Tag Archives: evolution

Nature’s missing evolutionary law added in new paper by leading scientists and philosophers

An October 22, 2023 commentary by Rae Hodge for Salon.com introduces the new work with a beautiful lede/lead and more,

A recently published scientific article proposes a sweeping new law of nature, approaching the matter with dry, clinical efficiency that still reads like poetry.

“A pervasive wonder of the natural world is the evolution of varied systems, including stars, minerals, atmospheres, and life,” the scientists write in the Proceedings of the National Academy of Sciences. “Evolving systems are asymmetrical with respect to time; they display temporal increases in diversity, distribution, and/or patterned behavior,” they continue, mounting their case from the shoulders of Charles Darwin, extending it toward all things living and not.

To join the known physics laws of thermodynamics, electromagnetism and Newton’s laws of motion and gravity, the nine scientists and philosophers behind the paper propose their “law of increasing functional information.”

In short, a complex and evolving system — whether that’s a flock of gold finches or a nebula or the English language — will produce ever more diverse and intricately detailed states and configurations of itself.

And here, any writer should find their breath caught in their throat. Any writer would have to pause and marvel.

It’s a rare thing to hear the voice of science singing toward its twin in the humanities. The scientists seem to be searching in their paper for the right words to describe the way the nested trills of a flautist rise through a vaulted cathedral to coalesce into notes themselves not played by human breath. And how, in the very same way, the oil-slick sheen of a June Bug wing may reveal its unseen spectra only against the brief-blooming dogwood in just the right season of sun.

Both intricate configurations of art and matter arise and fade according to their shared characteristic, long-known by students of the humanities: each have been graced with enough time to attend to the necessary affairs of their most enduring pleasures.

If you have the time, do read this October 22, 2023 commentary as Hodge waxes eloquent.

An October 16, 2023 news item on phys.org announces the work in a more prosaic fashion,

A paper published in the Proceedings of the National Academy of Sciences describes “a missing law of nature,” recognizing for the first time an important norm within the natural world’s workings.

In essence, the new law states that complex natural systems evolve to states of greater patterning, diversity, and complexity. In other words, evolution is not limited to life on Earth, it also occurs in other massively complex systems, from planets and stars to atoms, minerals, and more.

It was authored by a nine-member team— scientists from the Carnegie Institution for Science, the California Institute of Technology (Caltech) and Cornell University, and philosophers from the University of Colorado.

An October 16, 2023 Carnegie Science Earth and Planets Laboratory news release on EurekAlert (there is also a somewhat shorter October 16, 2023 version on the Carnegie Science [Carnegie Institution of Science] website), which originated the news item, provides a lot more detail,

“Macroscopic” laws of nature describe and explain phenomena experienced daily in the natural world. Natural laws related to forces and motion, gravity, electromagnetism, and energy, for example, were described more than 150 years ago. 

The new work presents a modern addition — a macroscopic law recognizing evolution as a common feature of the natural world’s complex systems, which are characterised as follows:

  • They are formed from many different components, such as atoms, molecules, or cells, that can be arranged and rearranged repeatedly
  • Are subject to natural processes that cause countless different arrangements to be formed
  • Only a small fraction of all these configurations survive in a process called “selection for function.”   

Regardless of whether the system is living or nonliving, when a novel configuration works well and function improves, evolution occurs. 

The authors’ “Law of Increasing Functional Information” states that the system will evolve “if many different configurations of the system undergo selection for one or more functions.”

“An important component of this proposed natural law is the idea of ‘selection for function,’” says Carnegie astrobiologist Dr. Michael L. Wong, first author of the study.

In the case of biology, Darwin equated function primarily with survival—the ability to live long enough to produce fertile offspring. 

The new study expands that perspective, noting that at least three kinds of function occur in nature. 

The most basic function is stability – stable arrangements of atoms or molecules are selected to continue. Also chosen to persist are dynamic systems with ongoing supplies of energy. 

The third and most interesting function is “novelty”—the tendency of evolving systems to explore new configurations that sometimes lead to startling new behaviors or characteristics. 

Life’s evolutionary history is rich with novelties—photosynthesis evolved when single cells learned to harness light energy, multicellular life evolved when cells learned to cooperate, and species evolved thanks to advantageous new behaviors such as swimming, walking, flying, and thinking. 

The same sort of evolution happens in the mineral kingdom. The earliest minerals represent particularly stable arrangements of atoms. Those primordial minerals provided foundations for the next generations of minerals, which participated in life’s origins. The evolution of life and minerals are intertwined, as life uses minerals for shells, teeth, and bones.

Indeed, Earth’s minerals, which began with about 20 at the dawn of our Solar System, now number almost 6,000 known today thanks to ever more complex physical, chemical, and ultimately biological processes over 4.5 billion years. 

In the case of stars, the paper notes that just two major elements – hydrogen and helium – formed the first stars shortly after the big bang. Those earliest stars used hydrogen and helium to make about 20 heavier chemical elements. And the next generation of stars built on that diversity to produce almost 100 more elements.

“Charles Darwin eloquently articulated the way plants and animals evolve by natural selection, with many variations and traits of individuals and many different configurations,” says co-author Robert M. Hazen of Carnegie Science, a leader of the research.

“We contend that Darwinian theory is just a very special, very important case within a far larger natural phenomenon. The notion that selection for function drives evolution applies equally to stars, atoms, minerals, and many other conceptually equivalent situations where many configurations are subjected to selective pressure.”

The co-authors themselves represent a unique multi-disciplinary configuration: three philosophers of science, two astrobiologists, a data scientist, a mineralogist, and a theoretical physicist.

Says Dr. Wong: “In this new paper, we consider evolution in the broadest sense—change over time—which subsumes Darwinian evolution based upon the particulars of ‘descent with modification.’”  

“The universe generates novel combinations of atoms, molecules, cells, etc. Those combinations that are stable and can go on to engender even more novelty will continue to evolve. This is what makes life the most striking example of evolution, but evolution is everywhere.”

Among many implications, the paper offers: 

  1. Understanding into how differing systems possess varying degrees to which they can continue to evolve. “Potential complexity” or “future complexity” have been proposed as metrics of how much more complex an evolving system might become
  2. Insights into how the rate of evolution of some systems can be influenced artificially. The notion of functional information suggests that the rate of evolution in a system might be increased in at least three ways: (1) by increasing the number and/or diversity of interacting agents, (2) by increasing the number of different configurations of the system; and/or 3) by enhancing the selective pressure on the system (for example, in chemical systems by more frequent cycles of heating/cooling or wetting/drying).
  3. A deeper understanding of generative forces behind the creation and existence of complex phenomena in the universe, and the role of information in describing them
  4. An understanding of life in the context of other complex evolving systems. Life shares certain conceptual equivalencies with other complex evolving systems, but the authors point to a future research direction, asking if there is something distinct about how life processes information on functionality (see also https://royalsocietypublishing.org/doi/10.1098/rsif.2022.0810).
  5. Aiding the search for life elsewhere: if there is a demarcation between life and non-life that has to do with selection for function, can we identify the “rules of life” that allow us to discriminate that biotic dividing line in astrobiological investigations? (See also https://conta.cc/3LwLRYS, “Did Life Exist on Mars? Other Planets? With AI’s Help, We May Know Soon”)
  6. At a time when evolving AI systems are an increasing concern, a predictive law of information that characterizes how both natural and symbolic systems evolve is especially welcome

Laws of nature – motion, gravity, electromagnetism, thermodynamics – etc. codify the general behavior of various macroscopic natural systems across space and time. 

The “law of increasing functional information” published today complements the 2nd law of thermodynamics, which states that the entropy (disorder) of an isolated system increases over time (and heat always flows from hotter to colder objects).

* * * * *

Comments

“This is a superb, bold, broad, and transformational article.  …  The authors are approaching the fundamental issue of the increase in complexity of the evolving universe. The purpose is a search for a ‘missing law’ that is consistent with the known laws.

“At this stage of the development of these ideas, rather like the early concepts in the mid-19th century of coming to understand ‘energy’ and ‘entropy,’ open broad discussion is now essential.”

