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Currently, in Japan, physics, chemistry, biology, and geology are taught independently in science education context. So I would like to know, has any country developed a curriculum that emphasizes the relationship or overlaps between these four fields? I know that similar movement is occurring under the name of "STEM integration." But how about the case of physics, chemistry, biology, and geology? (Or I should say "PCBG integration") I would appreciate it if you could let me know anything.
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My homestate Baden-Württemberg introduced an additional subject called NWT (Naturwissenschaft und Technik) a few years ago which is taught in middle grades starting in 8th grade. In principle this should be more of an integrated subject which should provide a connection once the individual subject groundwork has been laid.
At least in the introduction phase this didn't work well since the teachers did not receive proper training and new university students who wanted to teach this later were given way too hard curricula which contained basically the hardest courses from chemistry AND mechanical engineering which is absolutely unneccessary for teaching 8th graders. A lot of changes were made, but I don't have as much contact with students anymore since my current job does not involve teaching. You could ask the Fachschaft (students' interest representation group) at my alma mater for the current state:
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Olen R.Brown & David A.Hullender published a paper in Progress in Biophysics and Molecular Biology journal in August 2022 with the name ( Neo-Darwinism must Mutate to survive ) : https://www.sciencedirect.com/science/article/abs/pii/S0079610722000347
the writers doubt macroevolution or the ability of known mechanisms of evolution to explain macroevolution as they say :
The central focus of this perspective is to provide evidence to document that selection based on survival of the fittest is insufficient for other than microevolution. Realistic probability calculations based on probabilities associated with microevolution are presented. However, macroevolution (required for all speciation events and the complexifications appearing in the Cambrian explosion) are shown to be probabilistically highly implausible (on the order of 10−50) when based on selection by survival of the fittest. We conclude that macroevolution via survival of the fittest is not salvageable by arguments for random genetic drift and other proposed mechanisms.
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Fréderic:
1) The object of evolution is species, not ecosystem: ecosystem "evolves" only according to the evolutionary modifications of its constituting species.
2) In abundance of prey the population of predators increases - and opposite: when prey becomes scarce, less predators survive; in this way the proportions usually remain roughly near to "optimal" for the ecosystem.
3) Great population size makes, indeed, greater probability of appearance of advantageous mutation, but at the same time makes it much less likely to meet a mate with the same mutation, necessary for the mutation to persist (avoid quick "stochastic" elimination) and spread over the entire population.
4) The establishment in the prey population of the character making it difficult to seize by a predator, results in weakening of the selectiion pressure (and, consequently, tempo of further evolution) in prey and intensification in the predator, resulting in re-establishment of the balance.
5) Natural selection does not accept "good enough" for long: "still better" will always have prevalence, so what is "good enough" now will quickly become "not sufficiently good" (no, however ingenious, evolutionary modification can make the prey species absolutely out of the predator's reach: only the probabilities change!).
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Forests are the biodiversity wealth of natural ecosystems and a key factor in the wealth of the planet's biosphere. However, this natural wealth is rapidly being eroded by human civilisational activities. The scale of forest fires has been increasing in recent years. The increasing scale of forest fires is a result of the ongoing process of global warming. In some regions of the world, forests are also being burned in order to acquire more land for the cultivation of agricultural crops, which is usually carried out under predatory and unsustainable farming practices. It is well known that forests are one of the key factors in reducing the rate of increasing CO2 in the atmosphere, an important factor in slowing down the greenhouse effect and consequently also in slowing down global warming. It is therefore essential to increase the scale of forest fire protection.
The following questions are therefore becoming increasingly topical:
How to protect forests from fires?
What is your opinion on this subject?
What do you think about this topic?
Please reply,
I invite you all to discuss,
Thank you very much,
Regards,
Dariusz
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Remove all forest litter (dead branches from lower parts of trees). It provides the "fuel" for the next "wild" fire.
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Globally, deforestation processes continue to outpace aforestation processes.It is well known that forests are one of the key influences on the climate, on the stability and sustainability of the climate, the maintenance of a humid microclimate, local water management, the state of biodiversity in regions.
Forests are also one of the key factors in reducing the amount of CO2 entering the atmosphere. At the UN climate summit COP26, it was agreed that by the end of this decade, i.e. by the end of 2030, national and global forest deforestation processes should be completed and forest afforestation processes should be accelerated. The restoration of forest ecosystems should be carried out in accordance with the principles of ecology of specific environmental formations of forest ecosystems consisting of replacing monocultures of tree crops with biodiverse restored, tree-rich forest ecosystem formations adequate to the specific local environment, geological and climatic setting.
But why do we have to wait so many more years for this? Why have such decisions not been taken earlier?
Why do the processes of afforestation not already prevail over deforestation?
Why are forests still being cut down when we know how important they are for slowing down the progressive process of global warming?
What needs to be done so that aforestation processes already prevail over deforestation?
How can afforestation processes be implemented quickly and effectively?
How can afforestation processes in civilisationally degraded areas be carried out quickly and efficiently?
How can afforestation be carried out with a high level of biodiversity in restored natural forest ecosystems?
What do you think about it?
What is your opinion on this topic?
Please reply,
I invite everyone to the discussion,
Thank you very much,
Kind regards,
Dariusz
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Choose to plant trees as part of your life.
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
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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?
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To save life in desminopathy, can the body purposefully reduce muscle mass, for example, due to decreased heart function or for another reason?
It is known that when hypothermia, the body sacrifices limbs for survival. Is it possible with desminopathy a similar phenomenon?
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Dear Mozhgan Norouzi, thank you very much for your reply!
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A patient with desminopathy (mutation Thr341Pro DES in a heterozygous state) with the progression of the disease has a decrease in taste and smell, immunosuppression, and an increase in IgA in the blood.
Oddly enough, but all this is characteristic of infections, including viral ones. For example, it is known that if the hepatitis C virus is not treated, then death will occur in 20 years.
In the identified case of late onset desminopathy, muscle weakness manifests itself at the age of 30, and death occurs 20 years after the onset of the disease.
Could the desmin mutation in myofibrillar myopathy be caused by an infection?
Perhaps the infection contributes to the progression of desminopathy?
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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?
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What accounts for the solidifying of personally held narratives over time and how does it affect the way we interact with social affairs and politics?
All views welcome from a perspective of
-neuroscience
-psychology
-sociology
-biology
-political science
-education
Thank you so much for your inspiration!
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That is due to experiential learning, although it CAN become a problem if we allow "confirmation bias" (only accepting things that already agree with preconceptions) to ignore new data. We try to avoid it in science by constant questioning (not always successful, and almost never when appropriated by politics). For example, even what we call "Laws" in science are correctly understood as good interpretations of physical evidence that have not yet been refuted. It takes a long time for a theory to get enough evidence to become accepted, and much longer for one to be considered "law" of science.
