Bacteria, Elephants and Metabolic Activity

I'm sure someone, such as Coturnix at Science and Politics could write a better post on this subject, but I find it interesting so I'm going to have a go at it (although I'd love to see what Coturnix could make of it).

It is a truism in biology that smaller animals have higher metabolic rates than larger ones. Think of the shrew, and other such animals, that have to eat a large percentage of their body weight in order to survive. Recent research has qualified this picture somewhat. Researchers at the University of California have performed an extensive study and come up with some interesting results. A little background from Science Daily:

"...all living organisms have to transport energy obtained from food they eat to support the working of their internal organs, such as the brain or heart. The larger the organism, the further away are the organs from the body surface. “This makes energy supply more and more difficult for larger organisms,” he said. “For example, bacteria have to transport the obtained food over less than one micron, which is their body length, while the distance between an elephant's trunk and an organ such as its brain or heart is about ten million times longer."

With that in mind, the researchers compared metabolic rates in various groups of organisms ranging from bacteria (over 80 species were included) to elephants to test the idea that smaller animals are more metabolically active than larger animals:

But a new study led by Bai-Lian Li, professor of ecology at UC Riverside, shows that this is true only for organisms that are closely related evolutionarily and have body masses differing by no more than 6-7 orders of magnitude – about the difference in body mass between an elephant and a shrew.

For a pair of organisms that don't meet these conditions, that is, organisms that are not closely related evolutionarily and whose body mass difference exceeds the 6-7 orders of magnitude range, the researchers find that the small organism consumes about the same amount of energy per unit mass as the large organism: 1-10 watts per kilogram of body mass in the resting state of the organisms.

Since bacteria and elephants are not closely related, in evolutionary terms, and since an elephant is more than 6-7 times the size of bacteria:

"...elephants, ..., appear to be capable of supplying their tissues at a rate similar to that of tiny bacteria."

Even more interesting:

The researchers’ analysis also shows that the rate of energy consumption per unit body mass declines with growing body size in groups of evolutionarily close organisms, such as mammals. For example, one gram of an elephant’s body uses up 25 times less energy than does one gram of a shrew’s body, accounting for why shrews have to eat more often than elephants. On the other hand, a bacterium, which is not closely related to an elephant in an evolutionary sense, consumes approximately the same energy per unit body mass as the elephant.

Which may help explain trends towards large size in a lot of lineages throughout evolutionary history.

Finally, this is the most fascinating part:

So far, life scientists have held the view that the properties of living organisms are shaped by the changing external physical environment to which the organisms must continuously adapt. The new study posits, however, that living organisms are able to overcome the physical limitations imposed on them by their own physical properties and their external environment in order to maintain optimal, biochemical characteristics, such as the mass-specific metabolic rate the researchers studied.

Although, I'm not sure if the bolded sentence isn't just an alternative way of phrasing the first sentence. If organisms are continuosly adapting to the changing physical environment aren't they overcoming the physical limitations imposed on them by their own physical properties and their external environment in order to maintain optimal, biochemical characteristics?

Sigh

Oh, Well. Better luck next year...

GO CARDINALS!

GO CARDINALS!

More on Bone Eating Sea Worms

As I mentioned in a previous post some sea worms feed on whale bones. BBC News is reporting some have been discovered off the coast of Sweden (they were previously known only off the coast of California).



above is a picture of the Swedish species. Below is a scanning electron micrograph of the sea worm.



Here is another picture:



Here is what is know, so far:

Osedax worms are about 1-2cm in length.

A scanning electron micrograph shows up remarkable detail in the North Sea worm
They root themselves to the whale bones which they then plunder for oils with the help of symbiotic bacteria. The worms' flower-like plumes pull oxygen from the water.

There is a mystery:

Their reproductive system is extraordinary - certainly in the case of the Pacific Osedax.

"The female Pacific worms keep males inside their tube as a sort of little harem that fertilises eggs as they are released into the water column," explained Dr Glover.

"We're not sure what's happening with the reproductive biology of the Swedish worms yet. We've only got females; we haven't found any males. It's a bit weird."

Scientists have established that all of the Osedax species so far identified appear to be closely related to vestimentiferan tubeworms, which are found only at the volcanic cracks in the ocean floor called hydrothermal vents.

There is also a fly in the ointment. Since these worms live on whale falls (I. E. carcasses of dead whales that sink to the ocean floor) it is believed that whale carcasses act as stopping points that allow organisms to move around the ocean floor. If whales have low population numbers or are extinct this "island hopping" can't work:

What concerns researchers is that the commercial hunting which so devastated whaling populations would also have severely curtailed this activity by reducing the incidence of whale fall.