Stuart Kauffman
Institute for Systems Biology, Seattle WA

“The study of Wong et al. is like a breeze of fresh air blowing over the difficult terrain at the trijunction of astrobiology, systems science and evolutionary theory. It follows in the steps of giants such as Erwin Schrödinger, Ilya Prigogine, Freeman Dyson and James Lovelock. In particular, it was Schrödinger who formulated the perennial puzzle: how can complexity increase — and drastically so! — in living systems, while they remain bound by the Second Law of thermodynamics? In the pile of attempts to resolve this conundrum in the course of the last 80 years, Wong et al. offer perhaps the best shot so far.”

“Their central idea, the formulation of the law of increasing functional information, is simple but subtle: a system will manifest an increase in functional information if its various configurations generated in time are selected for one or more functions. This, the authors claim, is the controversial ‘missing law’ of complexity, and they provide a bunch of excellent examples. From my admittedly quite subjective point of view, the most interesting ones pertain to life in radically different habitats like Titan or to evolutionary trajectories characterized by multiple exaptations of traits resulting in a dramatic increase in complexity. Does the correct answer to Schrödinger’s question lie in this direction? Only time will tell, but both my head and my gut are curiously positive on that one. Finally, another great merit of this study is worth pointing out: in this day and age of rabid Counter-Enlightenment on the loose, as well as relentless attacks on the freedom of thought and speech, we certainly need more unabashedly multidisciplinary and multicultural projects like this one.”

Milan Cirkovic 
Astronomical Observatory of Belgrade, Serbia; The Future of Humanity Institute, Oxford University [University of Oxford]

The natural laws we recognize today cannot yet account for one astounding characteristic of our universe—the propensity of natural systems to “evolve.” As the authors of this study attest, the tendency to increase in complexity and function through time is not specific to biology, but is a fundamental property observed throughout the universe. Wong and colleagues have distilled a set of principles which provide a foundation for cross-disciplinary discourse on evolving systems. In so doing, their work will facilitate the study of self-organization and emergent complexity in the natural world.

Corday Selden
Department of Marine and Coastal Sciences, Rutgers University

The paper “On the roles of function and selection in evolving systems” provides an innovative, compelling, and sound theoretical framework for the evolution of complex systems, encompassing both living and non-living systems. Pivotal in this new law is functional information, which quantitatively captures the possibilities a system has to perform a function. As some functions are indeed crucial for the survival of a living organism, this theory addresses the core of evolution and is open to quantitative assessment. I believe this contribution has also the merit of speaking to different scientific communities that might find a common ground for open and fruitful discussions on complexity and evolution.

Andrea Roli
Assistant Professor, Università di Bologna.

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

On the roles of function and selection in evolving systems by Michael L. Wong, Carol E. Cleland, Daniel Arends Jr., Stuart Bartlett, H. James Cleaves, Heather Demarest, Anirudh Prabhu, Jonathan I. Lunine, and Robert M. Hazen. Proceedings of the National Academy of Sciences (PNAS) 120 (43) e2310223120 DOI: https://doi.org/10.1073/pnas.2310223120 Published: October 16, 2023

This paper is open access.

True love with AI (artificial intelligence): The Nature of Things explores emotional and creative AI (long read)

The Canadian Broadcasting Corporation’s (CBC) science television series,The Nature of Things, which has been broadcast since November 1960, explored the world of emotional, empathic and creative artificial intelligence (AI) in a Friday, November 19, 2021 telecast titled, The Machine That Feels,

The Machine That Feels explores how artificial intelligence (AI) is catching up to us in ways once thought to be uniquely human: empathy, emotional intelligence and creativity.

As AI moves closer to replicating humans, it has the potential to reshape every aspect of our world – but most of us are unaware of what looms on the horizon.

Scientists see AI technology as an opportunity to address inequities and make a better, more connected world. But it also has the capacity to do the opposite: to stoke division and inequality and disconnect us from fellow humans. The Machine That Feels, from The Nature of Things, shows viewers what they need to know about a field that is advancing at a dizzying pace, often away from the public eye.

What does it mean when AI makes art? Can AI interpret and understand human emotions? How is it possible that AI creates sophisticated neural networks that mimic the human brain? The Machine That Feels investigates these questions, and more.

In Vienna, composer Walter Werzowa has — with the help of AI — completed Beethoven’s previously unfinished 10th symphony. By feeding data about Beethoven, his music, his style and the original scribbles on the 10th symphony into an algorithm, AI has created an entirely new piece of art.

In Atlanta, Dr. Ayanna Howard and her robotics lab at Georgia Tech are teaching robots how to interpret human emotions. Where others see problems, Howard sees opportunity: how AI can help fill gaps in education and health care systems. She believes we need a fundamental shift in how we perceive robots: let’s get humans and robots to work together to help others.

At Tufts University in Boston, a new type of biological robot has been created: the xenobot. The size of a grain of sand, xenobots are grown from frog heart and skin cells, and combined with the “mind” of a computer. Programmed with a specific task, they can move together to complete it. In the future, they could be used for environmental cleanup, digesting microplastics and targeted drug delivery (like releasing chemotherapy compounds directly into tumours).

The film includes interviews with global leaders, commentators and innovators from the AI field, including Geoff Hinton, Yoshua Bengio, Ray Kurzweil and Douglas Coupland, who highlight some of the innovative and cutting-edge AI technologies that are changing our world.

The Machine That Feels focuses on one central question: in the flourishing age of artificial intelligence, what does it mean to be human?

I’ll get back to that last bit, “… what does it mean to be human?” later.

There’s a lot to appreciate in this 44 min. programme. As you’d expect, there was a significant chunk of time devoted to research being done in the US but Poland and Japan also featured and Canadian content was substantive. A number of tricky topics were covered and transitions from one topic to the next were smooth.

In the end credits, I counted over 40 source materials from Getty Images, Google Canada, Gatebox, amongst others. It would have been interesting to find out which segments were produced by CBC.

David Suzuki’s (programme host) script was well written and his narration was enjoyable, engaging, and non-intrusive. That last quality is not always true of CBC hosts who can fall into the trap of overdramatizing the text.

Drilling down

I have followed artificial intelligence stories in a passive way (i.e., I don’t seek them out) for many years. Even so, there was a lot of material in the programme that was new to me.

For example, there was this love story (from the ‘I love her and see her as a real woman.’ Meet a man who ‘married’ an artificial intelligence hologram webpage on the CBC),

In the The Machine That Feels, a documentary from The Nature of Things, we meet Kondo Akihiko, a Tokyo resident who “married” a hologram of virtual pop singer Hatsune Miku using a certificate issued by Gatebox (the marriage isn’t recognized by the state, and Gatebox acknowledges the union goes “beyond dimensions”).

I found Akihiko to be quite moving when he described his relationship, which is not unique. It seems some 4,000 men have ‘wed’ their digital companions, you can read about that and more on the ‘I love her and see her as a real woman.’ Meet a man who ‘married’ an artificial intelligence hologram webpage.

What does it mean to be human?

Overall, this Nature of Things episode embraces certainty, which means the question of what it means to human is referenced rather than seriously discussed. An unanswerable philosophical question, the programme is ill-equipped to address it, especially since none of the commentators are philosophers or seem inclined to philosophize.

The programme presents AI as a juggernaut. Briefly mentioned is the notion that we need to make some decisions about how our juggernaut is developed and utilized. No one discusses how we go about making changes to systems that are already making critical decisions for us. (For more about AI and decision-making, see my February 28, 2017 posting and scroll down to the ‘Algorithms and big data’ subhead for Cathy O’Neil’s description of how important decisions that affect us are being made by AI systems. She is the author of the 2016 book, ‘Weapons of Math Destruction: How Big Data Increases Inequality and Threatens Democracy’; still a timely read.)

In fact, the programme’s tone is mostly one of breathless excitement. A few misgivings are expressed, e.g,, one woman who has an artificial ‘texting friend’ (Replika; a chatbot app) noted that it can ‘get into your head’ when she had a chat where her ‘friend’ told her that all of a woman’s worth is based on her body; she pushed back but intimated that someone more vulnerable could find that messaging difficult to deal with.

The sequence featuring Akihiko and his hologram ‘wife’ is followed by one suggesting that people might become more isolated and emotionally stunted as they interact with artificial friends. It should be noted, Akihiko’s wife is described as ‘perfect’. I gather perfection means that you are always understanding and have no needs of your own. She also seems to be about 18″ high.

