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Kuru Disease: Bridging the Gap Between Prion Biology and Human Health – Cureus

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Kuru Disease: Bridging the Gap Between Prion Biology and Human Health - Cureus

UC biologist tells NY Post spiders are probably not attracted to Sephora body lotion – University of Cincinnati

The Post was following up on a one-star brand review posted to Reddit that suggested the lotion attracted spiders and not just any spiders but wolf spiders, which have a fearsome name but are actually so harmless that UC biology students routinely catch them by hand.

By Tuesday, the post on Reddit generated nearly 800 comments and reviewers on the brand page were promising new product reviews free of spider talk.

The brouhaha even made the storied pages of The New York Times.

The new urban legend gained traction when other posters suggested the body cream contained spider sex pheromonesor chemicals used to signal receptivity.

But Uetz, who has published more than 200 studies primarily on spiders, told the New York Post that pheromones are highly species-specific.

The internet is a great source of information, but its not always accurate, and someone putting a dab of body butter on a tissue and reporting in Reddit that it attracts spiders doesnt count as research, Uetz said.

Read the New York Post story.

Featured image at top: UC students study wolf spiders in a biology lab. Photo/Joseph Fuqua II/UC

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UC biologist tells NY Post spiders are probably not attracted to Sephora body lotion - University of Cincinnati

Feathers from deceased birds help scientists understand new threat to avian populations – EurekAlert

image:

A working turbine at a wind energy facility in Northern California

Credit: Todd Katzner

As concernsover the worlds declining bird population mount, animal ecologists developed an analytical approach to better understand one of the latest threats to feathered creatures: the rise of wind and solar energy facilities.

Bird mortality has become an unintended consequence of renewable energy development, said Hannah Vander Zanden, an assistant professor of biology at the University of Florida. If we want to minimize or even offset these fatalities, especially for vulnerable populations, we need to identify the geographic origin of affected birds. In other words, are the dead birds local or are they coming from other parts of North America?

Birds can be killed when they collide with wind turbines, fly into solar panels they mistake for bodies of water or become singed by the intense heat from concentrating solar power plants. While the death rate of birds due to these energy facilities is far less than deaths due to domestic cats and collisions with building, efforts to mitigate this problem is important, scientists say.

Vander Zanden and colleagues performed geospatial analyses of stable hydrogen isotope data obtained from feathers of 871 individual birds found dead at solar and wind energy facilities in California, representing 24 species.

Their analysis of natural-occurring markers in the feathers provided information about where the feathers were grown based on the water the birds consumed.

With these markers, we could determine whether the bird was local or if it was migrating from somewhere else, said Vander Zanden, who is the principal investigator of UFs Animal Migration and Ecology Lab.

Results from the study, which were published Friday in the journal Conservation Biology, show that the birds killed at the facilities were from a broad area across the continent. Their geographical origins varied among species and included a mix of local and nonlocal birds.

Researchers found most birds killed at solar facilities were nonlocal and peaked during the migratory periods of April and September through October. The percentage of migratory birds found at wind facilities nearly matched that of local birds, at 51%, Vander Zanden said.

This kind of data can help inform us about best strategies to use to minimize or mitigate the fatalities, she said. For example, facilities management could work with conservationists to improve the local habitat to help protect local birds or improve other parts of the species range where the migratory birds originate.

The results also illustrate the power of stable isotope data to assess future population growth or decline patterns for birds due to a variety of reasons.

Studying the remains of animals is a noninvasive approach to get information that is otherwise hard to track and apply to conservation, Vander Zanden said. Its a great way to understand the mysteries about animals.

Conservation Biology

The geographic extent of bird populations affected by renewable-energy development

5-Jan-2024

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Feathers from deceased birds help scientists understand new threat to avian populations - EurekAlert

Lighting the circuits to risky decision-making – EurekAlert

image:

Bananas represent the reward and the crocodile represents the risk. The blue path is a low risk-low return decision, while the pink path is a high risk-high return decision.

Credit: Trais/WPI-ASHBi

Life consists of infinite possibilities appearing in the real world as multiple choices, that then require decision-making in order to determine the best course of action. However, with every choice there also exists a certain amount of uncertainty or risk. Therefore, behind every decision, lies an intricate evaluation process that balances the risks and rewards associated with taking such actions. This can, in extreme cases, manifest itself as a pathological behavioral state of high risk-high return (HH) and low risk-low return (LL) decision processing that has been associated with gambling disorders.