It may even have led to the extinction of some bottom-dwelling organisms that depended on this rare but concentrated nutrient supply.

Swimming Dinosaurs

Recently tracks have been discovered in Wyoming that show that dinosaurs swam. According to the GSA this is the first evidence in Wyoming of this kind of behavior:

The tracks are embedded in a layer of rock known as the Middle Jurassic Bajocian Gypsum Spring Formation, a 165- to 167-million-year-old rock formation that contains fossilized remains of a marine shoreline and tidal flats. Geologists believe an inland sea, called the Sundance Sea, covered Wyoming, Colorado and a large area of the western United States during the Jurassic period from about 165 million years ago to 157 million years ago.

Debra Mickelson of CU-Boulder’s geological sciences department said the research team identified the tracks of the six-foot-tall, bipedal dinosaur at a number of sites in northern Wyoming, including the Bighorn Canyon National Recreation Area. “It was about the size of an ostrich, and it was a meat-eater,” she said. “The tracks suggest it waded along the shoreline and swam offshore, perhaps to feed on fish or carrion.”

The dinosaur does not have a name, although Mickelson is continuing to look for bones and other remains that could be used to identify and name the new species. “This dinosaur is similar to a Coelosaur,” she said. “It is a dinosaur with bird-like characteristics and is a possible ancestor of birds. It lived in a much earlier time period and was very different from larger dinosaurs like T-Rex or Allosaurus.”

The tracks are of different sizes and were deposited at about the same time, according to Mickelson, revealing that the dinosaurs likely traveled in packs and exhibited some variation in overall size. “Further research into the geologic record and depositional history of the region supports our conclusion that the dinosaurs were intentionally swimming out to sea, perhaps to feed,” she said.

Global Warming and Fossils

I'm still working on a post on Homo floresiensis. In the meantime...
"Prehistoric global warming episodes from massive atmospheric pollution involving carbon dioxide and methane could have created and preserved "mass kills" of wildlife..."

According to recent research previous episodes of global warming may have played a role in fossil preservation. The research, conducted by Oregon geologist Gregory Retallack, involved comparing thousands of well preserved assemblages of fish, crustaceans, insects, starfish among others. According to the article, during the past 500 million years there are 41 instances of exceptional preservation:

Such exceptional assemblages were thought to have been preserved in environments that were unusually low in oxygen, highly saline, very cold, or extremely dry. What was not suspected until the new compilation was the global distribution of other exceptional fossil deposits of the same ages. Independent estimates of atmospheric pollution crises come from studies of carbon anomalies, microscopic pores of fossil leaves and climatic indicators from fossil soils. Methane outbursts from volcanically intruded coals and submarine gas hydrates are prime suspects for these lethal atmospheric pollution events.

"Lowered levels of oxygen can kill fish and other creatures in marginally aerated environments, and also preserve their carcasses from dismemberment and decay," said Retallack. "Data from carbon anomalies and microscopic leaf pores indicate that some of these killer greenhouses ramped up, within only a few thousand years, to intolerable levels of more than 10 times the modern level of atmospheric carbon dioxide. What stopped them from continuing on to a sterile greenhouse atmosphere like that of Venus? It was the widespread death and burial of animals and their carbon which created fossil bonanzas, the likes of which may have saved us from the heat sterilization experienced by our sister planet."

Homo floresiensis: More Pieces of the Puzzle

The past week has seen a flurry of activity concerning Homo floresiensis. Starting with an article in the letters section of Nature (kindly sent to me by Aydin at Snail's Tales)and continuing with articles in Nature's News and News and Views Sections. Several bloggers have posted on it as well. Carl Zimmer at Corante has an interesting post on the subject. Orbis Quintus has some interesting thoughts as well. Perhaps, the most interesting though, is Hawks here, here and most importantly here.

My first thought on seeing the pictures of some of the other bones discovered was "Wow, they are really robust" but I'll get to that later. The main article ("Further Evidence for Small-Bodied Hominims from Late Pleistocene of Flores, Indonesia") gives some details on the stratigraphy of the cave where the fossils where found - including spots where samples for thermoluminescence were taken, talks about the tools and faunal remains and provides a table listing the remains that have been recovered so far. There is a new mandible (LB6/1) that is slightly smaller in size than the original. More importantly, there is some post cranial material. Which is were things really get interesting. As I mentioned above, the post cranial material is robust. The pictured bones are compared with similar bones from a human pygmy and the differences are noticable. For example, the humerus has a greater (midshaft circumference wise) as does the recovered tibia. The humerofemoral index (a ratio comparing the lengths of the humerus and femur) is the same as for AL-288-1 (Lucy) and the blades of the pelvis are flared antero-laterally which implies an australopithicine shaped thorax (and hence indicates some climbing behavior). Because of this the authors of the paper have moved away from intepreting H. floresiensis as a dwarf H. erectus. After reading the paper and seeing the pictures I would have to agree. For example, the trochlea and capitulum of the humerus look a lot like Australopithecus robustus - TM 1517 or KNM-ER 739 for example. One other interesting feature was the humeral torsion (rotation of the head of the humerus relative to the plane of the distal end) which is in the range of gibbons and macaques. Humeral torsion occurs mainly when there is a laterally facing shoulder joint and it is necessary for the elbow to flex and extend in an anteroposterior plane. Humans and the great apes have a large degree of humeral torsion (although gorillas, the most ground dwelling, have the least amount of the three). Overall, what the morphology says to me is that this is something new and we need to interpret it in it's own right rather than trying to force it into current species.

