Tag: University of Arizona

The science of dog learning.

A very interesting article in The Smithsonian Magazine.

There are countless breeds of dogs and they represent thousands of years of breeding.

But recent work in determining the genetic background behind the many different features of dogs has revealed so much.

The Smithsonian Magazine published an article nearly a month ago and hopefully it is alright to share it with you.

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What a Crowdsourced Study Taught Us About How Dogs Learn

A new study looks at the genes that underlie traits from self control to communication

 

 

Three dogs sit at attention ( MediaProduction

By Viviane Callier, July 31, 2020

Thousands of years of selective dog breeding has created a fantastic diversity of domestic canine companions, from the workaholic border collie to the perky Pomeranian. In cultures around the world, humans bred different dogs to be good at tasks including guarding, hunting and herding. Later, in Victorian England, kennel clubs established breed standards related not only to their behavior, but also their appearance.

As genomic sequencing has become more affordable, scientists have begun to understand the genes behind physical features such as body shape and size. But understanding the genes behind dog cognition—the mental processes that underlie dogs’ ability to learn, reason, communicate, remember, and solve problems—is a much trickier and thornier task. Now, in a pair of new studies published in Animal Cognition and in Integrative and Comparative Biology, a team of researchers has begun to quantify just how much variation in dog cognition exists, and to show how much of it has a genetic basis.

To study canine cognition, the studies’ authors turned to publicly available genetic information from a 2017 study, and a large community science project, Dognition.com, in which dog owners tested their own pets. “These papers offer an exciting integration of two forms of big data,” says Jeff Stevens, a psychologist at the University of Nebraska-Lincoln who was not involved in the study.

Previous studies often compared cognition in one breed against another using small sample sizes of dogs from each. This study, by contrast, is the first to examine the variation in cognition across three dozen breeds, and the genetic basis of that variation, explains Evan MacLean, a comparative psychologist at the University of Arizona who oversaw the pair of new studies. MacLean says dog breeds may be an ideal way to study the heritability of cognitive traits because breeds—all part of the same species—represent close genetic relatives with an incredibly diverse range of appearances and behaviors.

To gather a sufficient amount of data on how dogs reason and solve problems, the researchers looked to the Dognition.com portal. The initiative, created by Duke University dog researcher Brian Hare, started with tests in the lab. Researchers developed methods to understand how dogs think. They then stripped those methods down, and simplified them for dog owners to do themselves. In an earlier project, the researchers tested dogs in the lab and compared their results to those from owners testing the same dog at home. The results were the same, giving them confidence that the results from the citizen science project were reliable.

To participate in this project, dog owners tested their pups on 11 standardized tasks used by animal behaviorists on a variety of species that reflect four aspects of cognition: inhibitory control, communication, memory and physical reasoning. One task that measured inhibitory control, for example, involved having an owner put a treat on the floor in front of the dog and then verbally forbidding the dog from taking it. The owner then measured how long the dog would wait before eating the treat. In a task to assess communication skills, the dog owner placed two treats on the ground and gestured towards one of them. The owner then determined if the dog approached the indicated treat. To assess memory, the owner visibly placed food under one of two cups, waited for a few minutes, and then determined if the dog remembered which cup the food was placed under. To test physical reasoning, the owner hid food under one of two cups, out of view of the dog. The owner lifted the empty cup to show the dog that there was no food and then assessed whether the dog approached the cup with the food underneath.

The participating dog owners reported their dog’s scores and breed, producing a dataset with 1,508 dogs across 36 breeds. The researchers analyzed the scores and found that about 70 percent of the variance in inhibitory control was heritable, or attributable to genes. Communication was about 50 percent heritable, while memory and physical reasoning were about 20 percent heritable.

“What’s so cool about that is these two traits that are highly heritable [control and communication] are those that are thought to be linked to dogs’ domestication process,” says Zachary Silver, a graduate student in the Canine Cognition Center at Yale who was not involved in the study.