Although these higher cognitive processes occur seamlessly within the cerebral cortex of our brains dozens to hundreds of times daily the exact underlying neural circuits have remained elusive due to the technical difficulties of specifically targeting and manipulating these neural circuits.

A new study published Science, from a team of researchers led by Dr. Tadashi Isa at the Institute for the Advanced Study of Human Biology (WPI-ASHBi) and Graduate School of Medicine/Kyoto University, have identified and selectively manipulated using optogenetics a method that can modulate the activity of specific neurons with light the distinct neural circuits responsible for balancing risk vs. reward-return decision-making in primates. They show the behavioral changes resulting from stimulating these circuits accumulate over time and have long-term consequences independent of any stimulus providing insights into potential mechanisms underlying pathological risk-taking behaviors such as gambling disorders.

Various experimental paradigms have been developed to evaluate decision-making behavior, with the Iowa Gambling Task being arguably the most famous. However, such neuropsychological tasks are often limited by their design, as they cannot sufficiently uncouple higher-order cognitive processes.

To determine the pure choice bias between HH and LL decisions, Isa and colleagues first designed their own decision paradigm to uncouple risk-dependent choice behavior from other higher-order cognitive processes. Using eye movement to indicate their choice, macaque monkeys were trained to perform a cue/target choice task with water as their reward, consisting of 5 different HH-LL choices across 5 different sets of equivalent expected value (volume of reward awarded multiplied by probability), making a total of 25 potential options. Consistent with other primate studies that looked at risk-behavior, the authors found that primates had an inherent bias for HH over LL choices.

In the early 20th century, the cerebral cortex was mapped into 52 regions, known as Brodmann areas, based on their distinct cellular morphology and organization. The deeper, or ventral, parts of Brodmann area 6 (area 6V), were long thought to only function as a motor area in humans and primates. But more recently, regions overlapping area 6V have also been associated with decision-making processes, though direct evidence supporting such a function has been lacking.

By pharmacologically inactivating several candidate frontal brain regions, using the selective GABAA receptor agonist muscimol, the authors found that the ventral part of area 6V (area 6VV) to be responsible for the HH choice behavior. Interestingly, despite the orbitofrontal cortex (OFC) and the dorsal anterior cingulate cortex (aACC) being considered to play central roles in reward-based decision-making in monkeys, inactivating these regions had little effect on preference for HH choice.

Indeed, we were really surprised that neither the OFC nor the aACC were important for risk-dependent decision-making comments Dr. Ryo Sasaki, the first author of the study.

The ventral tegmental area (VTA) of the brain is essential for reward-associated processes, which is integral to risk-related decision-making. A subpopulation of dopaminergic neurons residing in the VTA are connected to the prefrontal cortex, including area 6V, also known as the mesofrontal (or the mesocortical) pathway.

To dissect the specific role of the mesofrontal pathway in risk-dependent decision-making, Isa and collaborators used an elegant optogenetic strategy, whereby an array consisting of 29 LED lights coupled to electrocorticogram (ECoG) electrodes was engineered (dimensions: 19mm x 12mm) and implanted into area 6V of primate brains expressing photoactivatable proteins in VTA neurons. During the narrow time window of decision-making, the authors precisely manipulated the neural activity of defined VTA terminals in area 6V by turning ON specific LEDs in their array, while simultaneously recording the activity within area 6V, that also included more superficial, or dorsal regions (area 6VD; approximately 2-3mm above area 6VV). The authors uncovered two subcircuits within the mesofrontal pathway with distinct roles in risk-dependent decision-making. They found HH-preference was dependent on the VTA-6VV pathway, whereas LL preference was dependent on the VTA-6VD pathway.

The spatiotemporal resolution of our LED/ECoG array was essential in distinguishing the VTA-6VV and VTA-6VD pathways and deciphering their distinct functional roles in risk-dependent decision-making claims Sasaki.

These findings were further validated by computational decoding, which recapitulated the choice preference behavior induced by photostimulation in primates in silico.

Interestingly, upon repetitive stimulation of either the VTA-6VV or the VTA-6VD pathways, Isa and coauthors observed cumulative effects that persisted over time, leading to long-term changes in preference for HH and LL choice in primates, respectively independent of any photostimulation. Isa comments, ...such long-term changes in choice behavior were rather unexpected and he adds, ... but this may now also offer a mechanistic explanation for how gambling disorders arise.

