Tag Archives: biodiversity

Taxonomies (classification schemes) rouse passions

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There seems to have been some lively debate among biologists about matters most of us treat as invisible: naming, establishing, and classifying categories. These activities can become quite visible when learning a new language, e.g., French which divides nouns into two genders or German which classifies nouns with any of three genders.

A July 26, 2020 essay by Stephen Garnett (Professor of Conservation and Sustainable Livelihoods, Charles Darwin University, Australia), Les Christidis (Professor, Southern Cross University, Australia), Richard L. Pyle (Associate lecturer, University of Hawaii, US), and Scott Thomson (Research associate, Universidade de São Paulo, Brazil) for The Conversation (also on phys.org but published July 27, 2020) describes a very heated debate over taxonomy,

Taxonomy, or the naming of species, is the foundation of modern biology. It might sound like a fairly straightforward exercise, but in fact it’s complicated and often controversial.

Why? Because there’s no one agreed list of all the world’s species. Competing lists exist for organisms such as mammals and birds, while other less well-known groups have none. And there are more than 30 definitions of what constitutes a species [emphasis mine]. This can make life difficult for biodiversity researchers and those working in areas such as conservation, biosecurity and regulation of the wildlife trade.

In the past few years, a public debate erupted among global taxonomists, including those who authored and contributed to this article, about whether the rules of taxonomy should be changed. Strongly worded ripostes were exchanged. A comparison to Stalin [emphasis mine] was floated.

…

Here’s how it started,

In May 2017 two of the authors, Stephen Garnett and Les Christidis, published an article in Nature. They argued taxonomy needed rules around what should be called a species, because currently there are none. They wrote:

” … for a discipline aiming to impose order on the natural world, taxonomy (the classification of complex organisms) is remarkably anarchic […] There is reasonable agreement among taxonomists that a species should represent a distinct evolutionary lineage. But there is none about how a lineage should be defined.

‘Species’ are often created or dismissed arbitrarily, according to the individual taxonomist’s adherence to one of at least 30 definitions. Crucially, there is no global oversight of taxonomic decisions — researchers can ‘split or lump’ species with no consideration of the consequences.”

Garnett and Christidis proposed that any changes to the taxonomy of complex organisms be overseen by the highest body in the global governance of biology, the International Union of Biological Sciences (IUBS), which would “restrict […] freedom of taxonomic action.”

…

… critics rejected the description of taxonomy as “anarchic”. In fact, they argued there are detailed rules around the naming of species administered by groups such as the International Commission on Zoological Nomenclature and the International Code of Nomenclature for algae, fungi, and plants. For 125 years, the codes have been almost universally adopted by scientists.

So in March 2018, 183 researchers – led by Scott Thomson and Richard Pyle – wrote an animated response to the Nature article, published in PLoS Biology [PLoS is Public Library of Science; it is an open access journal].

They wrote that Garnett and Christidis’ IUBS proposal was “flawed in terms of scientific integrity […] but is also untenable in practice”. They argued:

“Through taxonomic research, our understanding of biodiversity and classifications of living organisms will continue to progress. Any system that restricts such progress runs counter to basic scientific principles, which rely on peer review and subsequent acceptance or rejection by the community, rather than third-party regulation.”

In a separate paper, another group of taxonomists accused Garnett and Christidis of trying to suppress freedom of scientific thought, likening them to Stalin’s science advisor Trofim Lysenko.

…

The various parties did come together,

We hope by 2030, a scientific debate that began with claims of anarchy might lead to a clear governance system – and finally, the world’s first endorsed global list of species.

As for how they got to a “clear governance system”, there’s the rest of the July 26, 2020 essay on The Conversation or there’s the copy on phys.org (published July 27, 2020).

Monitoring forest soundscapes for conservation and more about whale songs

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I don’t understand why anyone would publicize science work featuring soundscapes without including an audio file. However, no one from Princeton University (US) phoned and asked for my advice :).

On the plus side, my whale story does have a sample audio file. However, I’m not sure if I can figure out how to embed it here.

Princeton and monitoring forests

In addition to a professor from Princeton University, there’s the founder of an environmental news organization and someone who’s both a professor at the University of Queensland (Australia) and affiliated with the Nature Conservancy making this of the more unusual collaborations I’ve seen.

Moving on to the news, a January 4, 2019 Princeton University news release (also on EurekAlert but published on Jan. 3, 2019) by B. Rose Kelly announces research into monitoring forests,

Recordings of the sounds in tropical forests could unlock secrets about biodiversity and aid conservation efforts around the world, according to a perspective paper published in Science.

Compared to on-the-ground fieldwork, bioacoustics –recording entire soundscapes, including animal and human activity — is relatively inexpensive and produces powerful conservation insights. The result is troves of ecological data in a short amount of time.

Because these enormous datasets require robust computational power, the researchers argue that a global organization should be created to host an acoustic platform that produces on-the-fly analysis. Not only could the data be used for academic research, but it could also monitor conservation policies and strategies employed by companies around the world.

“Nongovernmental organizations and the conservation community need to be able to truly evaluate the effectiveness of conservation interventions. It’s in the interest of certification bodies to harness the developments in bioacoustics for better enforcement and effective measurements,” said Zuzana Burivalova, a postdoctoral research fellow in Professor David Wilcove’s lab at Princeton University’s Woodrow Wilson School of Public and International Affairs.

“Beyond measuring the effectiveness of conservation projects and monitoring compliance with forest protection commitments, networked bioacoustic monitoring systems could also generate a wealth of data for the scientific community,” said co-author Rhett Butler of the environmental news outlet Mongabay.

Burivalova and Butler co-authored the paper with Edward Game, who is based at the Nature Conservancy and the University of Queensland.

The researchers explain that while satellite imagery can be used to measure deforestation, it often fails to detect other subtle ecological degradations like overhunting, fires, or invasion by exotic species. Another common measure of biodiversity is field surveys, but those are often expensive, time consuming and cover limited ground.

