Biology - Science topic

@Ed Gerck

Irrational numbers are uncomputable with probability one

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My deepest apologies, but I have read your Answer dated December 14, 2022 in the FLT thread https://www.researchgate.net/post/Are-there-other-pieces-of-information-about-Victory-Road-to - FLT#view=641367549777ccc70c026256/234 .

There was a link to your own thread given by you. This thread gives your erroneous statement from the very beginning, namely: "Irrational numbers are uncomputable with probability one".

Please agree, Dear Professor Ed G., that any irrational number is calculated with 100% accuracy with a probability of 1 for any number of orders p-1, if you write down p orders. Thus, if you write for the root of 2 one order before point and three orders after point, you will have sqrt(2)=1.414..., i.e., you can consider that you have written 4 orders. At the same time, the accuracy of 100% with a probability of 1 is provided for 3 orders, i.e. 1.41, etc., for any number of orders...

Speaking of some kind of all orders "full notation" , as you would like to see it, it's not possible for such a representation of irrational numbers.

If you point out my mistake to me, I will be grateful.

Greetings,

SPK

Dear Thomas,

yes, the brain's internal energy arises from the quantum statistical washout at a higher scale. My proposal is that negentropic entanglement binds the information (intrinsic) into a structure that is labile or dynamic originating at the molecular to the whole brain and reflecting a consciousness code that is decoded by EM dipoles in brains.

This algorithm can be reproduced in machines.

Dear Ashok Kamalanathan,

I agree with what you say, however it should remain at the stage of post-experiment modeling tool and not become too much a prediction tool at the expense of traditional biology, that of laboratory experience and on the different fields of application.

Reversing the sequence that was given to you in the script may be necessary for certain analyses or experiments in biology. The sequence refers to the order of nucleotides (A, C, G, and T) in a DNA or RNA molecule.

In molecular biology, the sequence of nucleotides in a DNA or RNA molecule is typically read from the 5' end to the 3' end. This is referred to as the "forward" direction. However, in certain cases, it may be necessary to analyze the complementary strand, which is read in the opposite direction, referred to as the "reverse" direction.

For example, if you are designing PCR primers to amplify a specific region of DNA, you may need to analyze the complementary strand in order to identify potential primer binding sites. In this case, you would need to reverse the sequence in order to work with the complementary strand.

To determine whether you are using the forward or reverse sense, you should look at the orientation of the sequence. If the sequence is presented in the 5' to 3' direction, it is in the forward sense. If the sequence is presented in the 3' to 5' direction, it is in the reverse sense.

Jerry Waese thanks a lot for your nice software and the image. I will try to play with it and understand what is what.

Here are the general steps to conduct research on HIF signaling in fin or limb regeneration in the field of Development and Regeneration Biology:

1) Literature review: Conduct a comprehensive review of the existing literature on HIF signaling and its role in fin or limb regeneration. Identify key research questions, knowledge gaps, and potential areas for further investigation.

2) Study design: Develop a study design that addresses the research questions and hypotheses. This may involve designing experiments to manipulate HIF signaling, such as using genetic or pharmacological approaches.

3) Animal model: Select an appropriate animal model for the study, such as zebrafish or axolotl, which are commonly used for studying fin or limb regeneration.

4) Sample collection: Collect samples from the animal model at various time points after injury or manipulation of HIF signaling. These samples may include fins or limbs, as well as blood or tissue samples for analysis of HIF signaling pathways.

5) Data collection: Collect data on various parameters of regeneration, such as cell proliferation, differentiation, and tissue morphogenesis. This may involve imaging techniques, such as confocal microscopy or X-ray imaging.

6) Data analysis: Analyze the data using appropriate statistical methods and software tools. This may involve comparing the regeneration outcomes between control and experimental groups, as well as identifying correlations between HIF signaling and regeneration outcomes.

7) Interpretation and conclusions: Interpret the results of the study in the context of the existing literature and draw conclusions about the role of HIF signaling in fin or limb regeneration. Identify areas for future research and potential applications of the findings.

8) Communication and dissemination: Communicate the findings of the study to the scientific community through publications in peer-reviewed journals and presentations at conferences. This may also involve communicating the findings to the general public through outreach activities and media engagement.

Note: The above steps are general guidelines and may vary depending on the specific research question and experimental design.

Jerry Waese to Larry Carlson:

Larry Carlson memory content can be stronger in so many ways but the memory engram is never any stronger than any other memory engram except in terms of accessibility of it.

i.e. how many different things lead to the reflex activation of the engram.

Greater access is afforded by the extent of interconnection with other engram patterns, while greater clarity is afforded by the extent of difference or uniqueness to other engrams.

I may have 500 "master engrams" that are instrumental in my most salient reflexes as I sit before the laptop screen in my bath. AND I may have 500 similarly instrumental salient reflex perturbing engrams that govern driving while seated in my car.

In the first case, what I am typing may have or may not have any effect on where I go, or what others think. In the second case my own life and others lives depend on what those reflexes do while driving.

The many conditions that lead to me hitting the brakes make that set of braking engrams (maybe 20/500 "master braking engrams" (i.e. administrative controlling engrams that cascade into multiple body articulation and movement engrams)) more accessible than the left turn engrams (maybe 100/500 deal with left turn considerations)

Fortunately I spend more time typing (not always in the bath) than driving.

