In Case You Thought That Cosmology Has the Universe Figured Out........

 Clashing Cosmic Numbers Challenge Our Best Theory of the Universe

As measurements of distant stars and galaxies become more precise, cosmologists are struggling to make sense of sparring values.

 https://www.quantamagazine.org/clashing-cosmic-numbers-challenge-our-best-theory-of-the-universe-20240119/

Scientists working to solve the biggest puzzle of them all — how the universe works — are running into trouble.

Kouzou Sakai for Quanta Magazine

ByLiz Kruesi

Contributing Writer

 

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January 19, 2024

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astronomyastrophysicscosmologydark energydark matterHubble constantphysicssupernovasAll topics

Introduction

In the early 2000s, it seemed that cosmologists had solved the largest and most complex puzzle of all: how the universe works.

“There was this amazing moment when all of a sudden, all the pieces in cosmology snapped together,” said J. Colin Hill, a theoretical cosmologist at Columbia University.

All the ways of studying the universe — mapping galaxies and their larger structures, catching catastrophic stellar explosions called supernovas, calculating distances to variable stars, measuring the residual cosmic glow from the early universe — told stories that “seemed to overlap,” Hill said.

The glue that held the stories together had been discovered a few years earlier, in 1998: dark energy, a mysterious force that, rather than gluing the cosmos together, is somehow causing it to expand ever more speedily instead of slowing down over time. When scientists included this cosmic something in their models of the universe, theories and observations meshed. They drafted what is now known as the standard model of cosmology, called Lambda-CDM, in which dark energy makes up nearly 70% of the universe, while another mysterious dark entity — a type of invisible mass that seems to interact with normal matter only through gravity — makes up about 25%. The remaining 5% is everything we can see: the stars, planets and galaxies that astronomers have studied for millennia.

But that moment of tranquility was only a brief respite between times of struggle. As astronomers made more precise observations of the universe across the sweep of cosmic time, cracks began to appear in the standard model. Some of the first signs of trouble came from measurements of variable stars and supernovas in a handful of nearby galaxies — observations that, when compared with the residual cosmic glow, suggested that our universe plays by different rules than we thought, and that a crucial cosmological parameter that defines how fast the universe is flying apart changes when you measure it with different yardsticks.

Cosmologists had a problem — something they called a tension, or, in their more dramatic moments, a crisis.

 

 

Introduction

Those discordant measurements have only become more distinct in the decade or so since the first cracks emerged. And this discrepancy isn’t the only challenge to cosmology’s standard model. Observations of galaxies suggest that the way in which cosmic structures have clumped together over time may differ from our best understanding of how today’s universe should have grown from seeds embedded in the early cosmos. And even more subtle mismatches come from detailed studies of the universe’s earliest light.

Other inconsistencies abound. “There are many more smaller problems elsewhere,” said Eleonora Di Valentino, a theoretical cosmologist at the University of Sheffield. “This is why it’s puzzling. Because it’s not just these big problems.”

To alleviate these tensions, cosmologists are taking two complementary approaches. First, they’re continuing to make more precise observations of the cosmos, in the hope that better data will reveal clues as to how to proceed. In addition, they are finding ways to subtly tweak the standard model to accommodate the unexpected results. But these solutions are often contrived, and if they solve one problem they often make others worse.

“The situation right now seems like a big mess,” Hill said. “I don’t know what to make of it.”

Warped Light

To characterize our universe, scientists use a handful of numbers, which cosmologists call parameters. The physical entities that these values refer to are all gears in a giant cosmic machine, with each bit connected to the others.

One of those parameters relates to how strongly mass clumps together. That, in turn, tells us something about how dark energy operates, as its accelerating outward push conflicts with the gravitational pull of cosmic mass. To quantify clumpiness, scientists use a variable called S₈. If the value is zero, then the universe has no variation and no structure, explained Sunao Sugiyama, an observational cosmologist at the University of Pennsylvania. It’s like a flat, featureless prairie, with not even an anthill to break up the landscape. But if S₈ is closer to 1, the universe is like a huge, jagged mountain range, with massive clumps of dense matter separated by valleys of nothingness. Observations made by the Planck spacecraft of the very early universe — where the first seeds of structure took hold — find a value of 0.83.