Depending on the vegetation of the area and the animals living there, bioacoustics can record animal sounds and songs from several hundred meters away. Devices can be programmed to record at specific times or continuously if there is solar polar or a cellular network signal. They can also record a range of taxonomic groups including birds, mammals, insects, and amphibians. To date, several multiyear recordings have already been completed.

Bioacoustics can help effectively enforce policy efforts as well. Many companies are engaged in zero-deforestation efforts, which means they are legally obligated to produce goods without clearing large forests. Bioacoustics can quickly and cheaply determine how much forest has been left standing.

“Companies are adopting zero deforestation commitments, but these policies do not always translate to protecting biodiversity due to hunting, habitat degradation, and sub-canopy fires. Bioacoustic monitoring could be used to augment satellites and other systems to monitor compliance with these commitments, support real-time action against prohibited activities like illegal logging and poaching, and potentially document habitat and species recovery,” Butler said.

Further, these recordings can be used to measure climate change effects. While the sounds might not be able to assess slow, gradual changes, they could help determine the influence of abrupt, quick differences to land caused by manufacturing or hunting, for example.

Burivalova and Game have worked together previously as you can see in a July 24, 2017 article by Justine E. Hausheer for a nature.org blog ‘Cool Green Science’ (Note: Links have been removed),

Morning in Musiamunat village. Across the river and up a steep mountainside, birds-of-paradise call raucously through the rainforest canopy, adding their calls to the nearly deafening insect chorus. Less than a kilometer away, small birds flit through a grove of banana trees, taro and pumpkin vines winding across the rough clearing. Here too, the cicadas howl.

To the ear, both garden and forest are awash with noise. But hidden within this dawn chorus are clues to the forest’s health.

New acoustic research from Nature Conservancy scientists indicates that forest fragmentation drives distinct changes in the dawn and dusk choruses of forests in Papua New Guinea. And this innovative method can help evaluate the conservation benefits of land-use planning efforts with local communities, reducing the cost of biodiversity monitoring in the rugged tropics.

…

“It’s one thing for a community to say that they cut fewer trees, or restricted hunting, or set aside a protected area, but it’s very difficult for small groups to demonstrate the effectiveness of those efforts,” says Eddie Game, The Nature Conservancy’s lead scientist for the Asia-Pacific region.

Aside from the ever-present logging and oil palm, another threat to PNG’s forests is subsistence agriculture, which feeds a majority of the population. In the late 1990s, The Nature Conservancy worked with 11 communities in the Adelbert Mountains to create land-use plans, dividing each community’s lands into different zones for hunting, gardening, extracting forest products, village development, and conservation. The goal was to limit degradation to specific areas of the forest, while keeping the rest intact.

But both communities and conservationists needed a way to evaluate their efforts, before the national government considered expanding the program beyond Madang province. So in July 2015, Game and two other scientists, Zuzana Burivalova and Timothy Boucher, spent two weeks gathering data in the Adelbert Mountains, a rugged lowland mountain range in Papua New Guinea’s Madang province.

Working with conservation rangers from Musiamunat, Yavera, and Iwarame communities, the research team tested an innovative method — acoustic sampling — to measure biodiversity across the community forests. Game and his team used small acoustic recorders placed throughout the forest to record 24-hours of sound from locations in each of the different land zones.

Soundscapes from healthy, biodiverse forests are more complex, so the scientists hoped that these recordings would show if parts of the community forests, like the conservation zones, were more biodiverse than others. “Acoustic recordings won’t pick up every species, but we don’t need that level of detail to know if a forest is healthy,” explains Boucher, a conservation geographer with the Conservancy.

…

Here’s a link to and a citation for the latest work from Burivalova and Game,

The sound of a tropical forest by Zuzana Burivalova, Edward T. Game, Rhett A. Butler. Science 04 Jan 2019: Vol. 363, Issue 6422, pp. 28-29 DOI: 10.1126/science.aav1902

This paper is behind a paywall. You can find out more about Mongabay and Rhett Butler in its Wikipedia entry.

***ETA July 18, 2019: Cara Cannon Byington, Associate Director, Science Communications for the Nature Conservancy emailed to say that a January 3, 2019 posting on the conservancy’s Cool Green Science Blog features audio files from the research published in ‘The sound of a tropical forest. Scroll down about 75% of the way for the audio.***

Whale songs

Whales share songs when they meet and a January 8, 2019 Wildlife Conservation Society news release (also on EurekAlert) describes how that sharing takes place,

Singing humpback whales from different ocean basins seem to be picking up musical ideas from afar, and incorporating these new phrases and themes into the latest song, according to a newly published study in Royal Society Open Science that’s helping scientists better understand how whales learn and change their musical compositions.

The new research shows that two humpback whale populations in different ocean basins (the South Atlantic and Indian Oceans) in the Southern Hemisphere sing similar song types, but the amount of similarity differs across years. This suggests that males from these two populations come into contact at some point in the year to hear and learn songs from each other.

The study titled “Culturally transmitted song exchange between humpback whales (Megaptera novaeangliae) in the southeast Atlantic and southwest Indian Ocean basins” appears in the latest edition of the Royal Society Open Science journal. The authors are: Melinda L. Rekdahl, Carissa D. King, Tim Collins, and Howard Rosenbaum of WCS (Wildlife Conservation Society); Ellen C. Garland of the University of St. Andrews; Gabriella A. Carvajal of WCS and Stony Brook University; and Yvette Razafindrakoto of COSAP [ (Committee for the Management of the Protected Area of Bezà Mahafaly ] and Madagascar National Parks.

“Song sharing between populations tends to happen more in the Northern Hemisphere where there are fewer physical barriers to movement of individuals between populations on the breeding grounds, where they do the majority of their singing. In some populations in the Southern Hemisphere song sharing appears to be more complex, with little song similarity within years but entire songs can spread to neighboring populations leading to song similarity across years,” said Dr. Melinda Rekdahl, marine conservation scientist for WCS’s Ocean Giants Program and lead author of the study. “Our study shows that this is not always the case in Southern Hemisphere populations, with similarities between both ocean basin songs occurring within years to different degrees over a 5-year period.”