Humans naturally look for patterns and consistency to survive the normal changes of the universe. Thus, anything that seems to be either consistent or part of a pattern becomes more "accepted" by a person, and thus harder to adapt or replace even in the face of new evidence that modifies or contradicts it.
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Hello!
I was wondering if anyone could point me to any references that show that with increasing oligo length, there is a significant reduction in ssDNA generation efficiency. Im specifically curious at what point heating to separate dsDNA becomes ineffective and some sort of legitimate physical experiment to quantify this reduction with increasing DNA length.
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found an assay here, thank you all!
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Hi
Some authors use either correlation matrices or VIF to identify collinearity between variables, while others apply both to improve model performance and interpretability. Therefore, I would be happy to get statistical explanations from anyone about the tools used separately and simultaneously or I want to know if other robust mechanisms to check collinearity are extant.
Thank you in advance!
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Both can be used, but I will suggest you to isolate the variables through PCI
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I just received this email from Peer Review Department from "Insights in Biology and Medicine" Journal.
I think that this journal is not indexed.
Here is the email:
Dear Dr. Hany Mansour,
In the view of your eminence in the field, we kindly request you to review a manuscript from the Insights in Biology and Medicine.
This is to bring to your kind notice that we have received a manuscript entitled "Dead Sea Salt Solution: composition, lack of cytotoxicity and in vitro efficacy against oral leukotoxins, endotoxins, and glucansucrase"
We believe that your expertise and experience in the subject matter will certainly help in enhancing the quality of the manuscript.
We request you to accept this manuscript for review purpose and send the comments in the stipulated date.
Please find the attachments of the manuscript and Evaluation form.
Your support will be highly appreciated in publishing the research and development works in Open Access.
Best compliments,
Lisa
Peer-Review Department
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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.
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I'm using Sporosarcina pasteurii to remove heavy metals from wastewater by producing metal carbonates. The issue I encounter is that high metal concentrations (i.e. Co 2g/L) strongly inhibit bacterial growth and activity.
One of the existing solutions is to isolate another already metal-tolerant strain (such as Lysinibacillus sphaericus). (source :
I have read that it is possible to adapt a bacterial culture to a high concentration of metals by serial acclimatisation, where the bacteria are successively grown in a medium of increasing metal concentration. (source : 10.1016/j.wasman.2018.07.010)
Can this method be adapted to ureolytic bacteria? Are there any examples?
If not, what other methods would you suggest?
Thank you !!
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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.
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Kindly discuss your ideas and viewpoints on the origin of life and the RNA world hypothesis.
What are the contradictory views on why researchers are still unsure about the origin of life through RNA or such analogous molecular intermediate pre-cursors preceding its existence?
"The general notion of an “RNA World” is that, in the early development of life on the Earth, genetic continuity was assured by the replication of RNA and genetically encoded proteins were not involved as catalysts. There is now strong evidence indicating that an RNA World did indeed exist before DNA- and protein-based life. However, arguments regarding whether life on Earth began with RNA are more tenuous. It might be imagined that all of the components of RNA were available in some prebiotic pool and that these components assembled into replicating, evolving polynucleotides without the prior existence of any evolved macromolecules. A thorough consideration of this “RNA-first” view of the origin of life must reconcile concerns regarding the intractable mixtures that are obtained in experiments designed to simulate the chemistry of the primitive Earth. Perhaps these concerns will eventually be resolved, and recent experimental findings provide some reason for optimism. However, the problem of the origin of the RNA World is far from being solved, and it is fruitful to consider the alternative possibility that RNA was preceded by some other replicating, evolving molecule, just as DNA and proteins were preceded by RNA." - Robertson and Joyce
[This is as per the explanation by Michael P Robertson and Gerald F Joyce in the article: "The origins of the RNA world." published in the Cold Spring Harb. Perspect. Biol. 4, a003608 (2012).]
The scientific community must resolve this contradicting conjecture through rational discussion and debate backed by strong experimental evidence on what must be the pre-cursor molecule to the Origin of Life if it is not RNA!
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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.
"
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
"The scientific community must resolve this contradicting conjecture through rational discussion and debate backed by strong experimental evidence on what must be the pre-cursor molecule to the Origin of Life if it is not RNA!"
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.
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Good day,
i have a general question about tissue culture.
I have found the following recipe for Epipremnum Aureum "Marble Queen":
Leaf Explant: MS Medium + 4.54 µM TDZ + 1.07 µM NAA (Thidiazuron in Micropropagation of Aroid Plants by Chen and Wei (2018), p. 105, DOI: 10.1007/978-981-10-8004-3_4)
Specifically, I have the following questions.
1) Do i only need to autoclave the agar with distilled water (I use a pressure cooker for this) and when the agar has cooled down a bit just add the MS, TDZ and NAA and mix it or do i need to autoclave the MS as well?
2) Will the TDZ dissolve in the agar water at all and how hot can the agar water be to add the MS, TDZ and NAA?
3) Is it even necessary to autoclave the water incl. agar (in the pressure cooker) if I clean all the jars with NaClO (sodium hypochlorite)?
Thank you in advance!
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You could made the MS medium and pour in to the glass jar and autoclave with your pressure cooker. Once it cooled down add the hormone by filter sterilization. Good luck
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Does the DNA remain stable or degrade at this temperature? Would there be any difference in thermal stability between supercoiled and linear forms of say, 3 kb plasmid.
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Here`s the article `The conformation of double-stranded DNA` by B. Cyriax &  R. Gäth, Naturwissenschaften, v. 65, p.106–108 (1978).
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I am a student of biotechnology and an independent SARS CoV-2 researcher from India. For finding the academia research status and analysis of the integration of innovation with research, I have created a set of Multiple choice type questions about your experience as a researcher. The google form requires nothing but your honesty and openness for research. Feel free to ask questions and DM. The questions will assist in gauging the level of innovation and writing in academia.
If possible, please do forward this little form to your fellow researchers and other amazing scientists. I would be highly grateful.
Thank you
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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.
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Human activities have greatly changed the natural environment since the Industrial Revolution. Have migratory birds changed their migration routes? Why can migratory birds do this?
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Hi Shu, Yes, James is right, in Google Scholar you can fin many citations.
