genetics – Page 2 – Pain In The Bud

Wordy Wednesday: Critically Endangered Orangutan Babies

The palm oil and logging industries have killed so many orangutan mothers, there are now more than a dozen major orangutan orphanages in Borneo and Sumatra. The pressure on orangutans, with whom we share 97% of our DNA, shows no signs of abating.

Orangutans are critically endangered, and the biggest threat to their continued existence comes from the agricultural sector, which has razed 55 percent of the species’ habitat in recent decades.

Jarang, a baby orangutan born in 2023. Credit: Blackpool Zoo

Logging companies clearing irreplaceable, old-growth jungle to claim more land for palm oil plantations have no compunction when it comes to flattening jungles despite the presence of orangutans hiding in the trees. The loggers often shoot the large apes on sight, leaving terrified, traumatized babies still clinging to their dead mothers, or taking them to sell as pets.

Of those left to die, the lucky babies are rescued before they starve and are brought to one of the many orangutan orphanages in Borneo and Sumatra, where they attend “school” to learn how to do everything from climb to forage. It takes at least eight years to teach them how to survive on their own, which is about the time it takes orangutan mothers to do the same job in the wild.

The unlucky babies end up as local pets, sold off to entertainment troupes or shipped off to places like Dubai, where wealthy clients will pay a premium for them.

Caretakers must start by teaching rescued orphans the most basic things, like how to climb and move through the jungle Credit: Borneo Orangutan Survival Foundation

Logos, an orphaned baby orangutan who was rescued in 2023 by the Jakarta Animal Aid Network (JAAN) Credit: International Animal Welfare Fund (IAWF)

Baby Galaksi (Indonesian for galaxy), was found wandering the jungle without his mother in 2021 by a villager in Borneo. He’s now in a “school” that teaches orphaned orangutans how to do everything from evading predators to discerning edible fruit from harmful and poisonous varieties. Credit: Samboja Lestari Orangutan Rehabilitation Centre

So what is palm oil, and why are countries in Asia bulldozing ancient jungles and forests to clear room and make more plantations?

Per the WWF:

“Palm oil has been and continues to be a major driver of deforestation of some of the world’s most biodiverse forests, destroying the habitat of already endangered species like the Orangutan, pygmy elephant and Sumatran rhino. This forest loss coupled with conversion of carbon rich peat soils are throwing out millions of tonnes of greenhouse gases into the atmosphere and contributing to climate change. There also remains some exploitation of workers and child labour. These are serious issues that the whole palm oil sector needs to step up to address because it doesn’t have to be this way.

…

Palm oil is in nearly everything – it’s in close to 50% of the packaged products we find in supermarkets, everything from pizza, doughnuts and chocolate, to deodorant, shampoo, toothpaste and lipstick.”

Palm oil is in constant demand, and it’s an easy to grow, incredibly efficient crop. Indonesia and Malaysia, the only two countries in the world where orangutans exist, produce 85 percent of the world’s palm oil.

Images of orangutan babies in wheelbarrows are common on social media, but usually stripped of context. Orphanages use the wheelbarrows to bring infants and toddlers to and from “school” every day. Credit: International Animal Rescue

Asoka was found crying in the jungle by a fisherman in Borneo. He was brought to an orphanage in Borneo. Credit: International Animal Rescue’s rehabilitation Centre in Ketapang, West Kalimantan

We share 97 percent of our DNA with orangutans, making the species our second-closest cousins from a genetic standpoint. Some studies claim orangutans are our closest relatives based on our phenotypical similarities.

Orphaned orangutans attending “school” to learn how to survive in the wild. Credit: Borneo Orangutan Survival Foundation

A baby at an orangutan orphanage is fed by a caretaker. Credit: Borneo Orangutan Survival Foundation

Want to read more and learn how to help?

