proteins? Somehow, it found a way," Dr. Ranganathan said. "One implication of our work is that the evolutionary protein-design process may not be as complex as was previously thought." (oooh, Behe's going to be bummed - afarensis)

Earlier research has shown that for a given group of related proteins, or protein family, all family members share common structures and functions. By examining more than 100 members of one protein family, the UT Southwestern group found that the proteins share a specific pattern of amino acid selection rules that are unique to that family.

"What we have found is the body of information that is fundamentally ancient within each protein family, and that information is enough to specify the structure of modern-day proteins," Dr. Ranganathan said.

He and his team tested their newly discovered "rules" gleaned from the evolutionary record by feeding them into a computer program they developed. The program generated sequences of amino acids, which the researchers then "back-translated" to create artificial genes. Once inserted into laboratory bacteria, the genes produced artificial proteins as predicted.

"We found that when isolated, our artificial proteins exhibit the same range of structure and function that is exhibited by the starting set of natural proteins," Dr. Ranganathan said. "The real test will be to put them back into a living organism such as yeast or fruit flies and see how they compete with natural proteins in an evolutionary sense."

Put them all together and a theory about the origins of life begins to emerge. The is one caveat though (going back to the second article):

If the origins of life are a philosopher's dream, then they are also a historian's nightmare. There are no known "sources," no fossils, that show us what the very earliest life on earth looked like.

*snip*

Since the fossil record may not show us how life began, what scientists can do is to determine, in a general way, how life-like attributes can emerge within complex chemical systems. The goal is not necessarily to answer how life did emerge in our early, chemical world, but to discover how life does emerge in any chemical world--to ask not just what happens in the past, but what happens in general.

The part in bold is, if you ask me, the most important point of the second article. We may never be able to have an exact blow by blow account of life's origins. What we can do, however, is indicate that under a certain set of given conditions life can arise. More importantly, we should eventually be able to indicate the conditions under which life can be expected to arise. The two are different. In the first case (think the Miller-Urey experiments) the initial conditions are specified and life may or may not develop under those circumstances. The point is that you are applying a theory to a particular case. The second instance is more generalized - or better yet operates at a higher theoretical level. In this case we can specify a range of conditions under which life should develop.

But, those of you who know a lot about science may be thinking "what about Brownian Motion?" "Surely", you say "Einstein proves everything you have just written is wrong" This brings us to our sixth article which is actually about UV damage to DNA rather than Brownian Motion. It is relevant, however:

In the current issue of the journal Nature, Bern Kohler and his colleagues report that DNA dissipates the energy from ultraviolet (UV) radiation in a kind of energy wave that travels up the edge of the DNA molecule, as if the energy were climbing one side of the helical DNA “ladder.”

The finding lends insight into how DNA damage occurs along the ladder's edge.

It also counters what scientists proposed in the 1960s: that UV causes mutations by damaging the bonds between base pairs – the horizontal “rungs” on the ladder. The new study shows that UV energy moves vertically, between successive bases.

*snip*

In undamaged DNA, there are no chemical bonds between vertically stacked bases. But the bases do interact electronically, which is why Kohler thinks they form an efficient conduit for UV energy to flow through.

“Even though paired bases are connected by weak chemical bonds, it's the interactions that take place without chemical bonds – the interactions between stacked bases – that are much more important for dissipating UV energy,” Kohler said.

*snip*

Their new experiments show that the behavior of full DNA differs profoundly from that of isolated bases. When the chemists turned their strobe light on whole strands of novel DNA, the UV energy still changed to heat eventually, but the energy dissipated a thousand times more slowly.

That's an eternity in the DNA universe, where scientists need to use special equipment just to see these ultra-fast chemical reactions happen. Yet, Kohler's team saw no evidence that the UV affected the chemical bonds between the base pairs. They surmised that the UV energy was leaving the molecule by traveling along the edges instead.

“This slow relaxation of energy is utterly different from the mechanism in single bases that transforms the energy into heat in less than a trillionth of a second,” Kohler said.

“Eventually, the energy does turn into heat, but the important point is that the energy is retained within the molecule for much longer times,” he added. “This can cause all kinds of photochemical havoc.”

It could be that when base pairs are aligned in their natural state in a DNA strand, the electronic interactions along the stack provide an easier way for DNA to rid itself of UV energy, compared to passing the energy back and forth between the two bases in a base pair as scientists have previously thought.

Although Brownian Motion and UV radiation are two different things I would expect that the energy gained via the effects of Brownian Motion (I assume Birdnow meant that - well never mind I'm not sure what Birdnow meant)would be dissapated in a similar manner.

