Eggs Past and Eggs Future

The picture above is a shot of a Victorian-era museum collection of wild bird eggs. These kinds of fantastic collections began around the time of Darwin, with egg collection an outgrowth of egg collections gathered for scientific purposes and a spontaneous outgrowth of curiosity about the diversity of the natural world coupled with the kind of relative (and conspicuous) wealth that allows people to travel to collect, buy and display curiosities that otherwise have no useful and practical purpose.

Bird egg collecting proved to be such a fad that collection of rare bird eggs threatened to tip certain rare birds over the abyss into extinction. In 1954, the Wild Birds Protection Act in the U.K. made it illegal to posses or own any wild birds' eggs taken since that time, and today it is illegal to sell any wild bird's egg, irrespective of their age -- a fact that is now true in the U.S. as well.

Ironically, old bird egg collections are an important resource for scientists studying bird biology, enabling them to track the rise of pesticides and other contaminants in the food chain.




The eggs, above, are a couple of odd ones I had around the house.

The dark one is an emu, the largest eggs is an ostrich, and the other two are chicken eggs that I had for breakfast.

I include the chickens eggs to show the scale of the other two, but also to show the diversity of what eggs can look like. Egg identification, without benefit of a nest or provenance, can be pretty hard, as bird eggs can change shape to some extent. Coloration and markings may also shift from bird to bird as well. Egg identification is an in-egg-zact science, especially where speciation is not complete (a surprisingly large number of birds) and the number of look-alike eggs are quite numbing.

Another small thought: We have pushed a lot of birds over the edge to extinction and near-extinction, but I am always struck by the fact that we never give credit to the fact that a lot of species (or what we would call species if they were wild) are now being created by man.

Chickens alone present a startling array of expressed diversity, to say nothing of cattle, roses, corn, broccoli, etc. We are already creating new species of birds (falcon and parrot hybrids are examples) and fish (hybrid trout, salmon, pan fish, etc.). to say nothing of the many odd things being done with recombinant DNA to make animals and plants grow larger, be more resistant to disease, and ship better.

We stand in the door of one of the largest booms in species creation ever, and yet when was the last time anyone gave that idea a nod? And yet, take a look at the two chicken eggs, pictured above. Would any birder claim these eggs were from the same species?

The Beast of Exmoor and Other Nonsense

A repost from February 2009

Stories of feral "beasts" lurking in the darkness of the English countryside have been around for hundred of years, and were already old when Sir Arthur Conan Doyle used such a tale as the basis of The Hound of the Baskervilles.

The stories persist, of course.

Here are a few contemporary descriptions of various U.K. beasties:

• Beast of Muchty: "I was travelling to my work at 04:30 when a cat the size of a Lurcher, jet black, small head, very slim with a long tail ran in front of my car (about fifty yards). The whole incident was over in 2 seconds ... "
• Beast of Bont: "The main evidence for the existence of these sharp-clawed, but mysterious stalkers has been the death toll among vulnerable herds of sheep."
• Beast of Barford: "It is twice the size of a dog print and clearly shows three huge claws and a large pad at the back. Wildlife experts believe the print is the most conclusive evidence yet that big cats are roaming Warwickshire."
• The Beast of Gloucester and The Black Beast of Inkeberrow: "A 'huge black beast' ran in front of Ray Lock's car on the other side of the river near Lydney... one evening near Monmouth where it was described as 'jet black and about the size of a large dog.'"
• Beast of Burford: "A £5,000 reward has been offered for the capture of a 'big cat' which has been terrorising a farming community ..... Pc Ray Hamilton, wildlife crime officer at Thames Valley Police, admitted there had been several sightings - but said this was not unusual. 'We've had sightings of everything you could imagine - pink flamingos, lions, dingos, wolves and even a giant ant-eater in Pangbourne.'"

The human desire to create imaginary "beasts" seems to have some correlation to the loss of large predators and true wilderness.

With the extinction of the bear and the wolf, the U.K. has lost all large predators and now has to suffice with two rather unimpressive meso-predators, the fox (average weight 15 pounds and living almost entirely off of mice) and the badger (average weight around 25 to 30 pounds and living almost entirely off of worms, beetle grubs, and small bulbs).

So what are these large feral "beasts" seen in the English countryside, and why is it that they are never actually found?

The short answer is that these "beasts" are nothing more than large escaped lurchers (coursing dog crosses) that have taken to livestock-worrying. As an article on the Beast of Osset notes:

"On a parkland estate in rural Yorkshire a poacher's lurcher (a fast greyhound-like hunting dog) was at large for six months but was sighted only once during that period. The gamekeepers knew it was there because they found the roe deer that it had killed, but it took a concerted effort with volunteers to flush it out of the wood."

In fact, sheep worrying is a serious problem in the U.K., and while any dog can end up attacking sheep, it is the larger dogs such as Lurchers and Bandogs (mastiff crosses) that do the damage that lead some to think a large cat or lion is loose in the English countryside.

Sheep worrying by lurcher.

In fact, a lurcher really does look like a large cat if seen in the dark or fog, and especially if it is seen only briefly from a moving car, as most "big cat" sightings are.