Akihiko has obviously been asked about his ‘wife’ before as his answers are ready. They boil down to “there are many types of relationships” and there’s nothing wrong with that. It’s an intriguing thought which is not explored.

Also unexplored, these relationships could be said to resemble slavery. After all, you pay for these friends over which you have control. But perhaps that’s alright since AI friends don’t have consciousness. Or do they? In addition to not being able to answer the question, “what is it to be human?” we still can’t answer the question, “what is consciousness?”

AI and creativity

The Nature of Things team works fast. ‘Beethoven X – The AI Project’ had its first performance on October 9, 2021. (See my October 1, 2021 post ‘Finishing Beethoven’s unfinished 10th Symphony’ for more information from Ahmed Elgammal’s (Director of the Art & AI Lab at Rutgers University) technical perspective on the project.

Briefly, Beethoven died before completing his 10th symphony and a number of computer scientists, musicologists, AI, and musicians collaborated to finish the symphony.)

The one listener (Felix Mayer, music professor at the Technical University Munich) in the hall during a performance doesn’t consider the work to be a piece of music. He does have a point. Beethoven left some notes but this ’10th’ is at least partly mathematical guesswork. A set of probabilities where an algorithm chooses which note comes next based on probability.

There was another artist also represented in the programme. Puzzlingly, it was the still living Douglas Coupland. In my opinion, he’s better known as a visual artist than a writer (his Wikipedia entry lists him as a novelist first) but he has succeeded greatly in both fields.

What makes his inclusion in the Nature of Things ‘The Machine That Feels’ programme puzzling, is that it’s not clear how he worked with artificial intelligence in a collaborative fashion. Here’s a description of Coupland’s ‘AI’ project from a June 29, 2021 posting by Chris Henry on the Google Outreach blog (Note: Links have been removed),

… when the opportunity presented itself to explore how artificial intelligence (AI) inspires artistic expression — with the help of internationally renowned Canadian artist Douglas Coupland — the Google Research team jumped on it. This collaboration, with the support of Google Arts & Culture, culminated in a project called Slogans for the Class of 2030, which spotlights the experiences of the first generation of young people whose lives are fully intertwined with the existence of AI. 

This collaboration was brought to life by first introducing Coupland’s written work to a machine learning language model. Machine learning is a form of AI that provides computer systems the ability to automatically learn from data. In this case, Google research scientists tuned a machine learning algorithm with Coupland’s 30-year body of written work — more than a million words — so it would familiarize itself with the author’s unique style of writing. From there, curated general-public social media posts on selected topics were added to teach the algorithm how to craft short-form, topical statements. [emphases mine]

Once the algorithm was trained, the next step was to process and reassemble suggestions of text for Coupland to use as inspiration to create twenty-five Slogans for the Class of 2030. [emphasis mine]

I would comb through ‘data dumps’ where characters from one novel were speaking with those in other novels in ways that they might actually do. It felt like I was encountering a parallel universe Doug,” Coupland says. “And from these outputs, the statements you see here in this project appeared like gems. Did I write them? Yes. No. Could they have existed without me? No.” [emphases mine]

So, the algorithms crunched through Coupland’s word and social media texts to produce slogans, which Coupland then ‘combed through’ to pick out 25 slogans for the ‘Slogans For The Class of 2030’ project. (Note: In the programme, he says that he started a sentence and then the AI system completed that sentence with material gleaned from his own writings, which brings to Exquisite Corpse, a collaborative game for writers originated by the Surrealists, possibly as early as 1918.)

The ‘slogans’ project also reminds me of William S. Burroughs and the cut-up technique used in his work. From the William S. Burroughs Cut-up technique webpage on the Language is a Virus website (Thank you to Lake Rain Vajra for a very interesting website),

The cutup is a mechanical method of juxtaposition in which Burroughs literally cuts up passages of prose by himself and other writers and then pastes them back together at random. This literary version of the collage technique is also supplemented by literary use of other media. Burroughs transcribes taped cutups (several tapes spliced into each other), film cutups (montage), and mixed media experiments (results of combining tapes with television, movies, or actual events). Thus Burroughs’s use of cutups develops his juxtaposition technique to its logical conclusion as an experimental prose method, and he also makes use of all contemporary media, expanding his use of popular culture.

[Burroughs says] “All writing is in fact cut-ups. A collage of words read heard overheard. What else? Use of scissors renders the process explicit and subject to extension and variation. Clear classical prose can be composed entirely of rearranged cut-ups. Cutting and rearranging a page of written words introduces a new dimension into writing enabling the writer to turn images in cinematic variation. Images shift sense under the scissors smell images to sound sight to sound to kinesthetic. This is where Rimbaud was going with his color of vowels. And his “systematic derangement of the senses.” The place of mescaline hallucination: seeing colors tasting sounds smelling forms.

“The cut-ups can be applied to other fields than writing. Dr Neumann [emphasis mine] in his Theory of Games and Economic behavior introduces the cut-up method of random action into game and military strategy: assume that the worst has happened and act accordingly. … The cut-up method could be used to advantage in processing scientific data. [emphasis mine] How many discoveries have been made by accident? We cannot produce accidents to order. The cut-ups could add new dimension to films. Cut gambling scene in with a thousand gambling scenes all times and places. Cut back. Cut streets of the world. Cut and rearrange the word and image in films. There is no reason to accept a second-rate product when you can have the best. And the best is there for all. Poetry is for everyone . . .”

First, John von Neumann (1902 – 57) is a very important figure in the history of computing. From a February 25, 2017 John von Neumann and Modern Computer Architecture essay on the ncLab website, “… he invented the computer architecture that we use today.”

Here’s Burroughs on the history of writers and cutups (thank you to QUEDEAR for posting this clip),

You can hear Burroughs talk about the technique and how he started using it in 1959.

There is no explanation from Coupland as to how his project differs substantively from Burroughs’ cut-ups or a session of Exquisite Corpse. The use of a computer programme to crunch through data and give output doesn’t seem all that exciting. *(More about computers and chatbots at end of posting).* It’s hard to know if this was an interview situation where he wasn’t asked the question or if the editors decided against including it.

Kazuo Ishiguro?

Given that Ishiguro’s 2021 book (Klara and the Sun) is focused on an artificial friend and raises the question of ‘what does it mean to be human’, as well as the related question, ‘what is the nature of consciousness’, it would have been interesting to hear from him. He spent a fair amount of time looking into research on machine learning in preparation for his book. Maybe he was too busy?

AI and emotions

The work being done by Georgia Tech’s Dr. Ayanna Howard and her robotics lab is fascinating. They are teaching robots how to interpret human emotions. The segment which features researchers teaching and interacting with robots, Pepper and Salt, also touches on AI and bias.

Watching two African American researchers talk about the ways in which AI is unable to read emotions on ‘black’ faces as accurately as ‘white’ faces is quite compelling. It also reinforces the uneasiness you might feel after the ‘Replika’ segment where an artificial friend informs a woman that her only worth is her body.

(Interestingly, Pepper and Salt are produced by Softbank Robotics, part of Softbank, a multinational Japanese conglomerate, [see a June 28, 2021 article by Ian Carlos Campbell for The Verge] whose entire management team is male according to their About page.)

While Howard is very hopeful about the possibilities of a machine that can read emotions, she doesn’t explore (on camera) any means for pushing back against bias other than training AI by using more black faces to help them learn. Perhaps more representative management and coding teams in technology companies?

While the programme largely focused on AI as an algorithm on a computer, robots can be enabled by AI (as can be seen in the segment with Dr. Howard).

My February 14, 2019 posting features research with a completely different approach to emotions and machines,

“I’ve always felt that robots shouldn’t just be modeled after humans [emphasis mine] or be copies of humans,” he [Guy Hoffman, assistant professor at Cornell University)] said. “We have a lot of interesting relationships with other species. Robots could be thought of as one of those ‘other species,’ not trying to copy what we do but interacting with us with their own language, tapping into our own instincts.”

[from a July 16, 2018 Cornell University news release on EurekAlert]

This brings the question back to, what is consciousness?

What scientists aren’t taught

Dr. Howard notes that scientists are not taught to consider the implications of their work. Her comment reminded me of a question I was asked many years ago after a presentation, it concerned whether or not science had any morality. (I said, no.)