Dogs are better at following humans’ communicative cues than wolves, and this is something that seems to be highly heritable, explains Silver. In contrast, there’s some evidence that wolves are better than dogs at physical reasoning.

Some of these traits are also influenced by environment and how the dog was handled as a puppy, so there are both genetic and environmental components. In fact, there is so much environmental and experiential influence on these traits that Gitanjali Gnanadesikan, a graduate student in MacLean’s lab and lead author of the new studies, cautions against the idea that these findings support certain breed restrictions or stereotypes. “Even the highly heritable traits have a lot of room for environmental influence,” she says. “This shouldn’t be interpreted as, ‘each of these breeds is just the way they are, and there’s nothing that can be done about it.’”

In the same way that women are on average shorter than men, but there’s quite a lot of overlapping variation within each sex, dog breeds also show a lot of variation within each breed that overlaps with variation among breeds.

Previous work has linked differences in inhibitory control to the estimated size of dogs’ brains. Comparative studies across many different species, ranging from tiny rodents to elephants and chimpanzees, also show that some aspects of self-control are strongly related to brain size. The bigger the brain size, the more self-control the animals seem to have, MacLean says.

Stevens notes that a lot of things—not just inhibitory control—correlate with brain size across species. And brain size, metabolic rate, lifespan, home range size are all correlated with body size. When many traits are correlated with each other, it is not clear which of these factors may underlie the cognitive differences. So there are a number of questions remaining to be explored.

After showing the degree to which different aspects of dog cognition are heritable, Gnanadesikan and MacLean used publicly available information on the genomes of dog breeds to search for genetic variation that was associated with the cognitive traits of interest. The researchers found that, like many other complex traits, there were many genes, each with small effect, that contribute to dogs’ cognitive traits. That is in contrast to morphological features in dogs; about 50 percent of variation in dog body size can be accounted for by variation in a single gene.

One of the limitations of the study is that the researchers did not have cognitive and genetic information from the same dogs; the genomes were breed averages. In the future, the researchers are planning to collect genetic data from the very same dogs that are completing the cognitive tests, to get measures of cognitive and genetic variation at the level of individual dogs. “This gives us a roadmap for places that we might want to look at more carefully in the future,” MacLean explains.

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Now this is an article that deserves to be read carefully so if you are in a hurry bookmark this and wait until you can sit and absorb the messages the article contains.

I was minded to look up Gitanjali’s details and I am glad I did. These are the details:

Gitanjali Gnanadesikan
I am an evolutionary biologist and comparative psychologist who is interested in social behavior and cognition. I work with Evan MacLean in the Arizona Canine Cognition Center studying the development and evolution of behavior and cognition in dogs and wolves.

I think I will reach out to her and see if she has more information she would like to share with us all.

Doggedly seeking the truth.

As a dog follows a scent.

P1110019
Casey doing what dogs do so well – picking up a scent.

I have been pondering about how one gets to the truth of a complex issue.  And there’s none more complex nor more essential in terms of the truth of an issue than Anthropogenic Global Warming (AGW).

It was kicked off by an email received from Dan Gomez.  Followers of Learning from Dogs will have seen mention of Dan’s name as he regularly sends me bits and pieces.  Indeed, let me refer you to a post that came out last August, Feeling depressed? Join your pals in the pool! and this extract:

Regular followers of Learning from Dogs will know that Dan and I go back a long way; far too long! In fact the occasion of me becoming aware of Mr. Daniel Gomez was at a Commodore Computer dealers conference in Boston, Mass.

I was giving a talk promoting a UK word-processing program that I was marketing for the Commodore. That software was called Wordcraft and I think the year was 1979, possibly 1980. Anyway, I used the word ‘fortnight’, which back in England is a common word meaning two weeks. Immediately, a voice called out from the audience, “Hey Handover, what’s a fortnight?“

The session deteriorated rapidly thereafter! Dan and I became very good friends and his LA company Cimarron became my West Coast USA distributor for Wordcraft. And it was Dan’s sister, Suzann, who invited me down to Mexico for Christmas 2007 which led to me meeting my beloved Jeannie! Funny old world!