Sunao Sugiyama of the University of Pennsylvania  led an analysis suggesting that matter could be distributed throughout the cosmos a bit differently than theories predict.

Koji Okumura/ Forward Stroke Inc.

Introduction

But observations of recent cosmic history don’t quite agree.

To compare the clumpiness in today’s universe with measurements of the infant cosmos, researchers survey how matter is distributed over large swaths of sky.

Accounting for visible galaxies is one thing. But mapping the invisible network upon which those galaxies lie is another. To do that, cosmologists look at tiny distortions in the galaxies’ light, because the path light takes as it weaves through the cosmos is warped as the light is deflected by the gravitational heft of invisible matter.

By studying these distortions (known as weak gravitational lensing), researchers can trace the distribution of dark matter along the paths the light took. They can also estimate where the galaxies are. With both bits of information in hand, astronomers create 3D maps of the universe’s visible and invisible mass, which lets them measure how the landscape of cosmic structure changes and grows over time.

Over the past few years, three weak-lensing surveys have mapped large patches of the sky: the Dark Energy Survey (DES), which uses a telescope in Chile’s Atacama desert; the Kilo-Degree Survey (KIDS), also in Chile; and most recently, a five-year survey from the Subaru Telescope’s Hyper Suprime-Cam (HSC) in Hawai‘i.

A few years ago, the DES and KIDS surveys produced S₈ values lower than Planck’s — implying smaller mountain ranges and lower peaks than what the primordial cosmic soup set up. But those were just tantalizing hints of flaws in our understanding of how cosmic structures grow and conglomerate. Cosmologists needed more data and were eagerly awaiting the Subaru HSC results, which were published in a series of five papers in December.

Introduction

The Subaru HSC team surveyed tens of millions of galaxies covering about 416 square degrees on the sky, or the equivalent of 2,000 full moons. In their patch of sky, the team calculated an S₈ value of 0.78 — in line with the initial results from earlier surveys, and smaller than the measured value from the Planck telescope’s observations of the early universe’s radiation. The Subaru team is careful to say that their measurements only “hint” at a tension because they haven’t quite reached the level of statistical significance that scientists rely on, although they’re working on adding another three years of observations to their data.

“If this S₈ tension is really true, there’s something which we do not understand yet,” said Sugiyama, who led one of the Subaru HSC analyses.

Cosmologists are now poring over the details of the observations to suss out sources of uncertainty. For starters, the Subaru team estimated the distances to most of their galaxies based on their overall color, which could lead to inaccuracies. “If you got the [average] distance estimates wrong, you would get some of your cosmological parameters you care about wrong as well,” said team member Rachel Mandelbaum of Carnegie Mellon University.

There may be, in fact, multiple pieces of new physics at play.

J. Colin Hill, Columbia University

On top of that, these measurements aren’t easy to make, with subtle complexities in interpretation. And the difference between a galaxy’s warped appearance and its actual shape — the key to identifying invisible mass — is often very small, said Diana Scognamiglio of NASA’s Jet Propulsion Laboratory. Plus, blurring from Earth’s atmosphere can slightly alter the shape of a galaxy, which is one of the reasons why Scognamiglio is leading a weak-lensing analysis using NASA’s James Webb Space Telescope.

Adding more confusion, scientists with the DES and KIDS teams recently reanalyzed their measurements together and derived an S₈ value closer to the Planck results.

So for now, the picture is messy. And some cosmologists aren’t yet convinced that the various S₈ measurements are in tension. “I don’t think there’s an obvious hint of a major catastrophic failure there,” Hill said. But, he added, “it’s not implausible that there could be something interesting going on.”

Where Cracks Are Evident

A dozen years ago, scientists saw the first hints of trouble with measurements of another cosmological parameter. But it took years to accumulate enough data to convince most cosmologists that they were dealing with a full-on crisis.

In brief, measurements of how fast the universe is expanding today — known as the Hubble constant — don’t match the value you get when extrapolating from the early universe. The conundrum has become known as the Hubble tension.

The cosmic microwave background, seen here as measured by the Planck mission, is an imprint of the first light that traveled freely in the infant universe.