Perhaps, the saddest part is that the researchers have been denied permission to return to Liang Bua.

Which Dromaeosaurid Are You?

Via Pharyngula



Deinonychus - Fun and playful, yet very set on pack
structure. Often an annoyance to larger
'raptors, such as Utahraptor.


Which Dromaeosaurid Are You?
brought to you by Quizilla


Fun - Check
Playful - Check
Often an annoyance... - That's a big yes per Mrs. afarensis!

A Step Closer to Understanding Anthropoid Origins

Anthropologists in the Fayum (where else?) of Egypt have uncovered several interesting fossils that shed some light on the origins of anthropoids (old and new world monkies). Unlike previous finds, these fossils were found at a relatively new locality in the Fayum.

According to paper coauthor Elwyn Simons:

"...analyses of the teeth of the two species clearly place them as members of a group called parapithecoids, known as "stem" anthropoids because they constitute the species of early creatures from which the subsequent "crown" anthropoid line arose. "The finding of these parapithecoids from such an ancient time confirms that crown anthropoids -- a group including all modern anthropoids -- have their earliest known beginnings in Africa," said Simons. "They show that findings by other researchers of isolated examples of possible higher primate fossils in Asia do not constitute evidence of an ancestral crown anthropoid lineage there."

Leaving the cladistic terminology aside, what this means is that these fossils are on the main line of anthropoid evolution. One of the species, Biretia megalopsis, may have been nocturnal - also important for understanding anthropoid evolution. How do we know B. megalopsis was nocturnal and why is this important?

"...a tooth root from the species Biretia megalopsis is truncated, indicating that it had to make room for the larger eyesocket of a nocturnal animal."

"These finds seem to indicate that Biretia megalopsis must have had very large eyes, and so was likely nocturnal," said Seiffert. "This has never been documented in an early anthropoid. The simplest explanation is that Biretia's nocturnality represents an evolutionary reversal from a diurnal ancestor, but that conclusion is based solely on the probable pattern of relationships. If down the road we find out that our phylogeny was wrong, Biretia could end up being very significant for our understanding of the origin of anthropoid activity patterns."

In other words, being diurnal (active during the day) is the ancestral condition for anthropoids, apes and humans and B. megalopsis evolved away from that condition.

More Organic Chemicals Found in Space

Scientists associated with NASA's Spitzer Telescope have discovered polycyclic aromatic hydrocarbons:

"NASA's Spitzer Space Telescope has shown complex organic molecules called polycyclic aromatic hydrocarbons (PAHs) are found in every nook and cranny of our galaxy. While this is important to astronomers, it has been of little interest to astrobiologists, scientists who search for life beyond Earth. Normal PAHs aren't really important to biology," Hudgins said. "However, our work shows the lion's share of the PAHs in space also carry nitrogen in their structures. That changes everything."

This is important because:

"Much of the chemistry of life, including DNA, requires organic molecules that contain nitrogen," said team member Louis Allamandola, an astrochemist at Ames. "Chlorophyll, the substance that enables photosynthesis in plants, is a good example of this class of compounds, called polycyclic aromatic nitrogen heterocycles, or PANHs. Ironically, PANHs are formed in abundance around dying stars. So even in death, the seeds of life are sewn," Allamandola said.

Looking back over the years it is totally amazing to me how many different types of organic chemicals have been found in outer space. Once upon a time it used to be thought that outer space was barren of organic chemicals and origins of life research focused on chemicals believed to be present on early earth. It seems the picture is changing...

Blood Drinking Spiders!

The above is a jumping spider native to Africa:

Evarcha culicivora, is found only around Lake Victoria in Kenya and Uganda. A species of jumping spider, or salticid, it usually hunts insects on tree trunks and buildings. It stalks its prey rather than trapping it in a web.