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Hello everyone,
I did the assembly of chloroplast genomes for some Boraginaceae species, in a few species, I got an orientation problem where the rbcl gene position is within the circular shape in a clockwise direction, and the atpB and atpE genes position is are outside the circular shape in the anti-clockwise direction (please see the picture), and this is a different result from most assemblies of chloroplast genomes that have been published !!!. (usually, the rbcl gene is outside the circular shape and in the anti-clockwise direction while the atpB and atpE genes are within the circular shape and in a clockwise direction)
I am using Chlorobox to draw the gene map after Novoplast finishes the assembly, this issue happened with only two of 7 samples, the two samples are from the same family !!!, I change the seed and reference many times and still got the same result.
Any idea what I need to fix this?
Thanks!
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I think that maybe you have used blunt end digestion endonucleases, this makes inserts to be ligable in both directions (as your experimental results suggest). If that's the case, maybe this information is useful:
Both the Costa and Weiner or Delphi genetics Staby methods could fix this orientation problem.
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Hi,
I wonder if anyone knows how to use sample release reagent from Sansure Biotech ?
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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.
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The 2023 ranking is available through the following link:
QS ranking is relatively familiar in scientific circles. It ranks universities based on the following criteria:
1- Academic Reputation
2- Employer Reputation
3- Citations per Faculty
4- Faculty Student Ratio
5- International Students Ratio
6- International Faculty Ratio
7- International Research Network
8- Employment Outcomes
- Are these parameters enough to measure the superiority of a university?
- What other factors should also be taken into account?
Please share your personal experience with these criteria.
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Cenk Tan; There are, of course, several websites that rank the universities worldwide. However, QS is the most famous of which.
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I was able to study biology but not enough to understand the difference between B-phycoerythrin and R-phycoerythrin. Quite "simply" could someone answer to this question? Can we switch from one form to another? :)
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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.
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Hello everyone:
Like Darwin reading Malthus "for amusement", I've been reading the 2nd chapter, "Systematics and Evolution", of the 3rd edition of "Vertebrate Biology", by Donald W. Linzey (2020).
When reading the section on "Species and Speciation" in this chapter, and more specifically when reading about the founder effect and its relationship with the origin of new species, I found the following sentence: "(...) speciation can proceed rapidly since only a portion of the original gene pool is normally present in the small, newly relocated population, and NATURAL SELECTION CAN WORK MORE QUICKLY ON SMALLER GENE POOLS" (capital letters are mine).
To the best of my knowledge, mathematical models of natural selection include parameters like relative fitness and/or selection coefficients, whereas population size is included in models for the evolutionary effects of random genetic drift.
So, do you have any idea on the reasons why natural selection could go faster in small populations (i.e., small gene pools)?
Any help will be welcome. Best regards, and thanks in advance:
Jose.
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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
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Hi! I am a 3rd year biology student, and currently working on my undergraduate thesis, which has an objective to determine the presence of metallothioneins on several candidates from different microalgae genera. But, I don't have a background on various bioinformatics tool, may I ask if you know any software that could possible help me achieve my study's motive? Thank you
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You might want to look at this recent paper:
Bioinformatic prediction of putative metallothioneins in non-ciliate protists
Sergio Balzano and Angela Sardo
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If I wanted to introduce a foreign protein into the human stomach without it getting cleaved up by proteases such as trypsin, how would I do so?
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Hello Chris Lee
You may introduce protective groups that will help prevent enzymatic degradation of the foreign protein.
Cyclization of foreign protein can increase its half-life by protecting it from the digestion of exo- and endopeptidases. Cyclization of peptides and proteins generate more rigid conformations, and it exhibits decreased susceptibility to enzymatic degradation.
You can also protect the foreign protein from proteases by covalently attaching it to a biocompatible polymer, leading to reduced immunogenicity, enhanced bioavailability, and enriched pharmacokinetic profile.
For more information, you may refer to the attached paper.
Best.
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Complex systems are becoming one of very useful tools in the description of observed natural phenomena across all scientific disciplines. You are welcomed to share with us hot topics from your own area of research.
Nowadays, no one can encompass all scientific disciplines. Hence, it would be useful to all of us to know hot topics from various scientific fields.
Discussion about various methods and approaches applied to describe emergent behavior, self-organization, self-repair, multiscale phenomena, and other phenomena observed in complex systems are highly encouraged.
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Jiří Kroc: Greetings Prof. Kroc. In neurology the cutting-edge research is on 1) neurodegeneration, 2) neuroprotection, 3) the unification/entanglement between the nervous system and the immune system and 4) disorders of consciousness. thanks, Mustafa.
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In my previous question I suggested using the Research Gate platform to launch large-scale spatio temporal comparative researches.
The following is the description of one of the problems of pressing importance for humanitarian and educational sectors.
For the last several decades there has been a gradual loss in quality of education on all its levels . We can observe that our universities are progressively turning into entertaining institutions, where students parties, musical and sport activities are valued higher than studying in a library or working on painstaking calculations.
In 1998 Vladimir Arnold (1937 – 2010), one of the greatest mathematicians of our times, in his article “Mathematical Innumeracy Scarier Than Inquisition Fires” (newspaper “Izvestia”, Moscow) stated that the power players didn’t need all the people to be able to think and analyze, only “cogs in machines,” serving their interests and business processes. He also wrote that American students didn’t know how to sum up simple fractions. Most of them sum up numerator and denominators of one simple fraction with the ones of the other, i.e. as they did it, 1/2+ 1/3 according to their understand is equal to 2/5 . Vladimir Arnold pointed out that with this kind of education, students can’t think, prove and reason – they are easy to turn into a crowd, to be easily manipulated by cunning politicians because they don’t usually understand causes and effects of political acts. I would add, for myself, that this process is quite understandable and expected because computers, internet and consumer society lifestyle (with its continuous rush for more and newer commodities we are induced to regard as a healthy behavior) have wiped off young people’s skills in elementary logic and eagerness to study hard. And this is exactly what the consumer economics and its bosses, the owners of international businesses and local magnates, need.
I recall a funny incident that happened in Kharkov (Ukraine). One Biology student was asked what “two squared” was. He answered that it was the number 2 inscribed into a square.
The level and the scale of education and intellectual decline described can be easily measured with the help of the Research Gate platform. It could be appropriate to test students’ logic abilities, instead of guess-the-answer tests which have taken over all the universities within the framework of Bologna Process which victorious march on the territories of former Soviet states. Many people can remember the fact that Soviet education system was one of the best in the world. I have therefore suggested the following tests:
1. In a Nikolai Bogdanov-Belsky (1868-1945) painting “Oral accounting at Rachinsky's People's school”(1895) one could see boys in a village school at a mental arithmetic lesson. Their teacher, Sergei Rachinsky (1833-1902), the school headmaster and also a professor at the Moscow University in the 1860s, offered the children the following exercise to do a mental calculation (http://commons.wikimedia.org/wiki/File:BogdanovBelsky_UstnySchet.jpg?uselang=ru):
(10 х 10 + 11 х 11 + 12 х 12 + 13 х 13 + 14 х 14) / 365 = ?