Here are some links to get you started. PITB is a big fan of the Jakarta Animal Aid Network, which successfully pushed Jakarta’s municipal government to ban the incredibly cruel “topeng monyet” monkey street shows:

World Wildlife Fund: Orangutans
Jakarta Animal Aid Network
Borneo Orangutan Survival Foundation
The Orangutan Project
Rainforest Trust

When Cute Is Cruel: Breed Beloved By Celebrities Like Taylor Swift Suffers Painful Genetic Mutation

Scottish Folds are cute, but the genetic mutation responsible for their folded ears also causes lifelong pain, joint problems and misshapen bones.

In 1961, a shepherd named William Ross found a barn cat with a curious feature: instead of the upright, swiveling, satellite dish ears of a normal feline, this cat’s ears were floppy and shapeless, resting atop her head like a tiny knitted cap.

Ross took the cat home and named her Susie. Susie gave birth to a litter of kittens with the same floppy ears, and it all gets a bit murky from there, with a dozen variations of the story online claiming it was Ross himself or a neighbor who “created” the breed.

Regardless of who it was, the floppy ears were transformed from an abnormal feature into the unmistakable characteristic of a breed, and the Scottish Fold was born.

The cute cats quickly caught on and were officially recognized in competitions by 1971.

Now they’re more in vogue than ever. They’re the preferred pets of music superstars Taylor Swift and Ed Sheeran, who regularly feature photos and videos of their Scottish Folds in social media posts. People across the world are buying them, and they routinely appear in “best breed” lists online, lauded for being cuddly and docile in addition to adorable.

Ed Sheeran with his Scottish Fold cat. Credit: Ed Sheeran/Instagram

But they’ve also been banned by the same cat fancy groups that initially welcomed them, they’re prohibited outright in some countries, and animal welfare groups are begging people to stop emulating celebrities by buying them.

That’s because the same deformity that gives Scottish Folds their distinctive ears is also responsible for weak and brittle cartilage and bones elsewhere in the body, which results in lifelong pain and disability.

According to the RSPCA:

“The disease is evident on x-rays of cats from as young as seven weeks of age. Serious abnormalities in joints and bone growth lead to arthritis (painful, swollen joints), short, abnormally thick, and inflexible tails, spinal abnormalities and short, stiff legs. The welfare impacts of Scottish Fold Osteochondrodysplasia can be severe in terms of pain and inability to perform natural behaviours, as these cats can be lame, walk with an abnormal gait, can be reluctant to engage in normal movements such as walking or jumping, and can even become completely crippled.

There is no cure for this progressive condition.”

Sadly, the deformities and resulting pain may be the reason Scottish Folds are considered docile and cuddly: they may simply be in too much pain to move or protest when their humans hug them or pick them up.

Ross and Turner didn’t know it in 1961, but the folded ears and brittle cartilage were the result of a genetic mutation. It wasn’t until 2016 that a group of American and Australian scientists found a mutation in a single gene, TRPV4, was responsible for weak cartilage and bones, leading to the deformities highlighted by the RSPCA in the passage above, as well as “progressive joint destruction.” The condition is called osteochondrodysplasia.

Taylor Swift and Scottish Fold cat — Swift’s cats have appeared in her music videos, feature prominently in her online posts, and were photographed in her arms for her 2024 post announcing she was supporting Vice President Kamala Harris in November’s presidential election.

Cats Protection, a UK charity, raised the issue in 2024, warning that Scottish Folds were becoming even more popular, with breeders struggling to meet high demand. The group issued a public statement asking cat lovers and Swift fans to avoid buying Scottish Folds. Scottish Folds are equally popular in the US, spurring resistance from stateside animal welfare groups as well.

The Governing Council of Cat Fancy, which registers breeds in the UK — and no longer recognizes Scottish Folds — was even more direct.

“We strongly advise members of the public not to try to acquire cats of this breed,” Steve Crow, chairman of Cat Fancy’s governing board, told The Guardian.

Scientists Finally Figure Out Why Some Cats Are Orange, PLUS: Are Street Cats Really ‘Taking Over?’

More Americans say they can’t afford to keep their cats because of inflation, leading to an increase in surrendered and dumped cats in some places.

More than 110 years ago, American geneticist Clarence Cook Little developed a theory explaining why some cats have orange coloring and some don’t.

