Michael J. Behe's Blog, page 63
June 12, 2022
Decoding a key part of the cell, atom by atom
In an article published in Science, researchers report progress on the determination of the structure of the nuclear pore complex, “an incredibly discriminating gatekeeper for the cell’s nucleus.”
Credit: Valerie AltounianWhatever you are doing, whether it is driving a car, going for a jog, or even at your laziest, eating chips and watching TV on the couch, there is an entire suite of molecular machinery inside each of your cells hard at work. That machinery, far too small to see with the naked eye or even with many microscopes, creates energy for the cell, manufactures its proteins, makes copies of its DNA, and much more.
Among those pieces of machinery, and one of the most complex, is something known as the nuclear pore complex (NPC). The NPC, which is made of more than 1,000 individual proteins, is an incredibly discriminating gatekeeper for the cell’s nucleus, the membrane-bound region inside a cell that holds that cell’s genetic material. Anything going in or out of the nucleus has to pass through the NPC on its way.
The NPC’s role as a gatekeeper of the nucleus means it is vital for the operations of the cell. Within the nucleus, DNA, the cell’s permanent genetic code, is copied into RNA. That RNA is then carried out of the nucleus so it can be used to manufacture the proteins the cell needs. The NPC ensures the nucleus gets the materials it needs for synthesizing RNA, while also protecting the DNA from the harsh environment outside the nucleus and enabling the RNA to leave the nucleus after it has been made.
The implications of this research are potentially huge. Not only is the NPC central to the operations of the cell, it is also involved in many diseases. Mutations in the NPC are responsible for some incurable cancers, for neurodegenerative and autoimmune diseases such as amyotrophic lateral sclerosis (ALS) and acute necrotizing encephalopathy, and for heart conditions including atrial fibrillation and early sudden cardiac death. Additionally, many viruses, including the one responsible for COVID-19, target and shutdown the NPC during the course of their lifecycles.
The assembly of the NPC’s outer face also helped solve a longtime mystery about the nuclear envelope, the double membrane system that surrounds the nucleus. Like the membrane of the cell within which the nucleus resides, the nuclear membrane is not perfectly smooth. Rather, it is studded with molecules called integral membrane proteins (IMPs) that serve in a variety of roles, including acting as receptors and helping to catalyze biochemical reactions.
Phys.Org
The nuclear pore complex is said to be composed of more than 1000 proteins, operating to form one of most complex pieces of molecular machinery within the cell. Consider that the probability of forming even one protein is miniscule, given the laws of physics in our universe, let alone 1000 proteins operating in concert. And yet some would claim that there is no evidence for intelligent design!
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June 11, 2022
L&FP, 56: Can we invent or define a nine-sided hexagon?
One of the many fundamental errors of nominalism is to confuse labels with logic of being substance.
To clarify the matter, let us ponder:
As was noted in the ongoing defending thread:
KF, 839: As a start point for rethinking, please, show us a nine sided hexagon.
(What, you can’t, isn’t the term hexagon just a word we can apply as we please, rewriting the dictionary at will, there is no such thing as a nature so there is no difference. So, on such radical nominalism, there is no difference between truth and error, truthfulness and willful deceit, justice and injustice, male and female, knowledge and myth, indoctrination and education, acquitting the innocent and knowingly condemning such, sound policing and the gestapo. See the nihilistic pattern?)
Believe it or not, there are many otherwise vexed issues that resolve themselves once we recognise this issue. END
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June 10, 2022
Scientists determine structure of key factor in RNA quality control
Science Daily reports:
In biology, getting rid of stuff can be just as important as making it. A buildup of cells, proteins, or other molecules that are no longer needed can cause problems, so living things have evolved several ways to clean house.
A prime example is the RNA exosome. RNA molecules perform many roles in cells. Some of them are translated into proteins; others form a cell’s protein-building machinery. The RNA exosome is a cellular machine that degrades RNA molecules that are faulty, harmful, or no longer needed. Without this microscopic Marie Kondo to prune what doesn’t spark joy, our cells would become dysfunctional hoarders, unable to function.