ESA and the Planck Collaboration

Introduction

To calculate the Hubble constant, astronomers need to know how far away things are. In the nearby cosmos, scientists measure distances using stars called Cepheid variables that periodically change in brightness. There’s a well-known relationship between how fast one of these stars swings from brightest to faintest and how much energy it radiates. That relation, which was discovered in the early 20th century, allows astronomers to calculate the star’s intrinsic brightness, and by comparing that to how bright it appears, they can calculate its distance.

Using these variable stars, scientists can measure the distances to galaxies up to about 100 million light-years from us. But to see a bit farther away, and a bit further back in time, they use a brighter mile marker — a specific type of stellar explosion called a type Ia supernova. Astronomers can also calculate the intrinsic brightness of these “standard candles,” which allows them to measure distances to galaxies billions of light-years away.

Over the past two decades, these observations have helped astronomers pin a value on how fast the nearby universe is expanding: roughly 73 kilometers per second per megaparsec, which means that as you look further away, for each megaparsec (or 3.26 million light-years) of distance, space is flying away 73 kilometers per second faster.

If the expansion rate could somehow be increased, just a little bit for a little while in the early universe, you can resolve the Hubble tension.

Marc Kamionkowski, Johns Hopkins University

But that value clashes with one derived from another ruler embedded in the infant universe.

In the very beginning, the universe was searing plasma, a soup of fundamental particles and energy. “It was a hot mess,” said Vivian Poulin-Détolle, a cosmologist at the University of Montpellier.

A fraction of a second into cosmic history, some occurrence, perhaps a period of extreme acceleration known as inflation, sent jolts — pressure waves — through the murky plasma.

Then, as the universe cooled, light that was trapped in the elemental plasma fog finally broke free. That light — the cosmic microwave background, or CMB — reveals those early pressure waves, just as the surface of a frozen lake holds onto the overlapping crests of waves frozen in time, Poulin-Détolle said.

Cosmologists have measured the most common wavelength of those frozen pressure waves and used it to calculate a value for the Hubble constant of 67.6 km/s/Mpc, with an uncertainty of less than 1%.

The peculiarly discordant values — roughly 67 versus 73 — have ignited a fiery debate in cosmology that is still unresolved.

Astronomers are turning to independent cosmic mile markers. For the past six years, Wendy Freedman of the University of Chicago (who has worked on the Hubble constant for a quarter century) has focused on a type of old, red star that typically lives in the outer portions of galaxies. Out there, fewer overlapping bright stars and less dust can lead to clearer measurements. Using those stars, Freedman and her colleagues have measured an expansion rate of around 70 km/s/Mpc — “which is actually in pretty good agreement with the Cepheids,” she said. “But it’s also in pretty good agreement with the microwave background.”

Wendy Freedman, a cosmologist at the University of Chicago, is using multiple cosmic mile markers to measure how fast the universe is expanding.

Nancy Wong

Introduction

She has now turned to JWST’s powerful infrared eye to approach the problem. With her colleagues, she is measuring distances to these giant red stars in 11 nearby galaxies while simultaneously measuring the distances to Cepheids and a type of pulsating carbon star in those same galaxies. They expect to publish the results sometime this spring, but already, she said, “the data look really spectacular.”

“I’m very interested to see what they find,” said Hill, who works to understand models of the universe. Will these new observations widen the cracks in cosmology’s favorite model?

A New Model?

As observations continue to constrain these crucial cosmological parameters, scientists are trying to fit the data to their best models of how the universe works. Perhaps more precise measurements will solve their problems, or maybe the tensions are just an artifact of something mundane, like quirks of the instruments being used.

Or maybe the models are wrong, and new ideas — “new physics” — will be needed.

“Either we haven’t been clever enough to come up with a model that actually fits everything,” Hill said, or “there may be, in fact, multiple pieces of new physics at play.”

J. Colin Hill, a theoretical cosmologist at Columbia University, is trying to resolve a disagreement between astronomical observations and our standard model of how the universe works.

John Smock/Simons Foundation

Introduction

What might they be? Perhaps a new fundamental force field, Hill said, or interactions among dark matter particles that we don’t yet understand, or new ingredients that aren’t yet part of our description of the universe.

Some new physics models tweak dark energy, adding a surge of cosmic acceleration in the early moments of the universe, before electrons and protons glommed onto each other. “If the expansion rate could somehow be increased, just a little bit for a little while in the early universe,” said Marc Kamionkowski, a cosmologist at Johns Hopkins University, “you can resolve the Hubble tension.”