The relation to intelligence and thermodynamics is a different story, but if we make it the same story it probably will not matter if I get clean (in the bath), communicate well (at RG) or drive into a wall.

Daniil ( Даниил ) Александрович Fedorov ( Федоров )

Difference equations can be useful for modeling discrete events in biological systems, such as the discrete stages of a cell cycle or the discrete events of a neural network firing. However, they may not be ideal for modeling continuous processes, such as the dynamics of a chemical reaction or the movement of a fluid through a network of vessels. In these cases, continuous models, such as differential equations or agent-based models, may provide a more accurate representation of the underlying biology.

One limitation of difference equations is that they assume that the changes in a system occur in discrete steps, and do not account for small changes that occur continuously over time. Additionally, they may not be able to capture the effects of small perturbations in the system, which can have a significant impact on the overall behaviour of the system.

I stumbled upon some interesting information: theoretical physicist and writer Alan Lightman asked a group of leading scientists: if you were offered the answer to a scientific puzzle, would you take it? Surprisingly, half of the scientists said no — too much would be lost by not engaging in the act of discovery.

Yes, for science it is important WHAT, but for scientists it is important WHO.

Hello Claudia,

My name is Fernando and I work as a medical physicist in a Hospital. I made my thesis about radiobiology. The thesis was about statistical concepts like Tumour Control Probability or Normal Tissue Complication Probability...,

I am just an example how you can do your PhD in this subject. You can start visiting a Hospital with a radiotherapy department in Bucharest, there you can find people like me, they can inform you.

Good Luck and go for it.

Dear Duan Xian Xiang,

Your words "The law of biology can be described by "program", but this "program" is not a computer program, computer program is only one of it, "program" or "calculation" includes psychological program, economic activity program, political activity program, gene program of organism, etc." are consistent with my review paper where are explained examples and methodologies used in biology and medicine to describe, simulate, and predict the behavior of biological systems.

The book you mentioned sounds interesting, but I do not know it.

According to my understanding, emergents and their mutual interactions are the best current methodological description of biological and many physical phenomena observed. In many cases, there exists no alternative to such descriptions, as demonstrated on medical applications in my review.

The review describing the basic principles of complex systems descriptions in biology:

"Complex Systems and Their Use in Medicine: Concepts, Methods and Bio-Medical Applications"

More information of how to use receptor for biosensor application!

Of course, time is a significant factor for spheroids' size and viability of cells, due to when you seed the cells to the generation of spheroids after the cells are in the proliferative stage. More time (days) can lead to the big size of spheroids, in addition, the cells located in the core zone are suffered from nutrients, oxygen, and ...

I suggest you set up the best time to achieve reliable results too

Vahid Rakhshan I will definitely spread the word about this amazing initiative. It's great to know that we can contribute to such a noble cause by simply utilizing our excess computer power. Thank you for bringing this opportunity to my attention. Let's join hands in making a difference in the fight against diseases.

Thank you for the offer, Petr! Someone was able to send me a digital version.

Kseniya Kondrasheva Nikhita Madhav Chambhare Thank you very much, The Goal is Pyocyanin production, we tried 1:100 and yes by micropipette because the loop carry small volume

Yes. Naturopathy and phytopharmacology, for example, make great sense, especially as balancing treatments and therapies.

Add Chloroform to a total of 50% total volume and vortex vigorously for a min or half. Let the sample settle for 10 minutes

Errami Ahmed answer is correct. 52 is the atomic weight of Cr and 294.18 is the molecular weigh of potassium dichromate. 2 is the stechiometric conversion factor.

To reach the Scopus document search module, you should use academic IPs. If your institute has been listed in the Scopus database, you have permission to search documents in Scopus. It is not free of charge, and your university should pay its share to Scopus to provide this service for its academic researchers.

It is generally recommended to amplify your targets at a single temperature in a qPCR experiment, as the efficiency of the polymerase reaction can vary with temperature and amplifying at a single temperature allows for more accurate and consistent results. However, if you have identified that the optimal annealing temperature for your target gene and housekeeping gene are different, it is possible to use a gradient temperature protocol in your qPCR experiment to optimize the amplification of each gene.

In this case, you can set up two separate qPCR reactions, one with a gradient temperature that is optimized for your target gene and one with a gradient temperature that is optimized for your housekeeping gene. You can then run these reactions in parallel, either in separate wells of the same qPCR plate or in separate qPCR plates, depending on the capacity of your qPCR machine. As long as the qPCR machine is able to read the signals from both reactions at the same time, it should not pose a problem.

It is important to note that using a gradient temperature protocol can be more time-consuming and may require specialized equipment. It is also worth noting that optimizing the annealing temperature of the primers is generally not necessary for most qPCR experiments, and a single temperature protocol is often sufficient.

Dear Yosef Scolnik ,

I am not sure whether Peter Donkor talks about the journal asked here. I presume the questions is about yet another initiative of Academia.edu: https://www.academia.edu/journals/2/academia_biology Do realize that Academia.edu started a journal before called “Academia Letters” and stopped this initiative already within less than two years. Have a look at https://www.academia.edu/journals/1/academia_letters/submission_faq where they state, “Academia Letters is no longer publishing articles and has stopped accepting submissions.”. See also here on RG: https://www.researchgate.net/post/Is_Academia_Letters_a_Recommendable_option_for_publishing_orphan_papers

The new title “Academia Biology” will start in 2023 to charge an APC which will be a staggering 2000 USD for a basically non-indexed journal published by a ‘publisher’ with no experience and reputation in publishing. Their misleadingly remark about the impact factor suggests that they will have an impact factor in 2025 which is theoretically correct but highly unlikely to happen with this ‘organization’ behind it.