A Bandog (what the Hound of the Baskervilles was) really does look like a lion if seen under the same circumstances.

What is amazing about the "big cat" stories in the U.K., however, is how easy they are disprove, and yet how utterly resistant people are to having their bubbles burst.

Take the issue of "big cat footprints". Most of these footprints are clearly large dog prints. How can we be sure? Simple -- all the footprints show claw marks. All the large cats, except the cheetah, however, walk with retracted claws, otherwise they would quickly dull

This foot print of the "Beast of Barford"
is held up by a young hopeful.

The other issue has to do with hounds -- the U.K. is crawling with fox packs, and yet none has ever chased and cornered a large cat other than the now very rare native Scottish Wildcat, which is not much larger than a tabby.

You can be sure that if the big cats were out there, British fox hounds would have found them by now! In the U.S., small teams of less experienced hounds manage to track down marauding farm-country cougars in only a few hours time.

Finally, we come to the issue of rub strips -- bits of carpet and tacks impregnated with a mixture of catnip and beaver castoreum -- that have failed to turn up any positive large cat hits in the U.K.

Wherever these rub strips are used -- whether in North America, South American, Europe, Africa, or Asia -- they are quickly found and rubbed against by large cats and other predators.

A DNA analysis of fur caught on the hooks of the carpet tacks can not only identify what species of animal has left it behind, it can identify what specific animal has come by in the night.

Rub strips are so accurate they are now routinely used to survey population densities of such elusive large cats as leopard, lynx, cougar, and jaguar, as well as badger, wolverine, bear, wolf, coyote and bobcat.

Of course, "Beast of" stories are not unique to the U.K.

Here in the United States we have Sasquatch and some local tales of little green men, swamp creatures, and even a werewolf or two (all delivered with a wink to small children).

In truth, however, we have far fewer fantasy "Beast" stories than the U.K. for a simple reason: we have more real top end predators.

In states like Minnesota, Wyoming, Idaho, Montana and North Carolina we really do have wolves prowling the remote sections.

In Florida, Louisiana and South Carolina we really do have 12 foot lizards slithering out of drainage ditches and quite capable of eating an old lady alive.

Mountain lions really do prowl the remote sections of Idaho, Wyoming, Montana, New Mexico, Colorado and even Texas, and are now being found as far east as Iowa.

Black bears number well over 400,000 in the lower 48 states, and there are over 100,000 more in Alaska.

Bobcats are everywhere, as are coyotes -- the later so common that there are bounties on them, including in my home state of Virginia.

No one living in a large America city today lives more than two hours away from a major top-end predator of some kind.

This is a glorious thing, and something we should count among our greatest national treasures.

But a "Beast of Bondwynn?" No, we don't have that.

In a world in which top-end predators are still common, there is no reason to invent ghost stories.

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The Kennel Club's Scheme

The Kennel Club has a scheme, and they want you to know about it.

I found out about this scheme while cruising The U.K. Kennel Club web site and clicking on the ad/link for their "Puppy Sales Register."

Here's what it says:

"Buyers of puppies from Accredited Breeders will gain the assurance that the breeder has undertaken to follow basic good practice as laid out by the scheme."

The scheme? Now there's truth in advertising!

So what is "the scheme"?

Well, let's start with what it is NOT. While the above paragraph offers "assurance," be forewarned that there is no insurance that a Kennel Club dog will not be an expensive genetic nightmare for you and your family.

As this bold faced warning on The Kennel Club web site notes:

"The Kennel Club makes no warranty as to the quality or fitness of any puppies offered for sale and can accept no responsibility for any transaction between purchaser and vendor arising from publication of the listing."

So "the scheme" is not an assurance of quality. They make no warranty and accept no responsibility. Good luck, and you're on your own. Don't let us know if it doesn't work out.

So then, what is "the scheme" all about?

Well, apparently, "the scheme" is all about overcoming the information people are hearing about the problems associated with Kennel Club dogs. As The Kennel Club web site notes:

"Some canine commentators have written and filmed recently with regard to the disadvantages of pedigree dog ownership, including expense and the possible health problems that owners may inherit when they take on a pedigree puppy."

Good God! These people have passed on information.

And they have even stooped to FILMING.

The bastards! Come on people, who are you going to believe, the Kennel Club, or your lying eyes?

Never mind that the problems associated with inbreeding are so well-known that they are warned about in the Bible (see Deuteronomy 27:22).

Never mind that genetic problems foisted on dogs by the Kennel Club's closed registry system are so legion they serve as a genetic gold mine for dysfunction and disease. As William Saletan noted in the Slate Magazine of Dec. 14, 2005:

"The reason we targeted the dog genome for decoding is that it's useful for genetic research. The reason it's useful for genetic research is that dogs are neatly divided into breeds, each of which is plagued by specific diseases. And the reason dogs are divided into diseased breeds is that we made them that way. Dogs are the world's longest self-serving, ecologically reckless genetic experiment, perpetrated by the world's first genetically engineering species: us. . . .