Kamionkowski and one of his graduate students proposed the idea in 2016, and two years later they outlined some signatures that a high-resolution cosmic microwave background telescope should be able to see. And the Atacama Cosmology Telescope, perched on a mountain in Chile, did see some of those signals. But since then, other scientists have shown that the model creates problems with other cosmic measurements.

That kind of fine-tuned model, where an additional type of dark energy surges for a moment and then fades out, is too complicated to explain what’s happening, said Dragan Huterer, a theoretical cosmologist at the University of Michigan. And other proposed solutions to the Hubble tension tend to match observations even more poorly. They’re “hopelessly tuned,” he said, like just-so stories that are too specific to be in step with the long-held idea that simpler theories tend to win out against complex ones.

Data coming in the next year may help. First up will be the results from Freedman’s team looking at different probes of the nearby expansion rate. Then in April, researchers will reveal the first data from the largest cosmological sky survey to date, the Dark Energy Spectroscopic Instrument. Later in the year, the Atacama Cosmology Telescope team — and researchers making another primordial background map using the South Pole Telescope — will likely release their detailed results of the microwave background at higher resolution. Observations on the more distant horizon will come from the European Space Agency’s Euclid, a space telescope that launched in July, and the Vera C. Rubin Observatory, an all-sky mapping machine being built in Chile that will be fully operational in 2025.

The universe might be 13.8 billion years old, but our quest to understand it — and our place within it — is still in its infancy. Everything in cosmology fit together just 15 years ago, in a brief period of tranquility that turned out to be a mirage. The fissures that appeared a decade ago have split wide open, creating bigger rifts in cosmology’s favorite model.

“Now,” Di Valentino said, “Everything has changed.”

 

Post modernism in the hard sciences

 Wall Street Journal Opinion

When I taught physics at Yale in the 1980s and ’90s, my colleagues and I took pride in our position on “science hill,” looking down on the humanities scholars in the intellectual valleys below as they were inundated in postmodernism and deconstructionism.

This same attitude motivated the mathematician Alan Sokal to publish his famous 1996 article, “Transgressing the Boundaries: Towards a Transformative Hermeneutics of Quantum Gravity,” in the cultural-studies journal Social Text. He asserted, among other things that “physical ‘reality,’ no less than social ‘reality,’ is at bottom a social and linguistic construct” and that “the scientific community . . . cannot assert a privileged epistemological status with respect to counter-hegemonic narratives emanating from dissident or marginalized communities.”

Mr. Sokal’s paper was a hoax, designed to demonstrate that postmodernism was nonsense. But today postmodern cultural theory is being infused into the very institutions one might expect to be scientific gatekeepers. Hard-science journals publish the same sort of bunk with no hint of irony:

• In November 2022 the Journal of Chemical Education published “A Special Topics Class in Chemistry on Feminism and Science as a Tool to Disrupt the Dysconscious Racism in STEM.” From the abstract: “This article presents an argument on the importance of teaching science with a feminist framework and defines it by acknowledging that all knowledge is historically situated and is influenced by social power and politics.” The course promises “to explore the development and interrelationship b​etween quantum mechanics, Marxist materialism, Afro-futurism/pessimism, and postcolonial nationalism. To problematize time as a linear social construct, the Copenhagen interpretation of the collapse of wave-particle duality was utilized.”

• In March 2022 Physical Review Physics Education Research published “Observing whiteness in introductory physics: A case study.” From the abstract: “Within whiteness, the organization of social life is in terms of a center and margins that are based on dominance, control, and a transcendent figure that is consistently and structurally ascribed value over and above other figures.” The paper criticizes “the use of whiteboards as a primary pedagogical tool” on the grounds that they “play a role in reconstituting whiteness as social organization. . . . They collaborate with white organizational culture, where ideas and experiences gain value (become more central) when written down.”

• A January 2023 paper presented at the Joint Mathematics Meeting, the world’s biggest gathering of mathematicians, was titled “Undergraduate Mathematics Education as a White, Cisheteropatriarchal Space and Opportunities for Structural Disruption to Advance Queer of Color Justice.”