The study authors examined humpback whale song recordings from both sides of the African continent–from animals off the coasts of Gabon and Madagascar respectively–and transcribed more than 1,500 individual sounds that were recorded between 2001-2005. Song similarity was quantified using statistical methods.

Male humpback whales are one of the animal kingdom’s most noteworthy singers, and individual animals sing complex compositions consisting of moans, cries, and other vocalizations called “song units.” Song units are composed into larger phrases, which are repeated to form “themes.” Different themes are produced in a sequence to form a song cycle that are then repeated for hours, or even days. For the most part, all males within the same population sing the same song type, and this population-wide song similarity is maintained despite continual evolution or change to the song leading to seasonal “hit songs.” Some song learning can occur between populations that are in close proximity and may be able to hear the other population’s song.

Over time, the researchers detected shared phrases and themes in both populations, with some years exhibiting more similarities than others. In the beginning of the study, whale populations in both locations shared five “themes.” One of the shared themes, however, had differences. Gabon’s version of Theme 1, the researchers found, consisted of a descending “cry-woop”, whereas the Madagascar singers split Theme 1 into two parts: a descending cry followed by a separate woop or “trumpet.”

Other differences soon emerged over time. By 2003, the song sung by whales in Gabon became more elaborate than their counterparts in Madagascar. In 2004, both population song types shared the same themes, with the whales in Gabon’s waters singing three additional themes. Interestingly, both whale groups had dropped the same two themes from the previous year’s song types. By 2005, songs being sung on both sides of Africa were largely similar, with individuals in both locations singing songs with the same themes and order. However, there were exceptions, including one whale that revived two discontinued themes from the previous year.

The study’s results stands in contrast to other research in which a song in one part of an ocean basin replaces or “revolutionizes” another population’s song preference. In this instance, the gradual changes and degrees of similarity shared by humpbacks on both sides of Africa was more gradual and subtle.

“Studies such as this one are an important means of understanding connectivity between different whale populations and how they move between different seascapes,” said Dr. Howard Rosenbaum, Director of WCS’s Ocean Giants Program and one of the co-authors of the new paper. “Insights on how different populations interact with one another and the factors that drive the movements of these animals can lead to more effective plans for conservation.”

The humpback whale is one of the world’s best-studied marine mammal species, well known for its boisterous surface behavior and migrations stretching thousands of miles. The animal grows up to 50 feet in length and has been globally protected from commercial whaling since the 1960s. WCS has studied humpback whales since that time and–as the New York Zoological Society–played a key role in the discovery that humpback whales sing songs. The organization continues to study humpback whale populations around the world and right here in the waters of New York; research efforts on humpback and other whales in New York Bight are currently coordinated through the New York Aquarium’s New York Seascape program.

I’m not able to embed the audio file here but, for the curious, there is a portion of a humpback whale song from Gabon here at EurekAlert.

Here’s a link to and a citation for the research paper,

Culturally transmitted song exchange between humpback whales (Megaptera novaeangliae) in the southeast Atlantic and southwest Indian Ocean basins by Melinda L. Rekdahl, Ellen C. Garland, Gabriella A. Carvajal, Carissa D. King, Tim Collins, Yvette Razafindrakoto and Howard Rosenbaum. Royal Society Open Science 21 November 2018 Volume 5 Issue 11 https://doi.org/10.1098/rsos.172305 Published:28 November 2018

This is an open access paper.

I found it at the movies: a commentary on/review of “Films from the Future”

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Kudos to anyone who recognized the reference to Pauline Kael (she changed film criticism forever) and her book “I Lost it at the Movies.” Of course, her book title was a bit of sexual innuendo, quite risqué for an important film critic in 1965 but appropriate for a period (the 1960s) associated with a sexual revolution. (There’s more about the 1960’s sexual revolution in the US along with mention of a prior sexual revolution in the 1920s in this Wikipedia entry.)

The title for this commentary is based on an anecdote from Dr. Andrew Maynard’s (director of the Arizona State University [ASU] Risk Innovation Lab) popular science and technology book, “Films from the Future: The Technology and Morality of Sci-Fi Movies.”

The ‘title-inspiring’ anecdote concerns Maynard’s first viewing of ‘2001: A Space Odyssey, when as a rather “bratty” 16-year-old who preferred to read science fiction, he discovered new ways of seeing and imaging the world. Maynard isn’t explicit about when he became a ‘techno nerd’ or how movies gave him an experience books couldn’t but presumably at 16 he was already gearing up for a career in the sciences. That ‘movie’ revelation received in front of a black and white television on January 1,1982 eventually led him to write, “Films from the Future.” (He has a PhD in physics which he is now applying to the field of risk innovation. For a more detailed description of Dr. Maynard and his work, there’s his ASU profile webpage and, of course, the introduction to his book.)

The book is quite timely. I don’t know how many people have noticed but science and scientific innovation is being covered more frequently in the media than it has been in many years. Science fairs and festivals are being founded on what seems to be a daily basis and you can now find science in art galleries. (Not to mention the movies and television where science topics are covered in comic book adaptations, in comedy, and in standard science fiction style.) Much of this activity is centered on what’s called ’emerging technologies’. These technologies are why people argue for what’s known as ‘blue sky’ or ‘basic’ or ‘fundamental’ science for without that science there would be no emerging technology.

