Tangled Bank #86

Welcome to Fish Feet, host of the 86th Tangled Bank blog carnival!

The Scientific Process
• Kevin of The Other 95% discusses metrics of scientific advancement and their impact on progress.

• Sunil at Balancing Life gives readers invaluable advice on writing grant proposals.

• Christian of Med Journal Watch writes about the artificial settings of diet trials and the value of their findings.

Evolution
• Shalini at Scientia Natura debates the impact of a recent palaeoanthropological discovery on the theory of evolution?

• CAD of VWXYNot? describes how the progression of tumorigenesis mirrors the process of evolution by natural selection.

• Eric of The Primate Diaries discusses offspring abandonment in the ancient and natural world.

Ecology
• Jeremy at The Voltage Gate contributes a riveting article on the ecology of fear in Yellowstone National Park.

• Scott of Dammit Jim! I’m a biologist not a… posts a cool youtube video and explores the curious mating rituals of jumping spiders.

• Mike at 10,000 Birds explores the diversity of Waxwings.

Agriculture and Environment
• Matthew of Behavioral Ecology muses about how even parasite-resistant sheep avoid eating shit!

• Jeremy of Agricultural Biodiversity Weblog discusses variation in the glycaemic index of various crops.

• Emmett from The Natural Patriot shares his perspective on the writing and philosophy of author and environmentalist, Richard Louv.

• Martin of Aardvarchaeology reviews Alan Weisman’s book, the The World Without Us

Human Biology, Diet and Medicine
• Paddy of Swedish Extravaganza writes a balanced discussion on the ethical aspects of vegetarianism.

• Cathy of Lab Cat talks about pre and probiotics.

• GrrlScientist of Living the Scientific Life talks about a bone hormone, which is linked to obesity and Type 2 Diabetes.

• Alvaro of Sharp Brains has submitted a podcast interview with neuropsychologist Dr. Elkhonon Goldberg who talks about brain improvement research.

• FitBuff of Total Mind and Body Fitness reports on a recent study which examines the unconscious signals we use to find Mr. or Mrs. Right!

Genetics
• Hsien of Eye on DNA imagines the possibility of genome sequencing being available to the public.

• Lev at Ouroboros writes an article about protein abundance in long-lived worm mutants.

• Jeremy at Another Blasted Weblog discusses restriction endonucleases, the molecular scissors that allow biologists to cut DNA.

I’m glad to have hosted the carnival and have enjoyed reading all of the great submissions! Two weeks from now on August 29, visit Tangled Bank again at Balancing Life.

Long Absence

Sorry I have been absent for so long. Life has been getting pretty busy, with grad school and a new baby on the way. But I hope to be back to blogging (at least once a week, if not more often) and Tangled Bank has given me the kick in the pants I need to get back to it! Visit us on August 15 to check Tangled Bank #86!

Monster Pig Debuked!

Apparently this 'Monster Pig' shot by an 11-year old boy in rural Alabama is a fake (big surprise) Check out the full story of photo manipulation here.

The cat with 26 toes

Thanks to Janine for sending in this story about a VERY polydactyl cat. Last month I wrote about the evolution of five fingers and toes and the constraints on this arrangement. Though loss of digits is not an uncommon evolutionary change, gaining digits is very rare. It is a phenomenon seen in polydacyl cats; however, I don't think anyone understands why cats are able to increase the number of their digits without 'repercussions' to the rest of their patterning. Anyway, click here to read about the polydactyl cat who has 26 fingers and toes!

Cretaion Museum reveals Adam's sordid past

I took a long weekend so I guess this story is a few days old but I had to rely it because it is so funny! Thanks to Hank Campbell who organizes Scientific Blogging for sending it along.

The Creation Museum of Petersburg, Kansas has been wrought with criticism since before it even opened, but most recently, they have been embroiled in a ‘moral scandal’ by an employ hired to tell the story of the fall of man.

A variety of actors were hired to play out scenes from the bible and the man chosen to play God’s golden boy, Adam, has now been revealed to have a ‘sordid’ history. Eric Linden, owns a website called Bedroom Acrobat, on which he is (allegedly -I cannot say this myself as the site has apparently crashed due to traffic overload) pictured. Linden, a graphic designer, model and actor purchased the domain name for this site which mostly sells clothing.

