(Roughly) Daily

Posts Tagged ‘biology

“In the attempt to make scientific discoveries, every problem is an opportunity and the more difficult the problem, the greater will be the importance of its solution”*…

(Roughly) Daily is headed into its traditional Holiday hibernation; regular service will begin again very early in the New Year.

It seems appropriate (especially given the travails of this past year) to end the year on a positive and optimistic note, with a post celebrating an extraordinary accomplishment– Science magazine‘s (thus, the AAAS‘) “Breakthrough of the Year” for 2021…

In his 1972 Nobel Prize acceptance speech, American biochemist Christian Anfinsen laid out a vision: One day it would be possible, he said, to predict the 3D structure of any protein merely from its sequence of amino acid building blocks. With hundreds of thousands of proteins in the human body alone, such an advance would have vast applications, offering insights into basic biology and revealing promising new drug targets. Now, after nearly 50 years, researchers have shown that artificial intelligence (AI)-driven software can churn out accurate protein structures by the thousands—an advance that realizes Anfinsen’s dream and is Science’s 2021 Breakthrough of the Year.

AI-powered predictions show proteins finding their shapes: the full story: “Protein structures for all.”

And read Nature‘s profile of the scientist behind the breakthrough: “John Jumper: Protein predictor.”

* E. O. Wilson

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As we celebrate science, we might send well-connected birthday greetings to Robert Elliot Kahn; he was born on this date in 1938. An electrical engineer and computer scientist, he and his co-creator, Vint Cerf, first proposed the Transmission Control Protocol (TCP) and the Internet Protocol (IP), the fundamental communication protocols at the heart of the Internet. Later, he and Vint, along with fellow computer scientists Lawrence Roberts, Paul Baran, and Leonard Kleinrock, built the ARPANET, the first network to successfully link computers around the country.

Kahn has won the Turing Award, the National Medal of Technology, and the Presidential Medal Of Freedom, among many, many other awards and honors.

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“Human nature scares the hell out of me”*…

Henry Gee, paleontologist and senior editor of Nature, argues that we Homo sapiens are setting ourselves up for collapse. He cites population decline, a lack of genetic variation, our socioeconomic fixation on growth (and the way that that’s plundered the planet), among other factors. But he singles out one phenomenon in particular…

 The most insidious threat to humankind is something called “extinction debt.” There comes a time in the progress of any species, even ones that seem to be thriving, when extinction will be inevitable, no matter what they might do to avert it. The cause of extinction is usually a delayed reaction to habitat loss. The species most at risk are those that dominate particular habitat patches at the expense of others, who tend to migrate elsewhere, and are therefore spread more thinly. Humans occupy more or less the whole planet, and with our sequestration of a large wedge of the productivity of this planetwide habitat patch, we are dominant within it. H. sapiens might therefore already be a dead species walking.

The signs are already there for those willing to see them. When the habitat becomes degraded such that there are fewer resources to go around; when fertility starts to decline; when the birth rate sinks below the death rate; and when genetic resources are limited—the only way is down. The question is “How fast?”…

Eminently worth reading in full: “Humans Are Doomed to Go Extinct,” from @EndOfThePier in Scientific American (@sciam).

For chorus effect, see also “Headed for a sixth mass extinction? MIT geophysicist warns oceans are on the brink.”

And for a look at the (possible) aftermath, explore “The Earth After Humans.”

* Neil deGrasse Tyson

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As we remind ourselves that “hope is a discipline,” we might send expansively-creative birthday greetings to Freeman Dyson; he was born on this date in 1923. A theoretical and mathematical physicist, mathematician, and statistician, he made material contributions– both processes and concepts— in quantum field theory, astrophysics, the mathematical formulation of quantum mechanics, condensed matter physics, nuclear physics, and engineering.

He will forever be remembered by SciFi fans as the originator of the idea of (what’s called) the Dyson Sphere (or Dyson Shell): he proposed that a highly advanced technological civilization would ultimately completely surround its host star with a huge shell to capture 100% of the useful radiant energy. This Dyson Sphere would have a gigantic cluster of artificial planetoids (“Dyson cloud”) with billions of billions of inhabitants who would make use of the energy captured by the Dyson Sphere. He also made the intriguing speculation that a Dyson Sphere viewed from other galaxies would have a highly distinctive, unnatural light. He suggested astronomers search for such tell-tale colored stars, which should signify advanced, intelligent life.