My reply angered an audience member (a visual artist who was working with scientists at the time) as she took it personally and started defending scientists as good people who care and have morals and values. She failed to understand that the way in which we teach science conforms to a notion that somewhere there are scientific facts which are neutral and objective. Society and its values are irrelevant in the face of the larger ‘scientific truth’ and, as a consequence, you don’t need to teach or discuss how your values or morals affect that truth or what the social implications of your work might be.

Science is practiced without much if any thought to values. By contrast, there is the medical injunction, “Do no harm,” which suggests to me that someone recognized competing values. E.g., If your important and worthwhile research is harming people, you should ‘do no harm’.

The experts, the connections, and the Canadian content

It’s been a while since I’ve seen Ray Kurzweil mentioned but he seems to be getting more attention these days. (See this November 16, 2021 posting by Jonny Thomson titled, “The Singularity: When will we all become super-humans? Are we really only a moment away from “The Singularity,” a technological epoch that will usher in a new era in human evolution?” on The Big Think for more). Note: I will have a little more about evolution later in this post.

Interestingly, Kurzweil is employed by Google these days (see his Wikipedia entry, the column to the right). So is Geoffrey Hinton, another one of the experts in the programme (see Hinton’s Wikipedia entry, the column to the right, under Institutions).

I’m not sure about Yoshu Bengio’s relationship with Google but he’s a professor at the Université de Montréal, and he’s the Scientific Director for Mila ((Quebec’s Artificial Intelligence research institute)) & IVADO (Institut de valorisation des données), Note: IVADO is not particularly relevant to what’s being discussed in this post.

As for Mila, the Canada Google blog in a November 21, 2016 posting notes a $4.5M grant to the institution,

Google invests $4.5 Million in Montreal AI Research

A new grant from Google for the Montreal Institute for Learning Algorithms (MILA) will fund seven faculty across a number of Montreal institutions and will help tackle some of the biggest challenges in machine learning and AI, including applications in the realm of systems that can understand and generate natural language. In other words, better understand a fan’s enthusiasm for Les Canadien [sic].

Google is expanding its academic support of deep learning at MILA, renewing Yoshua Bengio’s Focused Research Award and offering Focused Research Awards to MILA faculty at University of Montreal and McGill University:

Google reaffirmed their commitment to Mila in 2020 with a grant worth almost $4M (from a November 13, 2020 posting on the Mila website, Note: A link has been removed),

Google Canada announced today [November 13, 2020] that it will be renewing its funding of Mila – Quebec Artificial Intelligence Institute, with a generous pledge of nearly $4M over a three-year period. Google previously invested $4.5M US in 2016, enabling Mila to grow from 25 to 519 researchers.

In a piece written for Google’s Official Canada Blog, Yoshua Bengio, Mila Scientific Director, says that this year marked a “watershed moment for the Canadian AI community,” as the COVID-19 pandemic created unprecedented challenges that demanded rapid innovation and increased interdisciplinary collaboration between researchers in Canada and around the world.

COVID-19 has changed the world forever and many industries, from healthcare to retail, will need to adapt to thrive in our ‘new normal.’ As we look to the future and how priorities will shift, it is clear that AI is no longer an emerging technology but a useful tool that can serve to solve world problems. Google Canada recognizes not only this opportunity but the important task at hand and I’m thrilled they have reconfirmed their support of Mila with an additional $3,95 million funding grant until 22.

– Yoshua Bengio, for Google’s Official Canada Blog

Interesting, eh? Of course, Douglas Coupland is working with Google, presumably for money, and that would connect over 50% of the Canadian content (Douglas Coupland, Yoshua Bengio, and Geoffrey Hinton; Kurzweil is an American) in the programme to Google.

My hat’s off to Google’s marketing communications and public relations teams.

Anthony Morgan of Science Everywhere also provided some Canadian content. His LinkedIn profile indicates that he’s working on a PhD in molecular science, which is described this way, “My work explores the characteristics of learning environments, that support critical thinking and the relationship between critical thinking and wisdom.”

Morgan is also the founder and creative director of Science Everywhere, from his LinkedIn profile, “An events & media company supporting knowledge mobilization, community engagement, entrepreneurship and critical thinking. We build social tools for better thinking.”

There is this from his LinkedIn profile,

I develop, create and host engaging live experiences & media to foster critical thinking.

I’ve spent my 15+ years studying and working in psychology and science communication, thinking deeply about the most common individual and societal barriers to critical thinking. As an entrepreneur, I lead a team to create, develop and deploy cultural tools designed to address those barriers. As a researcher I study what we can do to reduce polarization around science.

There’s a lot more to Morgan (do look him up; he has connections to the CBC and other media outlets). The difficulty is: why was he chosen to talk about artificial intelligence and emotions and creativity when he doesn’t seem to know much about the topic? He does mention GPT-3, an AI programming language. He seems to be acting as an advocate for AI although he offers this bit of almost cautionary wisdom, “… algorithms are sets of instructions.” (You can can find out more about it in my April 27, 2021 posting. There’s also this November 26, 2021 posting [The Inherent Limitations of GPT-3] by Andrey Kurenkov, a PhD student with the Stanford [University] Vision and Learning Lab.)

Most of the cautionary commentary comes from Luke Stark, assistant professor at Western [Ontario] University’s Faculty of Information and Media Studies. He’s the one who mentions stunted emotional growth.

Before moving on, there is another set of connections through the Pan-Canadian Artificial Intelligence Strategy, a Canadian government science funding initiative announced in the 2017 federal budget. The funds allocated to the strategy are administered by the Canadian Institute for Advanced Research (CIFAR). Yoshua Bengio through Mila is associated with the strategy and CIFAR, as is Geoffrey Hinton through his position as Chief Scientific Advisor for the Vector Institute.

Evolution

Getting back to “The Singularity: When will we all become super-humans? Are we really only a moment away from “The Singularity,” a technological epoch that will usher in a new era in human evolution?” Xenobots point in a disconcerting (for some of us) evolutionary direction.

I featured the work, which is being done at Tufts University in the US, in my June 21, 2021 posting, which includes an embedded video,

From a March 31, 2021 news item on ScienceDaily,

Last year, a team of biologists and computer scientists from Tufts University and the University of Vermont (UVM) created novel, tiny self-healing biological machines from frog cells called “Xenobots” that could move around, push a payload, and even exhibit collective behavior in the presence of a swarm of other Xenobots.

Get ready for Xenobots 2.0.

Also from an excerpt in the posting, the team has “created life forms that self-assemble a body from single cells, do not require muscle cells to move, and even demonstrate the capability of recordable memory.”

Memory is key to intelligence and this work introduces the notion of ‘living’ robots which leads to questioning what constitutes life. ‘The Machine That Feels’ is already grappling with far too many questions to address this development but introducing the research here might have laid the groundwork for the next episode, The New Human, telecast on November 26, 2021,

While no one can be certain what will happen, evolutionary biologists and statisticians are observing trends that could mean our future feet only have four toes (so long, pinky toe) or our faces may have new combinations of features. The new humans might be much taller than their parents or grandparents, or have darker hair and eyes.

And while evolution takes a lot of time, we might not have to wait too long for a new version of ourselves.

Technology is redesigning the way we look and function — at a much faster pace than evolution. We are merging with technology more than ever before: our bodies may now have implanted chips, smart limbs, exoskeletons and 3D-printed organs. A revolutionary gene editing technique has given us the power to take evolution into our own hands and alter our own DNA. How long will it be before we are designing our children?

As the story about the xenobots doesn’t say, we could also take the evolution of another species into our hands.

David Suzuki, where are you?

Our programme host, David Suzuki surprised me. I thought that as an environmentalist he’d point out that the huge amounts of computing power needed for artificial intelligence as mentioned in the programme, constitutes an environmental issue. I also would have expected a geneticist like Suzuki might have some concerns with regard to xenobots but perhaps that’s being saved for the next episode (The New Human) of the Nature of Things.

Artificial stupidity

Thanks to Will Knight for introducing me to the term ‘artificial stupidity’. Knight, a senior writer covers artificial intelligence for WIRED magazine. According to its Wikipedia entry,

Artificial stupidity is commonly used as a humorous opposite of the term artificial intelligence (AI), often as a derogatory reference to the inability of AI technology to adequately perform its tasks.[1] However, within the field of computer science, artificial stupidity is also used to refer to a technique of “dumbing down” computer programs in order to deliberately introduce errors in their responses.