"In the course of engineering dogs to look, feel, and act as we wanted, we ruined millions of them. We gave them legs so short they couldn't run, noses so flat they couldn't breathe, tempers so hostile they couldn't function in society. Even our best intentions backfired. Nature invented sexual reproduction to diversify gene pools and dilute bad variants. By forcing dogs into incest (which we ban among humans, in part for biological reasons), we defied nature. We concentrated each bad gene in a breed, magnifying its damage: epilepsy for springer spaniels, diabetes for Samoyeds, bone cancer for Rottweilers. That's why the dog genome is so nifty: We can find disease genes just by comparing one breed's DNA to another's."

Does The Kennel Club admit they have anything to do with the genetic problems within their own closed registry system?

Of course not! Instead, they say:

"Many breeds benefit from health screening schemes ... There is huge potential for wiping out diseases in pedigree dogs, and within a matter of a few generations of rigorous DNA testing and selection of appropriate breeding mates, faulty genes can be removed from the breed's gene pool. This benefit simply does not exist in the cross breed or mongrel population, primarily due to the fact that the dog’s parentage is unknown, while it is a myth that these types are healthier than their pedigree cousins and do not suffer from inherited problems."

This is, of course, complete nonsense, on a par with the Vietnam-era mantra, "We must burn down the village to save it." In fact, no one has ever said that non-pedigree dogs do not have genetic disorders. What is being said is that non-pedigree dogs are far less likely to have specific genetic disorders, and that the chance of getting a specific (and often quite serious) genetic problem is directly linked to the narrowness of a gene pool.

And so what is the Kennel Club's answer to the very real problems associated with having too narrow a gene pool in the world of show-bred dogs?

It's narrowing the gene pool even further through a program of expensive genetic testing followed by a program of culling, exclusion and sterlization.

Their genius idea is that if they just keep cutting away at the rotten wood, they'll eventually get a solid boat.

Or not. Maybe they'll just end up in the water.

You see, the problem is not a handful of "bad dogs" with "defective" genes; it's the closed registry system itself. No mattter how "good" a gene pool is, if it is very narrow and inbreeding, it will produce defective stock, and culling an already narrow gene pool will only exacerbate the underlying problem. You may get rid of one problem, such as catacts, by culling a narrow gene pool, but another defect will soon crop up due to the doubling down of the invisible recessive genetic load. An eye disease may be scrubbed out, but a liver disease will crop up. Keep testing and culling, and a breed's genetic base will get narrower and narrower, and more problems (albeit different ones) will pop up and express themselves in an increasingly-inbred population of animals.

Or to put it simply: There is a reason that Mother Nature outcrosses animals, and there is a reason the Law of the Land affirmatively prevents you from marrying your sister, and there is a reason that Zoo's all over the world are shipping animals from one country and continent to another in order to increase genetic variability.

But of course, the Kennel Club does not want you to think clearly on this matter, do they?

Above all, they do not want you to consider that specific genetic disorders are being bred for in Kennel Club dogs.

• Ignore the Dachshund, the Basset Hound and the Skye Terrier, which suffer from achondroplasia (dwarfism) which is associated with heart, back and patella problems.
  
  
• Ignore the English Bull dog, the Lhaso Apso, the Pekingese, the French Bulldog, the Pug, the Boston Terrier, and the Cavalier King Charles Spaniel which suffer from brachycephalic syndrome and have such difficulty breathing that they often have sudden deaths which are written off as "heart attacks."



• Ignore the dogs bred for merle and piebald coats which are often deaf -- dogs like Dalmatians and Harlequin Great Danes.



• Ignore dogs like the Boston terrier and the Bulldog whose heads are now so large they must be born Caesarean-section.
  

How is the Kennel Club going to breed out these genetic problems when in most cases these genetic problems are written into the Kennel Club standards for these dogs?

The Kennel Club does not want you to think about that.

Nor do they want you to focus too much attention on all the breeds that are wracked by hip dysplasia, skin diseases, cataracts, liver failure, von Willebrand’s Disease, and the rest.

Never mind that there is now a veritable online catalog of breed-specific diseases in which you can "pick a breed, any breed".

Above all, gloss over that little disclaimer in which The Kennel Club specifically warns you that buying a dog from a kennel that is enrolled in their "Puppy Sales Register" does not ensure that you will get a healthy dog.

Instead, focus on "the scheme."

So what is "the scheme"? Why should anyone buy a Kennel Club dog? Well, to their credit, they are pretty straight up about it:

"[Buying a Kennel Club registered dogs] ensures that money is being put back into the canine world and enables the Kennel Club to run many schemes for the good of dogs and also be the voice for dogs on behalf of all their registered owners."

In other words, you should buy a Kennel Club dog so that the Kennel Club can perpetuate itself and the closed registry system that is wrecking dogs.

That's the scheme! And you are being invited to participate.

Oh, and good news -- the Pug has "Gone Top 20" thanks to rising breed popularity.

Never mind the atopy, the Brachycephalic syndrome, or the Demodicosis.

Let's not mention Entropion, Exposure keratopathy syndrome, Fold dermatitis, Hemivertebra, Pug encephalitis, or Sick sinus syndrome.

The slightly undershot jaw is supposed to be how they look.

And the snorting? That's normal too.

Woo-hoo, the Pug has gone Top 20. This is a dog that's part of "The Scheme!"