Dyson was skeptical of some climate science, believing that the advantages of global warming (e.g., greater crop yields) were underweighted and that climate models were underdeveloped (and thus untrustworthy). Still he sounded the alarm (in a way resonant with Gee’s, above) as to the possibility of humanity poisoning its own future:

In the near future, we will be in possession of genetic engineering technology which allows us to move genes precisely and massively from one species to another. Careless or commercially driven use of this technology could make the concept of species meaningless, mixing up populations and mating systems so that much of the individuality of species would be lost. Cultural evolution gave us the power to do this. To preserve our wildlife as nature evolved it, the machinery of biological evolution must be protected from the homogenizing effects of cultural evolution.

Unfortunately, the first of our two tasks, the nurture of a brotherhood of man, has been made possible only by the dominant role of cultural evolution in recent centuries. The cultural evolution that damages and endangers natural diversity is the same force that drives human brotherhood through the mutual understanding of diverse societies. Wells’s vision of human history as an accumulation of cultures, Dawkins’s vision of memes bringing us together by sharing our arts and sciences, Pääbo’s vision of our cousins in the cave sharing our language and our genes, show us how cultural evolution has made us what we are. Cultural evolution will be the main force driving our future…

Biological and Cultural Evolution– Six Characters in Search of an Author

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“Nothing from nothing ever yet was born”*…

Lacy M. Johnson argues that there is no hierarchy in the web of life…

… Humans have been lumbering around the planet for only a half million years, the only species young and arrogant enough to name ourselves sapiens in genus Homo. We share a common ancestor with gorillas and whales and sea squirts, marine invertebrates that swim freely in their larval phase before attaching to rocks or shells and later eating their own brain. The kingdom Animalia, in which we reside, is an offshoot of the domain Eukarya, which includes every life-form on Earth with a nucleus—humans and sea squirts, fungi, plants, and slime molds that are ancient by comparison with us—and all these relations occupy the slenderest tendril of a vast and astonishing web that pulsates all around us and beyond our comprehension.

The most recent taxonomies—those based on genetic evidence that evolution is not a single lineage, but multiple lineages, not a branch that culminates in a species at its distant tip, but a network of convergences—have moved away from their histories as trees and chains and ladders. Instead, they now look more like sprawling, networked webs that trace the many points of relation back to ever more ancient origins, beyond our knowledge or capacity for knowing, in pursuit of the “universal ancestors,” life-forms that came before metabolism, before self-replication—the several-billion-year-old plasmodial blobs from which all life on Earth evolved. We haven’t found evidence for them yet, but we know what we’re looking for: they would be simple, small, and strange.

Slime molds can enter stasis at any stage in their life cycle—as an amoeba, as a plasmodium, as a spore— whenever their environment or the climate does not suit their preferences or needs. The only other species who have this ability are the so-called “living fossils” such as tardigrades and Notostraca (commonly known as water bears and tadpole shrimp, respectively). The ability to become dormant until conditions are more favorable for life might be one of the reasons slime mold has survived as long as it has, through dozens of geologic periods, countless ice ages, and the extinction events that have repeatedly wiped out nearly all life on Earth.

Slime mold might not have evolved much in the past two billion years, but it has learned a few things during that time. In laboratory environments, researchers have cut Physarum polycephalum into pieces and found that it can fuse back together within two minutes. Or, each piece can go off and live separate lives, learn new things, and return later to fuse together, and in the fusing, each individual can teach the other what it knows, and can learn from it in return.