Personally, I would avoid this one.

Best regards.

I am sorry I am not familiar with either gromacs or Cygwin specifically so cannot speak to that. I am also not familiar with conda on Windows.

One option may be to use Windows Subsystem for Linux (https://learn.microsoft.com/en-us/windows/wsl/about) and install Ubuntu or another linux distro. There you would be able to use conda and other tools freely (including sudo).

A second option may be to alter your Windows PATH to include where gromacs is located. If you are unfamiliar, the PATH is where Windows searches for programs and exectuables, so if you place your desired program locations in PATH they should be able to run. This will not place gromacs into a conda environment but may allow you to use how you desire.

Thanks Ruben, I'll take that into consideration.

ICHAMS – a scientific meeting founded and completely run by our students in the Royal College of Surgeons University. Do I sound proud of them? By golly, I am!

This depends also a lot on our degree of free choice, but I do principally agree to your statement ! As I was never interested in greater intellectual puzzles, my choice was limited by the personal preference for practical problem-solving methods (’human action’) and the study of scientific methodology applications ( ‚real range of our methods‘ ).

———-—

Economics is a living thing—and to live implies both imperfection and change. There is joint action, but no joint thinking. There is only tradition which preserves thoughts and communicates them to others as a stimulus to their thinking. Human action is purposeful behavior. Science does not give us absolute and final certainty. It only gives us assurance within the limits of our mental abilities and the prevailing state of scientific thought.

Ludwig von Mises, Human Action: A Treatise On Economics

Best regards, sorry for the inconvenience, as I asked in my previous publication, this time I need another answer from another biologist or biology in order to complete my investigation and have different points of view. Thanks for your attention

Hello Juan; All of conservation science is biosocial. Our interactions with the natural world have proven to be pretty damaging and fixing the problems is often a social solution. Social scientists and conservation advocates have a critical, cooperative role to play is helping get us out of our present dilemmas. Best regards, Jim Des Lauriers

origin

Hello Rh Rj

Aldehyde-based fixatives such as formaldehyde (4% formaldehyde) react with and crosslink cellular proteins, stabilizing and hardening the sample. Aldehydes cross the plasma membrane and fix soluble proteins. Some targets can lose their antigenicity with aldehyde crosslinking.

To allow antibody access, detergents like Saponin and Triton X-100 remove different molecules from cellular membranes and create variable pore sizes.

Each detergent has different chemical properties that will impact the level of permeabilization and membrane integrity. For example, saponin interacts with cholesterol in cell membranes and leaves many membrane-associated proteins in place. In contrast, Triton X-100 and Tween-20 are examples of non-ionic detergents that interact with lipids and proteins in membranes and permeabilize non-selectively. This non-selectivity is helpful when trying to pass tough-to-permeabilize membranes. However, detergents can lyse cells or cause you to lose soluble proteins from the sample, if left on for too long or used at too high a concentration.

Thank you for your feedback on my discussion topic. I agree, such phenomena are possible, just statistically extremely rare.

Also I should point out that I was assuming strict determinism only for the sake mathematical simplicity.

The present format does not allow me to be more precise about the ideas presented above. Later on I plan to write a more concrete and rigorous presentation of these ideas terms of cellular automata and dynamical systems.

Thermofisher Scientific has a virtual lab training option on cell culture. You can check here: https://www.thermofisher.com/bd/en/home/global/forms/cell-culture-basics.html

You can use primers that amplify products of different lengths. In low-integrity samples you then observe an increased shift between Ct values of shorter and of longer products. I used this to get a hold of RNA integrity of laser-microdissected samples where the amount of RNA was not sufficient to see peaks in electropherograms ("Bioanalyzer") and not to mention bands in agarose gels. As I used oligo-dT priming in the RT, I amplified equally sized products that were located at different distances from the poly-A tail. If you use randompriming, it should work also with the amplification of products of different lengths.

You will need a standard of known good quality to compare against. If nothing else works, you can make a synthetic standard by mixing purified PCR products (in equimolar ratios). But take care of cross-contaminations (prepare/purify the standard in a different lab, ideally in a differn building!).

Hola Dr. Luis.

Logró identificar la especie de Coniopterygidae?

podría compartir información y fotos de las larvas, pupas y adulto.

Muchas gracias de antemano, saludos desde Guatemala

The most significant extinction for ecosystems is insect pollinators, as well as groups of coprophages and necrophages. But any other species of insect will have an impact on the ecosystem when it disappears. For many species, participation in ecosystem trophism has not yet been clarified.