“RNA surveillance and degradation pathways exist in all forms of life,” explains Christopher Lima, Chair of the Structural Biology Program in the Sloan Kettering Institute. “From bacteria to humans, all living things have mechanisms to monitor the quality of RNA and to purposely degrade it.”
For a long time, Dr. Lima says, these pathways were considered, like housework, kind of boring. But it turns out that these degradation pathways are highly regulated and control everything from embryonic development to the progression of the cell cycle.
What’s more, errors in these pathways can lead to many types of disease, from cancer to neurodegeneration.
Notice the descriptions consistent with intelligent design that seem unavoidable in this report.
RNA Degradation and Disease
There are big stakes involved. An indication of just how important RNA degradation is comes from the long list of diseases that result from defective or poorly controlled degradation. Perhaps the most famous example is cystic fibrosis. In this case, the messenger RNA encoding a protein that shuttles ions across cell membranes is degraded by RNA decay pathways. As a result, the protein is not present in mucous membranes of the lungs, which leads to a buildup of mucus there and results in severely impaired breathing.
“It’s a famous example of RNA quality control with bad results.”
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“The reality is if you have defective RNA quality-control pathways, your ribosomes don’t work, your transfer RNAs don’t work, your spliceosomes don’t work.” The list goes on and on.
ScienceDaily
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Scientist determine structure of key factor in RNA quality control
Science Daily reports:
In biology, getting rid of stuff can be just as important as making it. A buildup of cells, proteins, or other molecules that are no longer needed can cause problems, so living things have evolved several ways to clean house.
A prime example is the RNA exosome. RNA molecules perform many roles in cells. Some of them are translated into proteins; others form a cell’s protein-building machinery. The RNA exosome is a cellular machine that degrades RNA molecules that are faulty, harmful, or no longer needed. Without this microscopic Marie Kondo to prune what doesn’t spark joy, our cells would become dysfunctional hoarders, unable to function.
“RNA surveillance and degradation pathways exist in all forms of life,” explains Christopher Lima, Chair of the Structural Biology Program in the Sloan Kettering Institute. “From bacteria to humans, all living things have mechanisms to monitor the quality of RNA and to purposely degrade it.”
For a long time, Dr. Lima says, these pathways were considered, like housework, kind of boring. But it turns out that these degradation pathways are highly regulated and control everything from embryonic development to the progression of the cell cycle.
What’s more, errors in these pathways can lead to many types of disease, from cancer to neurodegeneration.
Notice the descriptions consistent with intelligent design that seem unavoidable in this report.
RNA Degradation and Disease
There are big stakes involved. An indication of just how important RNA degradation is comes from the long list of diseases that result from defective or poorly controlled degradation. Perhaps the most famous example is cystic fibrosis. In this case, the messenger RNA encoding a protein that shuttles ions across cell membranes is degraded by RNA decay pathways. As a result, the protein is not present in mucous membranes of the lungs, which leads to a buildup of mucus there and results in severely impaired breathing.
“It’s a famous example of RNA quality control with bad results.”
Copyright © 2022 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
“The reality is if you have defective RNA quality-control pathways, your ribosomes don’t work, your transfer RNAs don’t work, your spliceosomes don’t work.” The list goes on and on.
ScienceDaily
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June 9, 2022
At Phys.org: NASA gets serious about UFOs
What are the implications of NASA’s public involvement in this issue?
NASA is officially joining the hunt for UFOs. The space agency on Thursday announced a new study that will recruit leading scientists to examine unidentified aerial phenomena—a subject that has long fascinated the public and recently gained high-level attention from Congress.
The project will begin early this fall and last around nine months, focusing on identifying available data, how to gather more data in future, and how NASA can analyze the findings to try to move the needle on scientific understanding.
“Over the decades, NASA has answered the call to tackle some of the most perplexing mysteries we know of, and this is no different,” Daniel Evans, the NASA scientist responsible for coordinating the study, told reporters on a call.