________________

• To read more, see: Inbred Thinking on this blog
  

Cats Came from Iraq 100,000 Years ago

A look at mitochondrial DNA suggests that cats orinated in Iraq and other parts of the fertile crescent and not in Africa, Europe or North Africa as others have suggested, and that domestication began perhaps 100,000 years ago. A cat is a domesticated animal? Good to know, as most of the ones I know sure deny it. >> For more information.

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Coffee and Provocation

More Pet Food Recalls:
The massive recall continues, with more pet food brands being added and melamine-tainted corn and rice gluten now added to the list, along with tainted wheat gluten. Corn and rice gluten is often labeled "corn protein," or "rice protein" on dog food labels. Up to now, the concern had just been about tainted wheat gluten. It turns out that melamine may have been deliberately added to pet food stocks in China in order to boost their protein content during testing. For the record, there is no reason at all to think these poisons did not make it into the U.S. food supply, so if you are a vegan that eats seitan, you might reconsider your menu -- at least for a few weeks. See Google News for more information -- there are a million links out there.

FDA is the Problem, Not the SolutionCheck out what the FDA did when dogs started dropping over dead from Proheart 6, an injected drug to prevent heartworm. Hint: they did exactly what Wyeth told them to do and all-but-fired the FDA researcher who reported the problem. Talk about a captive agency!

Canine PerversionNow you can let your dog gets its kink on with this new canine sex toy/doll. And yes, apparently it's real. God help us all.

A Dubious DNA Test:
If you simply have to know what kind of dog might be in the mix of your mutt, there's a company that claims to do that. On the other hand, if you send me $50 and a picture of your dog, I'm pretty sure I can do just as good a job.
Pennsylvania Foxing Stories:
Pete Bassani has recently published a small (85 pg.) soft cover book called "Memories of a Fox Huntin' Terrierman." Each chapter is about driving a fox, mainly grays, in the mountains of New Jersey and Pennsylvania. The book is available from Pete at RR #1, PO Box 479, Hawley, Pa. 18428, for $17.50, postage included. Teddy Moritz says it's a good history of pre-Jack Russell terriers in the eastern U.S.

Will the Energy Crisis Bring Back the Great Plains?
It turns out that native prairie grasses are more effecient at producing ethanol than corn. It's a little early to tell if this might lead to further expansion of the Conservation Reserve Program and a turn around in grass nesting birds, but it's a glimmer of something positive in the middle of a $3-a-gallon world.

Working Pets Store:
An online store in Ohio called WorkingPets.com sells the new Deben locators, so it's not just the JRTCA anymore. Check out both stores and then join the JRTCA for all the reason given here. See below for an example.

Pennsylvania Scraps Poorly Written Law:
Pennsylvania has scrapped regulations that would have made it much more expensive (and perhaps impossible) to breed and raise hounds and hunting dogs in the state. A wide coalition of hunting dog groups, including the Jack Russell Terrier Club of America, helped send the law packing.

Cloned Dog Not a Fake

A Korean science company has run tests on the dog that Korean scientists claimed they had cloned and they say the dog is indeed the result of a cloning process. The Korean scientists tnat made the claim, HwangWoo-suk, is under fire for fabricating virtually all of his embryonic stem cell research. The Korean institute HumanPass ran tests and determined that Snuppy is the world's first cloned dog. It said DNA fingerprint tests showed cells from Snuppy matched those of its cell donor, an Afghan hound named Thai.

FrankenFido

William Saletan, one of Slate's national correspondents, wrote the piece below, which I hope folks will circulate widely as it may get people to thinking about where closed dog registries lead -- concentrated genetic defects without hope of outcross.

I suppose the breed clubs will have their own spin on this: "show ring breeders help cure cancer." And of course, it will be true, though not the whole story by any measure. . . .

By William Saletan, Slate Magagine, Dec. 14, 2005


Dogs: Made to order

Have you heard the latest news? We've decoded the DNA of dogs. Here's how the media-approved version of the story goes: We're showing our love for "man's best friend" by discovering and treating the genetic causes of his ailments. In return, we'll learn to treat the same ailments in ourselves.

It's a heartwarming story, but it's a fraud. The reason we targeted the dog genome for decoding is that it's useful for genetic research. The reason it's useful for genetic research is that dogs are neatly divided into breeds, each of which is plagued by specific diseases. And the reason dogs are divided into diseased breeds is that we made them that way. Dogs are the world's longest self-serving, ecologically reckless genetic experiment, perpetrated by the world's first genetically engineering species: us.

Dogs were just a loose category of wolves until around 15,000 years ago, when our ancestors tamed and began to manage them. We fed them, bred them, and spread them from continent to continent. While other wolf descendants died out, dogs grew into a new species. We invented the dog.

We didn't pick just any wolves for this project. We picked the ones that could help us and get along with us. Dogs are dumber than monkeys and other mammals in many ways, but they excel at one thing: interpreting human behavior. Three years ago, scientists tested this talent in wolves, adult dogs, puppies raised in households, and puppies raised in kennels. The wolves couldn't read humans well, but the puppies could — even the puppies raised in kennels. Through selection, we've hardwired human compatibility into dogs. We've made a species in our image.