(there is no provision here on Research Gate to write square of the numbers,thats why I have writen through multiplication of the numbers )
19th century peasant children with basted shoes (“lapti”) were able to solve such task mentally. This year, in September, this very exercise was given to the senior high school pupils and the first year students of a university with major in Physics and Technology in Kyiv (the capital of Ukraine) and no one could solve it.
2. Exercise of a famous mathematician Johann Carl Friedrich Gauss (1777–1855): to calculate mentally the sum of the first one hundred positive integers:
1+2+3+4+…+100 = ?
3. Albrecht Dürer’s (1471-1528) magic square (http://en.wikipedia.org/wiki/Magic_square)
The German Renaissance painter was amazed by the mathematical properties of the magic square, which were described in Europe firstly in Spanish (the 1280s) and Italian (14th century) manuscripts. He used the image of the square as a detail for in his Melancholia I painting , which was drawn in 1514, and included the numbers 15 and 14 in his magic square:
16 3 2 13
5 10 11 8
9 6 7 12
4 15 14 1
Ask your students to find regularities in this magic square. In case this exercise seems hard, you can offer them Lo Shu (2200 BC) square, a simpler variant of magic square of the third order (minimal non-trivial case):
4 9 2
3 5 7
8 1 6
4. Summing up of simple fractions.
According to Vladimir Arnold’s popular articles, in the era of computers and Internet, this test becomes an absolute obstacle for more and more students all over the world. Any exercises of the following type will be appropriate at this part:
3/7 + 7/3 = ? and 5/6 + 7/15=?
I think these four tests will be enough. All of them are for logical skills, unlike the tests created under Bologna Process.
Dear colleagues, professors and teachers,
You can offer these tasks to the students at your colleges and universities and share the results here, at the Research Gate platform, so that we all can see the landscape of the wretchedness and misery resulted from neoliberal economics and globalization.
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Every time i working with hyaluronic acid I got some bubbles inside gel. It desn't matter in lab and do not affect on the acid. Few days ago I saw syringe (with a needle) with clear hyaluronic acid without any bubbles. Friend send me a photo of bottle with the product without bubbles too. How do they made it??? I was trying vacuum suction but did not get proper effect.
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Problem solved. Thanks to all!
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Hello everyone, any system can be thought of as a collection of its fundamental building blocks. There are well defined fundamental parts in certain systems (attached image) like the basis vectors for a vector space or the 5 fundamental tastes. Then there are systems where the fundamental parts aren't as well defined but we can still think of the best candidate parts for such systems. For example,
  1. Colours: RGB
  2. Nations: Government, Bureaucracy, Civilians, Judiciary.
Which principal or fundamental parts can be thought of as the building blocks of fruits and vegetables? I can think of a few:
  1. Sugar content
  2. Vitamin content
  3. Citric acid content
  4. Skin
Can we come up with a master list of all possible principal components which are the bare minimum to construct any fruit or vegetable?
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A rephrasing of the question to make it a bit clearer:
Imagine you have the power to create any fruit/vegetable out of thin air (F&Vman). What minimum amount of data would you need to make a specific fruit/vegetable with your power? (let's use apple as an example for the discussion)
You want to earn a living by doing this so you wish to standardize the process. For that, you need an exact list of basic/fundamental characteristics of F&V (both, regarding their physicality and their chemical make-up) from your customers that can be used to make almost any, if not all, F&V.
That list is what I'm looking for.
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Also, kindly check the following link that may be useful:
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Compiled allometric data might help to detect scaling patterns.
Or similarities in the scaling relationships might suggest connections otherwise too subtle to find.
Does such a list exist?
Does such a list exist for biological phenomena?
If such lists do not exist should they?
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No such compilation that I know of (only some reviews, for the scaling of a specific trait in a specific group). So regarding your last question "should it exist", I think creating such a list would be an admirable but difficult task - depends on what you're thinking of exactly as "all known instances". Using all the raw data available would basically be a "database of everything", virtually impossible. It would still take a ton of work to even make a list of every allometric equation ever explicitly stated for every trait in every organism, and you'd also need to be able to update it, and to subset it by trait, taxa (down to intraspecific resolution, don't forget), external factors such as region/temperature/season/age/sex, etc.
(btw if somebody does go and make such a database it should definitely be named ALLometric right?)
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Hello everyone,
I need help understanding whether my two groups are paired or not.
I am collecting data from one group of cells. We have developed two different workflows (let's call them A, and B) for data analysis. We want to test whether these two workflows give the 'same' results for the same set of cells.
At the end, I obtain:
  1. Group 1 (contains the variable obtained with workflow A)
  2. Group 2 (contains the variable obtained with workflow B).
I have been considering the two groups as independent because the two workflows do not interfere with each other. However, the fact that both workflows operate on the same cells is throwing me off and I am wondering if these groups are actually paired.
Could you advise me on this and on what test is best to use?
The hypothesis for the test would be:
  • the distributions of the variable is the same with both workflow A and B; and/or
  • the median of the distribution from workflow A equals the one from workflow B
Thank you.
GN
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If you have two samples, from two measurement methods (workflows), but from the same subject (single group of cells), then you can use a paired samples test.
The benefit of this is that it has more statistical power than an unpaired test.
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Over the last few months, I have come across several posts on social media where scientists/researchers even Universities are flaunting their ranking as per AD Scientific Index https://www.adscientificindex.com/.
When I clicked on the website, I was surprised to discover that they are charging a fee (~24-30 USD) to add the information of an individual researcher.
So I started wondering if it's another scam of ‘predatory’ rankings.
What's your opinion in this regard?
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Dear friends, I am a master's student in biology. Now I need to added drug to the medium after being diluted into PBS. How much PBS can be added to the medium without affecting the cell growth. The medium I use is DMEM and 10% serums
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Hello Chaoqun Huang,
Its seems that the drug of your interest is water soluble. If it is so, then I would suggest to make the stock solution fist in sterile distilled water and then final working concentrations in Dulbecco′s Modified Eagle′s Medium (DMEM) culture medium. Make sure that the solvent (here water or PBS) final amount should not literally exceed more than 1% in culture medium in order to avoid disturbance in physical, chemical proprieties, and concentrations of other component of the culture medium.