While NASA probes and rovers scour the solar system for the fossils of ancient microbes, and its astronomers look for so-called “technosignatures” on distant planets for signs of intelligent civilizations, this is the first time the agency will investigate unexplained phenomena in Earth’s skies.
The announcement comes as the field of UFO study, once a poorly-regarded research backwater, is gaining more mainstream traction.
Copyright © 2022 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.“One of the things we tangentially hope to do as part of this study, simply by talking about it in the open, is to help to remove some of the stigma associated with it, and that will yield obviously, increased access to data, more reports, more sightings.”
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At EurekAlert: Antarctic glaciers losing ice at fastest rate for 5,500 years, finds study
At the current rate of retreat the vast glaciers, which extend deep into the heart of the ice sheet, could contribute as much as 3.4 metres to global sea level rise over the next several centuries.
Antarctica is covered by two huge ice masses: the East and West Antarctic Ice Sheets, which feed many individual glaciers. Because of the warming climate, the WAIS has been thinning at accelerated rates over the past few decades. Within the ice sheet, the Thwaites and Pine Island glaciers are particularly vulnerable to global warming and are already contributing to rises in sea level.
Now, a new study led by the University of Maine and the British Antarctic Survey, including academics from Imperial College London, has measured the rate of local sea level change – an indirect way to measure ice loss – around these particularly vulnerable glaciers.
They found that the glaciers have begun retreating at a rate not seen in the last 5,500 years. With areas of 192,000 km2 (nearly the size of the island of Great Britain) and 162,300 km2 respectively, the Thwaites and Pine Island glaciers have the potential to cause large rises in global sea level.
“These currently elevated rates of ice melting may signal that those vital arteries from the heart of the West Antarctic Ice Sheet have been ruptured, leading to accelerating flow into the ocean that is potentially disastrous for future global sea level in a warming world. Is it too late to stop the bleeding?”
During the mid-Holocene period, over 5,000 years ago, the climate was warmer than today and thus sea levels were higher and glaciers smaller. The researchers wanted to study fluctuations in sea level since the mid-Holocene, so studied the remnants of old Antarctic beaches, which are today elevated above modern sea level.
They examined seashells and penguin bones on these beaches using radiocarbon dating – a technique that uses the radioactive decay of carbon locked in the shells and bones as a clock to tell us how long they have sat above sea level.
When heavy glaciers sit on the land, they push down or ‘load’ the Earth’s surface. After the glaciers’ ice melts or ‘unloads’, the land ‘bounces back’ so that what once was a beach is now higher than sea level. This explains why the local sea level for this land fell, while globally the water from the melting ice caused global sea levels to rise.
By pinpointing the precise age of these beaches, they could tell when each beach appeared and therefore reconstruct changes in local, or ‘relative’, sea level over time.
The results showed a steady fall in relative sea level over the last 5,500 years, which the researchers interpret as a result of ice loss just prior to that time. This pattern is consistent with relatively stable glacier behaviour with no evidence of large-scale glacier loss or advance.
The paper is published in Nature Geoscience.
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June 8, 2022
The Death of Neutral Theory
In today’s Nature, we find this article:
“Synonymous mutations in representative yeast genes are mostly strongly non-neutral.”
They investigated what effect “synonymous, nonsynonymous and nonsense” mutations involving “21 endogenous genes” would have on yeast. The fitness levels of synonymous and nonsynonymous fell in equal (though not ‘identical’) measure–around 75%.
I don’t have access to the article itself, only the abstract. The abstract begins thusly:
Synonymous mutations in protein-coding genes do not alter protein sequences and are thus generally presumed to be neutral or nearly neutral[1,2,3,4,5]
1 through 5 are citations. Who are they: Kimura, King and Jukes, Nei and Kumar, Li and Dan Graur. The heavyweights of neutral theory.
The abstract ends:
The strong non-neutrality of most synonymous mutations, if it holds true for other genes and in other organisms, would require re-examination of numerous biological conclusions about mutation, selection, effective population size, divergence time and disease mechanisms that rely on the assumption that synonymous mutations are neutral.