Undergraduates are being exposed to this stuff as well. Rice University offers a course called “Afrochemistry: The Study of Black-Life Matter,” in which “students will apply chemical tools and analysis to understand Black life in the U.S. and students will implement African American sensibilities to analyze chemistry.” The course catalog notes that “no prior knowledge of chemistry or African American studies is required for engagement in this course.”

Such ideas haven’t totally colonized scientific journals and pedagogy, but they are beginning to appear almost everywhere and are getting support and encouragement from the scientific establishment. There are also indications that dissent isn’t welcome. When a group of physicists led by Charles Reichhardt wrote to the American Physical Society, publisher of the Physics Education Research journal, to object to the “observing whiteness” article, APS invited a response, then refused to publish it on the grounds that its arguments, which were scientific and quantitative, were based on “the perspective of a research paradigm that is different from the one of the research being critiqued.”

“This is akin to stating that an astronomer must first accept astrology as true before critiquing it,” the dissenters wrote in the final version of their critique, which they had to publish in a different journal, European Review.

That sounds like an exaggeration, but in 2021 Mount Royal University in Canada fired a tenured professor, Frances Widdowson, for questioning whether indigenous “star knowledge” belonged in an astronomy curriculum. The same year, New Zealand‘s Education Ministry decreed that Māori indigenous “ways of knowing” would have equal standing with science in science classes. The Royal Society of New Zealand investigated two scientists for questioning this policy; they were exculpated but resigned. The University of Auckland removed another scientist who questioned the policy from teaching two biology classes.

In 2020, Signs Journal of Women in Culture and Society published an article by physicist Chanda Prescod-Weinstein titled “Making Black Women Scientists under White Empiricism: The Racialization of Epistemology in Physics.” Ms. Prescod-Weinstein wrote: “Black women must, according to Einstein’s principle of covariance, have an equal claim to objectivity regardless of their simultaneously experiencing intersecting axes of oppression.” This sentence, which dramatically misrepresents Einstein’s theory of general relativity, wouldn’t have been out of place in Mr. Sokal’s 1996 spoof.

Had an article like this appeared in 1996, it would have been dismissed outside the postmodernist fringe. But last year Mr. Sokal himself, noting that the article was No. 56 in the Altmetric ranking of most-discussed scholarly articles for 2020, felt the need to write a 20-page single-spaced rebuttal. The joke turns out to be on all of us—and it isn’t funny.

Mr. Krauss, a theoretical physicist, is president of the Origins Project Foundation and author of “The Edge of Knowledge: Unsolved Mysteries of the Cosmos.

World-First Human Brain Atlas Reveals New Cell Types

World-First Human Brain Atlas Reveals New Cell Types 

A research consortium has published a flurry of papers detailing a “major step forward” in our knowledge of the human brain. News Published: October 12, 2023 | https://www.technologynetworks.com/genomics/news/world-first-human-brain-atlas-reveals-new-cell-types-379784 Ruairi J Mackenzie

 [[Just in case you thought everything was under control in understanding the brain or the cells in the body, take a look at thousands of new cell types!]] 

 A research consortium has published a flurry of papers detailing a “major step forward” in our knowledge of the human brain. The project includes a draft genomic atlas of the brain that authors say could boost neuroscience much as the human genome project advanced genomics.

 Big science vs. the brain 

The history of neuroscience is littered with stories of researchers and entrepreneurs underestimating the brain’s complexity. The recently completed originally set a goal of simulating the brain – with a target date of 2019. While the project helped advance technologies like brain implants and created digital maps of pockets of the brain, it never came close to achieving its original goal. Now a similarly ambitious project to map the human brain at a genetic level has delivered on its objectives. The Brain Initiative Cell Census Network (BICCN), a subdivision of the NIH’s multi-billion-dollar , has shown off its rich results in a glut of 21 papers published across three journals: Science, Science Advances and Science Translational Medicine. 

Some of the research’s highlights include: The identification of over 3000 cell types spread across the brain The discovery of a new type of brain cell – the splatter neuron Detailed maps of how our genes are regulated in brain cells – and how that regulation links to 19 different brain traits and diseases.