Knight was using the term in its humorous, derogatory form.

Finally

The episode certainly got me thinking if not quite in the way producers might have hoped. ‘The Machine That Feels’ is a glossy, pretty well researched piece of infotainment.

To be blunt, I like and have no problems with infotainment but it can be seductive. I found it easier to remember the artificial friends, wife, xenobots, and symphony than the critiques and concerns.

Hopefully, ‘The Machine That Feels’ stimulates more interest in some very important topics. If you missed the telecast, you can catch the episode here.

For anyone curious about predictive policing, which was mentioned in the Ayanna Howard segment, see my November 23, 2017 posting about Vancouver’s plunge into AI and car theft.

*ETA December 6, 2021: One of the first ‘chatterbots’ was ELIZA, a computer programme developed from1964 to 1966. The most famous ELIZA script was DOCTOR, where the programme simulated a therapist. Many early users believed ELIZA understood and could respond as a human would despite Joseph Weizenbaum’s (creator of the programme) insistence otherwise.

Of musical parodies, Despacito, and evolution

What great timing, I just found out about a musical science parody featuring evolution and biology and learned of the latest news about the study of evolution on one of the islands in the Galapagos (where Charles Darwin made some of his observations). Thanks to Stacey Johnson for her November 24, 2017 posting on the Signals blog for featuring Evo-Devo (Despacito Biology Parody), an A Capella Science music video from Tim Blais,

Now, for the latest regarding the Galapagos and evolution (from a November 24, 2017 news item on ScienceDaily),

The arrival 36 years ago of a strange bird to a remote island in the Galapagos archipelago has provided direct genetic evidence of a novel way in which new species arise.

In this week’s issue of the journal Science, researchers from Princeton University and Uppsala University in Sweden report that the newcomer belonging to one species mated with a member of another species resident on the island, giving rise to a new species that today consists of roughly 30 individuals.

The study comes from work conducted on Darwin’s finches, which live on the Galapagos Islands in the Pacific Ocean. The remote location has enabled researchers to study the evolution of biodiversity due to natural selection.

The direct observation of the origin of this new species occurred during field work carried out over the last four decades by B. Rosemary and Peter Grant, two scientists from Princeton, on the small island of Daphne Major.

A November 23, 2017 Princeton University news release on EurekAlert, which originated the news item, provides more detail,

“The novelty of this study is that we can follow the emergence of new species in the wild,” said B. Rosemary Grant, a senior research biologist, emeritus, and a senior biologist in the Department of Ecology and Evolutionary Biology. “Through our work on Daphne Major, we were able to observe the pairing up of two birds from different species and then follow what happened to see how speciation occurred.”

In 1981, a graduate student working with the Grants on Daphne Major noticed the newcomer, a male that sang an unusual song and was much larger in body and beak size than the three resident species of birds on the island.

“We didn’t see him fly in from over the sea, but we noticed him shortly after he arrived. He was so different from the other birds that we knew he did not hatch from an egg on Daphne Major,” said Peter Grant, the Class of 1877 Professor of Zoology, Emeritus, and a professor of ecology and evolutionary biology, emeritus.

The researchers took a blood sample and released the bird, which later bred with a resident medium ground finch of the species Geospiz fortis, initiating a new lineage. The Grants and their research team followed the new “Big Bird lineage” for six generations, taking blood samples for use in genetic analysis.

In the current study, researchers from Uppsala University analyzed DNA collected from the parent birds and their offspring over the years. The investigators discovered that the original male parent was a large cactus finch of the species Geospiza conirostris from Española island, which is more than 100 kilometers (about 62 miles) to the southeast in the archipelago.

The remarkable distance meant that the male finch was not able to return home to mate with a member of his own species and so chose a mate from among the three species already on Daphne Major. This reproductive isolation is considered a critical step in the development of a new species when two separate species interbreed.

The offspring were also reproductively isolated because their song, which is used to attract mates, was unusual and failed to attract females from the resident species. The offspring also differed from the resident species in beak size and shape, which is a major cue for mate choice. As a result, the offspring mated with members of their own lineage, strengthening the development of the new species.

Researchers previously assumed that the formation of a new species takes a very long time, but in the Big Bird lineage it happened in just two generations, according to observations made by the Grants in the field in combination with the genetic studies.

All 18 species of Darwin’s finches derived from a single ancestral species that colonized the Galápagos about one to two million years ago. The finches have since diversified into different species, and changes in beak shape and size have allowed different species to utilize different food sources on the Galápagos. A critical requirement for speciation to occur through hybridization of two distinct species is that the new lineage must be ecologically competitive — that is, good at competing for food and other resources with the other species — and this has been the case for the Big Bird lineage.

“It is very striking that when we compare the size and shape of the Big Bird beaks with the beak morphologies of the other three species inhabiting Daphne Major, the Big Birds occupy their own niche in the beak morphology space,” said Sangeet Lamichhaney, a postdoctoral fellow at Harvard University and the first author on the study. “Thus, the combination of gene variants contributed from the two interbreeding species in combination with natural selection led to the evolution of a beak morphology that was competitive and unique.”

The definition of a species has traditionally included the inability to produce fully fertile progeny from interbreeding species, as is the case for the horse and the donkey, for example. However, in recent years it has become clear that some closely related species, which normally avoid breeding with each other, do indeed produce offspring that can pass genes to subsequent generations. The authors of the study have previously reported that there has been a considerable amount of gene flow among species of Darwin’s finches over the last several thousands of years.

One of the most striking aspects of this study is that hybridization between two distinct species led to the development of a new lineage that after only two generations behaved as any other species of Darwin’s finches, explained Leif Andersson, a professor at Uppsala University who is also affiliated with the Swedish University of Agricultural Sciences and Texas A&M University. “A naturalist who came to Daphne Major without knowing that this lineage arose very recently would have recognized this lineage as one of the four species on the island. This clearly demonstrates the value of long-running field studies,” he said.

It is likely that new lineages like the Big Birds have originated many times during the evolution of Darwin’s finches, according to the authors. The majority of these lineages have gone extinct but some may have led to the evolution of contemporary species. “We have no indication about the long-term survival of the Big Bird lineage, but it has the potential to become a success, and it provides a beautiful example of one way in which speciation occurs,” said Andersson. “Charles Darwin would have been excited to read this paper.”

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

Rapid hybrid speciation in Darwin’s finches by Sangeet Lamichhaney, Fan Han, Matthew T. Webster, Leif Andersson, B. Rosemary Grant, Peter R. Grant. Science 23 Nov 2017: eaao4593 DOI: 10.1126/science.aao4593

This paper is behind a paywall.

Happy weekend! And for those who love their Despacito, there’s this parody featuring three Italians in a small car (thanks again to Stacey Johnson’s blog posting),

Julie Payette, Canada’s Governor General, takes on science deniers and bogus science at 2017 Canadian Science Policy Conference

On the first day of the 2017 Canadian Science Policy Conference (Nov. 1 -3, 2017 in Ottawa, Ontario), Governor General Julie Payette’s speech encouraged listeners to grapple with science deniers, fake news, and more (from a Nov. 2, 2017 article by Mia Rabson in the Huffington Post, Canada edition),

Payette was the keynote speaker at the ninth annual Canadian Science Policy Convention in Ottawa Wednesday night [Nov. 1, 2017] where she urged her friends and former colleagues to take responsibility to shut down the misinformation about everything from health and medicine to climate change and even horoscopes that has flourished with the explosion of digital media.

“Can you believe that still today in learned society, in houses of government, unfortunately, we’re still debating and still questioning whether humans have a role in the Earth warming up or whether even the Earth is warming up, period,” she asked, her voice incredulous.

She generated giggles and even some guffaws from the audience when she said too many people still believe “taking a sugar pill will cure cancer if you will it good enough and that your future and every single one of the people here’s personalities can be determined by looking at planets coming in front of invented constellations.”

Payette was trained as a computer engineer and later became an astronaut and licensed pilot and in 1999 was the first Canadian to board the International Space Station.