Museum administrators were swift in removing the 40-second video in which he appeared from the display. “We are currently investigating the veracity of these serious claims of his participation in projects that don’t align with the biblical standards and moral code upon which the ministry was founded,” Answers for Genesis spokesman Mark Looy said in an electronic statement.

T. rex didn't turn on a dime

Scientists now say that the "Terror of the Cretaceous" may not have been that bad after all. A new study indicates that T. rex had a hard time getting its jaws into fast, agile prey.

An American team of palaeontologists have used detailed computer models to work out the weight of a typical Tyrannosaurus and determine how it ran and turned. The results indicate a 6 to 8-tonne T. rex was unlikely to have topped 40km/h (25mph) and would have taken a few seconds to swivel 45 degrees.

The computer model estimated that a high center of mass and large inertia would have had been responsible for the slow movement and that T. rex could have been out-maneuvered by agile prey.

Dr Paul Barrett, of London's Natural History Museum, commented, "This is another finding that undermines the kind of idea of T. rex as a super-predator. But it has this huge mouth filled with 60-odd, 30cm-long teeth, so it was still a formidable animal."

The research was published in the Journal of Theoretical Biology.

The Starbucker Meme!

I have been Memed from PetLvr, who asks:

1) How full is your glass?
2) What kind of glass is it?
3) What’s in the glass?
4) Reasons for #1, #2, and #3

I admit, I am a slave to the large capitalist evil known as Starbucks. Did you know they actually have a Starbucks inside the Forbidden City in Beijing?!?!?

Well my glass is always full on account of me buying venti lattes which take me a while to drink. I get gingerbread lattes, a seasonal drink which Starbucks typically only does around Christmas but the cafe I go to still has ingredients left (Thank God for preservatives!)

If you are a Starbucks lover, consider yourself memed and pass it on!

(Re)burying Dinosaur Tracks in Pinon Canyon, Colorado

Dustin on Dysfunctional Analysis posted today about the Pinon Canyon development in Colorado.

The Pinon Canyon training ground is a military facility that will soon be extended, engulfing several townships and ranches. It is also the largest dinosaur track site in North America and the site contains ruins of the Dolores Mission, an old graveyard, and Native American petroglyphs. The historical and scientific value of the canyon is incredible.

Around The World Today

To many weird stories to blog about today so here are some links:

Poland inquiry to probe 'gay' teletubbies
Poland's conservative government sees the teletubbies as homosexual propaganda on the small screen, and is taking aim at Tinky Winky and his friends. Ewa Sowinska, government-appointed children rights watchdog, told a local magazine published on Monday she was concerned the popular BBC children's show promoted homosexuality.

Bonnethead Sharks and Komodo Dragons reproduce without sex
Sex is not necessary for all members of the animal kingdom. Of course it has its advantages, primarily, combining genetic material adds to the diversity of a species and makes it more ‘hardy’. But in vertebrates, organisms that are considered ‘more complex’ (ie. fish, amphibians, reptiles, birds and mammals) asexual reproductions is extremely rare and is thought to be limited because of the complexity of vertebrate genetics and body plans.

New Zealand cows produce skimmed milk
Experts at a biotechnology company in New Zealand have discovered that some cows have a gene giving them a natural ability to produce skimmed milk. The finding could be used to develop a dairy herd that produces low-fat milk. A cow with the "skimmed milk" gene was identified in 2001, and the team have since been able to breed calves that also produce the low-fat variety.

Outcry over TV kidney competition
The show comes from Big Brother creators Endemol. A Dutch TV station says it will go ahead with a programme in which a terminally ill woman selects one of three patients to receive her kidneys. Political parties have called for The Big Donor Show to be scrapped, but broadcaster BNN says it will highlight the country's shortage of organ donors.

Spiders on Drugs: Part 2

Some of you may recall the 'Hinterland Who's Who' parody that I posted back in March about spiders on drugs. Well Shelley Batts of Retrospectacle actually found an article on the effects of psychoactive drugs on the web-building activities of spiders published in NASA Tech Brief. Click on the image below to enlarge it and see the crazy webs stoned spiders make.