At the moment it is pretty unique. You see it has a taste for mammal - and human - blood! How do we know this? Scientists recently conducted prey preference experiments. This is how it works:

Lab experiments conducted near Lake Victoria showed the spider preferred female mosquitoes fed with human blood over all other prey, including male mosquitoes, which don't feed on animal blood.

Tests of the spider's prey preferences showed it went for blood-engorged female mosquitoes in 83 percent of cases when offered a choice of two similar-size insects.

When it came to making a choice based on smell alone, with the two meal options hidden from view, around 90 percent of jumping spiders selected the blood-filled mosquito.

Although many spiders have relatively poor eyesight—those that use webs to trap prey have no need for acute vision, Nelson says—jumping spiders are an exception.

"Salticids are predators that actively search for prey and mates and typically do not build webs," she said. "They have evolved eyes that support high-acuity vision suited to their active lifestyle."

Spiders don't have the skin-piercing mouth parts needed to feed directly on human blood, but the mosquito-munching jumping spider appears to have got around this. The strategy has other advantages as well, Nelson points out.

"Blood-feeding is a dangerous activity," she said. "Animals that are bitten have a swatting response, and often the insect is killed."

So, essentially the spider has come up with a method to avoid being swatted and still specialize on blood.

The study team suspects a blood meal is also biologically important to E. culicivora.

They say spiders expend a lot of energy breaking solid food down into liquid by injecting their prey with digestive enzymes.

"Perhaps blood is a ready-made, nutrient-rich liquid meal," Nelson said.

Although spiders creep me out, I think this is a fascinating study in evolution. Mosquitos specialize on blood as a food source as does E. culicivora but both have evolved different methods to obtain it. It would be interesting to find out if mosquitos were E. culicivora's primary prey or if this is a recent addition to their diet. It would also be interesting to see if there is a closely related species that doesn't feed on mosquitos (I'm thinking of Rhagoletis pomonella).

I'mmm Baaack!

Tokk a few days longer than I thought to get moved. Today was actually the first day I'v had to mess with the computer. I'll be visiting some friends in the blogosphere and start regular posting tomorrow.

Poor Me

Since I'm moving during the next couple of days I will be without the internet until Mondayish (assuming my DSL provider isn't fibbing) so if you seen a haunted, haggered man roaming your neighborhood crying "My kingdom for a modem connection" take pity - it will probably be me...
When the move is done and DSL restored I will have plenty to blog about - I've been collecting ideas all week!

On the Other Hand...

Little Blunt doesn't want to violate the law:

Robinson said that governors who order flags flown at half-staff in response to a soldier being killed while serving the country as opposed to the state are in violation of the law, according to general counsel Terry M. Jarrett's interpretation.

Here is what it's about:

Two St. Louis anti-war activists are challenging Gov. Matt Blunt to respond to the deaths of soldiers as several other states do: by flying flags at half-staff when a soldier from the state dies in the line of duty.

*snip*

Several other governors, including Illinois', issue such orders when soldiers from their states are killed. But Jessica Robinson, Blunt's press secretary, said Wednesday that neither Blunt nor any other governor had the authority to make such an order.

"As a veteran, Gov. Blunt deeply respects the sacrifices and has personally mourned the loss of those who have been killed in action," Robinson said. "But lowering the flags would actually be contingent on a presidential directive. ... Our general counsel's interpretation of the law is that the opportunity and authority rest with the governor when it's (a situation involving) state service and with the president when it's federal service."

*snip*

Joyce Doody, executive director of the National Flag Foundation in Pittsburgh, said governors do have the authority to order flags flown at half-staff. If asked, however, her organization suggests governors opt to fly state flags instead of U.S. flags so that the U.S. flag isn't too often at half-staff.

Her organization has not tallied how many states fly flags at half-staff in response to the deaths of soldiers. A review of news releases and articles shows that Illinois, California, Michigan, New Mexico, New Jersey, Kentucky, Oregon, Minnesota, Wisconsin, Indiana, Vermont and Pennsylvania are among the states whose governors have ordered either U.S., state or both flags to be flown at half-staff in response to the deaths of soldiers.

*snip*

Gerardo Cardenas, a spokesman for Blagojevich, said the governor had the authority to make the proclamation because he is commander in chief of the state's National Guard.

"This does not constitute any violation or any trespassing on presidential authority," Cardenas said. "This is a gesture that shows our respect for these soldiers who give up their lives ... We're respecting their sacrifice and honoring their service in a proper way."

Thank God we have Blunt to stand up for the President and law and order! Unlike all those other governors in Illinois, California, Michigan, New Mexico, New Jersey, Kentucky, Oregon, Minnesota, Wisconsin, Indiana, Vermont and Pennsylvania who hate America and violate the law. Even more horrifying they usurp presidential privilege! To Gitmo with them, I say! (Note to conservatives: I do not really mean this, I'm being sarcastic, so as much as you'd like to, please do not send all those governors to Gitmo.)