Mia Rabson in another Nov. 2, 2017 article (this time for 680news.com) presents responses to the speech from various interested parties,

According to popular Canadian astrologer Georgia Nicols, Canada’s Governor General should be doing what she can to “keep the peace” with loved ones today and avoid the “planetary vibe” that is urging people to engage in power struggles and disputes.

The advice, contained in Julie Payette’s Nov. 2 [2017] horoscope on Nicols’ website, might have come a day late, though Payette likely wouldn’t have listened to it anyway.

The Governor General made clear in a speech to scientists at an Ottawa convention Wednesday she has a very low opinion of the validity of horoscopes, people who believe in creationism or those who don’t believe in climate change.

Emmett Macfarlane, a political professor at the University of Waterloo said nothing stops a governor general from stating opinions and while there have been unwritten traditions against it, Payette’s most recent predecessors did not always hold their tongues.

Conservative political strategist Alise Mills said Payette went way over the line with her speech, which she characterized as not only political but “mean-spirited.”

“I definitely agree science is key but I think there is a better way to do that without making fun of other people,” Mills said.

There isn’t a lot of data on horoscope and astrology beliefs in Canada but a 2005 Gallup poll suggested around one in four Canadians believed in astrology.

Prime Minister Justin Trudeau didn’t seem to have any issue with what Payette said, saying his government and Canadians understand the value of science.

Mills said Payette wasn’t just promoting science, she was mocking people with religious beliefs, and specifically, evangelical Christians who don’t believe evolutionary science.

Astrologer Nicols said she had “no wish to take on a woman who is as accomplished as Julie Payette,” whom she notes is a “feisty Libra with three planets in Scorpio.”

But she did suggest Payette would be better to stick to what she knows.

“Astrology is not the stuff of horoscopes in newspapers, albeit I do write them,” wrote Nicols in an e-mail. “It is actually a complex study based on mathematics. Not fairy dust falling from the stars.”

There is one thing I find a bit surprising, Payette doesn’t seem to have taken on the vaccination issue. In any event, it looks like the conference had an exciting start.

Monster science (a book announcement and interview)

Helaine Becker has launched a new children’s science book incorporating monsters with science. The title, unsurprisingly, is: ‘Monster Science’. Here’s more about the book from Helaine’s Oct. 14, 2016 post on Sci/Why where she shares two reviews,

“From Frankenstein’s creation to Nessie, Becker uses the creatures of our scariest stories as a springboard for an introduction to the scientific understandings that might make such creatures possible—or impossible. In addition to man-made monsters and legendary sea creatures, she covers vampires, zombies, werewolves, and wild, humanlike creatures like Bigfoot. Chapter by chapter, she provides references from literature, film, and popular culture, including a bit of science, a bit of history, and a plentiful helping of humor. She includes numerous monster facts, suggests weapons of defense, and concludes each section with a test-yourself quiz. Science topics covered range widely: electricity, genetic engineering, “demonic diseases,” the nature of our blood and the circulatory system, the possibility of immortality, animal classification, evolution, cannibalism, optical illusions, heredity, hoaxes, and the very real profession of cryptozoology, or the search for hitherto unidentified creatures. … Kirkus

Then, there’s this one,

A highlight of this work is its exploration of the often symbiotic relationship between culture and science; figures such as Shelley, John Polidori (The Vampyre), and filmmaker George Romero (Night of the Living Dead) merged cultural fascination with scientific development to create truly inspiring works and further public interest in science… School Library Journal

Interview with Helaine Becker

Not to be confused with ‘Interview with a vampire’, this one is not novel-length and includes a scoop about an upcoming book in 2017,

Were you surprised by anything when you were researching and/or witting the book?

I learned so much while writing Monster Science – it’s one of the reasons I enjoy writing nonfiction, especially for kids. I always turn up fascinating stuff. I was surprised to learn that werewolves were rounded up and burned at the stake, just like witches, during the period of the Inquisition. Werewolves, it turns out, were thought to be witches – usually male ones – who could shape shift.

My fave fact of all is that vampires would still have to eat their vegetables.

Did you have to leave any monsters/pop culture references/science out of the book? And, why?

Children’s books have very tight space constraints, but my research is comprehensive and complete. That means we have to pick and choose what stays in. It’s gotta be the very best! I work closely with my editors on this, and sometimes we have, shall we say, “heated” discussions.” For Monster Science, I was particularly sorry to see the fascinating back story of the mad scientist trope end up with a stake in its heart.

Did you have a favourite monster before you started? If so, has your favourite changed? Or if you didn’t have one before writing the book, have you since developed a favourite monster?

I’ve had an uneasy relationship with vampires from the age of about 7, after watching an episode of Gilligan’s Island. It featured a “humorous” dream sequence with Gilligan as the vampire. I failed to see the humor at that tender age, and was terrified out of my socks. And anyone remember the original Dark Shadows? Barnabus Collins? Yeah. That show should have never been on in the afternoon. I slept with the blankies up to my ears until my mid-thirties. (Who am I kidding? I still do!)

Are you hoping to tie this book into the Frankenstein bicentennial celebrations?

Illustrated children’s books have very long time lines from concept to finished book. I wrote Monster Science several years ago, before I had any notion of Frankenstein bicentennials. But now that we’ve arrived at this auspicious date, I’m excited! I’d love to participate in some way. I will put on my zzz zzzz zzzt thinking cap.

Where can your fans come to a reading or some other event?

I do dozens of school visits and festival events every year. Some of them might be focused on a specific book, like Monster Science, but most usually feature discussions around several of my titles. This holiday season, for example, I will be doing events around my latest picture book, a very Canadian Christmas-themed title called Deck the Halls. It’s the third in a very popular series. Anyone can drop in to the Sherway Gardens branch of Indigo Book Store [in Toronto] at noon on Sunday, Dec. 4 [2016], to take part in that.

I’ll be doing many events in association with the Forest of Reading, one of North America’s largest children’s choice award programs this spring. More than 250,000 children participate! I am honored to have two science-related books nominated this year, Worms for Breakfast: How to Feed a Zoo (Owlkids) and Everything: Space (National Geographic Kids). I will also be the keynote at the Killaloe Literary Festival in beautiful northern Ontario at the end of May. Best place to look for my latest book and schedule info is my blog, http://helainebecker.blogspot.ca/.

Is there anything you’d like to add?

For insiders only: Coming soon! Look for my upcoming picture book biography of William Playfair, the Victorian era scoundrel who single-handedly invented the field of infographics. It’s called Lines, Bars and Circles and will be published by Kids Can Press early in 2017.

Thank you, Helaine! (I usually don’t get funny interviews. It makes for a good change of pace.)

Getting back to ‘Monster Science’, you can purchase the book here.

ISEA (International Symposium on Electronic Arts) 2015 and the pronoun ‘I’

The 2015 International Symposium on Electronic Arts (or ISEA 2015) held  in Vancouver ended yesterday, Aug. 19, 2015. It was quite an experience both as a participant and as a presenter (mentioned in my Aug. 14, 2015 posting, Sneak peek: Steep (1): a digital poetry of gold nanoparticles). Both this ISEA and the one I attended previously in 2009 (Belfast, Northern Ireland, and Dublin, Ireland) were jampacked with sessions, keynote addresses, special events, and exhibitions of various artworks. Exhilarating and exhausting, that is the ISEA experience for me and just about anyone else I talked to here in Vancouver (Canada). In terms of organization, I have to give props to the Irish. Unfortunately, the Vancouver team didn’t seem to have given their volunteers any training and technical difficulties abounded. Basics such as having a poster outside a room noting what session was taking place, signage indicating which artist’s work was being featured, and good technical support (my guy managed to plug in a few things but seemed disinclined or perhaps didn’t have the technical expertise (?) to troubleshoot prior to the presentation) seemed elusive (a keynote presentation had to be moved due to technical requirements [!] plus no one told the volunteer staff who consequently misdirected people). Ooops.

Despite the difficulties, people remained enthusiastic and that’s a tribute to both the participants and, importantly, the organizers. The Vancouver ISEA was a huge undertaking with over 1000 presentation submissions made and over 1800 art work submissions. They had 900+ register and were the first ISEA able to offer payment to artists for their installations. Bravo to Philippe Pasquier, Thecla Schiphorst, Kate Armstrong, Malcolm Levy, and all the others who worked hard to pull this off.