Films from the Future

Isn’t reading the Table of Contents (ToC) the best way to approach a book? (From Films from the Future; Note: The formatting has been altered),

Table of Contents
Chapter One
In the Beginning 14
Beginnings 14
Welcome to the Future 16
The Power of Convergence 18
Socially Responsible Innovation 21
A Common Point of Focus 25
Spoiler Alert 26
Chapter Two
Jurassic Park: The Rise of Resurrection Biology 27
When Dinosaurs Ruled the World 27
De-Extinction 31
Could We, Should We? 36
The Butterfly Effect 39
Visions of Power 43
Chapter Three
Never Let Me Go: A Cautionary Tale of Human Cloning 46
Sins of Futures Past 46
Cloning 51
Genuinely Human? 56
Too Valuable to Fail? 62
Chapter Four
Minority Report: Predicting Criminal Intent 64
Criminal Intent 64
The “Science” of Predicting Bad Behavior 69
Criminal Brain Scans 74
Machine Learning-Based Precognition 77
Big Brother, Meet Big Data 79
Chapter Five
Limitless: Pharmaceutically-enhanced Intelligence 86
A Pill for Everything 86
The Seduction of Self-Enhancement 89
Nootropics 91
If You Could, Would You? 97
Privileged Technology 101
Our Obsession with Intelligence 105
Chapter Six
Elysium: Social Inequity in an Age of Technological
Extremes 110
The Poor Shall Inherit the Earth 110
Bioprinting Our Future Bodies 115
The Disposable Workforce 119
Living in an Automated Future 124
Chapter Seven
Ghost in the Shell: Being Human in an
Augmented Future 129
Through a Glass Darkly 129
Body Hacking 135
More than “Human”? 137
Plugged In, Hacked Out 142
Your Corporate Body 147
Chapter Eight
Ex Machina: AI and the Art of Manipulation 154
Plato’s Cave 154
The Lure of Permissionless Innovation 160
Technologies of Hubris 164
Superintelligence 169
Defining Artificial Intelligence 172
Artificial Manipulation 175
Chapter Nine
Transcendence: Welcome to the Singularity 180
Visions of the Future 180
Technological Convergence 184
Enter the Neo-Luddites 190
Techno-Terrorism 194
Exponential Extrapolation 200
Make-Believe in the Age of the Singularity 203
Chapter Ten
The Man in the White Suit: Living in a Material World 208
There’s Plenty of Room at the Bottom 208
Mastering the Material World 213
Myopically Benevolent Science 220
Never Underestimate the Status Quo 224
It’s Good to Talk 227
Chapter Eleven
Inferno: Immoral Logic in an Age of
Genetic Manipulation 231
Decoding Make-Believe 231
Weaponizing the Genome 234
Immoral Logic? 238
The Honest Broker 242
Dictating the Future 248
Chapter Twelve
The Day After Tomorrow: Riding the Wave of
Climate Change 251
Our Changing Climate 251
Fragile States 255
A Planetary “Microbiome” 258
The Rise of the Anthropocene 260
Building Resiliency 262
Geoengineering the Future 266
Chapter Thirteen
Contact: Living by More than Science Alone 272
An Awful Waste of Space 272
More than Science Alone 277
Occam’s Razor 280
What If We’re Not Alone? 283
Chapter Fourteen
Looking to the Future 288
Acknowledgments 293

The ToC gives the reader a pretty clue as to where the author is going with their book and Maynard explains how he chose his movies in his introductory chapter (from Films from the Future),

“There are some quite wonderful science fiction movies that didn’t make the cut because they didn’t fit the overarching narrative (Blade Runner and its sequel Blade Runner 2049, for instance, and the first of the Matrix trilogy). There are also movies that bombed with the critics, but were included because they ably fill a gap in the bigger story around emerging and converging technologies. Ultimately, the movies that made the cut were chosen because, together, they create an overarching narrative around emerging trends in biotechnologies, cybertechnologies, and materials-based technologies, and they illuminate a broader landscape around our evolving relationship with science and technology. And, to be honest, they are all movies that I get a kick out of watching.” (p. 17)

Jurassic Park (Chapter Two)

Dinosaurs do not interest me—they never have. Despite my profound indifference I did see the movie, Jurassic Park, when it was first released (someone talked me into going). And, I am still profoundly indifferent. Thankfully, Dr. Maynard finds meaning and a connection to current trends in biotechnology,

Jurassic Park is unabashedly a movie about dinosaurs. But it’s also a movie about greed, ambition, genetic engineering, and human folly—all rich pickings for thinking about the future, and what could possibly go wrong. (p. 28)

…

What really stands out with Jurassic Park, over twenty-five years later, is how it reveals a very human side of science and technology. This comes out in questions around when we should tinker with technology and when we should leave well enough alone. But there is also a narrative here that appears time and time again with the movies in this book, and that is how we get our heads around the sometimes oversized roles mega-entrepreneurs play in dictating how new tech is used, and possibly abused. These are all issues that are just as relevant now as they were in 1993, and are front and center of ensuring that the technologyenabled future we’re building is one where we want to live, and not one where we’re constantly fighting for our lives.  (pp. 30-1)

He also describes a connection to current trends in biotechnology,

De-Extinction

In a far corner of Siberia, two Russians—Sergey Zimov and his son Nikita—are attempting to recreate the Ice Age. More precisely, their vision is to reconstruct the landscape and ecosystem of northern Siberia in the Pleistocene, a period in Earth’s history that stretches from around two and a half million years ago to eleven thousand years ago. This was a time when the environment was much colder than now, with huge glaciers and ice sheets flowing over much of the Earth’s northern hemisphere. It was also a time when humans
coexisted with animals that are long extinct, including saber-tooth cats, giant ground sloths, and woolly mammoths.

The Zimovs’ ambitions are an extreme example of “Pleistocene rewilding,” a movement to reintroduce relatively recently extinct large animals, or their close modern-day equivalents, to regions where they were once common. In the case of the Zimovs, the
father-and-son team believe that, by reconstructing the Pleistocene ecosystem in the Siberian steppes and elsewhere, they can slow down the impacts of climate change on these regions. These areas are dominated by permafrost, ground that never thaws through
the year. Permafrost ecosystems have developed and survived over millennia, but a warming global climate (a theme we’ll come back to in chapter twelve and the movie The Day After Tomorrow) threatens to catastrophically disrupt them, and as this happens, the impacts
on biodiversity could be devastating. But what gets climate scientists even more worried is potentially massive releases of trapped methane as the permafrost disappears.