Exactly how these distinct circuits contribute to balancing our day-to-day decision-making remains unclear, but the authors believe other brain regions are likely to also contribute to this process.

Considering the similarities (in structure and function) between human and non-human primate brains, our findings may have potential therapeutic implications, and even applications in the future, for the treatment of pathological forms of risk-taking such as gambling disorders, he says.

These findings were published in Science on January 5th 2024.

By

Spyros Goulas, Ph.D.

Scientific Advisor

Institute for the Advanced Study of Human Biology (WPI-ASHBi) / Kyoto University

Email: goulas.spyros.3n@kyoto-u.ac.jp

First/Corresponding Author of Study

Ryo Sasaki, Ph.D.

Assistant Professor

Department of Neuroscience, Graduate School of Medicine / Kyoto University

Email: sasaki.ryo.3r@kyoto-u.ac.jp

Lead Principal Investigator/Corresponding Author of Study

Tadashi Isa, M.D., Ph.D.

Professor

Department of Neuroscience, Graduate School of Medicine

Institute for the Advanced Study of Human Biology (WPI-ASHBi) / Kyoto University

Email: isa.tadashi.7u@kyoto-u.ac.jp

###

About Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University

What key biological traits make us human, and how can knowing these lead us to better cures for disease? ASHBi investigates the core concepts of human biology with a particular focus on genome regulation and disease modeling, creating a foundation of knowledge for developing innovative and unique human-centric therapies.

About the World Premier International Research Center Initiative (WPI)

The WPI program was launched in 2007 by Japan's Ministry of Education, Culture, Sports, Science and Technology (MEXT) to foster globally visible research centers boasting the highest standards and outstanding research environments. Numbering more than a dozen and operating at institutions throughout the country, these centers are given a high degree of autonomy, allowing them to engage in innovative modes of management and research. The program is administered by the Japan Society for the Promotion of Science (JSPS).

Experimental study

Animals

Balancing risk-return decisions by manipulating the mesofrontal circuits in primates

5-Jan-2024

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Lighting the circuits to risky decision-making - EurekAlert

Inside Science: Revolution in Biology and Its Impact, by Benjamin Lewin – Shepherd Express

WithInside Science, veteran science writer-editor Benjamin Lewin wonders about the changes coming to research methods from the application of AI, which can sort through massive amounts of raw data. And yet, who will have the final interpretation of that data, if there ever is a final interpretation?

Lewin is concerned about the increasing specialization within science, whose researchers know absolutely everything about one thing, but often at the price of being unable to see the broad picture. Coauthors of a single research paper are often unable to understanding the papers meaning beyond their own contributions. Lewin has no patience with the postmodern idea of science as culturally constructed, yet acknowledges how the rise and fall of dogmas illustrate the role of fashion in science. He focuses on biology inInside Science, his own area of specialty as editor ofCell, a leading journal in that field.

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David Luhrssen lectured at UWM and the MIAD. He is author of The Vietnam War on Film, Encyclopedia of Classic Rock, and Hammer of the Gods: Thule Society and the Birth of Nazism.

Jan. 05, 2024

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Inside Science: Revolution in Biology and Its Impact, by Benjamin Lewin - Shepherd Express

Spain to launch an atlas of all living beings cell by cell – EL PAS USA

Some of the worlds top scientists met on May 15 in Barcelona to discuss the crazy idea of studying each species of living being, cell by cell, in order to complete an atlas capable of shedding light on the evolution of life on Earth and the origin of human thought and disease. Seemingly over-ambitious, the idea came to Arnau Seb Pedrs, 37, a biologist from the village of La Fuliola in Lleida, in Catalonia, Spain. Seb Pedrs studies cells, but his real passion is ornithology. He travels to exotic places and makes a point of catching sight of absolutely all bird species in the region, even if he has to spend a week chasing a nondescript brown bird. This all-encompassing ambition may explain his determination to compile what he has called the Cellular Atlas of Biodiversity.

Seb Pedrs works at the Center for Genomic Regulation, close to Barcelonas Somorrostro beach, once a district of shantytowns and now home to half a dozen cutting-edge scientific institutes. The biologists office is small and simple. Three jellyfish, named Gary, Gerry and Cherry, swim around a circular fish tank. From his desk, the researcher proclaims that his project is no longer a pipe dream. The Gordon and Betty Moore Foundation, established in California by the co-founder of Intel and his wife, has just put up 3.6 million to launch the initiative.