This is going to be cell type dependent mostly, but one consideration is that a fibronectin, being extremely sticky, will attach to collagen type I (i.e. 10% serum fibronectin is about 30 ug/ml). So unless you are blocking the surface with heat-denatured 1% BSA it likely will still be a fibronectin coating. Usually 1-10 ug/ml fibronectin is ample, but 100 ug/ml of collagen type I is needed. Also collagen solutions are pH sensitive and will self polymerize. If using a collagen coating add cold (4C) PBS and coat for 4 hours at 4C to stop the polymerization from occurring. Fibronectin is best coated at 37C for 1 hour diluted in PBS (it can precipitate at 4C).

you can do it by xlstst to make a hierarchical clustering

for creating graphic images I recommend you biorender.com you have on this website all the templates also they are for free, you can register and start creating your first graphic abstract and images. in many articles and reviews, all the graphics are made via this website.

No, the standard free energy of hydrolysis of the phosphodiester bond in DNA is -5.3 kcal/mol. It requires energy to forge a phosphodiester bond, while to break one requires only enough energy to overcome the activation energy barrier, which is lowered by enzymatic- , acid- or base catalysis. Under physiological conditions, hydrolysis is further facilitated by the high water concentration.

Dear Shahina Akter ,

Adjust your question by adding the proper link https://www.researchgate.net/post/Scientific_Journals_with_Open_Access_and_no_APC_free_charges_for_authors and give the proper credits to Jeysson Sánchez-Suárez who built up the list.

Best regards.

Here is an interesting read:

Christian; Well, I'm baffled. Adding fluid at the top will probably form a bubble, but try it and see what happens. Jim Des Lauriers

Thank you for your kind response.

In Australia, we have lost around 50-60% of the population of most larger marsupials due to habitat clearing and clearfell forestry. The 2019 drought and mega-bushfires (and some other intensive fires in the previous decade or so) which in part were fuelled by climate change have further reduced populations of many marsupials by around half again. Some 20-25% of some species remain. In the case of the koala I have seen estimates of only 140,000 remaining in the wild. These are all preliminary and longer term data may show some bounce-back or some further declines (as recently record flooding also fueled in part by climate change has also impacted many of the areas impacted by the major drought and unprecedented bushfires.

Possibly the phrase is part of the dogma of our knowledge of physics (for now)... Perhaps the correct phrase would be "life as we know it..."

Navjot Singh This might surprise you but I recommend you analyse the problem without using quantum theory. If you take a look at the preprint linked below you will see a different approach to the analysis of molecular bonds:

This is based on the Spacetime Wave theory and shows how a stable bond is formed when the electrostatic and electromagnetic forces are in balance.

Richard

At the secondary level, the courses are integrated with each other. Mathematics exercises are related to chemistry, physics, biology, engineering, environment, and space sciences. We adopt the methodology of lesson research in education.

Hello Boudjema; Your last reply to Mr. Dsugutov is perfect! The Grants' research is the clearest demonstration of the phenomenon available to a nonspecialist audience. Well done! Best regards, Jim Des Lauriers

Dear Colleagues and Friends from the Research Gate portal,

Thanks for the answers given. From the answers above, it is clear that there are various ways and methods to protect forests from fires. Some of them are already in use but need to be scaled up, such as educating the public about the importance of the role of forests for the survival of most of the planet's biodiversity, the role of forests in limiting the scale and effects of the progressive process of global warming and therefore also in terms of human survival on the planet over the next at least several decades. On the other hand, some of these methods need to be further improved and also scaled up. These include, for example, creating new species of trees and shrubs that will be more resistant to abiotic (e.g. climate warming) and biotic (viral, bacterial, fungal, parasitic diseases) environmental factors. In addition to this, improving forest planning and management techniques by replacing disease- and fire-prone forest monocultures with multi-species, biodiverse forests, rich in natural forest ecosystems. Forest harvesting techniques are also among the methods that need to be further improved and developed. Well, instead of full felling, full deforestation in a specific area of the forest, which leads to rapid sterilisation and reduction of soil moisture, it is necessary (if at all) to cut only some, selected, individual trees in areas where the forest was planted without devastating the surrounding biosphere, without destroying the rest of the biodiverse natural forest ecosystem. It is also necessary to improve forest fire extinguishing techniques, creation of reservoirs for extinguishing water from rainfall, creation of systems limiting the rapid spread of a forest fire (clearing belts devoid of dry undergrowth, etc.), limiting the scale of draining of areas adjacent to forests, improving the system for detecting low levels of moisture of litter and undergrowth, improving systems for noticing micro-fires in order to increase the efficiency of action and shorten the time of fire development and its extinguishing by fire brigades. To this end, the new information technologies of ICT, the Internet and Industry 4.0 and satellite analytics should be used, as well as rapid transmission of information and informing specific public services and citizens as quickly as possible. In view of the ever-increasing scale of forest fires, which are increasingly caused by the progressive process of global warming and by their deliberate burning by humans, the problem is still very serious. In my country from January to July 2022, the number of forest fires increased compared to previous years and was already the same as in the whole of 2021. By 25.7.2022, there were already more forest fires in Poland than in the whole of last year 2021. In addition, an unusually high number of hot days have already been recorded. The scale of forest fires occurring in different regions of the world has once again intensified in recent months. In recent months, there have been forest fires in many countries in Europe, North America and on other continents. In some countries, record-breaking forest fires are still developing. Firefighters from various countries are involved in extinguishing them as part of international assistance. The problem is serious. The level of seriousness of this problem will increase in the years to come if mankind does not stop the increasingly rapid process of global warming. In addition, in the context of the above problem, it is particularly important to significantly increase the scale of afforestation in wasteland and post-industrial areas, areas degraded by civilisation. It is urgently necessary to bring about the prevalence of afforestation processes over deforestation on a global scale and to stop the deforestation of natural, biodiverse forest ecosystems. Why should we wait until the end of this decade to do so, as agreed at the UN-ET Climate Conference COP26. After all, what we do now in terms of a pro-environmental transformation of the economy on an individual, one-year scale translates into a potential slowdown in the progressive process of global warming on a multi-year scale. In some countries, the issue of the need to urgently and swiftly carry out a pro-environmental transformation of the economy is still downplayed and ignored in the political and business spheres. This is also the case in the country in which I operate. The issue of the key determinants of carrying out a pro-environmental transformation of the classic growth, brown, linear economy of excess to a sustainable, green, zero-carbon zero-growth and closed loop economy, in which the issue of the development of aforestation programmes and the protection of the planet's biosphere and climate is one of the essential elements, is described in my articles posted on my profile of this RG portal. Links to these articles can be found on the homepage of my RG profile. I invite you to collaborate, to set up joint international research projects in this important issue for the future of humanity, the biosphere and the planetary climate. I also invite you to continue discussions on the important issue of improving techniques, instruments and systems for forest fire protection.