Dan is a smart cookie. He holds a degree in psychology, as well as being a very easy guy to get along with.  We have been good friends for more than 30 years.

Anyway, back to the theme of the post; determining the truth of a complex issue.

Recently, Dan sent me an email with the subject heading of The Controversy Continues – A couple of Articles for your Digestive Tract….

The first article was:

Report shows UN admitting solar activity may play significant role in global warming

A leaked report by a United Nations’ group dedicated to climate studies says that heat from the sun may play a larger role than previously thought.

“[Results] do suggest the possibility of a much larger impact of solar variations on the stratosphere than previously thought, and some studies have suggested that this may lead to significant regional impacts on climate,” reads a draft copy of a major, upcoming report from the U.N.’s Intergovernmental Panel on Climate Change (IPCC).

The man who leaked the report, StopGreenSuicide blogger Alec Rawls, told FoxNews.com that the U.N.’s statements on solar activity were his main motivation for leaking the document.

The second article was from the Dick Morris website, from which I offer this extract (if, like me, you hadn’t heard of Mr. Morris before, details are here):

According to Bloomberg News, US carbon emissions are down 13% over the past five years and that they are now the lowest since 1994. In fact, we are more than halfway to President Obama’s goal of a 17% reduction below our peak year of 2007.

….

Coal has fallen to only 18% of our energy use (down from 23% in 2007) and natural gas is up to 31%. Natural gas has half the carbon emissions of coal.

Evidence suggests that climate change and global warming are happening, but at a much slower rate than doomsday warnings suggested. We are now on track for an increase in global temperatures of one degree centigrade by 2100. This increase is not enough to cause major flooding or rises in sea levels.

Please feel free to read the whole Dick Morris piece here.

So on the face of it, two convincing reports, especially the one from Alec Rawls.

Professor McPherson
Professor McPherson

Now let me turn to Professor Guy McPherson; professor emeritus at the University of Arizona.  Just take a peek at the professional recognition granted to Professor McPherson.

Guy McPherson writes a blog called Nature Bats Last.  It is described thus:

This blog focuses on the natural world, with a particular emphasis on the twin sides of our fossil-fuel addiction: (1) global climate change and (2) energy decline. Because these phenomena impact every aspect of life on Earth, specific topics range widely, and include philosophy, evolution, economics, humanity, politics, current events, and many aspects of the human condition.

Less than 3 months ago, Guy McPherson visited Greenfield Community College in western Massachusetts to deliver his presentation “The Twin Sides of the Fossil-Fuel Coin: Developing Durable Living Arrangements in Light of Climate Change and Energy Decline.

It lasts for just 40 minutes and needs to be watched.  Why do I say needs to be watched?  Because tomorrow I delve deeper into the challenges facing ordinary folk and watching the presentation and reflecting on the start of this post are very pertinent to following the scent of truth.

An ancient bond, indeed!

The mystery of the call of a dog in need of help.

Two days ago, I wrote a piece about how the evolution of the domestic dog has been reliably re-calibrated back to around 33,000 years ago.  I quoted from an article in the Arizona Republic, here are the opening paragraphs of that article.

Tamed dogs may go back 33,000 years

by Anne Ryman – Jan. 24, 2012 11:33 PM
The Republic | azcentral.com

Dogs have been “man’s best friend” longer than any other animal. And, as it turns out, longer than previously thought.

A pair of research papers published in the past few years, one most recently by a team that includes the University of Arizona, significantly pushes back the timeline for domestication of dogs from about 14,000 years ago to more than 30,000 years ago.

Researchers at UA and universities in England and the Netherlands used radiocarbon dating to determine that the skull of a Siberian dog was about 33,000 years old. Slightly older dog remains were identified in Belgium a few years ago by a separate research team.

The full Post is here.

So moving on, and apologies for a bit of a personal muse.