Moving on to ‘I’, while the theme for ISEA 2015 was Disruption, I noticed a number of presentations focused on biology and on networks (in particular, generative networks). In some ways this parallels what’s happening in the sciences where more notice is being given to networks and network communications of all sorts.  For example, there’s an Aug. 19, 2015 news item on ScienceDaily suggesting that our use of the pronoun ‘I’ may become outdated.  What we consider to be an individual may be better understood as a host for a number of communities or networks,

Recent microbiological research has shown that thinking of plants and animals, including humans, as autonomous individuals is a serious over-simplification.

A series of groundbreaking studies have revealed that what we have always thought of as individuals are actually “biomolecular networks” that consist of visible hosts plus millions of invisible microbes that have a significant effect on how the host develops, the diseases it catches, how it behaves and possibly even its social interactions.

“It’s a case of the whole being greater than the sum of its parts,” said Seth Bordenstein, associate professor of biological sciences at Vanderbilt University, who has contributed to the body of scientific knowledge that is pointing to the conclusion that symbiotic microbes play a fundamental role in virtually all aspects of plant and animal biology, including the origin of new species.

In this case, the parts are the host and its genome plus the thousands of different species of bacteria living in or on the host, along with all their genomes, collectively known as the microbiome. (The host is something like the tip of the iceberg while the bacteria are like the part of the iceberg that is underwater: Nine out of every 10 cells in plant and animal bodies are bacterial. But bacterial cells are so much smaller than host cells that they have generally gone unnoticed.)

An Aug. 19, 2015 Vanderbilt University news release, which originated the news item, describes this provocative idea (no more ‘I’)  further,

Microbiologists have coined new terms for these collective entities — holobiont — and for their genomes — hologenome. “These terms are needed to define the assemblage of organisms that makes up the so-called individual,” said Bordenstein.

In the article “Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes” published online Aug. 18 [2015] in the open access journal PLOS Biology, Bordenstein and his colleague Kevin Theis from the University of Michigan take the general concepts involved in this new paradigm and break them down into underlying principles that apply to the entire field of biology.

They make specific and refutable predictions based on these principles and call for other biologists to test them theoretically and experimentally.

“One of the basic expectations from this conceptual framework is that animal and plant experiments that do not account for what is happening at the microbiological level will be incomplete and, in some cases, will be misleading as well,” said Bordenstein.

The first principle they advance is that holobionts and hologenomes are fundamental units of biological organization.

Another is that evolutionary forces such as natural selection and drift may act on the hologenome not just on the genome. So mutations in the microbiome that affect the fitness of a holobiont are just as important as mutations in the host’s genome. However, they argue that this does not change the basic rules of evolution but simply upgrades the types of biological units that the rules may act upon.

Although it does not change the basic rules of evolution, holobionts do have a way to respond to environmental challenges that is not available to individual organisms: They can alter the composition of their bacterial communities. For example, if a holobiont is attacked by a pathogen that the host cannot defend against, another symbiont may fulfill the job by manufacturing a toxin that can kill the invader. In this light, the microbes are as much part of the holobiont immune system as the host immune genes themselves.

According to Bordenstein, these ideas are gaining acceptance in the microbiology community. At the American Society of Microbiology General Meeting in June [2015], he convened the inaugural session on “Holobionts and Their Hologenomes” and ASM’s flagship journal mBio plans to publish a special issue on the topic in the coming year. [emphases are mine]

However, adoption of these ideas has been slower in other fields.

“Currently, the field of biology has reached an inflection point. The silos of microbiology, zoology and botany are breaking down and we hope that this framework will help further unify these fields,” said Bordenstein.

Not only will this powerful holistic approach affect the basic biological sciences but it also is likely to impact the practice of personalized medicine as well, Bordenstein said.

Take the missing heritability problem, for example. Although genome-wide studies have provided valuable insights into the genetic basis of a number of simple diseases, they have only found a small portion of the genetic causes of a number of more complex conditions such as autoimmune and metabolic diseases.

These may in part be “missing” because the genetic factors that cause them are in the microbiome, he pointed out.

“Instead of being so ‘germophobic,’ we need to accept the fact that we live in and benefit from a microbial world. We are as much an environment for microbes as microbes are for us,” said Bordenstein.

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

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes by Seth R. Bordenstein and Kevin R. Theis. PLOS DOI: 10.1371/journal.pbio.1002226 Published: August 18, 2015

This is an open access paper.

It’s intriguing to see artists and scientists exploring ideas that resonate with each other. In fact, ISEA 2015 hosted a couple of sessions on BioArt, as well as, having sessions devoted to networks. While, I wasn’t thinking about networks or biological systems when I wrote my poem on gold nanoparticles, I did pose this possibility (how we become the sum of our parts) at the end:

Nature’s alchemy
breathing them
eating them
drinking them
we become gold
discovering what we are

As for how Raewyn handled the idea, words fail, please do go here to see the video here.

Science cakery

I have to thank Dean Burnett for his science cake extravagance on the Guardian science blogs. Here’s a few pictures of cake to tantalize you from Burnett’s Aug. 12, 2015 posting,

An evolution-of-life cake from @OxUniEarthSci Palaeontology Group. Bizarre how this life-sciences cake seems to defy physics with its structure. Photograph: @JackJMatthews

An evolution-of-life cake from @OxUniEarthSci Palaeontology Group. Bizarre how this life-sciences cake seems to defy physics with its structure.
Photograph: @JackJMatthews

A cake shaped like a subject entering an MRI scanner for @ImanovaImaging’s 1st birthday party. Because why not? Photograph: @M_Wall

A cake shaped like a subject entering an MRI scanner for @ImanovaImaging’s 1st birthday party. Because why not?
Photograph: @M_Wall

Katie Watkins created TMS coils on talking brains. For the record, it is not necessary or even helpful for the brain to be exposed during TMS. Photograph: Kate Watkins

Katie Watkins created TMS coils on talking brains. For the record, it is not necessary or even helpful for the brain to be exposed during TMS. Photograph: Kate Watkins

Katie Grifiths, posing with a DNA cake made by her sister Emma. What’s with these biology-themed cakes and their ability to overrule gravity? Do NASA know about this? Photograph: Katie Griffiths

Katie Grifiths, posing with a DNA cake made by her sister Emma. What’s with these biology-themed cakes and their ability to overrule gravity? Do NASA know about this?
Photograph: Katie Griffiths

Marilyn Audlsey produced this particles-in-a-cloud-chamber ginger cake. I’m not even going to pretend to know what that is, but it makes for a nice looking cake. Photograph: Marilyn Audsley

Marilyn Audlsey produced this particles-in-a-cloud-chamber ginger cake. I’m not even going to pretend to know what that is, but it makes for a nice looking cake. Photograph: Marilyn Audsley

And this is the last one I’m including,

Sara Barnes did this @ATLASexperiment. At last, the money spent on the Lare Hadron Collider starts to show useful results. Photograph: Sarah Barnes

Sara Barnes did this @ATLASexperiment. At last, the money spent on the Lare Hadron Collider starts to show useful results.
Photograph: Sarah Barnes

Burnett has many more areas of science memorialized in cake in his Aug. 12, 2015 posting.

I last featured science and cakes in a March 31, 2012 posting about the periodic table of elements and cupcakes. On a closely related note, I wrote about mathematics and baking in a June 28, 2013 posting.

Self-organizing nanotubes and nonequilibrium systems provide insights into evolution and artificial life

If you’re interested in the second law of thermodynamics, this Feb. 10, 2015 news item on ScienceDaily provides some insight into the second law, self-organized systems, and evolution,

The second law of thermodynamics tells us that all systems evolve toward a state of maximum entropy, wherein all energy is dissipated as heat, and no available energy remains to do work. Since the mid-20th century, research has pointed to an extension of the second law for nonequilibrium systems: the Maximum Entropy Production Principle (MEPP) states that a system away from equilibrium evolves in such a way as to maximize entropy production, given present constraints.