Thank you very much,

Best regards,

Dariusz Prokopowicz

Navjot Singh I define consciousness as the subjective experience that we each have arising from the operation of the brain.

In the paper titled the conscious brain, I have identified the importance of understanding how we control our focus of attention.

The brain is a particular combination of biology chemistry and physics and it is a lack of understanding of fundamental physics that has held us back.

Neuroscience has revealed the brain activity in the form of the network of neurons but we have to understand the effect of the electromagnetic wave activity generated by the brain on the operation of the brain as a whole.

Richard

I think we have choices about what we focus on as a culture. While none of us has the power to decide that, we can decide for ourselves and those around us what activities we engage in. We decide to promote reading and learning or not. We decide to promote diversity and freedom, or the censorship and oppression of those around us. We create our culture via many small decisions.

Likewise, we can decide to make planting trees part of out culture or not. And not just one day a year when we plant a tree,... that means not much.

How can afforestation be increased? - Quora

Dear Mozhgan Norouzi, thank you very much for your reply!

A patient with desminopathy survived Covid-19 six months ago without pneumonia, but with a temporary loss of smell and taste. After Covid-19, we note an accelerated progression of desminopathy, penetration accelerates, new muscles are quickly involved in the pathological process, muscle mass decreases, and heart function worsens. Perhaps the infection or its consequences are somehow connected with the mechanism of progression of desminopathy?

found an assay here, thank you all!

Both can be used, but I will suggest you to isolate the variables through PCI

Dear Hany Samy ,

In addition to what Anton Vrdoljak already indicated I can tell that the publisher behind the journal “Insights in Biology and Medicine” is “Heighten Science Publications” (https://www.hspioa.org ). A publisher mentioned in the Beall’s list of predatory publishers (https://beallslist.net ). This is a red flag but there are more:

-On their website https://www.biologymedjournal.com they prominently mention “Pubmed NLM Abbr: Insights Biol Med” misleadingly suggesting PubMed indexing

-They are not mentioned positively here:

So, better ignore.

Best regards.

In general, all things associated with tissue culture need to be properly sterilized. For me, I autoclave the complete media (MS, hormones(I use 2.4-D, NAA, BAP, Kinetin), and agar) along with the culture vessel (petri dish or test tube). But it is better to filter sterilize (.2 micron) the hormones and vitamins (of the media) and add them to MS media (agar mixed) when the temperature drops to about 50 degrees celcius.

You can do it by adapting bacterial culture to a high concentration of metals by serial acclimatization. and I can suggest you to induce mutation in your strain, using a UV lamp. this process is called"induced mutagenesis" it's easy and generally used for random selection of mutants. in your case, it's a positive selection of high-concentration heavy metals resistant mutants. good luck.

One of the issues that is holding the concept of an RNA world back from being more scientifically useful - irrespective of whether there ever was such a thing - is that we don't use the idea in the scientific way it was intended. Just like any other prebiotic scenario, it is not (nor has it ever been) a scientific hypothesis. In fact, scenarios are usually not intended as such. Scenario authors from all niches (including RNA world) have pointed out that scenarios themselves are untestable. However, they guide thinking and allow to conceive of hypotheses that are testable. If we go through the old literature we find very explicit passages to support this fact.

For the specific authors advanced in the question, G.F. Joyce and L.E. Orgel, we have a passage from 1999 in "prospects for understanding the origins of the RNA world". (The RNA World 2nd ed. 49-77).

"The presumed RNA World should be viewed as a milestone, a plateau in the early history of life on earth. So too, the concept of an RNA World has been a milestone in the scientific study of life's origins. Although this concept does not explain how life originated, it has helped to guide scientific thinking and has served to focus experimental efforts."

You can find this point of view expressed in foundational work for all niches related to the popular scenarios today. But you can also find it for scenarios most people in origins have never heard of. E.g. the idea that celllular life started with terpenoids found in G. Ourisson and Y. Nakatomi's "the terpenoid theory of the origin of cellular life: the evolution of terpenoids to cholesterol. (1994) Chem & Biol. 1 11-23".