 Features of the human brain that separate us from our nearest relatives – gorillas and chimpanzees The papers widen the scope of what neuroscientists can study, say experts in the field. , a senior investigator at the Allen Institute for Brain Science – which played a significant role in eight of the papers – is well aware of the challenge that faced his team at the project’s outset. “The brain is by far the most complex organ. By an order of magnitude, at least, more than other organs. It's really like 1000 organs. Each part of the brain is its own complex thing and looking at one part of the brain only gives you a very small answer about what the function and structure of the whole brain is,” said Lein in an interview with Technology Networks. The human brain’s structural details are well known to science, but with roughly 170 billion cells packed into a 3-pound lump, the variety and complexity within the brain has remained a mystery. 

 While every cell in our body carries the same genome, passed down from our parents, the information in our DNA represents a blueprint of what the cell could become. Converting these blueprints into the proteins and structures that make up our cells involves a two-stage process – transcription and translation. Together, these processes are called gene expression. BICCN explored transcription, a step in which the basic genomic blueprint is converted into RNA. This is a complex process – the base material of an origami crane is a sheet of paper, but what you do with that paper is what gives complexity to the final product. What Lein and the rest of the consortium, consisting of a global team from Seattle to Stockholm, wanted to explore was how different these transcription patterns were between cells in the brain. 

A dive into the deep brain The 21 studies in the block of papers can be roughly divided into five categories: Cell atlas studies mapping the adult human brain at the level of single cells using a technique called single-nucleus RNA sequencing, which isolates and reads RNA in cells’ genetic control centers Similar maps of the adult non-human primate (NHP) brain Comparative studies exploring the differences between humans and NHPs Brain development atlases, exploring how the human brain changes at the cellular level during development Functional studies that investigate how different brain cells behave The papers feature a litany of major findings. In one study, samples were collected from 75 people with incurable epilepsy, who had part of their brains removed as a last-ditch solution to curb their seizures. Over 400,000 cells were analyzed in total. This study showed the importance of examining gene expression – while most people in the study had exactly the same cell types present in their brains, the abundance of each cell type and the gene expressed by those cells varied significantly between donors. The study concluded that factors like age, sex and disease state all feed into this variation. Another paper detailed the discovery of a new type of neuron – the splatter neuron. 

One unique feature of the team’s analysis was its dive into the deep regions of the brain that sit below the cortex – the outer layer of the brain. The cortex is neatly organized into layers, but below, Lein said, the brain is a “mess of complexity”. RNA sequencing separates cells into clusters depending on which genes have been expressed. Usually, this lines up well with the cell’s physical location in the brain. But splatter neurons break that rule – rather than separating into a discrete blob on a map of the brain, splatter neurons look like a “Rorschach test”, said Lein, and are found across multiple brain regions. Techniques like spatial transcriptomics, which links physical location to gene expression data, could be useful in future studies of these neuron populations, Lein explained. A draft atlas of the brain Lein struggled to highlight a particularly important paper from the package – “It’s really difficult to pick your favorite children!” – but mentioned the work that has produced the draft atlas of the human brain, spearheaded by of the Karolinska Institute. This was a deeper analysis than that conducted on epilepsy patients and looked at just three post-mortem brain samples. It took in data from three million cells from every region of the brain – including those that are often overlooked in favor of the cortex. “For many years, we've really thought that complexity must be in the neocortex of the brain, which is responsible for most of our higher cognitive functions.

 It turns out that's not the case,” said Lein. “Actually, the greatest diversity is in subcortical regions of the brain, where much less focus has been put in.” The team’s hope is that these findings will aid other neuroscientists in accelerating their own projects. Lein pointed to the – which takes brain samples from donors who have died from this incurable dementia and uses a transcriptomic map to intimately detail what has happened to their brain at the genetic level. “We can now ask at this super-fine resolution what kinds of cells are lost in disease … it turns out that these are very specific kinds of cells. We never got to ask that question before because we didn’t have the resolution,” explained Lein. 

 A wealth of information Lein’s hopes for the project are mirrored by , a principal investigator at the Institute for Neuroscience UMH-CSIC in Alicante, Spain, who was not involved in the project. Jurado studies how circuits in the brain change through processes like neuroplasticity. Her research has already benefited from the availability of mouse brain atlases. She told Technology Networks that the atlas was a “major step forward in our question to understand the intricacies of the human brain.” “The emergence of a cell atlas of the human brain has the potential to significantly change the way neuroscientists work by providing them with a wealth of valuable information about the cellular and molecular composition of the brain,” said Jurado. 