But that wasn't enough. We had specific needs. We bred hunting dogs, herding dogs, sled dogs, and guard dogs. (We also tried a few unauthorized uses.) We turned reproductive separation and inbreeding into a science, multiplying and dividing the species into more than 400 breeds. The American Kennel Club sorts them into the Sporting Group, Working Group, Herding Group, Hound Group (whose ancestors were "used for hunting"), Terrier Group (whose ancestors "were bred to hunt and kill vermin"), and Toy Group. "The diminutive size and winsome expressions of Toy dogs illustrate the main function of this Group: to embody sheer delight," says the club's Web site. Every dog has his duty.

Each need, each breed, called for special traits. We bred collies for vigilance, Rottweilers for aggression, retrievers for obedience. In a span of decades, we bred ferocity into Dobermans and then, with equal deliberateness, bred it out. We treated dogs like guns. We designed and bought them for protection, then complained when they hurt us. When cities banned pit bulls, we bought Rottweilers. It was as easy as replacing an illegal assault weapon with a legal one.

Not all our designs were utilitarian. We made some breeds just for fun. Some, like the Pharaoh Hound, were thought to be ancient because they looked like dogs drawn on Egyptian tombs. But last year, when we checked their DNA, we found no evidence they were older than modern breeds. Apparently, breeders crafted them by mating dogs that looked like the drawings. Life imitated art.

In the course of engineering dogs to look, feel, and act as we wanted, we ruined millions of them. We gave them legs so short they couldn't run, noses so flat they couldn't breathe, tempers so hostile they couldn't function in society. Even our best intentions backfired. Nature invented sexual reproduction to diversify gene pools and dilute bad variants. By forcing dogs into incest (which we ban among humans, in part for biological reasons), we defied nature. We concentrated each bad gene in a breed, magnifying its damage: epilepsy for springer spaniels, diabetes for Samoyeds, bone cancer for Rottweilers. That's why the dog genome is so nifty: We can find disease genes just by comparing one breed's DNA to another's.

Well, too bad for the dogs. But three cheers for us and our experiment. "The dog genome is a wonderful playground for geneticists," exults the New York Times. "A treasure trove," says the San Francisco Chronicle. "A convenient laboratory," agrees Reuters.

Man's best friend, indeed.

Canine Genetics Made Easy?

First we had artificial insemination, then we had artificial insemination with frozen sperm ("pupcicles"), and then we had dogs being cloned ("Clone, clone on the range, where the dogs and the puppies all play ..."

Now scientists have mapped almost the entire canine genome. The article below, from The Boston Globe, gives the details:

Team of Scientists Maps Out 99% of Dog Genome

Scientists have finished a sophisticated map of a dog's genes, providing new insights into the deep links between humans and one of their most treasured animals, as well as creating a unique tool for studying a range of diseases, from cancer to blindness, that affect people and their dogs.

The team of scientists, led by the Broad Institute of Harvard and MIT, determined virtually the entire genetic code, or genome, of the dog, making the achievement the canine equivalent of the completion two years ago of the Human Genome Project, the scientists said yesterday. Rough drafts of the dog genome have been released over the past several years, but the new work represents the first highly accurate version and also includes, for the first time, a detailed library of common genetic variations seen in dogs -- making possible a new generation of fast, accurate genetic studies of diseases and other traits.

Biologists have taken up the genetics of many animals, but the dog is uniquely interesting and useful, the scientists said, because of its history. The modern dog, including several hundred breeds, is the product of thousands of years of careful breeding, aimed at drawing out specific behaviors, such as the obsessive herding of the Border collie, or appearances, such as the hairless Chinese crested. By applying the modern tools of genetics to these breeds, it is now easy to find the small genetic variations responsible for the differences, with applications from dog breeding to human psychiatry. The genetic map of the dog announced yesterday should also accelerate the search for the genetic causes of diseases that plague certain breeds, perhaps leading to cures for dog and man alike.

''It is a historic day in the relationship between man and dog," said Eric S. Lander at a press conference yesterday, as a pug and an Akita tussled in the back of the room at the Bayside Exposition Center, where a dog show was being set up. Lander is the director of the Broad Institute and the owner of two golden retrievers.

Scientists said that the dog also stands as a testament to the power of evolution -- and its importance -- at a time when some are challenging its teaching in public schools. Looking for the genetic causes of human diseases in dogs makes sense only if humans and dogs are close evolutionary relatives that share a common ancestor -- a fact that is strongly supported by the genetic map Lander and his colleagues found.

''Biomedical research today depends on evolution," said Lander. ''It is hard to say that it is 'just a theory.' "

The research, which is reported today in the journal Nature, was led by Kerstin Lindblad-Toh, co-director of genome sequencing and analysis at the Broad Institute. Using a blood sample from a boxer named Tasha, the team determined about 99 percent of the sequence of DNA that makes up the dog genome.

The team, which included researchers across the United States as well as in France and the United Kingdom, also compiled a list of 2.5 million places in this sequence where there are common differences among dogs. This was done, according to the Nature paper, by comparing Tasha's DNA with DNA from a poodle and a number of other breeds -- enough, the scientists said, to record many of the most common variations in dogs.