Methane is a powerful greenhouse gas—some eighty times more effective at exacerbating global warming than carbon dioxide— and large-scale releases from warming permafrost could trigger catastrophic changes in climate. As a result, finding ways to keep it in the ground is important. And here the Zimovs came up with a rather unusual idea: maintaining the stability of the environment by reintroducing long-extinct species that could help prevent its destruction, even in a warmer world. It’s a wild idea, but one that has some merit.8 As a proof of concept, though, the Zimovs needed somewhere to start. And so they set out to create a park for deextinct Siberian animals: Pleistocene Park.9

Pleistocene Park is by no stretch of the imagination a modern-day Jurassic Park. The dinosaurs in Hammond’s park date back to the Mesozoic period, from around 250 million years ago to sixty-five million years ago. By comparison, the Pleistocene is relatively modern history, ending a mere eleven and a half thousand years ago. And the vision behind Pleistocene Park is not thrills, spills, and profit, but the serious use of science and technology to stabilize an increasingly unstable environment. Yet there is one thread that ties them together, and that’s using genetic engineering to reintroduce extinct species. In this case, the species in question is warm-blooded and furry: the woolly mammoth.

The idea of de-extinction, or bringing back species from extinction (it’s even called “resurrection biology” in some circles), has been around for a while. It’s a controversial idea, and it raises a lot of tough ethical questions. But proponents of de-extinction argue
that we’re losing species and ecosystems at such a rate that we can’t afford not to explore technological interventions to help stem the flow.

Early approaches to bringing species back from the dead have involved selective breeding. The idea was simple—if you have modern ancestors of a recently extinct species, selectively breeding specimens that have a higher genetic similarity to their forebears can potentially help reconstruct their genome in living animals. This approach is being used in attempts to bring back the aurochs, an ancestor of modern cattle.10 But it’s slow, and it depends on
the fragmented genome of the extinct species still surviving in its modern-day equivalents.

An alternative to selective breeding is cloning. This involves finding a viable cell, or cell nucleus, in an extinct but well-preserved animal and growing a new living clone from it. It’s definitely a more appealing route for impatient resurrection biologists, but it does mean getting your hands on intact cells from long-dead animals and devising ways to “resurrect” these, which is no mean feat. Cloning has potential when it comes to recently extinct species whose cells have been well preserved—for instance, where the whole animal has become frozen in ice. But it’s still a slow and extremely limited option.

Which is where advances in genetic engineering come in.

The technological premise of Jurassic Park is that scientists can reconstruct the genome of long-dead animals from preserved DNA fragments. It’s a compelling idea, if you think of DNA as a massively long and complex instruction set that tells a group of biological molecules how to build an animal. In principle, if we could reconstruct the genome of an extinct species, we would have the basic instruction set—the biological software—to reconstruct
individual members of it.

The bad news is that DNA-reconstruction-based de-extinction is far more complex than this. First you need intact fragments of DNA, which is not easy, as DNA degrades easily (and is pretty much impossible to obtain, as far as we know, for dinosaurs). Then you
need to be able to stitch all of your fragments together, which is akin to completing a billion-piece jigsaw puzzle without knowing what the final picture looks like. This is a Herculean task, although with breakthroughs in data manipulation and machine learning,
scientists are getting better at it. But even when you have your reconstructed genome, you need the biological “wetware”—all the stuff that’s needed to create, incubate, and nurture a new living thing, like eggs, nutrients, a safe space to grow and mature, and so on. Within all this complexity, it turns out that getting your DNA sequence right is just the beginning of translating that genetic code into a living, breathing entity. But in some cases, it might be possible.

In 2013, Sergey Zimov was introduced to the geneticist George Church at a conference on de-extinction. Church is an accomplished scientist in the field of DNA analysis and reconstruction, and a thought leader in the field of synthetic biology (which we’ll come
back to in chapter nine). It was a match made in resurrection biology heaven. Zimov wanted to populate his Pleistocene Park with mammoths, and Church thought he could see a way of
achieving this.

What resulted was an ambitious project to de-extinct the woolly mammoth. Church and others who are working on this have faced plenty of hurdles. But the technology has been advancing so fast that, as of 2017, scientists were predicting they would be able to reproduce the woolly mammoth within the next two years.

One of those hurdles was the lack of solid DNA sequences to work from. Frustratingly, although there are many instances of well preserved woolly mammoths, their DNA rarely survives being frozen for tens of thousands of years. To overcome this, Church and others
have taken a different tack: Take a modern, living relative of the mammoth, and engineer into it traits that would allow it to live on the Siberian tundra, just like its woolly ancestors.

Church’s team’s starting point has been the Asian elephant. This is their source of base DNA for their “woolly mammoth 2.0”—their starting source code, if you like. So far, they’ve identified fifty plus gene sequences they think they can play with to give their modern-day woolly mammoth the traits it would need to thrive in Pleistocene Park, including a coat of hair, smaller ears, and a constitution adapted to cold.

The next hurdle they face is how to translate the code embedded in their new woolly mammoth genome into a living, breathing animal. The most obvious route would be to impregnate a female Asian elephant with a fertilized egg containing the new code. But Asian elephants are endangered, and no one’s likely to allow such cutting edge experimentation on the precious few that are still around, so scientists are working on an artificial womb for their reinvented woolly mammoth. They’re making progress with mice and hope to crack the motherless mammoth challenge relatively soon.

It’s perhaps a stretch to call this creative approach to recreating a species (or “reanimation” as Church refers to it) “de-extinction,” as what is being formed is a new species. … (pp. 31-4)

This selection illustrates what Maynard does so very well throughout the book where he uses each film as a launching pad for a clear, readable description of relevant bits of science so you understand why the premise was likely, unlikely, or pure fantasy while linking it to contemporary practices, efforts, and issues. In the context of Jurassic Park, Maynard goes on to raise some fascinating questions such as: Should we revive animals rendered extinct (due to obsolescence or inability to adapt to new conditions) when we could develop new animals?