Now Little has been proven correct thanks to the work of separate teams in Japan and the US, which discovered the mechanism that leads to orange coloring, including fully ginger felines as well as calicos and tortoiseshells.

The explanation may be a bit too heavy on genetics for some readers, but essentially the researchers found the specific gene that leads to the growth or orange fur. They’ve known about the gene for a long time, but didn’t realize the totality of its function. Its official name is ARHGAP36, but for the sake of simplicity, scientists are calling it “the orange gene.”

“The orange gene has a known role in hair follicle development, but scientists didn’t previously know it is also involved in pigment production,” a team of geneticists and biotechnologists wrote in The Conversation, a science publication. “This means that a new pathway for pigment production has been discovered, opening the way for exciting and important research into a basic biological process.”

calico cat relaxing on wooden bench outdoors — In partially orange cats like calicos and tortoiseshells, the blotches of color are the result of imperfect gene copies and a secondary pigment-related gene switching “on and off.” Credit: Mehmet Guzel/Pexels

Ginger cats are usually male, but the pigmant can also appear in female cats due to an error in gene copying which deletes one segment of the orange pigment-producing genetic code.

That’s why calicos and tortoiseshells have orange blotches or mixed orange fur. “[T]he orange gene is persistently switched on in orange areas but is mostly switched off in non-orange areas of a cat’s coat,” the authors wrote.

Are there more strays in 2024?

Time magazine has a story examining the problem of stray cats in America’s urban and suburban population centers, why it’s happening, and what can be done about it.

First, might as well get this out of the way: We don’t know if there are “more” cats. The claim that there are more relies on anecdotes, and there’s no hard data to back that up. You have to be highly motivated to invest the time and money into a proper census like the D.C. Cat Count, and it’s an understatement to say most towns and cities are either not willing to do that, or don’t have the resources.

What we do know is there may be more cats in certain areas, with individual shelters in some places reporting record numbers of surrenders and cats scooped up by animal control.

close up of a stray cat on the metal railing — Rescuers say people who can’t afford food, supplies and veterinary care are surrendering or dumping their cats in larger numbers than in years past. Credit: Dou011fu Tunce/Pexels

The story quotes rescuers who say they’ve seen more surrendered pets, as well as data from Shelter Animals Count, which tallies self-reported information from shelters and rescues. The latter says 32 percent of cats taken in were owner surrenders in 2024, compared to 30.5 percent in 2019.

“It’s a combination of people surrendering their pets and people not adopting because they’re not sure they can take on the financial commitment,” Animal Care Centers of NYC’s Katy Hansen told Time.

Rescuers say that’s reflected in their experiences trapping the felines, who are friendly and acclimated to humans.

The people surrendering their pets cite inflation, not only impacting the cost of essentials like food and litter, but also more expensive veterinary care.

The story additionally includes this eye-popping detail:

“At Veterinary Care Group, a private equity-owned practice in Brooklyn, the cost of spaying or neutering a cat has soared to $850 per animal. By contrast, at the nonprofit veterinary clinic Zweigart recently founded in Brooklyn, the cost of spaying or neutering a cat is $225 and a mid-sized dog is $300.”

The lesson here: Steer well clear of veterinary clinics that aren’t vet-owned or are obtuse about their ownership. Private equity groups don’t buy clinics out of love for animals.

a close up shot of a tabby cat — The cost of spay/neuter procedures ranges dramatically at different veterinary practices. Credit: Tima Miroshnichenko/Pexels

As for solutions to local spikes in stray populations, the story doesn’t offer any. It mentions TNR (trap, neuter, return) but only in the context of a lawsuit against the San Diego Humane Society for its neuter/vaccination program.

That said, there probably isn’t a one-size-fits-all technique. What works for a small town won’t necessarily work in a city, and there are dozens of factors that could influence the prevalence of stray cats and colonies. Still, city councils and town boards don’t need to reinvent the wheel. Chances are if they look, they’ll find a municipality similar to their own where locals have successfully stabilized feline populations.