And in case you missed the HWW parody, here it is:

Snake explodes after swallowing alligator

Thanks to Janine for pointing out this story of a python which burst open after gobbling up a Florida gator.

The strange scene was found by park rangers in the Everglades National Park. The Burmese python is likely an escaped pet or perhaps a descendant of one. In recent years many guilt-ridden owners release their exotic pets into the hot and wet swampy environment because they are no longer able to take care of them and do not want them put down.

Because pythons are not natural to the environment, the rangers suspect that they challenge the alligators' position as apex predators in the food chain. Frank Mazzotti, a University of Florida wildlife professor, says "Encounters like that are almost never seen in the wild. They were probably evenly matched in size. If the python got a good grip on the alligator before the alligator got a good grip on him, he could win." He also suggested that the alligator may have clawed at the python's stomach, leading it to burst.

This is not the first encounter between the two giant reptiles, at least three other similar incidents have been recorded in the past.

The picture (click to enlarge) depicts a 2m long alligator partially swallowed by 4m long python, whose belly ruptured during the process. The victim's tail and hindlimbs are protruding from the predator’s burst abdomen. The head of the python was missing, perhaps due to scavenging by other wildlife.

Fossil tracks suggest dinosaurs could swim

Ancient footprints have provided compelling evidence that some dinosaurs were able to swim. The 15m (50ft) trackway was discovered in the Cameros Basin in Spain, which, 125 million years ago, in the Early Cretaceous was a vast lake.

The unusual-shaped prints suggest the animal clawed at sediment on the lake bottom as it swam in about 3m (10ft) of water. Though it has been suggested that large sauropods occasionally waded through shallow waters, it is thought that these tracks were left by a large, bipedal, carnivorous dinosaur that was not wading, but rather was using the water to support its body.

Dr Loic Costeur, a palaeontologist at the University of Nantes, France, says "The Cameros Basin has thousands of walking footprints from diverse dinosaur fauna, but when we saw these it was obvious straightaway that this was a swimming dinosaur."

The underwater trackway is well-preserved in sandstone and is made up of 12 consecutive prints each consisting of two to three scratch marks. Ripple marks around the track suggest the dinosaur was swimming against a current, attempting to keep a straight path. Dr Costeur also stated that "The dinosaur swam with alternating movements of the two hind limbs: a pelvic paddle swimming motion."

I guess it was a sort of a prehistoric doggie paddle:)

Lion vs. Buffalo vs. Croc

Check out this amazing video: a lionesses snags a water buffalo calf but ends up having to fight over it when a hungry croc decides he wants his piece.

A story about a polydactyl cat

Well, I have caught a bad cold and been stuck in bed for almost a week. So since I haven't been able to blog much, I thought I would take advantage of Benj Arriola's comment about a polydactyl cat he had when he was young, left in response to my blog about the evolution of five fingers and toes. Benj Arriola writes Global Warming Awareness and off-handedly mentioned that his comment was good enough as a blog post, I agree so I hope you don’t mind me stealing your writing, Benj :)

Benj Arriola writes…
I'm back and was searching about the ostrich people, and found it on Wikipedia. And in my search for photos, I also found this site with a page on polydactyl cats. I remember my own cat having an extra useless "thumb." Useless because they were like dead and was just hanging there. But I think that cat was a real genetic disorder in many ways, since one paw had an extra "thumb." The other paw had two nails on one digit. The cat was pure white that his eyes were very noticeable. One was blue and the other was green.

But just a background on it... when it was still a kitten, it was a stray kitten that took a ride in our car, that seemed to climb under the car and ended it's way near an area near the car battery and was securely there until we got home from a bowling trip that was just about 1 kilometer away. He was kitten although he was big enough not to depend on his mother. For me he was the best cat I had. I had cats since 1978 up to today.

When ever we go back to the bowling alley we kept going to... I noticed by the side of the building, is a big trash can and some trash dumps near it where several stay cats go to. I am not surprised if my cat's mother was probably one of them feeding on all these trash while she was pregnant.