DMEM is a modification of Basal Medium Eagle (BME) that contains four-fold concentrations of the amino acids and vitamins. The original formulation contained 1000 mg/L of glucose and was used to culture embryonic mouse cells. Since then, it has been modified in several ways to support primary cultures of mouse and chicken cells, as well as a variety of normal and transformed cells. It is a widely used basal medium for supporting the growth of many different mammalian cells including primary fibroblasts, neurons, glial cells, smooth muscle cells, as well as cell lines such as HeLa, 293, Cos-7, and PC-12 etc.
Hence, addition of large amount of solvent (here water or PBS) may alter/dilute the constituents of DMEM specifically made for specific type of cell culture or purpose. In any condition, try to ensure that the solvent present in final working concentration is not more that 1% (v/v) in DMEM culture medium in order to retain the osmolarity and other ingredients concentration in culture medium.
Good luck
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Example:
1. You use Material 1 in Biology and after using it, you recycle it in Chemistry to come up with Material 2.
2. You use Material 1 in Biology and then its product is used in Chemistry, Physics, Earth Science.
3. Or any related activities that make use of similar or related ideas.
If you can share also your related studies, I highly appreciate it. Thanks!
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I used 1 material in biology lab and recycle it that's used it in Field work
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Like I want to prepare a senior secondary Biology Subject curriculum block for instruction.
I need the block format, the contents examples etc
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I'm a maths teacher by profession - but here's a few bullet points:
* allow time to pre-assess find out what learners know already
* allow time to cycle through the curriculum twice,
* once at the level the pre assess indicates and to set the ground work of the big picture,
* cycle through the curriculum a 2nd time to either review what wasn't learned or teach to greater depth what was learned
* use retrieval practice questions to follow on from teaching (in maths about 30% of learners forget what they learned in less than a week, but if reviewed by questions within e.g. 5 days and depending on response 2 further weeks or fewer, the retention for learners will be much higher).
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As far as I know it has been dismissed as a closed cased of the history of science having no defenders left. However, that's not the feeling I get when the issue comes up in private discussions. I'm wondering if I have missed something, and if and how vitalism (or some refined modern form of it) is still considered to be a viable option by some biologists?
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Vital force(s) are beyond materialistic description as is very carefully explained by @Reza Sayed . Yet, the recent discoveries on the effects of cell membrane potential on cancerous growth, morphological development, regrowth of organs and limbs that is led by Professor @Michael Levin [1,2] are telling us that it is possible to shift materialistic description of forces shaping living entities a bit further into that was up to a recent time assumed to be undescribable using materialistic science. Electricity plays indispensable role in morphogenesis.
The way, the biological systems think is closely related to self-organizational and their emergent properties when observed from the materialistic point of view. There are observed some very interesting effects within experimental and computational studies, many of them are shared in my projects and are part of my research on emergents in biology [4-6].
Emergents are one of the crucial parts of every single living system in existence. As already said in one of the first answers, emergents are not equal to living systems because we do observe them in non-living systems too.
As a mathematician working in complex system applied to living entities, it is well-known fact to me that emergent behavior is one of the crucial parts of living creatures. Emergence is not sufficient to explain life, but it is its inseparable constituting and organizational feature.
My research brings me in this area and hence, I decided to find out robust emergent structures in simple (very primitive) massive-parallel computational environment called a cellular automaton, which serves as an oversimplified proxy of living system [3].
Surprisingly, it was found that we can construct a simple cellular automaton called r-GoL (robust Game of Life), which is resistant against random injection of one percent of errors into the computation. In other words, emergents do not collapse when subjected to a certain fraction of faulty operations [3].
From the point of view of living systems, it means that we do have means of construction of deterministic rules, which produces emergent structures, that are resilient against errors. This means nothing less than that we are capable to construct reliable computations above unreliable hardware/wetware.
Life itself is very probably exploiting unreliable computational media that is giving rise to very robust emergent and reliable emergent structures. 
###
[1] Brook Chernet, Dany S Adams, Maria Lobikin, and Michael Levin: "Use of genetically encoded, light-gated ion translocators to control tumorigenesis", Oncotarget 7(15):19575-19588 (March 2016) DOI: 10.18632/oncotarget.8036
[2] Chris Fields and Michael Levin: "Does evolution have a target morphology?", Organisms: Journal of Biological Sciences 4: 1, 57-76. (August 2020) DOI: 10.13133/2532-5876/16814
[3] Jiri Kroc: "Why Do Biology and Medicine Need to Study Robust Massive Parallel Information Processing Environments: Explained on the Game of Life and Its Generalization?", ResearchGate (Feb 2022) https://www.researchgate.net/publication/358446061_Why_Do_Biology_and_Medicine_Need_to_Study_Robust_Massive_Parallel_Information_Processing_Environments_Explained_on_the_Game_of_Life_and_Its_Generalization
[4] Project: "Complexity in Medicine: Practical Problems, Their Definitions, Models, and Solutions", ResearchGate, March 7, 2020,
[5] Project: "Complex Systems in Physics, Biology, and Medicine: Backgrounds, Understanding, Modeling, and Software", ResearchGate, April 3, 2017, https://www.researchgate.net/project/Complex-Systems-in-Physics-Biology-and-Medicine-Backgrounds-Understanding-Modeling-and-Software
[6] Project: "Complexity Digest -- Toolkit Containing Root Research Results, Articles, Books, and Software -- Covers Emergence, Self-Organization, and Beyond", ResearchGate, February 11, 2020, https://www.researchgate.net/project/Complexity-Digest--Toolkit-Containing-Root-Research-Results-Articles-Books-and-Software--Covers-Emergence-Self-Organization-and-Beyond
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Most biologists and philosophers understand vitalism as the doctrine of the entelechy, originally proposed by the German biologist Hans Driesch in the early twentieth century. According to Driesch, entelechies were nonmaterial, bio-specific agents responsible for governing a few peculiar biological phenomena. Current attitudes towards vitalism and the doctrine of the entelechy are almost universally negative. Numerous biologists and philosophers today endorse this metaphysical refutation of vitalism. For them, since all events and processes in the world, from the metaphysical point of view, must be identical or reducible to some material (or physical) events and processes, there is no room for nonmaterial agents such as entelechies. The addition of the information instead of the concept of entelechy will change the perspective on vitalism.,
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You might dispense with entelechy or élan vital in favor of information (à la Shannon & Weaver), but wouldn't the resulting theory be a replacement of vitalism with an information-theoretic biology rather than an updated vitalism?
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Hello,
my name is Carolin Fischer, a sociology student from the Friedrich-Schiller-University Jena. I am currently writing my Bachelor's Thesis in the field of Cultural and Environmental Sociology. As this will be a qualitative study on environmental topics I am looking for interview partners, who work (or used to work) in the field of environmental and climate change research. The interviews will be held via video chat either in German or English.