Now, physicists Alexey Bezryadin, Alfred Hubler, and Andrey Belkin from the University of Illinois at Urbana-Champaign, have demonstrated the emergence of self-organized structures that drive the evolution of a non-equilibrium system to a state of maximum entropy production. The authors suggest MEPP underlies the evolution of the artificial system’s self-organization, in the same way that it underlies the evolution of ordered systems (biological life) on Earth. …

A Feb. 10, 2015 University of Illinois College of Engineering news release (also on EurekAlert), which originated the news item, provides more detail about the theory and the research,

MEPP may have profound implications for our understanding of the evolution of biological life on Earth and of the underlying rules that govern the behavior and evolution of all nonequilibrium systems. Life emerged on Earth from the strongly nonequilibrium energy distribution created by the Sun’s hot photons striking a cooler planet. Plants evolved to capture high energy photons and produce heat, generating entropy. Then animals evolved to eat plants increasing the dissipation of heat energy and maximizing entropy production.

In their experiment, the researchers suspended a large number of carbon nanotubes in a non-conducting non-polar fluid and drove the system out of equilibrium by applying a strong electric field. Once electrically charged, the system evolved toward maximum entropy through two distinct intermediate states, with the spontaneous emergence of self-assembled conducting nanotube chains.

In the first state, the “avalanche” regime, the conductive chains aligned themselves according to the polarity of the applied voltage, allowing the system to carry current and thus to dissipate heat and produce entropy. The chains appeared to sprout appendages as nanotubes aligned themselves so as to adjoin adjacent parallel chains, effectively increasing entropy production. But frequently, this self-organization was destroyed through avalanches triggered by the heating and charging that emanates from the emerging electric current streams. (…)

“The avalanches were apparent in the changes of the electric current over time,” said Bezryadin.

“Toward the final stages of this regime, the appendages were not destroyed during the avalanches, but rather retracted until the avalanche ended, then reformed their connection. So it was obvious that the avalanches correspond to the ‘feeding cycle’ of the ‘nanotube inset’,” comments Bezryadin.

In the second relatively stable stage of evolution, the entropy production rate reached maximum or near maximum. This state is quasi-stable in that there were no destructive avalanches.

The study points to a possible classification scheme for evolutionary stages and a criterium for the point at which evolution of the system is irreversible—wherein entropy production in the self-organizing subsystem reaches its maximum possible value. Further experimentation on a larger scale is necessary to affirm these underlying principals, but if they hold true, they will prove a great advantage in predicting behavioral and evolutionary trends in nonequilibrium systems.

The authors draw an analogy between the evolution of intelligent life forms on Earth and the emergence of the wiggling bugs in their experiment. The researchers note that further quantitative studies are needed to round out this comparison. In particular, they would need to demonstrate that their “wiggling bugs” can multiply, which would require the experiment be reproduced on a significantly larger scale.

Such a study, if successful, would have implications for the eventual development of technologies that feature self-organized artificial intelligence, an idea explored elsewhere by co-author Alfred Hubler, funded by the Defense Advanced Research Projects Agency [DARPA]. [emphasis mine]

“The general trend of the evolution of biological systems seems to be this: more advanced life forms tend to dissipate more energy by broadening their access to various forms of stored energy,” Bezryadin proposes. “Thus a common underlying principle can be suggested between our self-organized clouds of nanotubes, which generate more and more heat by reducing their electrical resistance and thus allow more current to flow, and the biological systems which look for new means to find food, either through biological adaptation or by inventing more technologies.

“Extended sources of food allow biological forms to further grow, multiply, consume more food and thus produce more heat and generate entropy. It seems reasonable to say that real life organisms are still far from the absolute maximum of the entropy production rate. In both cases, there are ‘avalanches’ or ‘extinction events’, which set back this evolution. Only if all free energy given by the Sun is consumed, by building a Dyson sphere for example, and converted into heat then a definitely stable phase of the evolution can be expected.”

“Intelligence, as far as we know, is inseparable from life,” he adds. “Thus, to achieve artificial life or artificial intelligence, our recommendation would be to study systems which are far from equilibrium, with many degrees of freedom—many building blocks—so that they can self-organize and participate in some evolution. The entropy production criterium appears to be the guiding principle of the evolution efficiency.”

I am fascinated

  • (a) because this piece took an unexpected turn onto the topic of artificial life/artificial intelligence,
  • (b) because of my longstanding interest in artificial life/artificial intelligence,
  • (c) because of the military connection, and
  • (d) because this is the first time I’ve come across something that provides a bridge from fundamental particles to nanoparticles.

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

Self-Assembled Wiggling Nano-Structures and the Principle of Maximum Entropy Production by A. Belkin, A. Hubler, & A. Bezryadin. Scientific Reports 5, Article number: 8323 doi:10.1038/srep08323 Published 09 February 2015

Adding to my delight, this paper is open access.

Islam and evolution

Yasmin Khan’s Jan. 9, 2013 posting on the Guardian science blogs provides some fascinating insight and I strongly encourage this piece in its totality but for anyone who likes -previews, here’s the opening paragraph (Note: Links have been removed),

More than 850 delegates flocked to a seminal conference [Have Muslims Misunderstood Evolution?]  in London on Saturday about the compatibility of modern evolutionary theory and Islamic theology – despite scaremongering and the refusal of Islamic student societies to participate. Determined organisers had overcome pressure to cancel by changing the venue from Imperial College to Logan Hall at the University of London. The event was the brainchild of the Deen Institute, which runs courses to promote critical thinking among Muslim students and kindle rational dialogue within Islam. The need for dialogue is urgent, because to date there has been little open discussion within British Muslim communities on this divisive subject. Recent debates in the US suggest that evolution is not as much of a problem theologically to Muslims as it is to Christian creationists, but there is work to be done to clarify the situation.

Here’s another snippet of what appears to have been a very lively dialogue (Note: Links have been removed),

Fatima Jackson, a biological anthropologist at the University of Maryland, offered a compelling alternative narrative. Nothing in biology would make sense outside the evolution paradigm, which she defined as a “basic organising tool”. She reconciled her faith with science by holding to the belief that the singularity of life is a manifestation of the unity of God. In her view, exploring natural phenomena helps to bring us closer to God. “Evolution doesn’t replace faith, it complements it.”

Each primate, she said, “has its own trajectory from a common ancestor which has diversified”. Humans are a part of the natural world and not a unique creation. “You can’t just push the fossils away,” she cautioned, citing an article by Sheikh al-Turayri, who asserts that the question of evolution is purely a matter for scientific inquiry.

The Deen Institute mentioned as the ‘brains’ behind this initiative seems to have burst onto the scene in June 2012, from a June 22, 2012 Deen Institute press release (scroll down the page to the first press release),

Adam Deen, Co-Founder and Director of the Institute, explains: “People of faith are viewed in some quarters as uneducated, blindly and unquestioningly following outmoded ideologies, which they have not chosen, but rather inherited. The Deen Institute is about challenging that view, about emphasising that faith is the result of rigorous critical thinking and intellectual thought.”

Through dialogue and discussion, The Deen Institute aims to foster engagement with society and contribute to highlighting the fact that Islam is as relevant today as it was fourteen hundred years ago.

The institute will provide academic courses, devised and taught by qualified and experienced instructors, aimed at bridging the gap between the precepts of the faith as enshrined in their historical context and their application to the contemporary era. Courses will center on ethics, philosophy, history and science, and the Institute will also host forums, roundtables and debates aimed at challenging prevailing assumptions. The contents will be summarized in regular publications and online.

The Deen Institute considers the Qur’an and the example of the Prophet Muhammad (the Sunnah) to be the ethical benchmark in the elaboration of an enlightened philosophy and this premise will be reflected in the organisation’s work. However, the Institute is not exclusive to any particular Muslim group or perspective and features eminent scholars from all backgrounds. It also welcomes students from all faiths or none.

The Deen Institute seeks to provide a platform from which shared concerns and questions can be openly discussed and examined, in an atmosphere of respect, civility and mutual understanding.

The Institute and this recent discussion of evolution and Islam puts me in mind of the  House of Wisdom (mentioned in my Sept. 24, 2009 posting in reference to the opening of the King Abdullah University of Science and Technology in Saudi Arabia),

The House of Wisdom existed from the 9th to 13th centuries CE (common era) in Baghdad. Originally intended as a library whose main purpose was for the translation of books from Persian into Arabic, the House of Wisdom became a centre for the study of the humanities and sciences that was unrivaled in its time. One of its great scholars (Al-Khawarizmi) is known as the ‘father of algebra’. They invented the library catalogue where books were organized according to subjects.

All the best to the Deen Institute and their continued dialogue efforts.