"The hypothesis provides an attractive way of ordering the terpenoids: like all evolutionary theories, it cannot be tested directly. The ideas summarized here do, however, suggest a multitude of experiments having some bearing on the fundamental and fascinating question: how did the first cells appear? We hope to carry out some of them."

A related line of thought - but highly influential - is the exposition by Harold J. Morowitz from 1992 in his book "Beginnings of Cellular Life: Metabolism Recapitulates Biogenesis". If we go to the conclusion, we find this explicit clarification on the distinction between a genuine scientific theory and a scenario:

"at this stage of the thought process, it is important to focus on the hypothesis that intermediary metabolism recapitulates prebiotic chemical evolution. This hypothesis is not a strictly vulnerable theory in the Popperian sense, but it does provide us with a valuable heuristic method for using modern knowledge of biochemistry to search for events that have left their trace. If the intermediary metabolism of autotrophs does not recapitulate biogenesis, then the discontinuities will have to be explained."

More than 2 decades back, many authors made a clear distinction regarding this nuance. Scenarios are here to help: they guide thinking and design experiments. They only guide thinking in a scientifically meaningful direction as long as we can easily abondon scenarios and enthusiastically continue replacing them with new, more informed scenarios. A situation where a scenario gets entrenched and where researchers treat it as a scientific hypothesis is - by construction - hard to escape.

In fact, this is exactly the situation that many researchers have described around the 80s, when criticism mounted against the prebiotic broth scenario. The passage from Wächtershäuser's 1988 "Theory of a Surface Metabolism" is telling:

"The prebiotic broth theory has received devastating criticism for being logically paradoxical (11, 135), incompatible with thermodynamics (11, 144, 160), chemically and geochemically implausible (134, 136, 144), discontinuous with biology and biochemistry (160), and experimentally refuted (135, 160). The reason for the tenacity with which it is retained as accepted dogma has been forcefully and clearly stated by Scherer (126): "If this rejection is substantiated, there will remain no scientifically valid model of the selforganization of the first living cells on earth."

Clearly, the broth scenario had overstayed its welcome. One reason for this is that its 'claims' (which for a scenario can only be speculations) were too much in contradiction with claims from fields of science that do not suffer the same restrictions when it comes to testing and refuting their theories. One example of a very controversial idea that can be found in Haldane's formulation of a broth scenario, is the purported necessity of a long, highly functional protein randomly emerging from a soup, as an extremely rare event: we expect this to be prohibitively unlikely and hence a far from parsimonious explanation.

Quite a few of the critiques voiced against the prebiotic broth scenario are equally valid critiques of some scenarios we have today, including RNA world.

The RNA world is an old and multifaceted concept. There are contrasting formulations that make different claims (to be interpreted as speculations) about history. As with the prebiotic broth scenario (and any scenario), it has raised genuine scientific objections. These have remained largely unadressed, in spite of its long dominance.

It is instructive to bear in mind that scenarios don't come from nowhere. They're fairly detailed speculations about purported historical events. To make them, each author makes assumptions. Some of these concern speculations that later became testable, e.g. about chemistry and physics. You will find different scenario authors make different assumptions and different arguments (and flaws therein). There's an inevitable bias here with respect to the fields an author is trained in. Some of the foundational assumptions in popular scenarios like RNA world are at least 50 years old, but some unchallenged assumptions date back to a literature that is more than a century old. A time before IUPAC, modern quantum mechanics, genetics, and so forth.

That has been enough time to forget that scenarios like RNA world are by construction not testable hypotheses and that they were not intended as such. Scenarios are here to guide thinking, to inspire experiments. The best thing a scenario can do for us, is generate insights that spur us to change the way we think and thereby necessitate replacing our old scenarios with new ones, and repeat the cycle. The science coming out of the community today is a lot more conducive to doing that than previously.

The same cannot be said for the rather myopic RNA-centric framing of a question in the cited passage, which attempts to elevate RNA world to more than a scenario. Rather than forcing ourselves to think about the rather narrow and outdated proposal by Joyce and Robertson, ("consider the alternative possibility that RNA was preceded by some other replicating, evolving molecule"), it is more productive to critically revisit all the things that have been assumed and argued when the concept of an RNA world was conceived and how which of these premises are considered valid or plausible today, and which ones back then. Is there a formulation of RNA world for abiogenesis that is logically sufficient? And if so is it logically necessary that abiogenesis proceeded this way?

It is also instructive to check how much of the logic was sound. e.g. the rhetorical tricks employed in RNA world introduce all sorts of hidden assumptionsm.

As an example of the latter: some still justify an RNA world by the party trick 'chicken-and-egg' question 'protein or RNA, which came first?', only to conclude with 'RNA, it encodes proteins' and hastily conclude with an even stronger 'RNA-first' for abiogenesis. 'chicken-and-egg' fallacies are nothing new in origins. In fact, they were already identified as such long ago. E.g. in chapter 8 of "Seven Clues to the Origin of Life (1985)" by Cairns-Smith, there's an illustrated passage detailing that these types of paradoxes in origins frame the question in a manner that prevent us from considering scaffolds.