Seb Pedrs already made global headlines in September. His team analyzed the four known species of placozoans cell by cell strange creatures shaped like tiny pancakes. They are marine organisms barely a millimeter in size, which diverged from the human group 800 million years ago and consist of 50,000 cells each. The meticulous work of Seb Pedrs and his colleagues has revealed that these tiny beings, lacking a brain or any other organ, possess something similar to neurons, the cells responsible for thought.

The biologist argues that the Cellular Atlas of Biodiversity would reveal a multitude of natures secrets. We have to be prepared to come across unexpected findings, he says. Our study of placozoans was not undertaken with a view to understanding the evolution of neurons and the nervous system. That naturalistic motivation is what I like the most. We are explorers.

Every living being has a unique DNA, present in each of its cells. In the case of human beings, DNA is like a piano with 20,000 keys, which are the genes. All cells have the same piano, but each of them plays a different tune, which is why some are neurons in the brain and others are part of the muscle or the fat around our middle. According to Seb Pedrs, a couple of years ago, his group created the first cell-by-cell atlas of the cauliflower coral, an organism that forms reefs in the shallow waters of the Indian and Pacific oceans. The analysis revealed 40 different cell types. One of them, in charge of making the coral cling to the rock, constantly touches a key that triggers the production of an antimicrobial compound, as if it wanted to clean up its surroundings. The study of the corals cells brought to light a new substance with antibiotic potential during a global alert about the threat of superbugs resistant to all known drugs. It was a surprise, says Seb Pedrs. The potential for finding new genes with new functions is very high.

The May 15 meeting in Barcelona was a success, marking the first time that a scientific alliance of this size has been launched in Spain. It was attended by the leaders of the main international organizations in the field, such as the American biologist Harris Lewin, coordinator of the Earth BioGenome Project, which aims to read the DNA of all species of animals, plants, fungi and protists. Also participating were Stein Aerts, the Belgian bioengineer behind the Fly Cell Atlas, and British researcher Mark Blaxter, who studies 70,000 U.K. species in Darwins Tree of Life project. The heads of the Human Cell Atlas, the Israeli scientist Aviv Regev and the German Sarah Teichmann, joined via videoconference.

The 3.6 million from the Moore Foundation will be used to launch phase 0 of the project, according to Seb Pedrs. The biologist and his colleagues will fine-tune the methods for analyzing each species and prepare the infrastructure of the vast database, in collaboration with Irene Papatheodorou of the European Bioinformatics Institute in Hinxton, England. We want to have a home for the data we will start producing on a large scale already set up, he says.

There are a lot of people working on this in the world, but there is a lack of coordination, adds Seb Pedrs. When you want to access the results for a species, its absolute chaos. There are no standards of any kind. Nor is there a coordinated effort to see who does what. Its the Wild West.

Seb Pedrs is currently putting the finishing touches to an article on the initiative for a leading scientific journal. I know of many people who have done many experiments that have not worked out, wasting thousands and thousands of euros, but there is no culture of publishing your methods and explaining what has not worked for you, Seb Pedrs. The next person who tries it is back at square one. We want to open up the field and let no one keep their magic tricks to themselves.

Phase 0 of the project will investigate eight species that have already been analyzed cell by cell in order to test the protocols. This group will consist of the fruit fly, the worm Caenorhabditis elegans, an annelid (also from the worm group), a plant of the genus Marchantia, an anemone, a fungus, a brown algae, and possibly a sea urchin or a starfish. We want to study organisms that are difficult to handle, with hard casing, to test six cell-by-cell analysis methods, says Seb Pedrs. The usual techniques involve breaking the subject into pieces and obtaining a suspension of single cells using force, sound waves and enzymes. This is followed by examining which keys of the DNA piano each cell plays. We want to obtain a universal method, says Seb Pedrs.

The project will open up a new world for science. Cell atlases not only tell you about the biology of the organism you are analyzing, says Seb Pedrs. You can also study its interactions with what else is inside its cells. His team has investigated microalgal blooms in the ocean, linked to giant viruses that hijack cellular machinery. Scientists can analyze what type of cells the invaders are in and how they usurp the piano keys.

Seb Pedrs is already calculating what phase 1 of the project might look like. We could start with about 100 species spanning the entire tree of life, he says. We will need another 10 to 15 million. Ideally, we would like to sample organisms that are on both sides of major transitions, such as the emergence of multicellular beings and the origin of the nervous system.