The St. Louis Post-Dispatch Has Picked Up the Delay/Blunt Story

Here although it's basically the same as the story I linked to in the previous post.

Tom Delay and the Blunts

I just turned on KMOV (a CBS affiliate) in time to hear a story about Delay giving 100,000 to Blunt who gave it to the Missouri Republicam party. He also gave the MO Republican part 50,000 and the party turned around and gave it back. I am unclear about all the details. DeLay, Successor Blunt Swapped Donations:

WASHINGTON (AP) -- Tom DeLay deliberately raised more money than he needed to throw parties at the 2000 presidential convention, then diverted some of the excess to longtime ally Roy Blunt through a series of donations that benefited both men's causes.

When the financial carousel stopped, DeLay's private charity, the consulting firm that employed DeLay's wife and the Missouri campaign of Blunt's son all ended up with money, according to campaign documents reviewed by The Associated Press.

*snip*

The government's former chief election enforcement lawyer said the Blunt and DeLay transactions are similar to the Texas case and raise questions that should be investigated regarding whether donors were deceived or the true destination of their money was concealed.

*snip*

Hartley said he saw no similarity to the Texas case. The fact that DeLay's charity, Christine DeLay's consulting firm and Blunt's son were beneficiaries was a coincidence, Hartley said.

Much of the money - including one donation to Blunt from an Abramoff client accused of running a "sweatshop" garment factory in the Northern Mariana Islands - changed hands in the spring of 2000, a period of keen interest to federal prosecutors.

*snip*

Noble said investigators should examine whether the pattern of disguising the original source of money might have been an effort to hide the leaders' simultaneous financial and legislative dealings with Abramoff and his clients.

"You see Abramoff involved and see the meetings that were held and one gets the sense Abramoff is helping this along in order to get access and push his clients' interest," he said. "And at the same time, you see Delay and Blunt trying to hide the root of their funding.

*snip*

The DeLay group began transferring money to Blunt's group in two checks totaling $150,000 in the spring of 2000, well before Republicans actually met in Philadelphia for the convention. The transfers accounted for most of money Blunt's group received during that period.

DeLay's convention arm sent $50,000 on March 31, 2000. Eight days later, the Blunt group made a $10,000 donation to DeLay's private charity for children on April 7, 2000, and began the first of several payments totaling $40,000 to a northern Virginia-based political consulting firm formed by DeLay's former chief of staff, Ed Buckham.

That consulting firm at the time also employed DeLay's wife, Christine, according to DeLay's ethics disclosure report to Congress.

Hartley said Blunt was unaware that Mrs. DeLay worked at the firm when he made the payments, and that she had nothing to do with Blunt's group.

*snip*

On May 24, 2000 - just before DeLay left with Abramoff for the Scottish golfing trip - DeLay's convention fundraising group transferred $100,000 more to Blunt's group. Within three weeks, Blunt turned around and donated the same amount to the Missouri Republican Party.

The next month, the state GOP began spending large amounts of money to help Blunt's son, Matt, in his successful campaign to become Missouri secretary of state. On July 25, 2000, the state GOP made its first expenditure for the younger Blunt, totaling just over $11,000. By election day, that figure had grown to more than $160,000.

Hartley said Blunt always liked to help the state party and the fact that his son got party help after his donation was a coincidence. "They are unrelated activities," he said.

Exchanges of donations occurred again in the fall. Just a few days before the November election, DeLay's ARMPAC gave $50,000 to the Missouri GOP. A month later, the Missouri GOP sent $50,000 to DeLay's group.

More here.

The Meme

Aydin at Snail's Tales has tagged me with the meme that is going around. So without further ado...

What were you doing 10 years ago? Ten years ago I was beggining what would become the second worst semester in my educational career. I was actually looking forward to the semester because I was starting the research on my master's thesis. I was going to examine some recently created methods for determining gender from the tibial plateau (really more in the way of verification on modern forensic samples). I was also going to try and apply them to zooarchaeological situations. At any rate, during the course of the semester I came down with bronchitis on three separate occasions. The third time I developed cough syncopy to go along with the bronchits - which means I passed out almost every time I coughed. I managed to muddle through the semester with GPA intact.