As for the Buddies, I’d live in my car before giving Bud up. He wouldn’t be thrilled about that situation, and we’d have to head south because the winters here are brutal, but as long as Bud has his servant, he’s good.

A previous version of this post incorrectly described cat chromosomes. The story has been updated to remove the error.

Local Politicians Have No Clue How To Manage Cats

Feeding strays is now punishable by a $150 fine in an Ohio town, the latest municipality whose elected leaders chose to ignore expert guidelines on managing feline populations.

Every time the stray cat issue comes up, local town boards and city councils act as if they need to reinvent the wheel.

Imagining that they are the first to deal with this extremely common problem, they make decisions from positions of ignorance, dismissing the concerns of people who actually work with cats. Or they “do the research” and come up with their own ineffective policies instead of simply looking at what other towns and cities have tried in the past.

At least that way, you know what works and what doesn’t, and how much your decision’s going to cost taxpayers.

But that would be the smart thing to do, which is why our local elected leaders don’t do it. Instead they pull stunts like the village board of Mogadore, Ohio, a town of 3,700 about 10 miles east of Akron.

The Mogadore board just passed a law that makes feeding strays and ferals punishable by a fine of up to $150, as if that will stop cats from finding food and breeding.

Tellingly, Mogadore’s elected leaders say their ordinance applies to “wild, stray, or un-owned” cats, which means they don’t understand they’re all the same species.

Apparently neither do the reporters at WOIO, a local news station in Cleveland. A story from the station is confidently incorrect in telling readers “[d]omestic cats that have become wild, meaning live outdoors, roam free, and rarely interact with humans, are also considered feral.”

Stray cat and kitten — Credit: Sami Aksu/Pexels

Felis catus is a domestic animal. By definition a domestic cat is not wild and cannot become wild. Evolution cannot happen to a single animal.

While evolution is a constant process, speciation — wolves becoming dogs, wildcats becoming house cats, wild boar becoming docile farm pigs — is a species-wide shift that takes at least a few hundred years but often much longer, “from human-observable timescales to tens of millions of years” depending on the species.

The whole process results in changes at the genetic level. The transition from wildcats to domestic cats, for example, involved changing only 13 genes.

This is not rocket science, it’s basic stuff we all learned in high school science classes.

But that’s almost beside the point.

Fining people for feeding stray cats, including caretakers who voluntarily manage cat colonies, will not solve the problem. It doesn’t work. It has never worked in any town anywhere in the world.

It also creates a needlessly adversarial relationship with the passionate people doing the hard work of managing the feline population, often thanklessly and at their own expense. Why make enemies of them when they’re doing a public service?

Mogadore’s village board had a representative from Alley Cat Allies and people from local rescues on hand to inform them that fines don’t work, and to offer the humane and effective option of trap, neuter, return. TNR may not be perfect, but it’s better than anything else people have tried.

Mogadore’s board and mayor ignored the experts and went ahead with their plan to fine people instead.

They’re not alone. This happens thousands of times across the US, Europe, Australia and most other places where domestic cats live. Japan and Turkey take a more humane approach, and they’re better for it. But here in the US, we often deal with issues by ignoring precedent and engaging in wishful thinking.

If the residents of Mogadore are lucky, their elected officials will realize their mistake sooner rather than later.

Stray cat eating — Stray and feral cats already have a difficult existence without ill-advised laws making it illegal to care for them. Credit: Mehmet Fatih Bayram/Pexels

DNA From Dead Sheep In UK Matches Big Cats, But Is That Proof Of Their Presence?

Rumors of big cats in the UK countryside have persisted for years, with witness claims from all over the country. The latest reported sighting was in northern England.

People who really want to believe big cats are running around the British countryside are ecstatic with the news that a DNA sample from a dead sheep reportedly tested positive for panthera DNA.

The DNA sample was swabbed from a freshly-killed sheep carcass “at an undisclosed upland location” in Cumbria, northwest England, a witness told BBC Wildlife. It’s exactly the kind of countryside where people have been reporting big cat sightings for years, although the sightings aren’t confined to that area, with other witnesses claiming they’ve seen large felids as far as the UK’s southern coast.