Seb Pedrs grew up among the steppe birds typical of the drylands of Lleida. He has made expeditions to study bird life in North Africa, Turkey, Thailand, Chile and Israel, with more than 2,000 species observed. He recently saw his first Tengmalms owl in Spain. In the eastern jungles of Australia, he encountered the mythical cassowary, a bird measuring up to two meters that has been known to kill humans. In his small office in Barcelona there is no decoration, just a drawing of a tapaculo a brown bird from Chile and a postcard with the face of Charles Darwin, the father of the theory of evolution by natural selection. We are interested in studying the evolution of cell types, he says. But first there are a lot of technical questions that are dense and boring, but which we need to solve.

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Physics, Chemistry Couldnt Give Rise to Biology – Discovery Institute

Photo credit: Rmi Walle, via Unsplash.

The laws of nature provide stable conditions and physical boundaries within which biological outcomes are possible. Laws are, in effect, a chessboard. They provide a stable platform and non-negotiable boundaries. But they do not determine the movement of pieces or the outcome of the game.

Or do they? Rope Kojonen, a theologian at the University of Helsinki, argues for the compatibility of design and evolution. My colleagues Steve Dilley, Brian Miller, Casey Luskin, and Ipublished a reviewof Kojonens thoughtful book,The Compatibility of Evolution and Design, in the journalReligions.In a series atEvolution News, we have been expanding on our response to Dr. Kojonen. Here, I will shift gears to analyze his claims about the laws of nature and their role in the origin of biological complexity and diversity.

The laws of nature are at the heart of Kojonens model. They are the mechanisms of design, the linchpin of Kojonens project to wed design and evolution. To evaluate his model, however, we need to be clear about what exactly his position is. Kojonen is not entirely clear about how the laws of nature (and initial conditions) are said to bring about the origin of life, the diversification of life, and human cognition. However, there seem to be at least three possible ways to interpret Kojonens model:

Lets discuss point one, namely, that the laws of nature (and the like) have causal power or limit the possibility space enough that the diversity of plant and animal species observed today emerged from unicellular organisms. While I am personally convinced that design is evident in the very fabric of the universe and yes, in the laws of physics and chemistry, these material mechanisms do not have sufficient causal power or limit the possibilities sufficiently to explain how the diversity of organisms came to be (if these laws have stayed the same over time). To support this point, Ill talk about the capabilities of the laws of physics and chemistry and give examples of how they currently interact with biology.

In Kojonens model, the laws of nature do the heavy lifting in terms of creating biological complexity. While Kojonen cites an array of other factors e.g., environmental conditions, structuralism, convergence, and evolutionary algorithms its also clear that these factors are undergirded by the laws of nature themselves. But there are limits to the creative power of the laws of nature. If it turns out that the laws have limited ability to produce biological complexity, then other factors (such as the environment, convergence, etc.) thatdependupon the laws of nature likewise have limits. If Kojonen thinks that these other factors have creative powers thattranscendthe limits of the laws of nature, then the burden is on him to show that.Is it possible for the laws of nature to be a causal force or sufficiently constrain the possibility space?

According to one definition, a mechanism is a process that acts on objects to produce an outcome. Here I will define a material mechanism as a process by which a physical object is acted upon by one of the physical laws. Material objects are built from the elements of the periodic table, and the laws of physics and chemistry are the constant processes that constrain how material objects behave. To understand materialistic mechanisms, lets look at a few illustrations.

Definition:The law of universal gravitation says an object will attract another object proportionally to the product of their masses and inversely related to the square of their distance from each other.

This law tells us how objects behave toward one another. Gravity constrains motion, whether that motion is human, planetary, or light. A complex system may also be able to detect gravity and use it as a cue. Lets look at an example of plant growth. Leaves grow in the opposite direction of gravitational pull, but roots grow downward in the direction of gravitational pull. What causes this? Is it gravity? Definitely not. Root growth occurs through the division of stem cells in the root meristem, located at the tip of the root. Thus, root stem cells rely on gravity as a cue to be detected by their sensors, so that they know where to direct their growth. But gravity is not the mechanism that creates plant morphology. Rather, plants work within the constraints of gravity and exploit it via sensors to scaffold their architecture.