Having this list of common differences will make it far easier for researchers to do genetic studies involving large numbers of dogs, because they can focus on the places in the genome where dogs are likely to have differences that might explain why one dog gets bone cancer and another does not. For example, scientists who are interested in why some greyhounds get bone cancer, and others do not, can look at these places to see if there is a pattern, without having to determine the entire genetic code of each dog -- about 2.4 billion molecules long. ''This is really the big thing," said Gregory M. Acland, a senior research associate at the Institute for Animal Health at Cornell University.

Many ailments -- including cancer, epilepsy, and heart disease -- are thought to be similar in dogs and humans, but it will be easier to identify the genes involved using dogs, said Acland, who studies genetic diseases that affect vision. In contrast to humans, dog breeds are highly in-bred, making two dogs in the same breed more similar genetically than two humans. Thus, for example, scientists could compare Dalmatians that are deaf with those that are not deaf, and there would be fewer random genetic differences between the dogs clouding the picture than if the same study were done in humans.

The work described yesterday, and follow-up work planned to study specific diseases, were made possible by the efforts of the American Kennel Club and dog owners who agreed to send in blood samples from their pets. (Owners of pure-breed dogs who are interested in participating can find more information at www.dogdna.org.) The research was funded by the National Human Genome Research Institute, part of the National Institutes of Health.

Dogs themselves are a human creation, thought to have begun when people domesticated the wolf in East Asia. The new analysis suggests that this happened about 30,000 years ago, said Lindblad-Toh.

The researchers also compared the DNA of dogs with completed genomes for humans and mice, and what they found challenges one idea about what makes humans special. When the human genome was first compared with that of the mouse, several years ago, scientists found evidence that the genes that are active in the cells of the brain seem to have evolved more quickly in humans than in mice, hinting that this might explain the intellect of humans. The new analysis casts doubt on this theory, because it shows that the brain-related genes in dogs have been evolving just as fast as those of humans, according to Tarjei S. Mikkelsen, a scientist at the Broad. The dog has about 19,300 genes, slightly fewer than humans, who have about 20,000 genes, according to Lindblad-Toh.

The researchers also identified a portion of the genome, about 5 percent, that is shared by dogs, humans, and mice -- meaning this portion is apparently essential to mammals. Yet less than half of that is devoted to genes. What the rest of the genetic material does is a mystery, but it is thought that some of this material may regulate when the genes turn off and on in particular cells. Still, the fact that the function of this crucial part of the genome is unknown underlines how much there is to learn.

For those who have been involved in dog genetics for years, there is hope that the new work will put the dog on the same footing as other favorite research organisms, such as the fruit fly and the mouse. In a way, it is a logical next step for the dog, which has done so much for humans -- guardian, hunter, companion. Yet there is also irony in discovering the scientific potential of dogs, noted Mark W. Neff, a scientist at the Center for Veterinary Genetics at the University of California, Davis. ''We are so close to our pet dogs, that we stop thinking of them as this incredible, unique species," Neff said.

Is a Cloned Afghan the Beginning of End for Shows?

It's the first cloned dog -- an Afghan of all things. The process is very, very expensive and inefficient, but so was invitro fertilization 20 years ago; now it's how most of the top horse and cattle are being bred.

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Snuppy, the First Cloned Puppy
S. Korean scientists say creation will help in human disease research
By Joseph B. Verrengia, Associated Press, August 5, 2005

He could be just another frisky, long-haired puppy with a slightly dazed expression. But his genetic fingerprint says otherwise.

Meet Snuppy, the world's first cloned dog. Scientists duplicated this Afghan hound, born 14 weeks ago, using a skin cell plucked from another hound. The two dogs are three years apart but genetically identical, right down to their weird, tan eyebrows.

Snuppy was created by South Korea's pioneering stem cell scientist, smashing another biological barrier and reigniting a fierce ethical debate.

The researchers, led by Hwang Woo-suk, insist they cloned the Afghan hound, a resplendent supermodel in a world of mutts, only to help investigate human disease, including the possibility of cloning stem cells for treatment purposes.

The dog's appearance in Thursday's issue of the journal Nature stirred renewed calls for a global ban on the cloning of humans to produce babies.

"Successful cloning of an increasing number of species confirms the general impression that it would be possible to clone any mammalian species, including humans," said Ian Wilmut, a reproductive biologist at the University of Edinburgh who produced the first cloned mammal, Dolly the sheep, from an adult cell nearly a decade ago.

Researchers have since cloned cats, goats, cows, mice, pigs, rabbits, horses, deer, mules and gaur, a large wild ox of Southeast Asia. So far, efforts to clone a monkey or another primate with the same techniques have failed.

Uncertainties about the health and life span of cloned animals persist; Dolly died prematurely in 2003 after developing cancer and arthritis.

Wilmut and others complimented Hwang's achievement. But they said politicians and scientists must face the larger and more delicate issue — how to extend research without crossing the moral boundary of duplicating human life in the lab.

"The ability to use the underlying technology in developing research models and eventually therapies is incredibly promising," said Robert Schenken, president of the American Society for Reproductive Medicine. "However, the paper also points out that in dogs as in most species, cloning for reproductive purposes is unsafe."