General thoughts

‘Films for the Future’ offers readable (to non-scientific types) science, lively writing, and the occasional ‘memorish’ anecdote. As well, Dr. Maynard raises the curtain on aspects of the scientific enterprise that most of us do not get to see.  For example, the meeting  between Sergey Zimov and George Church and how it led to new ‘de-extinction’ work’. He also describes the problems that the scientists encountered and are encountering. This is in direct contrast to how scientific work is usually presented in the news media as one glorious breakthrough after the next.

Maynard does discuss the issues of social inequality and power and ownership. For example, who owns your transplant or data? Puzzlingly, he doesn’t touch on the current environment where scientists in the US and elsewhere are encouraged/pressured to start up companies commercializing their work.

Nor is there any mention of how universities are participating in this grand business experiment often called ‘innovation’. (My March 15, 2017 posting describes an outcome for the CRISPR [gene editing system] patent fight taking place between Harvard University’s & MIT’s [Massachusetts Institute of Technology] Broad Institute vs the University of California at Berkeley and my Sept. 11, 2018 posting about an art/science exhibit in Vancouver [Canada] provides an update for round 2 of the Broad Institute vs. UC Berkeley patent fight [scroll down about 65% of the way.) *To read about how my ‘cultural blindness’ shows up here scroll down to the single asterisk at the end.*

There’s a foray through machine-learning and big data as applied to predictive policing in Maynard’s ‘Minority Report’ chapter (my November 23, 2017 posting describes Vancouver’s predictive policing initiative [no psychics involved], the first such in Canada). There’s no mention of surveillance technology, which if I recall properly was part of the future environment, both by the state and by corporations. (Mia Armstrong’s November 15, 2018 article for Slate on Chinese surveillance being exported to Venezuela provides interesting insight.)

The gaps are interesting and various. This of course points to a problem all science writers have when attempting an overview of science. (Carl Zimmer’s latest, ‘She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity’] a doorstopping 574 pages, also has some gaps despite his focus on heredity,)

Maynard has worked hard to give an comprehensive overview in a remarkably compact 279 pages while developing his theme about science and the human element. In other words, science is not monolithic; it’s created by human beings and subject to all the flaws and benefits that humanity’s efforts are always subject to—scientists are people too.

The readership for ‘Films from the Future’ spans from the mildly interested science reader to someone like me who’s been writing/blogging about these topics (more or less) for about 10 years. I learned a lot reading this book.

Next time, I’m hopeful there’ll be a next time, Maynard might want to describe the parameters he’s set for his book in more detail that is possible in his chapter headings. He could have mentioned that he’s not a cinéaste so his descriptions of the movies are very much focused on the story as conveyed through words. He doesn’t mention colour palates, camera angles, or, even, cultural lenses.

Take for example, his chapter on ‘Ghost in the Shell’. Focused on the Japanese animation film and not the live action Hollywood version he talks about human enhancement and cyborgs. The Japanese have a different take on robots, inanimate objects, and, I assume, cyborgs than is found in Canada or the US or Great Britain, for that matter (according to a colleague of mine, an Englishwoman who lived in Japan for ten or more years). There’s also the chapter on the Ealing comedy, The Man in The White Suit, an English film from the 1950’s. That too has a cultural (as well as, historical) flavour but since Maynard is from England, he may take that cultural flavour for granted. ‘Never let me go’ in Chapter Two was also a UK production, albeit far more recent than the Ealing comedy and it’s interesting to consider how a UK production about cloning might differ from a US or Chinese or … production on the topic. I am hearkening back to Maynard’s anecdote about movies giving him new ways of seeing and imagining the world.

There’s a corrective. A couple of sentences in Maynard’s introductory chapter cautioning that in depth exploration of ‘cultural lenses’ was not possible without expanding the book to an unreadable size followed by a sentence in each of the two chapters that there are cultural differences.

One area where I had a significant problem was with regard to being “programmed” and having  “instinctual” behaviour,

As a species, we are embarrassingly programmed to see “different” as “threatening,” and to take instinctive action against it. It’s a trait that’s exploited in many science fiction novels and movies, including those in this book. If we want to see the rise of increasingly augmented individuals, we need to be prepared for some social strife. (p. 136)

These concepts are much debated in the social sciences and there are arguments for and against ‘instincts regarding strangers and their possible differences’. I gather Dr. Maynard hies to the ‘instinct to defend/attack’ school of thought.

One final quandary, there was no sex and I was expecting it in the Ex Machina chapter, especially now that sexbots are about to take over the world (I exaggerate). Certainly, if you’re talking about “social strife,” then sexbots would seem to be fruitful line of inquiry, especially when there’s talk of how they could benefit families (my August 29, 2018 posting). Again, there could have been a sentence explaining why Maynard focused almost exclusively in this chapter on the discussions about artificial intelligence and superintelligence.

Taken in the context of the book, these are trifling issues and shouldn’t stop you from reading Films from the Future. What Maynard has accomplished here is impressive and I hope it’s just the beginning.

Final note

Bravo Andrew! (Note: We’ve been ‘internet acquaintances/friends since the first year I started blogging. When I’m referring to him in his professional capacity, he’s Dr. Maynard and when it’s not strictly in his professional capacity, it’s Andrew. For this commentary/review I wanted to emphasize his professional status.)

If you need to see a few more samples of Andrew’s writing, there’s a Nov. 15, 2018 essay on The Conversation, Sci-fi movies are the secret weapon that could help Silicon Valley grow up and a Nov. 21, 2018 article on slate.com, The True Cost of Stain-Resistant Pants; The 1951 British comedy The Man in the White Suit anticipated our fears about nanotechnology. Enjoy.

****Added at 1700 hours on Nov. 22, 2018: You can purchase Films from the Future here.

*Nov. 23, 2018: I should have been more specific and said ‘academic scientists’. In Canada, the great percentage of scientists are academic. It’s to the point where the OECD (Organization for Economic Cooperation and Development) has noted that amongst industrialized countries, Canada has very few industrial scientists in comparison to the others.