Definition:The electrostatic laws state that charges attract or repel with a force that is proportional to the product of their charges and inversely proportional to the square of the distance between them, depending on whether they are alike or different.

Electrostatic laws describe the attraction of positively charged ions to negatively charged ions. These laws constrain (but do not cause) the way an electrochemical gradient can be formed and work across a membrane. The charge and concentration differential across a membrane creates an electrical field. The cell then uses the potential energy of the electrical field to generate energy, convey electrical signals, and power the delivery of nutrients into the cell. The crucial point here is that electrochemical gradients are not an emergent property of the electrostatic laws. Instead, they are caused by molecular machinery. As Elbert Branscomb and Michael J. Russell say in a recent BioEssays paper, to function, life has to take its transformations out of the hands of chemistry and operate them itself, using macromolecular mechano-chemical machines, requiring one machine (roughly) for each transformation; life must, in Nick Lanes evocative phrasing, transcend chemistry.(Branscomb and Russell 2018)

How do electrostatic laws interface with organisms body plans? Organism body patterning is formed in part by bioelectrical networks, which operate across cell fields to integrate information and mediate morphological decision-making. (Djamgoz and Levin 2022) The bioelectrical networks play critical roles by regulating gene expression, organ morphogenesis, and organ patterning. This is, of course, exactly what would be necessary as an emergent property from electrostatic laws for them to have generative capacity. But these bioelectric networks no more emerge from the electrostatic laws than do cellular networks; rather, these bioelectric networks are information rich networks which carry information in a bioelectric code which can be understood by the sender and receiver.(Levin 2014)

Now the electrostatic laws, in conjunction with the design of the periodic table of elements, constrain the possible chemical space of molecule bonding arrangements. For example, based on the chemical characteristics of hydrogen and oxygen as well as the electrostatic laws, H2O has a specific bonding configuration. These mechanisms can thus explain the origin and ready formation of some simple molecules. But what about more complex molecules like those used in life? According to a paper in the journalNature, Chemical space and biology, The chemical compounds used by biological systems represent a staggeringly small fraction of the total possible number of small carbon-based compounds with molecular masses in the same range as those of living systems (that is, less than about 500 daltons). Some estimates of this number are in excess of 1060.(Dobson 2004)This statement is consistent with our observation that complex molecules like glucose and nucleic acids result from enzymes. If one thinks that electrostatic laws and the periodic table limit the search space so that molecules like nucleic acids form on their own, then nucleic acids should form spontaneously from phosphate, nitrogen, carbon, hydrogen, and oxygen, just like water does. But this is not something that is observed. Instead, complex molecules in an appreciable quantity can only be built using enzymes (which are built using information in DNA) or in highly controlled laboratory synthesis environments. Not to mention the fact that there must be something in the natural laws that forces the chemistry of life to use only left-handed molecules. And if that is true, then why arent all molecules left-handed as this would seem to require a rule in the laws.

If one grants the first cell (supposing the origin of life is a miraculous event), there remain thousands of unique molecular compounds essential for the diversity of life to be selected from the chemical space. We know that many of these molecular structures are multipurpose, recyclable, and essential to other ecosystem members. The design of these molecules and the enzymes that make and break them down appears to have required foresight for the needs and functions of the ecosystem as well as an in-depth understanding of chemistry and biochemistry. Is this type of information and causal power available in the electrostatic laws or the other laws of nature?

Definition:The first law of thermodynamics says that matter and energy cannot be created or destroyed but can only change form. The second law of thermodynamics says that closed systems always move toward states of greater disorder. Open systems move toward equilibrium, where the disorder (aka entropy) of the universe is at its maximum.

The laws of thermodynamics place constraints on what biological organisms must do to remain alive. That is, organisms must capture, harness, and expend energy to maintain a state far from equilibrium. To do this, organisms must/do have incredibly designed architectures that reflect a highly advanced understanding and exploitation of the laws of nature. For example, in central carbon metabolism, energy is extracted from the molecule glucose in the most efficient way possible. But just because this biochemical pathway exhibits an architecture that is amazingly designed to leverage the constraints imposed by thermodynamics does not mean that the laws provide a mechanism by which these complex systems arose in the first place. In other words, simply because a vehicle is highly efficient does not imply that the laws of thermodynamics designed it. More likely, it means whoever designed the vehicle had a thorough understanding of thermodynamics.