New Meme

Via Profgrrrrl and Pharyngula

Rules:
1. Go into your archive.
2. Find your 23rd post (or closest to).

Mine's from 2/02/05, a post titled " Lest You Think It's Just Evolution"
3. Find the fifth sentence (or closest to).
4. Post the text of the sentence in your blog along with these instructions.

The fifth sentence reads:

Therefore, everything has meaning and reflection on his nature, whether it is math or history or science. Two plus two equals four because God created them that way,” (emphasis mine)said Glen Schultz, who heads the Baptists’ LifeWay curriculum program for church-based schools and home-schoolers.

Added Later: I left off two r's in Profgrrrrl's name - this has been corrected. You'd think I'd do better research - being a science blogger.

It's Lurker Day!

At least according to Pharyngula, Chris Clarke and Feministe anyway. So all you folks who lurk at my blog say Hi, tell me what you think (besides the fact that you think my blog is the greatist blog ever, etc), tell me what you like (wohoo more posts about bones, etc) or don't like (aack no more posts about bones, we will run away if you do, etc). Today, you lurkers can talk and I'll listen! Even if you only came for spider pics!

Neanderthal Teeth: How Did They Grow?

The above is a human tooth. If you look closely you can see faint grooves running horizontally across it's surface. These grooves are called perikymata and represent growth. More specifically they represent growth cycles of about 6-14 days. Below is a high magnification detail from a thin section.


High magnification detail from the same thin section showing the regular growth structures found in enamel (polarised transmitted light microscopy). The approximately weekly growth layers, known as brown striae of Retzius, can be seen running from bottom left to top right. The enamel prisms run across from left to right, along which cross-striations can be seen (arrows). The cross-striations represent circadian (i.e. daily) growth markers and can be used to determine the precise timing of crown formation, as well as the timing of any disruption to this formation.

In theory one could count the number of perikymata on a tooth multiply it by 6-12 days and come up with an estimate of how long it took the tooth to form - getting at the same time an estimate of the length of childhood. Such studies have a long history in anthropology and recently this idea was applied to Neanderthal teeth. At issue is how long Neanderthals took to reach maturity - if they took less time than anatomically modern humans then that would obviously have bearing on the whole "Out of Africa/Multiregional Continuity" debate.
Recently a team of researchers performed a study on the perikymata of Neanderthal teeth:

For the study, the researchers used precise dental impressions Guatelli-Steinberg and Larsen made of 55 teeth believed to come from 30 Neanderthal individuals. These were compared to 65 teeth from 17 Inuit, 134 teeth from 114 southern Africans and 115 teeth from as many Newcastle residents. In all cases, the researchers tallied the number of perikymata on the enamel surface of the teeth.

Guatelli-Steinberg said that the results showed that the enamel formation times for the Neanderthals fell easily within the range of time shown by teeth from the three modern populations – a conclusion that did not support a shorter childhood for the Neanderthals.

Enticing though it may be, these new findings haven't convinced the researchers that a Neanderthal childhood was equal to a modern human's.

“The missing key bit of data to show that would be evidence for when the first molar tooth erupted in the Neanderthals, and we simple have no evidence of when that occurred,” she said.

The length of time is important, the researchers say, because unlike all other primates, humans have an extended period of childhood growth, during which brain matures both in size and through experiences. Some earlier hominids matured far more quickly than modern humans.

“The question is when exactly did that pattern of development evolve in the growth of humans,” she said.

Tiger Salamanders and Evolutionary Change

A recent article published in BMC Ecology casts an interesting light on tiger salamander evolution:

Researchers analysed a late-Holocene fossil record to track morphological traits in the Tiger Salamander through the last 3,000 years. The team, led by Elizabeth Hadly from Stanford University, United States, analysed trends in the fossil record within the context of known climate change, to distinguish patterns of response correlating to specific climatic periods during this time.

The fossils were all collected from Lamar Cave in Yellowstone National Park in Wyoming, United States. The cave deposits were dated and divided into five time periods according to their estimated age. The researchers then grouped the fossils into four morphologically distinct groups: young larval, paedomorphic, young terrestrial or old terrestrial, and measured the body size index (BSI) of fossils in each group and time period.

The team found that paedomorphic individuals - sexually mature, yet still aquatic and retaining larval characteristics - were much smaller than terrestrial adult individuals, during the Medieval Warm Period (MWP). The authors claim that this is eveidence for a response to warm and dry climate conditions, which allowed a terrestrial ectotherm to flourish. They conclude that the fossil record of the Tiger Salamander reflects known climatic conditions during the MWP, a time period characterised by a warm and dry climate that occurred approximately 1150 to 650 years ago.

The entire paper can be found here