Last night (the night of the 30th/31st Jan.) a single, gentle yelp from Pharaoh had me instantly awake. Initially hadn’t a clue about the time but instinctively knew it was an un-Godly hour!  Jean and I had been late to bed and I was pretty tired when the lights went out – off to sleep in an instant.  Ergo, waking up at 2am as it turned out to be, the classic deep-sleep time of the night, was challenging!  It is also relevant to mention that Pharaoh is reliably a very good sleeper at night.

Yet, in literally an instant of time, I had transitioned from being totally asleep to being mentally alert wondering what had caused him to cry out.  Pharaoh came to the side of the bed and let me rub his head, then went back to near the door and uttered another soft yelp.  I knew without any doubt at all that he was in pain and lay on my back anticipating what would be coming – putting a dressing-gown on and leading his nibs out into a very cold and dark night!

Then a clawed paw on the door told me to get moving, and within moments of Pharaoh being outside, it was clear that he had a badly upset tummy.

The whole episode was repeated around 4.45 am.

It was later in the morning that I was reflecting with Jean about the evolution of the dog-human relationship that a) gave the dog the instinctive confidence to call out to his ‘master’ in a different ‘I need help‘ tone, and b) that the call was so rapidly interpreted by a human as a call for help from another species.

But dogs sleeping near or around their human companions for more than 30,000 years allows plenty of time for species bonding to develop in ways that are both beautiful and mysterious.  Long may that bonding remain beautiful and mysterious.

Fabulous animals!

Pharaoh. June 2008, 3 months before we both left for Mexico!

Consciousness, science or God?

More of Peter Russell’s insightful ideas.

It was back in March, the 8th to be precise, when I first wrote about Peter Russell.  Well just over a week ago, I came across another article by Russell from the Huffington Post.  It was then a moment’s work to find it on Peter Russell’s own website.  (This links to various essays on the topic.)

Here’s a ‘taste’ from the first essay.

The Anomaly of Consciousness

Excerpted from book From Science to God

Science has had remarkable success in explaining the structure and functioning of the material world, but when it comes to the inner world of the mind science falls curiously silent. There is nothing in physics, chemistry, biology, or any other science that can account for our having an interior world. In a strange way, scientists would be much happier if there were no such thing as consciousness.

David Chalmers, professor of philosophy at the University of Arizona, calls this the “hard problem” of consciousness. The so-called “easy problems” are those concerned with brain function and its correlation with mental phenomena: how, for example, we discriminate, categorize, and react to stimuli; how incoming sensory data are integrated with past experience; how we focus our attention; and what distinguishes wakefulness from sleep.

It would be wrong to publish anything more so if you are interested in more, then go here and pick away or better still buy the book!

If you have a quiet 30 minutes, settle down and watch these videos

Part One

Part Two

Part Three

Arizona geology

An interesting insight into Arizona geology.

I’m taking a little gamble that the owners of the copyright in the following article will not mind the complete re-publishing of this piece.

While I have practically zero knowledge of the geology of much of the USA living here close to the Mogollon Rim makes it almost impossible not to sense the ageless beauty of the surrounding hills and mountains.  Anyway, this article was found on the Arizona Geology website. It is called Putting Earth Science Back in its Place, written by STEVEN SEMKEN of ARIZONA STATE UNIVERSITY.

The ancient landscape of Arizona

One of the most universal and fundamental things that humans do is to make places. We do this by sensing and experiencing the space around us, and attaching meanings to parts of it: here is a beautiful mountain, here is where my house is, here is where we have found copper, here is where my ancestors lived.  The meanings that we affix to places can be aesthetic, ceremonial, historic, practical, and mythical, as well as scientific. Humans develop emotional attachments to meaningful places, sometimes to the point of making significant personal sacrifices to preserve or protect them. The combination of meanings and attachments that connect us to places is called the sense of place.