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The fact is that even the so-called simple organisms such as E. coli are very complex enterprises with all sorts of things going on together. There is plenty of scope for accidental discoveries of effective new combinations of subsystems. It seems inevitable that every so often an older way of doing things will be displaced by a newer way that depends on a new set of subsystems. It is then that seemingly paradoxical collaborations may come about.

To see how, consider this very simplified model - an arch of stones: This might seem to be a paradoxical structure if you had been told that it arose from a succession of small modifications, that it had been built one stone at a time.

scaffolds that starts like this:

This might seem to be a paradoxical structure if you had been told that it arose from a succession of small modifications, that it had been built one stone at a time. How can you build any kind of arch gradually? The answer is with a supporting scaffolding. In this case you might have used a scaffolding of stones. First you would build a wall, one stone at a time:

Then you would remove stones to leave the 'paradoxical' structure.

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It should be noted that in 2022, even in RNA-world, very few scholars remain that find RNA-first a convincing idea. As a scenario, however, it is not useless: it is instructive to consider what the underlying ideas are that at some point in time made such a highly specific idea compelling to so many of us.

A fixed motif in scenario papers is to start explicitly and implicitly assuming a few things about what chemistry can and cannot do and some properties of abiogenesis. These sort of assumptions used to be spelled out routinely, also outside scenario papers. Let me give two examples.

The original 1953 paper for the "Frank Model" "on spontaneous asymmetric synthesis", has the passages

".. the defining property of a living entity the ability to reproduce its own kind ...

confining attention to chemical molecules, the complexity of any having this essential property of life is likely to be great enough to make it highly improbable that it has a centre of symmetry."

(*I should point out that Frank makes an important error here: the capacity for molecular reproduction is not a molecular property but a property of a reaction network. If we add an additional thermodynamic criterion this property is autocatalysis and we can then check this claim from the IUPAC definition: https://goldbook.iupac.org/terms/view/C00876. It turns out there are trivial ways to make small networks that have this property https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d67469df42226f44295/original/emergent-autocat-animation.gif.)

The point to retain here is that Frank considers it to be generally accepted that one can assume this property to be prohibitively rare in chemistry. This belief was wideheld, and we can e.g. read in "the units of selection" (1970) by Lewontin a summary on scientific views on abiogenesis

"The present view ... Since there was no autocatalysis, there was no reproduction or heredity and so no possibility of natural selection."

The coacervates in Oparins scenario were notably invoked to adress this issue.

When it comes to assumptions in scenarios, this systematically involved conjecturing that chemistry 'in the wild' intrinsically and deterministically becomes a 'mess', undergoing no meaningful complexification, and for which no reproduction and evolution can reasonably be expected. From there, it appears that no process of abiogenesis should conceivably occur naturally, and thereafter some specific sequence of exceptional events is proposed as plausible, because it appears to be the sole contender.

Let us make more explicit why this is not an innocent procedure:

We still find our understanding of 'basic chemistry' to be plagued with limitations and long-lived misinterpretations (e.g. 2 days ago we learned that methyl substitution destabilizes radicals instead of the textbook knowledge that it stabilizes them ).

Moving beyond the basics, we by and large lack a lot of formal theory, experiment, or even a simple reference frame for the things that happen then. Joyce and Robertson honor the tradition of purporting from the outset that 'chemistry in the wild' becomes an intractable mess. The issue is that we don't know at all if that's the case. We cannot assume this from the outset, we need to extensively study it. We require extensive experiments and theory and a reference frame for all the phenomenology associatied with complex systems (e.g. multiple components, compartments, multiple forms of nonequilibrium driving, length scales, time scales).

In making the routine assumption of 'messy, intractable chemistry that can neither complexify nor multiply', we have decided in advance that, once we finally understand 'chemistry in the wild' with its 'so-called intractible mixtures', it cannot have any bearing on abiogenesis. Let alone explain it.

That is a disproportionately bold conjecture about fundamental science, and a very consequential one: all historical scenarios - RNA world being one out of many - have been justified by formulating conjectures of this sort (many authors also insist on other properties, e.g. chemistry being deterministic). Clearly, it should be the first priority of everyone in the field to test this conjecture, by extensively and rigorously studying complex chemical systems as an end in itself. If the conjecture is correct, it provides an important validation for historical scenario approaches. If the conjecture turn out wrong, we are in a much better position to conceive of more scientifically informed scenarios, but potentially the approach will change entirely.

In presenting it as such, I am making it appear as if it could be an open question whether the chemical conjectures underpinning our scenarios in origins may be true or not. In fact, we have learned quite a few things in the meantime. And some clumsy mistakes were made elsewhere.

- Determinism:

When it comes to chemistry being deterministic (a key tennet of e.g. Sutherlands scenario and Wächtershäusers surface metabolism): upon critical evaluation of what is known of basic chemistry this idea becomes unacceptable, especially when considering the chemical processes on the surface of a planet, as opposed to a quick reaction in pyrex.

1) insofar as it is reproducible, modern chemistry owes much of it to big strides of standardization in glassware, methodology, synthesis protocols (e.g. usage of stirring bars).

2) lab chemistry exhibits many forms of contingency. This is particularly the case when it comes to phase behavior, e.g. habit modification, polymorphism. Aspirin purportedly has 8 reported polymorphs, phenobarbitone 13.