The cloned puppy was the lone success from more than 100 dogs implanted with more than 1,000 cloned embryos.

In a news conference in Seoul, the cloning team also condemned the reproductive cloning of humans as "unsafe and inefficient." Human reproductive cloning already is banned in South Korea. Other nations, including the United States, are split over whether to ban just human cloning or cloning of all kinds, including the production of stem cells.

Embryonic stem cells are the source of all tissue. Researchers believe they can be coaxed to grow into heart, brain or nerve cells that could be used to renew ailing organs.

Last year, Hwang's team at Seoul National University created the world's first cloned human embryos. In May, they created the first embryonic stem cells that genetically match injured or sick patients.

The researchers insisted the dog experiment was aimed at creating a reliable research model.
Monkeys are the closest model to humans, and they are crucial to medical research, but Hwang told reporters that cloning a monkey "is technically impossible at the moment."

"Dogs share physiological characteristics with humans," he said. "A lot of diseases that occur in dogs can be directly transferred to humans."

Animal welfare groups criticized the experiment. "This technology could lead to a brave new world of puppy production if it were hijacked by profiteers seeking to use cloning to supply the pet trade," said Wayne Pacelle, president of the Humane Society of the United States.

The researchers nicknamed their canine creation Snuppy, for "Seoul National University puppy," a reference to Hwang's lab. One of the dog's co-creators, Gerald Schatten of the University of Pittsburgh School of Medicine, described Snuppy, now 14 weeks old, as "a frisky, healthy, normal, rambunctious puppy."

On scientific terms, the experiment's success was mixed. Like Dolly, Snuppy was created using a method called somatic cell nuclear transfer.

Scientists took a skin cell from the ear of a 3-year-old male Afghan hound and extracted genetic material from the nucleus. They transferred it to an unfertilized egg whose nucleus was removed. The reconstructed egg holding the DNA from the donor cell was zapped with an electric current to stimulate cell division.

Dog eggs have been problematic because they are released from the ovary at an earlier, less mature stage than in other mammals. This time, the researchers collected more mature eggs from the donors' fallopian tubes.

They implanted 1,095 cloned embryos into 123 dogs and just three pregnancies resulted. That's a cloning efficiency rate lower than experiments with cats and horses. One fetus miscarried and one puppy died of pneumonia 22 days after birth.

That left Snuppy. He was delivered by Caesarean section from his surrogate mother, a yellow Labrador retriever.

Thinking About Species Loss

Eskimo Curlew, which may be extinct.


We often hear about wildlife species loss, but only rarely is such species loss quantified, defined, or given proper causation.

Whenever I hear about species loss, I naturally ask five key questions --and I often find the answers surprising.


1. Do the animals exist at all?

This may sound like an odd question, but it's a pretty important one because a lot of what is written about species extinction is totally unsupported by observed data.

Here's the scoop: Over the course of the last 400 years, only about 820 species of vascular plants and vertebrate animals are listed as having gone extinct by the IUCN Red List. In addition, the IUCN reports several species being "rediscovered" every year after having previously listed them as "lost".

Though the IUCN cannot report on what has not been discovered, we have clearly discovered most of the mammals, birds, fish, snakes, frogs, shrubs, vines, grasses and trees in the world. While new species of wildlife are being discovered every day, there is no evidence to support the notion that even 50 vertebrates and vascular plants are going extinct every year, much less the 20,000 number commonly cited (invertebrates and fungi are very difficult to push into extinction as any farmer can tell you).

As odd as it may sound, even physical evidence of the existence of a species does not necessarily mean that this species has ever existed. Here, I am specifically talking about birds, where it turns out some "extinct" species are based on single skins collected in the 19th or early 20th Century. The cone-billed tanager is a good example (to read more about the hunt for this "extinct species" read "The Ghost With Trembling Wings" by Scott Weidensaul).

The problem with birds is that they hybridize a lot, and bird species are not always very distinct from each other. Along with the cone-billed tanager, for example, there are several species of hummingbirds that we know of only due to single examples collected for the millenary trade. These so-called "Bogotá Skins" (for their central shipping point out of South America to Europe) may in fact represent evidence of a new species of now extinct hummingbirds -- or they could simply represent hybrids of other hummingbirds. With about 10 percent of all bird species known to cross the "species barrier," it's hard to know.


2. Is the animal being described really a species?

In fact a lot of stories about species decline are NOT about the decline of a species, but about the decline of a SUB-species in a very specific area.

A sub-species is, by definition, NOT a species. In fact most subspecies are nothing more than slightly different colored animals that exhibit no other behavior differences and that freely breed with populations of other animals in their species (animals whose populations may in fact be quite large and growing).


Sub-species are an interesting thing. I have always found it ironic that many environmentalists place little value on the prolific creation of thousands of new subspecies of apples, potatoes, pigs, cattle, and chickens, but assign tremendous value to subspecies of cougars, lions and pronghorns (to give just three examples). In fact, many sub-species of wild animals are little more than political artifices designed to boost the careers or egos of the people naming them.