If you're interested in being interviewed and in helping me with my thesis please feel free to contact me via Research Gate or mail: fischer.carolin@uni-jena.de
Thank you and kind regards,
Carolin
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Hi there Carolin,
sounds like a great topic for a BA thesis :-) I'm interested in your project - potentially also in participating as an interviewee. What precisely are you investigating in your research?
Feel free to contact me at Julius.Riese@web.de
With best wishes from Berlin,
Julius
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Can you please suggest what could be the possible reasons for the confirmation of only 4 out of 13 genes (by qPCR), not all 13? Have anyone observed the same ChIP-qPCR validation issues? Any PubMed suggestion would be great. Thank you for your help in advance.
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Hi Amit
getting results from one experiment and failing to reproduce in an other experiment can allow you the differences and biases from both techniques. maybe you could look at the specificities of all your primers and see what's different in the 9 remaining genes. for instance you can check for specificity by testing your primers in silico at the UCSC website (http://genome.ucsc.edu/cgi-bin/hgPcr).
all the best
fred
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For thinking - in regard to overtaking "believes, dogmas"
Blind adoption of believes, dogmas by people in populations (Psychology of the Crowd, by Gustave Le Bon) seems to be psychologically coupled and physically from a social scientific point of view explainable:
here, too, synchronization within masses occurs
- and it seems also in accordance to the Kuramoto model.
For this, only a corresponding marketing strategy, seems to be necessary (applied maths / physics).
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Basis:  Yoshiki Kuramoto assumed in 1975 that there is a weak relationship (better coupling) of oscillating systems (oscillators) and that these are almost identical. Kuramoto found that mathematically between each pair of coupled oscillators, their interaction is sinusoidally dependent on the respective phase difference, resulting into the so-called *Kuramoto Model* This even can be illustrated using initially non-synchronous metronomes, which in the course (under certain conditions: moveable surface) synchronize themselves.
This even seems a basic model in nature, biology, chemistry, physics and/or social sciences: – synchronizing of coupled systems:
– collective flasing of fireflies [Buck 1988]
– collective oscillation of pancreatic beta cells [Sherman 1991]
– the heartbeat synchronized with ventilation [Schäfer 1998]
– pedestrian induced oscillations on bridges [Strogatz 2005]
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References
-Kuramoto, Yoshiki (1975) Self-entrainment of a population of coupled non-linear oscillators. In: Araki H (eds.) International Symposium on Mathematical Problems in Theoretical Physics, Lecture Notes in Physics, Volume 39, Springer-Verlag Berlin, Heidelberg. DOI: 10.1007/BFb0013365.
-Buck J (1988) Synchronous rhythmic flashing of fireflies, IIi. Q Rev Biol (63)3), 265–289. DOI: 10.1086/415929.
-Sherman A, Rinzel J (1991) Model for synchronization of pancreatic betacells by gap junction coupling. Biophysical journal 59(3), 547–559. DOI: 10.1016/S0006-3495(91)82271-8.
-Schäfer C, Rosenblum MG, Kurths J, Abel HH (1998) Heartbeat synchronized with ventilation, Nature 392(6673), 239–240. DOI: 10.1038/32567.
-Strogatz SH, Abrams DM, McRobie A, Eckhardt B, Ott E (2005) Theoretical mechanics: Crowd synchrony on the millennium bridge, Nature 438(7064), 43–44. DOI: 10.1038/43843a.
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Credit 'spontaneous synchronization of metronomes' video
#psychology #synchronization #nature #physics #chemistry #biology
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Yes, Björn, these phenomena of spontaneous synchronization of motions include the so-called nano-resonance or Egorov resonance, which explains, for example, the nature of the well-known narrow and intense optical J-band, where, under certain (resonant) conditions, the electronic motion and the motion of the nuclear reorganization of the environment are synchronized. There are good reasons to believe that nano-resonance plays an important role in the life of living organisms.
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Yesterday I have read a news stating that The embryo fossil, nicknamed “Baby Yingliang,” was discovered in Ganzhou, Jiangxi Province in southern China, and is believed to be at least 66 million years old. Researcher Dr. Fion Waisum Ma told the AFP news agency that the discovery is “the best dinosaur embryo ever found in history” (globalnews, 2021).
Although there were several discoveries of Dinosaur components such as:
Eggs
DNAs from thier remains
are frequently being discovered, Since the biotechnology development is in its Zenith at 2022, Why nobody has attempted to create a dinosaur?
What type of scientific constraints would be encountered in such a laboratory experiment?
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The science fiction book Jurassic Park and the movies based on it are about recreating dinosaurs by extracting their DNA from the guts of dinosaur-biting insects trapped in amber.
DNA is not sufficiently stable to survive for the necessary 65 million years or longer since dinosaurs roamed the Earth, so dinosaur DNA is not available. What you would do with it, if you could get it, in order to recreate dinosaurs is another issue.
The oldest DNA ever recovered was recently reported from 1.2 million year old mammoth teeth in Siberia.
It has been seriously proposed to recreate mammoths, which went extinct several thousand years ago. Mammoth DNA is available from animals preserved in permafrost.
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I consider doing research relating biomechanics to the quality of food people eat, but the methodology to access what people eat seems a strong limitation. Questionnaires/surveys seem to be the way, but the accuracy of the information may be questionable, and the reported habits may not necessarily explain the current biology of the cohort. How do you all approach investigating the quality/quantity of food intake?
I'm curious to know your thoughts!
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Another way is to utilise Computer vision /ML approaches to extract the food content, and from that, a picture of the dietary habit can be built. As an example
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Dear colleagues, our lab is having a new project in synovial fluid processing. We need filtered from all the cells SF.
Does anyone have experience in filtering the SF sample through 0.22 um filters? If it is possible to isolate the cells and keep them (maybe in case of filtering via a vacuum system, not via just syringe and filter).
One more question: what is your typical protocol to get synovial fluid cells spun?
Best regards,
Mariia, PhD in Biology, Ukraine
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Please check the following references :-
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Hi Academics,
Kindly could you clarify the meaning of the term " Researcher"?
Best.
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In my opinion, a true researcher is someone who try to find solutions for the well-being and prosperity of humanity and not to serve individual / personal interest.
That's why a good researcher should be modest, generous and have perseverance since this capacites or should I say personality traits make (in my own vision) a huge difference to qualify a person as a reserahcer since intelligence / competence alone are not enough.