‘Robomussels’ for climate change

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These ‘robomussels’ are not voting but they are being used to monitor mussel bed habitats according to an Oct. 17, 2016 news item on ScienceDaily,

Tiny robots have been helping researchers study how climate change affects biodiversity. Developed by Northeastern University scientist Brian Helmuth, the “robomussels” have the shape, size, and color of actual mussels, with miniature built-in sensors that track temperatures inside the mussel beds.

Caption: This is a robomussel, seen among living mussels and other sea creatures. Credit: Allison Matzelle

Caption: This is a robomussel, seen among living mussels and other sea creatures. Credit: Allison Matzelle

An Oct. 12, 2016 Northeastern University news release (also on EurekAlert), which originated the news item, describes a project some 20 years in the making,

For the past 18 years, every 10 to 15 minutes, Helmuth and a global research team of 48 scientists have used robomussels to track internal body temperature, which is determined by the temperature of the surrounding air or water, and the amount of solar radiation the devices absorb. They place the robots inside mussel beds in oceans around the globe and record temperatures. The researchers have built a database of nearly two decades worth of data enabling scientists to pinpoint areas of unusual warming, intervene to help curb damage to vital marine ecosystems, and develop strategies that could prevent extinction of certain species.

Housed at Northeastern’s Marine Science Center in Nahant, Massachusetts, this largest-ever database is not only a remarkable way to track the effects of climate change, the findings can also reveal emerging hotspots so policymakers and scientists can step in and relieve stressors such as erosion and water acidification before it’s too late.

“They look exactly like mussels but they have little green blinking lights in them,” says Helmuth. “You basically pluck out a mussel and then glue the device to the rock right inside the mussel bed. They enable us to link our field observations with the physiological impact of global climate change on these ecologically and economically important animals.”

…

For ecological forecasters such as Helmuth, mussels act as a barometer of climate change. That’s because they rely on external sources of heat such as air temperature and sun exposure for their body heat and thrive, or not, depending on those conditions. Using fieldwork along with mathematical and computational models, Helmuth forecasts the patterns of growth, reproduction, and survival of mussels in intertidal zones.

Over the years, he and his colleagues have found surprises: “Our expectations of where to look for the effects of climate change in nature are more complex than anticipated,” says Helmuth. For example, in an earlier paper in the journal Science, his team found that hotspots existed not only at the southern end of the species’ distribution, in this case, southern California; they also existed at sites up north, in Oregon and Washington state.

“These datasets tell us when and where to look for the effects of climate change,” he says. “Without them we could miss early warning signs of trouble.”

The robomussels’ near-continuous measurements serve as an early warning system. “If we start to see sites where the animals are regularly getting to temperatures that are right below what kills them, we know that any slight increase is likely to send them over the edge, and we can act,” says Helmuth.

It’s not only the mussels that may be pulled back from the brink. The advance notice could inform everything from maintaining the biodiversity of coastal systems to determining the best–and worst–places to locate mussel farms.

“Losing mussel beds is essentially like clearing a forest,” says Helmuth. “If they go, everything that’s living in them will go. They are a major food supply for many species, including lobsters and crabs. They also function as filters along near-shore waters, clearing huge amounts of particulates. So losing them can affect everything from the growth of species we care about because we want to eat them to water clarity to biodiversity of all the tiny animals that live on the insides of the beds.”

Here’s a link to and a citation for the paper,

Long-term, high frequency in situ measurements of intertidal mussel bed temperatures using biomimetic sensors by Brian Helmuth, Francis Choi, Gerardo Zardi.  Scientific Data 3, Article number: 160087 (2016) doi:10.1038/sdata.2016.87 Published online: 11 October 2016

This paper is open access.

Nearby Nature GigaBlitz—Summer Solstice 2012—get your science out

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The June 20 – 26, 2012 GigaBlitz event is an international citizen science project focused on biodiversity. From the June 13, 2012 news item on physorg.com,

A high-resolution image of a palm tree in Brazil, which under close examination shows bees, wasps and flies feasting on nectars and pollens, was the top jury selection among the images captured during last December’s Nearby Nature GigaBlitz. It’s also an example of what organizers hope participants will produce for the next GigaBlitz, June 20-26 [2012].

Here’s a close up from the Brazilian palm tree image,

Bee close up from Palmeira em flor, by Eduardo Frick (http://gigapan.com/gigapans/95168/)

This bee close up does not convey the full impact of an image that you can zoom from a standard size to extreme closeups of insects, other animals, portions of palm fronds, etc. To get the full impact go here.

Here’s more about the Nearby Nature GigaBlitz events from the June 13, 2012 Carnegie Mellon University news release,

The Nearby Nature GigaBlitz events are citizen science projects in which people use gigapixel imagery technology to document biodiversity in their backyards — if not literally in their backyards, then in a nearby woodlot or vacant field. These images are then shared and made available for analysis via the GigaPan website. The events are organized by a trio of biologists and their partners at Carnegie Mellon University’s CREATE Lab.

…

December’s GigaBlitz included contributors from the United States, Canada, Spain, Japan, South Africa, Brazil, Singapore, Indonesia and Australia. Ten of the best images are featured in the June issue of GigaPan Magazine, an online publication of CMU’s CREATE Lab.

The issue was guest-edited by the organizers of the GigaBlitz: Ken Tamminga, professor of landscape architecture at Penn State University; Dennis vanEngelsdorp, research scientist at the University of Maryland’s Department of Entomology; and M. Alex Smith, assistant professor of integrative biology at the University of Guelph, Ontario.

The inspiration for the gigablitz comes from the world of ornithology (bird watching), from the Carnegie Mellon University June 13, 2012 news release,

Tamminga, vanEngelsdorp and Smith envisioned something akin to a BioBlitz, an intensive survey of a park or nature preserve that attempts to identify all living species within an area at a given time, and citizen science efforts such as the Audubon Society’s Christmas Bird Count.

“We imagined using these widely separated, but nearby, panoramas as a way of collecting biodiversity data – similar to the Christmas bird count – where citizen scientists surveyed their world, then distributed and shared that data with the world through public GigaPans,” they wrote. “The plus of the GigaPan approach was that the sharing was bi-directional – not merely ‘This is what I saw,’ but also hearing someone say, ‘This is what I found in your GigaPan.'”