WOW! Is this the longest comment I made in history? Hahaha. This is good enough as a blog post. Haha. Well I guess there is no other place to share it but here.

Sarda sarda

This morning my friend John Orcutt sent me this great picture of a boat he and his Dad spotted while wine-touring along the Oregon coast.

Seeing my name always catches my attention because it is so unusual (on account of my Dad misspelling it on my birth certificate). However the boat is probably not named after me but rather Sarda sarda, a species of fish that is commonly called the Atlantic Bonito. It is my understanding that this fish received its name from the island of Sardinia around which it was caught but these days it is more commonly caught by commercial fishermen around New York's coast.

Sarda sarda is often used in cuisine, especially in Japanese food. It has a cosmopolitan distribution though the globe and to my knowledge is not currently threatened or endangered by overfishing.

Complete Book of Life from Aardvarks to Zorilla

The Encyclopedia of Life project will detail 1.8 million known plant and animal species in the format of an online archive. Each species will have its own page with descriptions, photographs, videos, and maps, compiled by experts.

It is hoped that the $100m USD (£50m GBP) archive will be complete in 10 years and that in addition to an educational tool, the archive will have value for conservation efforts.

The project will begin by harvesting information from existing databases, such as FishBase, which contains details of 29,900 extant fish species. Data input will begin with animals, then plants, fungi and microbes last. It is not clear when fossil species will be added.

Encyclopedia of Life began development January 2006 and is reminiscent of other ventures such as the Tree of Life, Catalogue of Life and Consortium for the Barcode of Life. The last was launched in 2005 and is attempting to identify all species through unique genetic markers (called ‘barcodes’) found in the mitochondria of cells. This project has so far identified more than 27,000 species.

Proponents claim the Encyclopedia of Life will be much more through and flexible in regards to structure compared to its predecessors and will include dynamic features such as live searches. Fast internet technology has meant that such a large-scale endeavor has only recently become possible.

It is unknown how many species currently live on our planet but estimate range form a modest 2 million to 100 million.

Life on Land: The evolution of five fingers and toes

Well it didn’t take long for avid readers to spot the oddity in Friday’s posted picture of the early tetrapod, Acanthostega. This strange animal did not have the ‘usual’ number of digits, instead it had eight. Having more than five fingers or toes is called polydactyly and is a rare condition.

Few examples of polydactyly occur in the animal kingdom today, the panda’s thumb though, is one classic example. The panda has five digits on its paw plus an opposable 'thumb' but this thumb is not a sixth digit like the others, but actually an unusual outgrowth of a wrist bone. Thus even the panda’s thumb is not truly an example of more than five digits.

So what about Acanthostega and his buddies? The Late Devonian was a busy time, plant life was diversifying and insect life was gaining ground on land. Tetrapods, were making their first steps on to land and living semi-aquatic lifestyles about 375 million years ago. These animals had many characteristics advantageous to aquatic life, such as streamlined bodies, webbed feet and tail fins. But they also had weight-bearing limbs with which they could lift themselves out of the water. Acanthostega had eight digits on its front and hind limbs and two other early tetrapods, Ichthyostega and Tulerpeton, also had more than five digits.

So how could these animals have had such a wide variety of limb structures when all of their descendants seem to have a variation upon the five digit structure? It is thought that pentadactyly evolved in an animal that was ancestral to all present day tetrapods (amphibians, reptiles, birds and mammals) and that this event event happened 340 million years ago in the Lower Carboniferous (about 35 million years after the first tetrapods evolved).

To be honest, we don#t understand how these animals could have been so experimental while their descendants were so conventional. And why 5 anyway? No one knows. And we have no examples to examine. There are few animals who have extra digits. The most common is the novelty polydactyl cat, but this species is the result of selective breeding of animals with a genetic anomaly.

In a general sense, we know that it easier to ‘lose’ a trait then to gain it, hence the large number of animals who have reduced digits. But the striking lack of polydactyl examples in the long history of tetrapods since the Devonian implies there may be an evolutionary constraint at work. For example, pleiotropy is the multiple effects of genes on more than one physical characteristic. Hand-Foot-Genital syndrome illustrates such a condition. This rare disorder malforms limbs and the urinary system because the same defective genes pattern both systems. So perhaps the constraint on tetrapod limb structure is part of a greater pattern.