Best wishes,
Sabri
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Hi everyone,
I seed MCF-7 cells (15000 cell/well) into 96-well plates using DMEM with 10% FBS. They seem equally distributed after seeding. However, after 24h incubation they kind of clump into each other and does not show their usual morphology. They just look very weird, I don't know how to describe it so please see the attached photo.They grow perfectly fine in flask with same growth medium (second photo, 24h incubation after splitting).
I do this procedure for 3 years and never had a problem like this. It would be highly appreciated if you could comment what can cause this.
Thank you
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Based on my experience, I would suggest you these points, that you may consider-
First, MCF7, growing in clumps is not an issue, but a common phenomenon. It shall depend on the density of cells. Simultaneously, I thing 15000 cells for a 96 well plate is on a higher side. You should try 7000 cells and repeat the same experiment. Let the cells settle and adhere for the 1st day, then you may start your treatment or further experiment. I have used this concentration for most of my experiments, that are published. Alternatively, you may try standardising the cell count from 5k to 15k, and use the cell density of your choice.
Secondly, I am presuming that there is no contamination and all your media constituents, pH, Incubator temperature, CO2 level, etc all are ok. You may consider analysing what exactly have changed in supplies. If any thing remarkable, like Brand of 96-well plate, new Medium, etc., consider reverting it back to that you were using initially.
And Finally and most important point is that the cells might have undergone many passages and entered Senescence Phase. Its then time to replace and discard cells and use a new stored vial or procure new lot of cells.
Try these and let me know, if it helps!!
Regards
Dr. Satyam Kumar Agrawal
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I'm looking for journals in the field of biology/ecology or on the topic of plastic pollution that publish short article types: a short communication or a natural history note for example. I have a few of these spin-off stories from my main research, which are interesting enough to publish but don't come close to a full research article. All suggestions would be welcome!
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You can check if "Microbiology resource announcement" will be good
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Is it possible to use Artificial Intelligence (AI) in Biological and Medical Sciences to search databases for potential candidate drugs/genes to solve global problems without first performing animal studies?
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We hypothesize that future generations of Artificial Intelligence (AI) technologies specifically adapted for biological sciences will help enable the reintegration of biology.
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Taxonomy (a branch of biology), for example, is a basic science discipline that primarily deals with the identification, classification, and nomenclature of plants. It also contributes to biodiversity and conservation. However, it has been largely overlooked in recent times due to the fact that it has been unable to grow broader impacts or, maybe, due to other emerging applied fields. This question is being posed to discuss the broader impacts of basic sciences in general, and taxonomy in particular.
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Basic science are the backbone of all advance research and technology..it will give you a proper insight for the innovative technology.for example if take aquaculture unless and until you are not able to identify the species your future research will be vain.so all basic science should be studied and then future research and enterpinersh I can be developed.
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How are "levels" of thought or processing validly seen as hierarchical? This turns out to be a very basic and important question, BECAUSE most often behavior Researcher(s) decide what is at one "level" and what is involved with another "level" and a [supposed] relationship is seen that is thought to be hierarchical (one level using the previous ones (which is fine and good), <- BUT all these "levels" are also seen subjectively). This is a damned poor way of classifying, if [supposedly] for science purposes: it is quite arbitrary and subjective (and task dependent). WHAT'S THE ANSWER?
For those who understand Piaget, the better Answer for what are hierarchical "levels" is: there is a hierarchy developing/unfolding/emerging where qualitative (big differences) in processing occur AND .... This also clearly indicates the Subject 'sees' differently .... The only strictly empirical way to account for all this is that a new "level" involves seeing more or different things or significantly seeing certain things ANEW (in a different way); all those possibilities, in Ethogram Theory, are explained by perceptual shifts (at the beginnings or inceptions of a new level). AND: This also more than strongly indicates that at each new level MORE types of objects/actions are involved.
THUS, for there to be a true empirical hierarchy, SOMETHING (_OR_ type of thing) NOT PRESENT BEFORE IS ADDED (in an objectively verifiable way).
Those who "define" hierarchies without this requirement have lost touch with empirical grounding and have lost touch with science itself. (In Psychology science (like with other real sciences): The SUBJECT, specifically BEHAVIOR PATTERNS, define ALL !; the Researcher(s) merely using his/their own imaginative thought/"analysis" DEFINES NOTHING. Try to remember that the organism, in all aspects of its behaving (including behavior (behavior patterns themselves, per se)) IS ORGANISMIC; if this does not "show", then you are off track and almost certainly in a way that will NOT SELF-CORRECT (as good science does).)
All the above is very much related to questions of concepts being concrete or "abstract" (INTEGRAL to the issue , in fact); AND, not understanding true ontogeny (cognitive development in childhood) leaves "levels of abstraction" in confusion (a pseudo-mystery, seen generously as simply [supposedly] a mystery .)
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Dear Professor, please look at this related reference.
Thank you
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Hello!
I isolated some T-cells with some very interesting TCRs from primary cultures. I sent them to Genewiz to get chromium single cell TCR sequencing done, however the sample viability was super low. I sent them 8 more vials so that they could do a dead cell removal and then isolate the live population and perform single cell sequencing on the remaining cells. The sequencing results show that whatever is left over after DCR is most likely another contaminant cell type, not a TCR. I now only have one vial left, so whatever I choose to do next is very critical and essentially has to work the first try.
At this point I dont care about chain pairing, I can piece that back together afterwards by trial and error, I just want to get some data from these cells. I was wondering if anyone knows if I can thaw my cells directly into RNA later and then do either normal NGS or another single cell sequencing method to get any info on the TCR sequences? Should I just amplify the TCR regions on thawing with some kind of primer pool and then send that for NGS? In general, what's the most robust process for getting out TCR information from low viability samples?
Some other notes:
1. I didnt personally do the T cell isolation but my thinking is they were pretty much exhausted at the time of freezing which is why we have viability issues on thawing
2. They were frozen in 10% glycerol + 10% FBS in a Mr Frosty at -80C and then maintained in LN2 and shipped on dry ice.
3. Observed viability is ~30% on thawing however this could just be the contaminant cell population....
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Definitely a fair assessment, Ive made other samples that have similar properties as this, but none of the other samples Ive generated have responded with as much vigor as this sample.
Definitely will invest in generating another panel of T-cells but from what I can tell so far, this sample had a particularly rare phenotype that i may or may not see again in a relatively limited panel size. every once in a while I remember I have this last vial and wonder if I can do anything with it, in the end its always for the birds...
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I propose the following idea.
1. attach ions to a virus
2. localize it with ion trap
3. burn a hole in the middle thus destroying DNA
4. put in water
I would like to hear both physicists and biologists? Is this possible?