Here’s an excerpt from the Nearby Nature gigablitz June 20 -26, 2012 Call for Entries,

The challenge: Gigapixel imaging can reveal a surprising range of animal and plant species in the ordinary and sometimes extraordinary settings in which we live, learn, and work. Your challenge is to capture panoramas of Nearby Nature and share them with your peers at gigapan.org for further exploration. We hope that shared panoramas and snapshotting will help the GigaPan community more deeply explore, document, and celebrate the diversity of life forms in their local habitats.

Gigablitz timing: The event will take place over a 7-day period – a gigablitz – that aligns with the June solstice. Please capture and upload your images to the gigapan.org website between 6am, June 20 and 11pm, June 26 (your local time).

Juried selections:    Panoramas that meet the criteria below are eligible for inclusion in the science.gigapan.org Nearby Nature collection. The best panoramas will be selected by a jury for publication in an issue of GigaPan Magazine dedicated to the Nearby Nature collection.  Selection criteria are as follows:

  • Biodiversity: the image is species rich.
  • Uniqueness: the image contains particularly interesting or unique species, or the image captures a sense of the resilience of life-forms in human-dominated settings.
  • Nearby Nature context: image habitat is part of, or very near, the everyday places that people inhabit.
  • Image quality: the image is of high quality and is visually captivating.

Subjects and locations: The gigablitz subject may be any “nearby” location in which you have a personal interest:  schoolyard garden, backyard habitat, balcony planter, village grove, nearby remnant woods, vacant lot meadow next door and others.  Panoramas with high species richness (the range of different species in a given area) that are part of everyday places are especially encouraged.  It is the process of making and sharing gigapans that will transform the ordinary into the extraordinary.

Here are 3 things to keep in mind when choosing a place:

  • The panorama should focus on organisms in a habitat near your home, school or place of work.
  • Any life-forms are acceptable, such as plants, insects, and other animals.
  • Rich, sharp detail will encourage snapshotters to help identify organisms in your panorama.  Thus, your gigapan unit should be positioned close to the subject habitat – within 100 feet (30 meters) away, and preferably much closer.  Up close mini-habitats in the near-macro range are welcome.

Please do check the Call for Entries for additional information about the submissions.

As for the website which hosts the contest, I checked the About GigaPan page and found this,

What is a GigaPan?

Gigapans are gigapixel panoramas, digital images with billions of pixels. They are huge panoramas with fascinating detail, all captured in the context of a single brilliant photo. Phenomenally large, yet remarkably crisp and vivid, gigapans are available to be explored at GigaPan.com. Zoom in and discover the detail of over 50,000 panoramas from around the world.

A New Dimension for Photography

GigaPan gives experienced and novice photographers the technology to create high-resolution panorama images more easily than ever before, and the resulting GigaPan images offer viewers a new, unique perspective on the world.

GigaPan offers the first solution for shooting, viewing and exploring high-resolution panoramic images in a single system: EPIC series of robotic camera mounts capture photos using almost any digital camera; GigaPan Stitch Software automatically combines the thousands of images taken into a single image; and GigaPan.com enables the unique mega-high resolution viewing experience.

GigaPan EPIC

GigaPan EPIC robotic mounts empower cameras to take hundreds, even thousands of photos, which are combined to create one highly detailed image with amazing depth and clarity.

The GigaPan EPIC and EPIC 100 are compatible with a broad range of point-and-shoot cameras and small DSLRs to capture gigapans, quickly and accurately. Light and compact, they are easy-to-use, and remarkably efficient. The EPIC Pro is designed to work with DSLR cameras and larger lenses, features advanced technology, and delivers stunning performance and precision. Strong enough to hold a camera and lens combination of up to 10 lbs, the EPIC Pro enables users to capture enormous panoramas with crisp, vivid detail.

Bringing Mars Rover Technology to Earth

The GigaPan EPIC series is based on the same technology employed by the Mars Rovers, Spirit and Opportunity, to capture the incredible images of the red planet. Now everyone has the opportunity to use technology developed for Mars to take their own incredible images.

GigaPan was formed in 2008 as a commercial spin-off of a successful research collaboration between a team of researchers at NASA and Carnegie Mellon University. The company’s mission is to bring this powerful, high-resolution imaging capability to a broad audience.

The original GigaPan prototype and related software were devised by a team led by Randy Sargent, a senior systems scientist at Carnegie Mellon West and the NASA Ames Research Center in Moffett Field, Calif., and Illah Nourbakhsh, an associate professor of robotics at Carnegie Mellon in Pittsburgh.

If I understand this rightly, this commercial enterprise (GigaPan), which offers hardware and software,  also supports a community-sharing platform for the types of images made possible by the equipment they sell.

Vancouver’s Café Scientifique March 27, 2012 meeting

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At the Railway Club (579 Dunsmuir Street, Vancouver, BC, Canada) as usual, this month’s Café Scientifique features (from the March 2012 announcement),

Dr. Bruce Archibald, a paleontologist from Simon Fraser University. His café will be:

How are global patterns of biodiversity affected by climate? The view from a fossil fly’s eye.

Understanding the way that large-scale patterns of biodiversity are affected by climate has been among the greatest outstanding problems in ecology. Why are there more species in the tropics? The answer isn’t as simple as it might seem at first, as some possible controlling factors change together with latitude, and so their individual affects are difficult to evaluate. This Gordian knot might be cut, though, by looking in deep time, when global climates followed different patterns than today. So, comparing both modern and fossil communities in their environmental contexts allows a novel view of this problem. Why do the species compositions of communities change differently across mountainous landscapes in the tropics than in the Temperate Zones? An intriguing hypothesis proposed by Dan Janzen in 1967 can be examined by this system. Fossil insect communities from our regions may provide answers to understanding some basic ways of how life in the modern world is organized.

The café will take place on

Tuesday, March 27, 2012
7:30 pm
Railway Club
579 Dunsmuir Street
Vancouver

The event is held in a side room and not in the bar proper.