In some cases there is another less vanity-centered reason to name a subspecies -- you can "up list" an animal (and its habitat) for protection by simply singling it out. The Sonoran pronghorn appears to be an example -- an animal made "rare" despite the fact it appears to be little more than a light-colored variant of an animal that actually numbers in the million.


3. Was the species ever very common?

Some threatened and endangered species are animals that were always rare and not very successful to begin with. Take the Whooping Crane, for example. DNA analysis suggests Whoopers never numbered more than about 5,000 individuals. The 1850 population of the bird (when most of the American West was still unsettled and very wild) is estimated to have been just 1,500 individuals. There are now 500 Whoopers in the world, with about 350 of them in the wild. I am very glad the Whooper was pulled back from the edge of extinction, but the fact that the bird was never common or genetically successful is not an inconsequential part of its story (though it is rarely told).


The Florida Manatee is another animal that was probably never terribly common. The Manatee population of Florida before there were outboard motors is estimated to have been around 10,000 or so. By the 1980s, the manatee population had declined to about 800, but it has since risen to over 3,000.
Again, bringing the American manatee (Trichechus manatus) back from extirpation in the U.S. is excellent, but we should not expect the population to ever get really huge. Note that the American manatee also exists in many other Caribbean countries south to Brazil, but it is a rare animal there due to hunting by indigenous people .


4. What is the population of the species now?

The point here is that numbers are only meaningful within context. Do I wish there were more pronghorn in America? Sure! But one million pronghorn -- up from just 13,000 individuals at the turn of the 20th Century -- is pretty good news and one we should be celebrating!


5. What has really caused the decline (or increase) of this species?

The death of any species is important, but I also want to know the circumstances of the decline or extinction. I consider the loss of the Passenger Pigeon and the Eskimo Curlew (there were once millions of these birds flying over vast areas of this continent) a much more significant tale than the loss of a species of flightless rail on a small island in the Pacific. One extinction signals the total loss of a once very common species that was successful over a very large area. The other signals the total loss of a very rare species that was NOT successful over a very large area. There are very different lessons to be learned from these very different stories.


Most people are surprised to learn that most extinctions are of the latter type (fairly unsuccessful species in very isolated locations) and not the former (fairly successful species in fairly common locations). They are further amazed to discover that habitat loss is a much rarer cause of species extinction than the introduction of rats, cats, goats and pigs -- or of indiscriminate hunting. If you go through the IUCN Redlist of extinct species, for example, you find zeros for most countries (no known endemic species pushed into extinction), but incredible numbers of extinctions for such tiny islands as Mauritius (41 extinct species), Réunion (16 extinct species), Saint Helena (29 extinct species), French Polynesia (67 extinct species), and the Cook Islands (15 extinct species). In fact, these little spots of land, along with Hawaii, account for about 200 of the 812 species pushed into extinction over the course of the last 400 years.

Is the loss of an "unsuccessful species" a bad thing? I think so. But it may not be quite as horrible or as unprecedented as it is commonly made out to be. In fact it may be part of the order of things. After all, instead of a living at a time when there is a "biodiversity bottleneck," as some texts would have you believe, we are actually living at a time of incredible genetic diversity. As the folks at the World Resources Institute note, "Global biological diversity is now close to its all time high. Floral diversity, for example, reached its highest level ever several tens of thousands of years ago. Similarly, the diversity of marine fauna has risen to a peak in the last few million years." In short, we live in a very bio-diverse time, and with diversity will come a lot of failure which is every bit as much a part of Darwin's evolutionary equation as success (if not more so).


It's also worth remembering that even as we are losing species, we are also gaining them -- new types of chickens, pigs, apples, corn, and trees. New hybrids of canaries, geese, ducks, pigeons, cattle, horses, falcons, eagles, dogs and cats. And we are doing it with wild birds too.


The last time I flipped through a Sibley's Audubon guide to birds, I counted one extinct species of parrot (the Carolina parakeet), but 27 new species of introduced parrots that are found in wild flocks in the U.S. (65 species have been encountered in Florida alone). In California and Florida these wild-flocking parrots are already creating new hybrids. Wild parrot colonies are not just found in warm climates by the way -- they are found near my home in suburban Virginia, and in downtown parks in Seattle and Chicago. One hundred and fifty years from now my great grandchildren may find hybridized variations of these same birds listed as entirely new "American" species of parrots (the Sibley guide already notes the presence of many Amazon hybrids in Florida and California).

Food for thought.

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Eastern Coyotes

Eastern coyotes are larger than their Western counterparts -- no one is quite sure why. One idea is that the Eastern coyote has cross-bred with wolves and farm dogs, but this is really unproven. What is clear, is that the so-called "Red Wolf" that once existed in the Eastern U.S. is really nothing more than a hybrid wolf-coyote cross. This has been proven with DNA tests of old "Red Wolf" skins kept at the Smithsonian, and also with DNA tests of the wild Red Wolves loose in the Alligator River National Wildlife Refuge in northeastern North Carolina.

The coyote, pictured above, was shot in the Adirondack's of New York and weighed 59 pounds -- a very, very large coyote. Most adult Eastern Coyotes weigh in at around 40 pounds.