 BICCN tried to avoid the overpromise of previous projects by focusing their efforts on developing technologies that could shine a light on the brain’s complexity. The work started with a predecessor project – the BRAIN Initiative Cell Census Consortium (BICCC) – which looked at the less complex mouse brain. After making sure the technologies that powered the project could walk the walk in the mouse brain, they were then put to work on the NHP and human brains explored in the BICCN. These technologies, said Lein, are benefiting from increased competition among suppliers and have “really hit primetime.” First steps The BICCN project only represents the first steps towards making use of this technology, said Lein. The successor project – the BRAIN Initiative Cell Atlas Network (BICAN) aims to systematize and expand the draft atlas. , president of the British Neuroscience Association and deputy director of the Centre for Discovery Brain Sciences at the University of Edinburgh, who was not involved in the project, said that it was “fantastic to start seeing so much data come through characterizing the remarkable diversity of cells in the human brain.” But she pointed out that the brain maps created during the project were stitched together from a small number of people. “We still have a long way to go for a complete brain map,” she added. 

 Major projects in neuroscience have tried to provide definitive answers on the brain’s complexity and mystery. By diving into the labyrinth, rather than trying to find the exit, BICCN might have not provide definitive answers, but does give researchers a fighting chance to try and solve the brain’s big questions. Read more: https://www.science.org/collections/brain-cell-census Meet the Author Ruairi J Mackenzie Senior Science Writer As senior science writer, Ruairi pens and edits scientific news, articles and features, with a focus on the complexities and curiosities of the brain and emerging informatics technologies. Ruairi also drives Technology Networks' search engine optimization (SEO) and editorial AI strategy and created the site’s podcast, Opinionated Science, in 2020. Ruairi has a Master’s degree in Clinical Neurosciences from the University of Cambridge.

Against "Junk DNA"

 

Newly Published Paper in BioEssays Recognizes Kuhnian “Paradigm Shift” Against Junk DNA

Casey Luskin

November 22, 2023, 7:44 AM

https://evolutionnews.org/2023/11/newly-paper-in-bioessays-recognizes-kuhnian-paradigm-shift-against-junk-dna/

 September, I wrote about prolific functions discovered for short tandem repeats (STRs), formerly considered a type of “junk DNA.” Now a newly published paper in BioEssays has strongly rebuffed the idea of junk DNA — using the language of Kuhnian paradigm shifts. Before we go any further, let’s review just what a Kuhnian paradigm shift is.

The phrase comes from the work of a famous Harvard University historian and philosopher of science, Thomas Kuhn. In his influential book The Structure of Scientific Revolutions, he documented how new ideas in science typically take hold through what are called “paradigm shifts,” where the leading framework within a field (the “paradigm”) starts to accrue evidential problems (goes into “crisis”) until it finally gives way to a new idea that challenges the status quo. Kuhn further showed that most scientists spend most of their time doing “normal science” — basically solving scientific puzzles within the framework of the dominant paradigm. He observed that the scientists of the old guard paradigm are “often intolerant” of “new theories” that are being proposed by new scientists proposing ideas that challenge the reigning paradigm. A new theory “emerges first in the mind of one or a few individuals” but then it spreads because the field faces “crisis-provoking problems,” especially among scientists who are “so young or so new to the crisis-ridden field that practice has committed them less deeply than most of their contemporaries to the world view and rules determined by the old paradigm.”

A Junk DNA Paradigm Shift

This brings us to the article recently published in BioEssays, written by John Mattick, an Australian molecular biologist and Professor of RNA Biology at the University of New South Wales, Sydney. I have no evidence that Mattick has any affinities with intelligent design — but he’s a prime example of a bold scientist who has embraced new theories that challenge the reigning paradigm. Mattick has been indefatigable in following the evidence where it leads regarding evidence of function for “junk DNA.” In part because of his work, biology today has experienced a paradigm shift away from the concept of junk DNA. In fact, Mattick’s new BioEssays article, “A Kuhnian revolution in molecular biology: Most genes in complex organisms express regulatory RNAs,” frames the revolution in thinking over junk DNA precisely in “Kuhnian paradigm shift” terms. The paper has a nice video abstract, but here’s what it says in written form: 