Sharon Larkin-Snowden, who lives nearby, told a big cat enthusiast podcaster that she disturbed the “big cat” while it was feeding. The startled felid took off and jumped a stone wall, leaving the partially-eaten sheep, Larkin-Snowden said.

“I assumed at first it was a sheepdog, but then I did a double take and realised it was a black cat,” she said. “It was big – the size of a German shepherd dog.”

Jaguar in a pub — “I could really go for a Chinese! Anyone else wanna go for a Chinese?”

A swab was collected — the details are sketchy on who did the collecting and when exactly they submitted the sample — and sent to the University of Warwick’s Robin Allaby, a professor of life sciences.

Allaby, whose specialty is studying the genetics and evolution of domesticated plants, began offering a DNA testing service for the public some 12 years ago in response to the persistent rumors of big cats in the countryside. In the past samples have yielded DNA from foxes and other animals, but Allaby says this one matched the genetic profile of a big cat, although he cannot say which species.

It’s not unusual for a DNA sample to match to a genus, in this case panthera, but not to a specific species if the sample was degraded or only partial.

Rick Minter, who has made a career of tracking alleged big cat sightings across the UK, says he believes the mystery cat is a leopard. Leopards and jaguars are the only two big cats who have true melanistic color morphs — meaning some of them have virtually all-black coats — and Minter says he believes it’s more likely the former.

Neither are native to the UK or Europe: Leopards range from Africa to Asia, while jaguars range from south to Central America, with some populations edging slightly into the US.

puma sits on tree — Britain’s big cat enthusiasts say they believe pumas are among the wild cats living in Credit: Jean Paul Montanaro/Pexels

Why isn’t a DNA match evidence of big cats in the UK?

If the lab results say the sample came from a big cat and that result is consistent with the witness account, what’s the problem?

Chain of custody, for one. We don’t know anything about who took the sample, where it was taken, the time elapsed between the kill and the sample swab, or who may have handled it before it reached Allaby.

In fact, we don’t know if there was a dead sheep to begin with.

If I were a prankster living in the UK, for example, and was friendly with a keeper at a local zoo, I could have the keeper swab an animal, bag it and hand it over to me. There are dozens of conceivable ways a person could obtain a sample even if they don’t know someone who works in a zoo.

Leopard in a pub — “So we left the sheep there at the edge of the field and made sure the lady saw us before we buggered off over the fence. Next day, we was in all the papers! A right laugh that was, mate.”

The problem is the provenance of the sample and what happens to it between the time it’s collected and ends up in the hands of a scientist like Allaby.

This is why chain of custody is paramount in criminal trials, and why there must be a complete record of who handled samples from collection in the field to the lab. Even in the absence of foul play, an improperly handled sample can be contaminated and render test results meaningless.

It’s not a matter of trust, it’s the simple fact that extraordinary claims require extraordary evidence, as Carl Sagan was fond of saying. Short of capturing one of these animals or getting clear, indisputable footage, any other claimed proof has to be ironclad.

Speaking of footage, that’s another issue. It’s extremely difficult to believe that a breeding population of big cats can exist in the UK countryside for years or even decades without a single definitive photo or video. The UK’s rural areas may not be blanketed by CCTV cameras like London, but they’re not the Amazon either. People live, work and farm in those regions, cameras are more ubiquitous than ever, and farmers take steps to protect their livestock, including installing cameras.

Big cats don’t just feed and vanish into the mist. They mark trees with their claws and urine, they leave distinct pug marks, they leave distinctive bite marks on their prey, and they make noise. To paraphrase one naturalist, when big cats are living nearby, you know it. Even if you don’t see them, signs of their presence are ubiquitous.

To accept the claims of tigers, leopards and pumas gallavanting in the fields around small towns and villages, we’d have to suspend disbelief or conclude that these are some sort of previously unknown ghost cats who can fade in and out of the physical plane.

I’m not a skeptic to be a killjoy. If big cats really were running around the UK, that would be a hell of a story. But we’d still need convincing evidence, and this isn’t it.