What were you doing five years ago? Five years ago I was working for a company that provided nurse case management for worker's comp claims (don't get hurt in Missouri is all I can say - Blunt's made it worse). I was also back at a community college taking Trigonometry and College Algebra. There is a silver lining in every cloud and somewhere along the line I saw the good in being knocked out of college (see the previous post). You see, I didn't really pick the master's thesis I wanted, mainly because I didn't have the math (if you are reading this post and want to be a physical anthropologist take math, a lot of math, chemistry, evolutionary biology and evo-devo wouldn't hurt either - neither would some good classes in comparitive anatomy). What I would have liked to have done was test Martin Bernal's theories developed in "Black Athena" concerning the ethnicity of the greeks. In particular I wanted to see if there was any biological admixture between the greeks and surrounding peoples. This would have required more math than I had so I was back in school trying to acquire the tools I needed to become the type of anthropologist I want to be.

What were you doing one year ago? One year ago I was starting the scanning department for my current employer. I was out of college, again, because my wife wanted to go and since I had a B.A. I felt it was her turn. I'm a very patient person - I'll have a Ph.D before all is said and done.

What were you doing yesterday? Writing a post on my one year anniversery as a blogger! Oh, and packing.

Five songs you know the words to? Well, that's kind of tough... Once upon a time I used to play a bamboo flute (I also used to play the trumpet - Louis Armstrong rules!) and had the sheet music to quite a lot of songs - play them enough and you learn them by heart. So, pretty much anything off Neil Young's Harvest, Stairway to Heaven, Ben (I don't know why I know the words to that - seen the movie once to often I guess). Anything off Black Sabbath's Paranoid.

Five snacks you like? Popcorn, Baby Ruth, Trail Mix, Bannanas, Milk Duds

Five things you would do with $100 million? I divide this into two sections. The selfish part: Finish my education, increase my library size significantly (this applies to books and monster movies - a weakness of mine), buy a 40 ft Hallberg-Rassy and sail to greece with my family:


They are beautiful, beautiful boats and cost a small fortune.

Then I would make sure several other family members are taken care of, which should really be included in the altruistic section. The altruistic part: endowe some scholarships in science so others could attend college. Either start an evolution research institute or maybe endowe the NCSE.

Five places I would run away to? Anyplace the sailing is good, in particular the Aegean. Greenland (as long as I wasn't unemployed). Aydin mentioned Darwin's house and that would be cool - as would the Galopagos Islands. Hadar would be fantastic as would Olduvai Gorge.

Five things I would never wear? Those skimpy swimming trunks Brazillian and Italian men wear at the beach (at least not without doing some serious exercising). This is a really tough question. I'm stumped...

Five greatest joys? Does Mrs. afarensis count? The little afarensis' too. The explosion in my brain when I have an "eureka" moment and solve a difficult problem. Sailing. Chess (although it's been awhile - I really admire the style of Aron Nimzovitch if that means anything to any of you). Fencing. Reading.

Five favorite toys: My computer obviously. Slide rules - I have five. Having a telescope and a microscope would be fun as would a digital camera.

Five people I'm tagging? Most of the bloggers I know have already done this so I'm leaving that open to whoever wants to do it.

Happy Blogiversary To Me

Yes, that's right! It was one year ago today that a blog named afarensis first blazed across the intellectual firmament, astounding all with it's brilliance! So I thought in this post I would look back at the past year.

Originally, I was going to name the blog "Insomnia" because I do suffer quite frequently with insomnia. The idea was to blog when I couldn't sleep. Didn't quite work out though because I tend to read when I can't sleep (for example I'm on page 526 of Gould's monumental "The Structure of Evolutionary Theory"). Here's my first post:

Up late

Well technically I woke up early and can't get back to sleep. This blog will be about science, politics and whatever else I can think of to say.

See what I mean about brilliant!

I posted six more times in October and seven times in November. In December I did not post at all. Mainly, because I was having a running battle with a creationist who claimed to be from Missouri over at Chris Mooney'sblog (whoooops! Just gave up my anonymity didn't I?).
In January I only put up three posts. I decided at that point that I needed to get more serious about blogging, so in February I vowed that I would try to post everyday and although I didn't quite reach that goal I did start posting a lot more frequently. This effort brought me my first commenter:

I was looking at various blogs and came across one that had the Book Meme. It looked like a lot of fun so while I was posting it on my own blog, I tracked it back several blogs. Anyway, I found this in one of the comment sections Good grief, there are 987 different posts referencing "page 123" in Technorati...
PSoTD | Email | Homepage | 02.17.05 - 9:28 pm | #
I clicked on that comment and one of the links was yours.

This commenter still shows up on a regular basis. Can anybody guess who it was?

Sometime during March some of the other blogs in the blogosphere started occasionally linking to my posts and several - such as Red State Rabble, Thoughts From Kansas, Dharma Bums, Pharyngula, It's Morning Somewhere and last, but not least Snail's Tails. Others started linking later, and you can find links to them in my blogroll, but these are the people primarily responsible for my sitmeter climbing.