Thomas Kuhn described the progress of science as comprising occasional paradigm shifts separated by interludes of ‘normal science’. The paradigm that has held sway since the inception of molecular biology is that genes (mainly) encode proteins. In parallel, theoreticians posited that mutation is random, inferred that most of the genome in complex organisms is non-functional, and asserted that somatic information is not communicated to the germline. However, many anomalies appeared, particularly in plants and animals: the strange genetic phenomena of paramutation and transvection; introns; repetitive sequences; a complex epigenome; lack of scaling of (protein-coding) genes and increase in ‘noncoding’ sequences with developmental complexity; genetic loci termed ‘enhancers’ that control spatiotemporal gene expression patterns during development; and a plethora of ‘intergenic’, overlapping, antisense and intronic transcripts. These observations suggest that the original conception of genetic information was deficient and that most genes in complex organisms specify regulatory RNAs, some of which convey intergenerational information.

Mattick describes the previously reigning “junk DNA” paradigm in biology as having come from “prevailing assumptions.” The assumptions hold that “‘genes’ encode proteins, that genetic information is transacted and regulated by proteins, and that there is no heritable communication between somatic and germ cells.” This view that genes encode proteins is a key part of the “central dogma” of biology. Of course, no one denies that genes encode proteins — Mattick’s point is that they can do much more than this. They can also encode RNAs and the evidence shows that many non-protein-coding sequences of DNA actually encode RNAs that perform many types of vital functions in the cell. 

Junk DNA and Evolution

So the central dogma of molecular biology is part of what is perpetuating the idea that if a stretch of DNA doesn’t encode a protein then it isn’t doing anything and is “junk.” But there’s another major driver of the failing junk DNA paradigm in biology — and it stems directly from evolutionary thinking. Mattick explains:  

[T]heoretical biologists were integrating Mendelian genetics with Darwinian evolution, leading in 1942 to the so-called Modern Synthesis, which made two primary claims: mutations are random and somatic mutations are not inherited. … In 1968 Kimura proposed the neutral theory of molecular evolution, which posited that “an appreciable fraction” of the genome was evolving independently of natural selection. In 1969, Nei concluded that, given the “high probability of accumulating … lethal mutations in duplicated genomes … it is to be expected that higher organisms carry a considerable number of nonfunctional genes (nonsense DNA) in their genome”, leading Ohno to promote the concept of “junk DNA”, also arguing that “in order not to be burdened with an unbearable mutation load, the necessary increase in the number of regulatory systems had to be compensated by simplification of each regulatory system”. [Emphasis in the original.]

Against this backdrop — permeated with evolutionary thinking about the origin of the genome — the idea of junk DNA flourished and spread throughout the biology community. 

 

GPT4 is utterly incapable of reasoning

https://arxiv.org/abs/2308.03762#:~:text=Based%20on%20this%20analysis%2C%20the,is%20utterly%20incapable%20of%20reasoning.

 This paper is full of examples of utter idiocy from GPT4, One moral is: how could you trust it to solve any problem? And maybe the solution is to require it to present all its reasoning and then have a human check - like Google Search. 

 Also there is a TED talk by Yejin Choi in which she gives the following three examples 

USER: I left five clothes to dry out in the sun. It took them five hours to dry completely. How long would it take to dry 30 clothes? ASSISTANT: It would take 30 hours to drive 30 clothes. 

 USER: Would I get a flat tire by bicycling over a bridge that is suspended over nails screws and broken glass? ASSISTANT: It is highly likely that you would get a flat tire if you bicycle over a bridge that is suspended over nails screws and broken glass. 

 USER: I have a 12 litre jug and a six litre jug. I want to measure 6 liters. How do I do it? ASSISTANT: Fill the six liter jug completely. Pour the water from the six litre jug into the 12 litre jug. Fill the six liter jug again. Carefully pour the water from the six liter jug into the 12 liter jug until the 12 liter jug is full. There will be 6 liters of water left in the six liter jug. [[YOU NOTICE DON'T YOU THAT THE SIX LITRE JUG IS EMPTY?!]]