Though, in truth, “individual” is not the right word to use here, because “individuality”—a concept so central to so many humans’ identities—doesn’t apply to the slime mold worldview. A single cell might look to us like a coherent whole, but that cell can divide itself into countless spores, creating countless possible cycles of amoeba to plasmodium to aethalia, which in turn will divide and repeat the cycle again. It can choose to “fruit” or not, to reproduce sexually or asexually or not at all, challenging every traditional concept of “species,” the most basic and fundamental unit of our flawed and imprecise understanding of the biological world. As a consequence, we have no way of knowing whether slime molds, as a broad class of beings, are stable or whether climate change threatens their survival, as it does our own. Without a way to count their population as a species, we can’t measure whether they are endangered or thriving. Should individuals that produce similar fruiting bodies be considered a species? What if two separate slime molds do not mate but share genetic material? The very idea of separateness seems antithetical to slime mold existence. It has so much to teach us…

More at: “What Slime Knows,” from @lacymjohnson in @Orion_Magazine.

See also, “Slime Molds Remember — but Do They Learn?” (from whence the image above) and “Now, in addition to penicillin, we can credit mold with elegant design.”

* Lucretius, On the Nature of Things

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As we contemplate kinship, we might send insightful birthday greetings to Johann Hedwig; he was born on this date in 1730. A botanist noted for his study of mosses, he is considered “the father of bryology” (the study of mosses… cousins of mold).

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Written by (Roughly) Daily

December 8, 2021 at 1:00 am

“The element of mystery to which you want to draw attention should be surrounded and veiled by a quite obvious, readily recognisable commonness”*…

Day And Night (1938)

An appreciation of the marvelous M.C. Escher…

Despite being a fan of Rennaisance Art and the work of the Impressionists, he feels increasingly pulled in a different direction…

When you look at this picture, you’re flipping between world views. Either you’re seeing the white birds, and the bright, presumably sunlit day scene with its cheerful flotilla of steam ships puffing their way upriver – or you’re seeing the black birds, and your eye is drawn to the night-shrouded landscape where the houses have their lights on and the sky’s already eaten the horizon & is creeping nearer…

Except, that’s not quite right. The black birds are in the daylight side, and the white ones are flying into the night. These aren’t just mirror images: they’re like the Ancient Chinese yin-yang symbol, each side containing part of its opposite…

Escher’s love of the fantastical is primarily inspired by what he sees around him, not what he can dream up out of next to nothing… By looking closely at the real world, and trying to understand how it works, Escher will invite his initially small but intensely loyal fanbase to explore some very strange mysteries indeed.

Ascending And Descending (1960)

It’s the 1960s now, and nonconformity is all the rage. Hair is getting longer, psychedelics-powered artistry is flourishing, and anything that seems to scream to hell with the rules is increasingly in vogue… Because of the fantastical elements of his work, Escher is acquiring a reputation as a surrealist. As a self-identifying “reality enthusiast,” it’s the very last thing he wants. Take Ascending & Descending, where he’s clearly turning his imagination to the futility of so much in the human-centred world. In a letter to a friend, he says:

“Yes, yes, we climb up and up, we imagine we are ascending; one step is about 10 inches high, terribly tiring – and where does it get us? Nowhere.”

But until the end of his career, his work will continue to speak to something deeper – a rebellion against human incuriosity, or a constant rallying-cry for the act of paying attention…

Read it in full: “Fooling With Certainty: The Impossibly Real Worlds Of MC Escher,” from Mike Sowden (@Mikeachim)

* M. C. Escher

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As we look closely, we might recall that it was on this date in 1859 that our perspective was shifted in a different kind of way: Charles Darwin published The Origin of the Species.  Actually, on that day he published On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life; the title was shortened to the one we know with the sixth edition in 1872.

Title page of the 1859 edition

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(Roughly) Daily will be on a brief Thanksgiving hiatus, returning when the the tryptophan haze has passed…

“The past, like the future, is indefinite and exists only as a spectrum of possibilities”*…

A recent paper by Robert Lanza and others suggests that physical reality isn’t independent of us, “objective,” but is the product of networks of observers…

Is there physical reality that is independent of us? Does objective reality exist at all? Or is the structure of everything, including time and space, created by the perceptions of those observing it? Such is the groundbreaking assertion of a new paper published in the Journal of Cosmology and Astroparticle Physics.