3) glassware is cleaned between reactions, thereby making successive reactions in the same glassware independent. In nature, this property of independence is absent. In fact, effort to make an evolutionary classification of minerals are rooted in the opposite: that certain minerals start to form conditional on the presence of certain others. (https://pubs.geoscienceworld.org/msa/ammin/article/104/6/810/570840/An-evolutionary-system-of-mineralogy-Proposal-for)

- Autocatalysis:

A first issue to get out of the way is the misconception that autocatalysis is prohibitively rare. A prominent PI in origins (RNA world, not a chemist) told me that chemists throughout history have found exactly one example. Claims about the contents of a literature one cannot realistically have read in a lifetime is a common error we can find in the origins literature. Below are some reviews.

I should stress that these reviews discuss examples from a few niches in chemistry. These reviews do at least allow to have 100s of counterexamples to dubious claims about no autocatalysis in chemistry, but it's only a small fraction. Virtually all branches of chemistry have regular reports of autocatalysis, but very few focus on autocatalysis in its own right. And hence most branches do not review their reported examples.

By critically examining the IUPAC definitions, one can show that autocatalysis is dramatially more widespread than long thought. In part, this is because the definition applies to a wealth of situations where the term is not routinely employed. By examinging the requirements of autocatalysis as an emergent network property, one can demonstrate that this property emerges particularly readily in a heterogeneous / multicompartment context. With the disclaimer that I'm an author I refer to the following:

- Messy chemistry:

Refreshing counterexamples are afforded by the literature on systems chemistry and dynamic combinatorial libraries.

In the context of origins, a recent work that is greatly aiding in fixing our misconceptions is : https://www.nature.com/articles/s41557-022-00956-7

Where a reaction of purported immense complexity is found to exhibit highly reproducible and ordered behavior as function of environmental inputs. How chemistry exactly works on this level is still poorly understood. I think I do, but it'll have to await peer review. But we cannot in good scientific conscience take for granted anymore that chemistry becomes messy and intractable. When we do the experiments, we see something very different.

in conclusion, I want to come back to the final point of the question

No. The sientific community should strive to do what it can justify scientifically. Those that find it fruitful to relegate the RNA world - which is not a hypothesis - are justified in doing so. Notably because it is is founded on scientifically refuted premises and logical errors.

Those that find ways to make it fruitful to keep it are justified in doing so: it's a scenario, one can draw inspiration from it. Perhaps a thoroughly altered version can be developed that fixes previous issues.

Above all else, RNA is an amazing molecule that has been used for fundamental research that concerns everyone in origins, and will continue to do so irrespective of how serious the RNA world scenario is still taken.

What the origins of life community needs, first and foremost, however, is concern itself with more important matters.

Complex chemistry needs to be studied thoroughly on an experimental and theoretical level.

New scenarios are needed. And these scenarios should no longer require chemistry to have properties it doesn't have, and vice versa. These scenarios should also explicitly be appraciated for what they are, an for what they're not. They're here to help, to guide thinking, inspire experiments, produce testable predictions, update our beliefs. They are not scientific hypotheses in and of themselves.

Hello sir, Asif Bilal

Just saw your response. It means a lot to me. Thank you so much for your time.

If possible, could you please forward the survey to other amazing scientists, It would help me a lot.

Hi,

The supplier claims that their "sample release reagent" (nucleic acid release technology), can lyse pathogens at room temperature very fast, with no need to heating, centrifuging or replacing tubes, the sample DNA/RNA can be extracted quickly through simple operations. The reagent is applied for the pretreatment of nucleic acid molecules, to release them from specimens, then the released nucleic acids can be used for clinical in vitro diagnosis or for the detection through appropriate apparatus.

Cenk Tan; There are, of course, several websites that rank the universities worldwide. However, QS is the most famous of which.

B-Phycoerythrin (B-PE), a fluorescent protein from phycobiliprotein family, is isolated from cyanobacteria and eukaryotic algae. Its primary absorption peak is at 545nm with a secondary peak at 563nm. B-PE consists of α, β and γ subunits and is present as (αβ)6γ. B-PE and the closely related R-PE are the most intensely fluorescent phycobiliproteins having orange fluorescence. They are significantly brighter and more photostable than conventional organic fluorophores. B-PE labeled streptavidin, primary and secondary antibodies have been widely used in applications such as flow cytometry and multi-color immunofluorescent staining.

While

R-phycoerythrin (R-PE) is an intensely bright phycobiliprotein isolated from red algae that exhibits extremely bright red-orange fluorescence with high quantum yields. It is excited by laser lines from 488 to 561 nm, with absorbance maxima at 496, 546, and 565 nm and a fluorescence emission peak at 578 nm. R-PE is a large molecule used for fluorescence-based detection, primarily in flow cytometry, microarray assays, ELISAs, and other applications that require high sensitivity but not photostability.

Hello; Small samples taken from a large pool will not reflect the gene distribution of the larger pool. Founders' effects, genetic bottlenecks, etc. are what are under discussion and the basis for many examples of speciation. The extreme example might be parthenogenetic species arising from hybridization. Fun stuff! Cheers, Jim Des Lauriers

You might want to look at this recent paper:

Bioinformatic prediction of putative metallothioneins in non-ciliate protists

Sergio Balzano and Angela Sardo

Published:13 April 2022