Definition:Quantum physics describes the physical properties at the level of atoms and subatomic particles using the wave function, which is determined by the Schrdinger equation. The Schrdinger equation is the quantum counterpart of Newtons second law, describing what happens in the quantum realm to systems of subatomic particles.

Schrdinger equations are linear equations, so when added, the outcome is also linear. This is very different from what is observed in the real world. For biology and complex systems, conditional branching occurs, as in the example:

If {antibiotic is detected} then (express antibiotic efflux pump). If {antibiotic decreases} then (decrease expression of antibiotic efflux pump).

This type of branching found in complex systems cannot be boiled down to a wave function. Thus, as George Ellis, a leading theorist in cosmology and complex systems, says [T]here is no single wave function for a living cell or macroscopic objects such as a cat or a brain. In short, the complex nonlinear world is unable to arise from a single wavefunction.

Definition:The behavior that an organism programmatically/cognitively undertakes to avoid death.

The laws of physics and chemistry do NOT include natural selection. Natural selection is an outcome of the programming of a specific goal:desire to survive. As such, I define natural selection as the change in populations that depends upon their programmed and, in some cases, cognitive capacity to survive and the environmental factors they face. Please note that this definition is different from how most people might think of natural selection, but one hopes it is more accurately aligned with how it actually works. To support this goal, the desire to survive, organisms have a variety of mechanisms that may include both voluntary and involuntary responses. For example, in humans, the immune system would be an example of an involuntary response (programmatically compiled) where the defenses of the body fight off invaders. An example of a voluntary response (a cognitive response) in humans might be when someone runs for their life from a bear or kills a poisonous snake. Another example of an involuntary mechanism is natural genetic engineering. In case you arent familiar with natural genetic engineering, it just means that cells have the capability to actively reorganize and modify their own genomes to enable survival. This involves mechanisms like transposition (movements of genetic elements within the genome), gene duplication, horizontal gene transfer (transfer of genetic material between different organisms), and other forms of genetic rearrangement. Another important example is phenotypic plasticity, which has frequently been confused for natural selection but is the ability of an individual organism to exhibit different phenotypes (observable characteristics or traits), for example, in response to changes it senses in the environment. Phenotypic plasticity occurs too rapidly to be driven by mutation and selection; thus, it is recognized as an innate adaptation algorithm embedded within an organism.

So, the desire to survive, coupled with environmental conditions and random mutations that favor some individuals over others, is natural selection. As natural selection relies on the agent- or life-specific mechanism of a desire to survive, it cannot account for anything related to the origin of life, only the diversification of life. The degree to which natural selection can account for the diversification of life is an active area of research, but ID proponents Douglas Axe and Brian Miller have discovered some important limits. Miller summarized decades of research on the topic of protein evolution, which relies on natural selection, in our response to Rope Kojonen. In short, they have shown that natural selection is not capable of creating a high-complexity enzyme from a random sequence of amino acids or of transforming one protein fold into a different fold without guidance. This is effectively an upper bound for what natural selection can accomplish, which bears not only on origin-of-life scenarios but also on the ability of life to diversify from a single organism into the diversity we see today.

The emergent properties of physics and chemistry are necessary, but not sufficient to explain the origin or diversification of biological organisms. Gravity can be used as a cue by biology to determine directionality, but gravity doesnt make a leaf grow up or a root grow down that happens only because a complex system is sensing, interpreting, and acting on the gravitational cue. The design of the periodic table of elements constrains the bonding pattern between hydrogen and oxygen and bestows upon water its life-giving properties, but these constraints on chemical bonding do not cause the formation of DNA or other complex molecules. Enzymes are necessary for more complex molecules to be formed at the rate required for life. The electrostatic laws describe how positive and negative charges attract one another, but these laws do not cause the formation of an electrochemical gradient across a membrane that only happens because molecular machines harness energy to push a system away from equilibrium. In quantum physics, the linear wave function describes the wave-particle duality of matter, but it cannot account for the conditional branching observed in complex systems.

In short, the best way to summarize the capacity of all these material mechanisms is in George Elliss words from his recent article, Quantum physics and biology: the local wavefunction approach: The laws of physics do not determine any specific outcomes whatsoever. Rather they determine the possibility space within which such outcomes can be designed.(Ellis 2023)

Tomorrow we will look at the second interpretation of Kojonens model for how the laws of nature and initial conditions could bring about life and its diversification.

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Physics, Chemistry Couldnt Give Rise to Biology - Discovery Institute