So let's talk about that for a few. My most popular post was Wells, Centrioles and Cancer: Bad things Happen when you Believe your own Metaphor. Pharyngula linked to it and I received over 2,500 hits - as a matter of fact I still get hits on it from that link!
Ian Musgrave even showed up and made a few snarky comments about Wells! I have been averaging around 280 hits a day for the last couple of months (although lately it has dropped below 200) and at last count I have had 44,393 hits. Which surprises the hell out of me. I never thought I would have that many hits after just a year. So, to those 44,393 people I say:

THANK YOU

Since my site is devoted to anthropology, evolution and science you would think that I get my fair share of creationist and Intelligent Design trolls, but you would be dead wrong! Pharyngula and The Panda's Thumb are hogging them all! Not that I object, you understand, because I would rather blog about science than argue with the brain dead. It's been my experience that people like that know little about evolution and are instead arguing against some weird mishmash they have created in their own imagination. On the other hand, I have had several wingnuts show up. The first showed up when I announced I had joined the Big Brass Alliance. Another wingnut showed up when I did my Cindy Sheehan. This is also the longest thread to date.

In June I started a new blog dedicated to Middle School (or Junior High) and High School students, as well as those who know little about evolution but wish to learn more. The blog is called Transistions: The Evolution of Life. Anyone can contibute posts to it by getting in touch with me. I have had a wide variety of people contribute to it, in addition to the posts I have written. I am always seeking good posts that fit in with the basic mission of the blog. I am also seeking links to websites, etc, you can go here for more info on what I'm looking for.

Since this blog is about anthropology, evolution and science I have always been a littled worried. I do have a Bachelor's degree in anthropology and did two years of grad school before a car accident (I was hit by a drunk driver) and a year long concussion (I really feel sorry for those professional athletes that get concussions, they are brutal and agonizing and really affect your life) knocked me out of school (I do plan on going back - maybe soon). So I do know something about the subjects I blog about. More importantly, I know how to research a subject befor I post on it. Which is not to say I haven't goofed a time or two. I have found, however, that if you do your research your posts will be well received by the scientific community at large - even if you are not a working scientist. For exammple, Per Ahlberg sent me a copy of his Nature article on Ichthyostega after reading my first post on the subject. So let me talk a little about my blogging philosophy. I consider one of my missions, as a science blogger, to be education. I try, whenever possible, to post items that demostrate not just what science is about, but how scientists learn about the world around them. For example, my recent post on the expansion of the universe. A second example, on how scientists can study the interactions of insects and plants in the past can be found here. To me, this is a really important issue. All to often I have encountered a basic misunderstanding about how science works - and here I'm not just talking about the scientific method (such as the difference between a fact and a theory or about what the word hypothesis means). Here I am referring to the "we can learn about it because we wern't there" criticism embraced by creationists.
Having said that, like other bloggers, I tend to blog about whatever interests me. So I treated you all to, for example, a long series on Kennewick and what can be learned from one skeleton.
Finally, I am not afraid to get a little silly or goofy:



Some have claimed this is a picture of Badtux at a recent party! It's really Opus - a picture I post whenever I feel silly - although the resemblance to Badtux is striking!

Expansion of the Universe

This is cool (yes I know, I should be packing). Physicist Richard Price was asked a simple question by a high school student:

"He asked me if, as space expands, we all get bigger too," says Price. "I knew the standard answer was 'no', but I couldn't explain why not. And when I consulted my colleagues, neither could they."

So he decided to investigate:

Since atoms are made up mostly of empty space, with electrons "orbiting" the nucleus at distances typically many hundreds of times its diameter, it seemed reasonable to ask whether the electrons would be dragged away from the nucleus by the stretching of space. Price decided to examine the simplest system, that of a hydrogen atom, with one negative electron orbiting a positive proton. He found if the force involved - electromagnetic in the case of atoms - binding the system together is stronger than a certain critical value, the system will be entirely unaffected by the cosmological expansion.

What does it all mean you ask:

"This means that the solar system - which is quite tightly bound by gravity - doesn't expand. Your desk doesn't expand. Your dog doesn't expand," says Price. "But clusters of galaxies, which are only loosely bound by gravity, will feel this effect."

Price also found that the atoms never experience just a little stretching - either they must totally ignore the expansion of the universe or they will be completely torn apart. "This all-or-nothing effect is a startling result," says Roy Maartens, a cosmologist at the University of Portsmouth in the UK. "This question has been knocking around since the 1930s, but nobody has found this before."

The moral of the story, to me, is that you should try to explain science to as many people as possible, because the questions they ask may lead you to some interesting research.