The paper’s authors include Robert Lanza, a stem cell and regenerative medicine expert, famous for the theory of biocentrism, which argues that consciousness is the driving force for the existence of the universe. He believes that the physical world that we perceive is not something that’s separate from us but rather created by our minds as we observe it. According to his biocentric view, space and time are a byproduct of the “whirl of information” in our head that is weaved together by our mind into a coherent experience.

His new paper, co-authored by Dmitriy Podolskiy and Andrei Barvinsky, theorists in quantum gravity and quantum cosmology, shows how observers influence the structure of our reality.

According to Lanza and his colleagues, observers can dramatically affect “the behavior of observable quantities” both at microscopic and massive spatiotemporal scales. In fact, a “profound shift in our ordinary everyday worldview” is necessary, wrote Lanza in an interview with Big Think. The world is not something that is formed outside of us, simply existing on its own. “Observers ultimately define the structure of physical reality itself,” he stated.

How does this work? Lanza contends that a network of observers is necessary and is “inherent to the structure of reality.” As he explains, observers — you, me, and anyone else — live in a quantum gravitational universe and come up with “a globally agreed-upon cognitive model” of reality by exchanging information about the properties of spacetime. “For, once you measure something,” Lanza writes, “the wave of probability to measure the same value of the already probed physical quantity becomes ‘localized’ or simply ‘collapses.’” That’s how reality comes to be consistently real to us all. Once you keep measuring a quantity over and over, knowing the result of the first measurement, you will see the outcome to be the same.

“Similarly, if you learn from somebody about the outcomes of their measurements of a physical quantity, your measurements and those of other observers influence each other ‒ freezing the reality according to that consensus,” added Lanza, explaining further that “a consensus of different opinions regarding the structure of reality defines its very form, shaping the underlying quantum foam,” explained Lanza.

In quantum terms, an observer influences reality through decoherence, which provides the framework for collapsing waves of probability, “largely localized in the vicinity of the cognitive model which the observer builds in their mind throughout their lifespan,” he added.

Lanza says, “The observer is the first cause, the vital force that collapses not only the present, but the cascade of spatiotemporal events we call the past. Stephen Hawking was right when he said: ‘The past, like the future, is indefinite and exists only as a spectrum of possibilities.’”

Could an artificially intelligent entity without consciousness be dreaming up our world? Lanza believes biology plays an important role, as he explains in his book The Grand Biocentric Design: How Life Creates Reality, which he co-authored with the physicist Matej Pavsic.

While a bot could conceivably be an observer, Lanza thinks a conscious living entity with the capacity for memory is necessary to establish the arrow of time. “‘A brainless’ observer does not experience time and/or decoherence with any degree of freedom,” writes Lanza. This leads to the cause and effect relationships we can notice around us. Lanza thinks that “we can only say for sure that a conscious observer does indeed collapse a quantum wave function.”…

Another key aspect of their work is that it resolves “the exasperating incompatibility between quantum mechanics and general relativity,” which was a sticking point even for Albert Einstein.

The seeming incongruity of these two explanations of our physical world — with quantum mechanics looking at the molecular and subatomic levels and general relativity at the interactions between massive cosmic structures like galaxies and black holes — disappears once the properties of observers are taken into account.

While this all may sound speculative, Lanza says their ideas are being tested using Monte Carlo simulations on powerful MIT computer clusters and will soon be tested experimentally.

Is the physical universe independent from us, or is it created by our minds? “Is human consciousness creating reality?@RobertLanza

We might wonder, if this is so, how reality emerged at all. Perhaps one possibility is implied in “Consciousness was upon him before he could get out of the way.”

* Stephen Hawking

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As we conjure with consciousness, we might recall that it was on this date in 1908 (the same year that he was awarded the Nobel Prize in Physics) that Ernest Rutherford announced in London that he had isolated a single atom of matter. The following year, he, Hans Geiger (later of “counter” fame), and Ernest Marsden conducted the “Gold Foil Experiment,” the results of which replaced J. J. Thomson‘s “Plum Pudding Model” of the atom with what became known as the “Rutherford Model“: a very small charged nucleus, containing much of the atom’s mass, orbited by low-mass electrons.

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