We study and teach about Earth through its places. From Monument Valley to Organ Pipe, the landscapes of Arizona are set with places that are not only great geological exemplars, but meaningful to people for all kinds of reasons. It is only human for us to become interested in these diverse place meanings even as we explore our surroundings scientifically. Our students may also have, or can be encouraged to develop, rich senses of these places—particularly ones that are relevant to their personal interests, family experiences, or cultural backgrounds. This is the nature ofplace-based teaching, which encourages students to explore, and become involved in, local environments and communities. Urban places are just as meaningful, and can be just as instructive, as rural or remote places.

It is not simply teaching about the geology of a place such as Grand Canyon or the Río Salado Valley. It is finding ways for your students to experience the place: if possible by bringing them there, but alternatively by bringing them local rock specimens, images, maps, and readings to investigate, or enabling them to explore virtually using Google Earth. It is also helping them to become moreinvested in local places: by being able to explain how they get their weather, drinking water, fuel, and electrical power; by doing a community-service project; by creating art that celebrates the beauty of land and environment. And authentically place-based teaching and learning are as trans-disciplinary as place meanings themselves are. Here are reason and motivation for Earth science teachers to collaborate with their colleagues in life sciences, geography, history, language, literature, and so on, to develop ways to explore and understand the natural and cultural landscapes of Arizona across the curriculum.

Why is this important? On one hand, cultural forces such as the pervasiveness and popularity of digital entertainment and the homogenizing effects of global commerce conspire against student and community interest in local places and concerns. There is mounting research and anecdotal evidence that children and families spend less time outdoors. To be oblivious to the importance of local places is to forego opportunities to learn from them and protect them from environmental and cultural degradation. On the other hand, right here in Arizona we are already faced with a number of what many scientists and policymakers have labeled “grand challenges” to sustainability if not human existence, including depletion of water resources, lessened biodiversity, declining air quality, continued dependence on fossil energy, and climate change.  Place-based teaching is an appropriate response. And it is intellectually and emotionally delightful to reacquaint yourself and your students with the places of home.

SELECTED, RECOMMENDED READINGS

ONE PLACE-BASED TEACHING AND LEARNING:
Gruenewald, D. A., & Smith, G. A. (Eds.). (2008). Place-Based Education In The Global Age: Local Diversity.
New York: Lawrence Erlbaum. ISBN 978-0-8058-5864-8.

Sobel, D. (2004). Place-Based Education: Connecting Classrooms And Communities.
Great Barrington, MA: The Orion Society. ISBN 0-913098-54-X.

ON THE MANY PLACE MEANINGS OF ARIZONA AND THE SOUTHWEST:
Basso, K. H. (1996). Wisdom Sits In Places: Landscape And Language Among The Western Apache.
Albuquerque, NM: University Of New Mexico Press. ISBN 0-8263-1724-3.

Ffolliott, P. F., & Davis, O. K. (2008).  Natural Environments Of Arizona: From Deserts To Mountains.
Tucson, AZ: University Of Arizona Press.  ISBN 978-0-8165-2697-0.

Granger, B.H. (1982).   Will C. Barnes’s Arizona Place Names, Facsimile Edition.
Tucson, AZ: University Of Arizona Press. ISBN 0-8165-0729-5.

Kamilli, R. J., & Richard, S. M. (Eds.). (1998). Geologic Highway Map Of Arizona, Map M-33.
Tucson, AZ: Arizona Geological Society And Arizona Geological Survey. ISBN 1-891924-00-1.

McNamee, G. (1993).  Named In Stone And Sky: An Arizona Anthology.
Tucson, AZ: University Of Arizona Press.  ISBN 0-8165-1348-1.

Nations, D., & Stump, E. (1996).  Geology Of Arizona, Second Edition.
Dubuque, IA: Kendall-Hunt Publishing.  ISBN 0-7872-2525-8.

Trimble, M. (1986).  Roadside History Of Arizona.
Missoula, MT:  Mountain Press Publishing Company.  ISBN 978-0-8784-2198-5.

Wiewandt, T., & Wilks, M. (2001). The Southwest Inside Out: An Illustrated Guide To The Land And Its History.
Tucson, Arizona: Wild Horizons Publishing. ISBN 1-879728-03-6.