Sorry I have been absent....

Sorry I have taken so long to add my Palaeozoic post but it will be up sometime tomorrow. Thanks for your enthusiastic responses to my Friday post.

BTW I have been posting some of my old posts on the Scientific Blogging website, which you should definitely check out. One of my posts, unfortunately not one of my more intelligent pieces, on T. rex eating coconuts was posted to Digg and racked up a whopping 35,000 hits. Fame and fortune may yet be mine, I just hope it doesn't go to my head!

My Research into Palaeozoic Communities

Yesterday I began writing a little bit about what I do, so if you want to catch up check out Part 1. My goal while I’m at Bristol is to compile a community-level study of tetrapod diversity and to compare it to Mike Benton’s global pattern of tetrapod diversity. I hope that my research will aid our understanding of some ‘big’ questions such as:
1) Is global diversity a reasonable measure of true biodiversity?
2) How did tetrapods diversify? Did they conquer new niches or expand into new habitats?
3) How did mass extinction events effect community structure?

But even more interestingly, this study has an application to our present situation. We are witnessing a biodiversity crisis right now and it is not clear whether it is simply a part of Earth’s natural cycle or massive impact by human presence (though to be honest I lean towards the latter). Studying past communities helps us understand more about our present situation.

The first part of my research covered the Palaeozoic, from the origin of tetrapods about 375 million years ago to about 250 million years ago. At this time there were no birds, no mammals and no dinosaurs. The landscape was dominated by large amphibians and the first reptiles. Amphibians at the time were not like frogs but more like very large salamanders, and the largest of these superficially resembled crocodiles (For example, see my post of Parotosuchus). This period of time ended with the largest mass extinction event, in Earth’s history, the Permo-Triassic event 251 million years ago, when over 90% of Earth’s species went extinct.

During the 125 million years though, a lot of changes took place. I realize this post has gotten long already so I will continue more next week starting with a look at the first tetrapods, who possessed a strange oddity that we rarely see today and one that has changed our understanding of the evolution of life on land. Can you spot this oddity in the image to the right?

Click to view a larger image at http://universe-review.ca/I10-72-Acanthostega.jpg

A little bit about my job…

I’m a palaeontologist at the University of Bristol, currently in the (yikes!) third year of my PhD. But what exactly DO I DO?!?!? Well I don’t fit into the stereotypes of Jurassic Park and Ross from Friends. I don’t spend most of my days in the hot Mongolian desert carefully brushing sand away to reveal amazing and perfectly intact dinosaur skeletons. Sometimes I wish I did though, because to be honest I spend most of my time in the office, counting.

Yes, counting, This is what I do, count animals form different parts of Earths’ past and from all over the world. But to what end? I’m a ‘Macroevolutionist’ so I like to think about the ‘Big picture’, which sounds grand but to be honest can be a bit tedious because big picture stuff often means gathering lots of data, compiling it, and producing graphs. To add a little excitement to my day sometimes I add colour to my graphs and occasionally throw in a pie chart just to be a little crazy.

Seriously though, my supervisor, Mike Benton, has spent a lot of his career counting and has come up with some pretty intriguing insights about biodiversity and Earth’s past. One of his biggest contributions has been the this graph, which is a count of the all of the tetrapods (amphibians, reptiles, mammals and birds) that we have found in the fossil record, from their origin, almost 400 million years ago to the present. As you can see the diversity of tetrapods has risen almost exponentially since their origin to the present day, punctuated occasionally by a mass extinction event, such as the Permo-Triassic event 250 million years ago, when over 90% of Earth’s species went extinct.

But the trouble with this graph is that counting the number of fossils we have from different times is Earth’s history reveals a similar pattern, so it is difficult to say whether Mike’s graph is a true reflection of diversity or simply an artifact of the rock record. This is where my research comes in. I am studying the diversity within communities through time, a study that is independent of these artifacts so I will see if community diversity is similar to global diversity and what the implications are. If you’re still with me and haven’t fallen asleep, tomorrow I will discuss some of early research, including (just for you Will:), Romer’s Gap.