In the Phys.Org press release, one of the authors is quoted saying:
“Since the genetic code was solved in the 1960s, synonymous mutations have been generally thought to be benign. We now show that this belief is false,” said study senior author Jianzhi “George” Zhang, the Marshall W. Nirenberg Collegiate Professor in the U-M Department of Ecology and Evolutionary Biology.
“Because many biological conclusions rely on the presumption that synonymous mutations are neutral, its invalidation has broad implications. For example, synonymous mutations are generally ignored in the study of disease-causing mutations, but they might be an underappreciated and common mechanism.”
I can hardly wait to see what Larry Moran says at his Sandwalk blog.
I have often made fun of those who hold to the Neutral Theory in the non–Kimuran sense. My problem with the idea of everything being ‘neutral’ was that, hypothetically, anything can become anything. There’s no start nor finish to this process. I thought it was extravagant; instead, it was just wrong. Modern techniques–the use of Crisper to make mutant genes, has now allowed us to see how NT is a ‘dead-end.’ We can only hope that evolutionary biologists can see this. But there’s really no reason for such hope, is there?
The authors tell us that there’s no reason to believe that what they found in yeast won’t be found in other eukaryotic species, but that this will have to be tested to confirm that this ‘dead-end’ generally holds. I’ll bet on it holding in most families with few, if any, exceptions. We’ll see. Science progresses (while Darwinism ebbs).
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At Reasons to Believe: Could Life Be Silicon-Based?
Biochemist Fuz Rana discusses a 2020 review article published in the journal Life in which a team of astrobiologists from MIT present a detailed evaluation of silicon’s life-support capacity.
Star Trek episode: The Devil in the DarkThe first scientific proposal for silicon-based life extends back to 1891 and the ideas of German astrophysicist Julius Scheiner. Since that time scientists have debated the prospects of silicon-based life—with some embracing its plausibility and others dismissing it. But as a team of astrobiologists from MIT have recently pointed out, to date no one has systematically and comprehensively assessed the capacity of silicon to support life in both a terrestrial environment and plausible nonterrestrial settings. They tackle this problem in a 2020 review article published in the journal Life in which they present a detailed evaluation of silicon’s life-support capacity.1
This work has obvious implications for astrobiology and origin-of-life models. But the implications extend beyond science. The research also highlights the design of the universe, our solar system, and the biochemical systems that constitute life.
Life’s Requirements
Before it’s possible to assess the usefulness of silicon as a chemical framework for life, it’s necessary to identify the general chemical requirements for life. The team from MIT notes that any life-supporting chemical element must display sufficient chemical diversity. This chemical diversity is required to produce the chemical complexity necessary to generate the diverse collection of molecular structures and chemical operations required to originate and sustain living systems.
There are two facets to this diversity: the capacity for an atom to produce molecules with a variety of shapes and the capacity of the atom to form compounds with a range of functional diversity. Both features are illustrated by carbon-based (organic) compounds.
This discussion of carbon’s diverse features leads to the question: Are there other atoms that display chemical diversity on par with carbon that could serve as the molecular basis for life?
Silicon Chemistry
Based on its position in the periodic table, at first blush silicon is expected to have the best chance of any other chemical element to rival carbon as a life-support system. Silicon has similar chemistry to carbon. It has a valence of four and forms Si-Si and Si-H bonds. It also forms bonds with heteroatoms such as oxygen.
But make no mistake, silicon chemistry only superficially resembles carbon’s chemistry. In many respects, silicon displays fundamentally distinct chemistry from carbon. This difference, I’ll explain, undermines silicon’s capacity to support life, at least in an aqueous environment.
As the authors of the Life paper state, “Silicon and carbon are ‘false twins.’ Their similarities are superficial and insufficient to mitigate their crucial differences. Chemistry that is stable and normal for carbon is unstable and exotic for silicon, and, similarly, chemistry that is unstable and impossible for carbon is stable and routine for silicon. Silicon’s distinct chemical characteristics and reactivity make it a challenging choice for life.”