Actually there is a second moral of the story:

Andrew Jaffe, an astrophysicist at Imperial College London in the UK believes the effect becomes interesting in so-called "big rip" cosmologies in which the universe is not only expanding, but the expansion is accelerating.

"Price's calculation still holds in this case, but you start to see the opposite effect," says Jaffe. The expansion of the universe accelerates drastically. First it overpowers gravity, ripping apart solar systems, and next the electromagnetic forces are overwhelmed. "The planets are torn apart, and then you and me, and finally the atoms that make us up are destroyed," says Jaffe. "That's not a particularly fun way to end."

Now if we could only get a restauraunt at the end of the universe...

Biblical Curse Generator

Red State Rabble has a link to a biblical curse genorator. It's very amusing. I tried it and got:

Harken, O ye bull of Bashan, for you will be swallowed by a whale with excessively bad breath!

I wonder if it will have legs or if it will be one of those modern evoluted types with no legs!

Follow the link to Red State Rabble if you want to try.

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

Museums and the Creationist challange

Via The Panda's Thumb comes this interesting article on how museums are responding to challanges by creationists. I think it's kind of sad that museums have to devote their resources to this kind of thing.

Challenged by Creationists, Museums Answer Back

IBM Promotes Science and Math Education

Arr! Me fine beauties at IBM be sailing on a fair tack and close hauled they be! From the lubbers at CNN:

"Over a quarter-million math and science teachers are needed, and it's hard to tell where the pipeline is," said Stanley Litow, head of the IBM Foundation, the Armonk, New York-based company's community service wing. "That is like a ticking time bomb not just for technology companies, but for business and the U.S. economy."

While many companies encourage their employees to tutor schoolchildren or do other things to get involved in education, IBM believes it's the first to guide workers toward switching into a teaching career.

Avast ye dogs, there be more to the story:

The company expects older workers nearing retirement to be the most likely candidates, partly because they would have more financial wherewithal to take the pay cut that becoming a teacher likely would entail.

The workers would have to get approval from their managers to participate. If selected, the employees would be allowed to take a leave of absence from the company, which includes full benefits and up to half their salary, depending on length of service.

In addition, the employees could get up to $15,000 in tuition reimbursements and stipends while they seek teaching credentials and begin student-teaching.

From then on, the IBM people would become school employees -- the program will encourage them to work in public schools but they can go private if they wish -- and leave Big Blue's payroll.

But IBM plans to offer a mentoring program that would give its former workers guidance and teaching materials over the Internet.

For you scurvey dog's who speak nary a drop of lubber this means they be takin older pirates fit for nought but a trip to Davy Jone's locker and be retrainin so's they can teach all the new cabin lads and lasses so's they can enjoy the booty that comes with a career in science and math.

Yo Ho, me hearties this be a worthy thing they do, lift yer Rum cups high and salute them or ye be walking the planks for sure.

Pirate Movie Sunday

Since I can't do too much to celebrate National Talk Like a Pirate tomorrow (other than talking like a pirate) I am doing a little celebrating today by watching a bunch of pirate movies. Here are the movies I'm hoping to get through:

The Seahawk - not a bad Errol Flynn movie, though Captain Blood was better
The Black Swan - Tyrone Powers at his best
The Swashbuckler - Robert Shaw rocks
Pirates of The Carribean - Geoffrey Rush steals this movie
Princess Bride - Dread Pirate Roberts and all

Talk Like a Pirate Day is Tomorrow

And for those who lack the proper verbal skills or vocabulary here is a primer.

And remember, the Code is more like guidelines than actual rules...

Frog Fungus (Batrachochytrium dendrobatidis) Found in Britain

According to theBBC a deadly frog fungus native to North America has been found in wild populations of British frogs.



The fungus - Batrachochytrium dendrobatidis, pictured above - is believed to have been introduced into Britain via american species (Rana catesbeiana) pictured below.



From the BBC:

"This disease is a major cause of amphibian population declines and extinctions worldwide. So it's pretty bad news that it has been found in the wild in this country."

*snip*

The fungus was identified six years ago and is firmly established in parts of the Americas, Australia and Europe. The disease it causes, chytridiomycosis, appears to kill amphibians by damaging their sensitive skins, blocking the passage of air and moisture.

"I think there is great concern," said Dr Richard Griffiths, an amphibian specialist at the University of Kent in Canterbury.

"It will take more work to see if infected animals can be taken out of the wild, cleaned up and released. At the moment, people are concentrating on keeping [the disease] out."

The fungus can be spread via the water:

"The fungus has turned up in many captive collections of exotic amphibians. And it can spread by motile zoospores in water," he explained.

"So someone washing out their vivarium and pouring the water into the garden could inadvertently bring native species into contact with it."

Below is a diagram of the fungus life cycle.