Copyright © 2022 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.In short, the fiction that permeates our culture about the prospects of silicon-based life—when carefully considered—leads us to a remarkable reality: A Mind must be responsible for the design of the universe. This Mind has a purpose for the universe—the advent of life.
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From Big Think: Chinese rover makes surprise discovery about liquid water on Mars
Kristin Houser writes:
Data from the Zhurong rover suggests the Red Planet was wet more recently than we thought.
A Chinese rover has found evidence that there was liquid water on Mars far more recently than we thought — a discovery that could affect plans to one day colonize the Red Planet.
Can we surmise that, just as Earth’s past history included conditions to facilitate human thriving (consider the vast deposits of fossil fuels that have powered our technological advances), that nearby solar system objects may also have properties that could further facilitate human exploration and technological development?
Credit: CNSALiquid water on Mars: Based on past research, scientists believed there was liquid water on Mars up until about 3 billion years ago — the point at which the planet’s dry “Amazonian” epoch began and the geological era before it (the “Hesperian” epoch) ended.
Understanding the history of liquid water on Mars can help us predict how much water remains on the Red Planet, in the form of ice or hydrated minerals. We might then be able to use that existing water on Mars to support crewed missions.
“One of the most important resources for human explorers is water,” lead study author Yang Liu from the Chinese Academy of Sciences (CAS) told CNN. “Hydrated minerals, which contain structural water, and ground ice can be used as the important water resource on Mars.”
What’s new? After landing on Mars in May 2021, China’s Zhurong rover began collecting data on soil samples. When researchers from CAS and the University of Copenhagen analyzed some of that data, they found evidence of water in samples that were just 700 million years old.
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This suggests that the area being explored by the Zhurong rover — Mars’ Utopia Planitia, a plain in a huge impact crater — was home to a “substantial” amount of liquid water at a time when we thought Mars’ surface was already dried up.
Big Think
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At Mind Matters News: Researchers: Our brains use data compression to get things right
A recent experiment with mice showed data compression at work when the mice were making decisions about how to get a reward:
000 –Sensory data are compressed when challenges loom; now researchers have shown that our brains use that AI-type technique for cognitive functions too…
Neuroscientists are well aware that, when processing data from our senses, our brains routinely block out information that is irrelevant to an immediate, pressing problem. A person who suddenly smells smoke from the kitchen might barely hear the ring tone of an anxiously awaited, important phone call just coming in.
But are the cognitive areas of our brains similarly adapted to priority processing? It can’t be done simply by simply blocking out irrelevant signals. The current research, using mice, points to a different technique for focused cognitive decision-making.
News, “Researchers: Our brains use data compression to get things right ” at Mind Matters News (June 8, 2022)
The researchers noted in a preprint of the study that the mice almost always made the correct choice, but that the results became more variable the closer they were to the 1.5-second target. Previous research has shown that animals estimate their own ability to correctly classify different stimuli.
Adam Schrader, “Brain applies ‘data compression’ when making decisions, study finds” at UPI (June 6, 2022)
And where does compressed data come in? Greater compression resulted in some information loss but not total failure:
The team discovered that only models with a compressed task representation could account for the data. “The brain seems to eliminate all irrelevant information. Curiously, it also apparently gets rid of some relevant information, but not enough to take a real hit on how much reward the animal collects overall. It clearly knows how to succeed in this game”, Machens said.
Champalimaud Centre for the Unknown, “The brain applies data compression for decision-making” at Eurekalert (June 6, 2022)
Eating very much concentrates the mouse mind; we just didn’t know that the mice use a technique somewhat like AI to do it. That fact may have implications for the future development of AI…
000 –Takehome: Curiously, we humans often invent things by design for a purpose and yet, when we find the same things in nature, some conclude that there is no design or purpose in nature…
You may also wish to read: A little-known structure tells our brains what matters now Work with monkeys and mice has shed light on the filtering role of a neglected feature of the mammalian brain. The cuneate nucleus (CN) in the brain stem turns out to communicate regularly with your prefrontal cortex and spine as to what you had better notice.
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