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Scientists exploring the physics of the virus which facilitate to study mode of infection and vaccine prepatation while both physics and chemistry will never tell us how to design an effective vaccination programm or solve the problem of the crossing pedestrain .Recently the science events to watch for in 2022 Nature Omicron,Moon missions and particle physics are among the theme set to .....make their vavvines more affordable for lower_income countries.mor detailed in the attached ref.
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I know that several genes come one after the other under a single promoter in an operon, but what is exactly between those genes? Does the start codon of the second ORF come right after the ORF of the first gene? If there is a specific example with the dna sequence, that would be great.
Also, does an operon always require an operator?
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ORFs of eukaryotes are typically different from those of prokaryotes. In eukaryotes, mostly, genes do not come as long ORFs; they are "mixed up" with introns. Thus, providing substantially large spaces for non-coding genes (which has been demonstrated to be as high as 62% in the human genome). In bacteria, there is relatively very low non-coding DNA in the genome (approx 11%) which therefore gives in a continuous ORFs. What may be located between ORF's of two different genes, or the intergenic regions may comprise of the list succinctly put by Dr Frank Burns. It is also however, important to remember that some overlaps do occur that complicates the assessment in a single shot.
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If I have an experience but no certificate in Machine Learning, and have both experience and certifcate in Medicine (Urology) ... and want to publish a peper that include an interaction between these 2 feilds, in either Urology or CS journals. Should i add a coauthor who is certified in Data science or CS? ... if not, Would it be necessary to prove my competency in ML by any means?
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Publishing on a particular area does not require one to necessarily have a certificate in that area. However, if you find yourself to be inadequately equipped with the requisite knowledge to do a good job in that specific field, you may overcome that by collaborating with someone with that knowledge so that together you can bring out a very good and scientific work.
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The Fig2A of the paper shows that a tiling library of a gene was prepared containing 50bp fragments. The fragments span over the entire gene sequence incrementing about 7bp from each other. Later this sample was used to study the sequence dependence on DNA bendability over genome scale. This is a very interesting study but I am unable to figure out how the tiling library was prepared. Is it done by preparing a sequences for primer pool for every fragment and ordering them? Can we prepare a tiling library with any amount of spacing between them? Please let me know if you have any idea.
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Red biotechnology: This area includes medical procedures such as utilizing organisms for the production of novel drugs or employing stem cells to replace/regenerate injured tissues and possibly regenerate whole organs. It could simply be called medical biotechnology.
nuha hamid taher
Senior lecturer
Faculty of Basic Education
Mustansiriya University
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In a patient with hereditary desminopathy (mutation Thr341Pro DES in the heterozygous state) over the past three years, an increase in the blood uric acid level up to 440-480 µmol / l was established by 1.5 times (the norm is 428.4 µmol / l). With the progression of the disease, the level has risen and is above normal. It is known that uric acid is an antioxidant. Is it necessary to reduce the level of uric acid? The patient has no problems with the joints.
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The change in the level of uric acid and biochemical parameters in a patient with an identified case of desminopathy is presented in the article https://www.researchgate.net/publication/357311034_CHANGE_IN_REDOX_STATUS_AND_BIOCHEMICAL_PARAMETERS_IN_PATIENT_WITH_DESMINOPATHY_T341P_SEVERAL_YEARS_AFTER_DISEASE_SYMPTOMS_ONSET
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In my personal experience I have find the higher rate of sprouting when fresh cow dung is applied on the top side of cutting what might be its reason.
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Metabolic rewiring and epigenetic remodeling, which are closely linked and reciprocally regulate each other, are among the well-known cancer hallmarks. Studies have reported use of Onco-metabolites to metabolically reprogram the epigenetic of cancer. I was wondering what might be major limitations of such techniques?
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Hello. This topic is not exactly my field, so I cannot give you a satisfactory answer. I will be happy to follow all the news and discussions in this field.
Regards, Zlata Felc.
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Hello.
I would like to check cell changes by culturing T cells isolated from PBMC in amino acid-rich or deficient medium. How long should I culture in rich and deficient mediums to check cell changes?
It is also a concern whether it should be cultured in rich/deficient medium from the beginning, or whether it should be cultured in normal medium at first and then moved to culture them.
I'm sorry that my English is not good! Please give me a lot of answers! :)
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Global warming affects many processes in biological ecosystems.
Different species of flora and fauna change their habitats and geographical areas according to climate change and specific geographical environments.
Areas of occurrence of specific species, for example insects in terrestrial areas and fish and arthropods in the seas and oceans, change.
For example bird habitats change, so migrations of some bird species may also be subject to modification. In the situation when forest areas dry out and turn into steppes and deserts, changes in natural habitats and areas of occurrence of species change and concern simultaneously many species of flora and fauna.
Do you agree with me on the above matter?
In the context of the above issues, I am asking you the following question:
What changes in natural ecosystems are caused by the ongoing global warming process?
Please reply
I invite you to the discussion
Thank you very much
Best wishes
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Dariusz Prokopowicz still learning from your questions...thanks
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I want to count these fragments for image analysis of autolysis. Please suggest good software, it is so critical in my work.
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Having a background in health science I am aware that the term "interphase" is a biological one which describes a stage of cell division. Specifically it is defined as the resting phase between successive mitotic divisions of a cell, or between the first and second divisions of meiosis.
This may be compared to a materials science definition for "interface" as the region formed when two phases (systems) are in contact through which the intensive properties of one phase transfer to the other.
When I would read "SEI" defined as solid electrolyte interphase in papers within my current field, I would always have a quiet giggle to myself and wonder how it gets past the editors, even in high impact publications. But I recently found myself forced to reassess my position, after digging around in foundational work on the SEI thing by Peled et al (1979). This paper has "interphase" in its title, and I believe there are peers who consider this to be the original work defining SEI. An excerpt from the paper:
It acts as an interphase between the metal and the solution and has the properties of solid electrolyte, through which electrons are not allowed to pass. Therefore, it is called "Solid Electrolyte Interphase (SEI)."
So the discussion is this, if these authors coined the term SEI, shouldn't it be acceptable for us as materials scientists to misappropriate "interphase" for our own purposes, and to hold our ground on it? On the other hand, what is science without clarity in our terminology? And how is "interphase" in a materials context saying anything more or less than the previously defined term "interface"?
The one thing I feel confident about is that we shouldn't be reading interchangeable definitions for the same thing, just depending on the source. Let alone seeing it arbitrarily interchanged within a single source - yes I have read individual papers where SEI is both "interphase" and "interface"...
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Hello. I received a compound with molecular weight 453.292 and the only mass information for it is 1 micromol. This is very confusing because usually chemicals have a mass in grams or milligrams. I do not know how to calculate from this. I need to make up either 10mM or 1mM of the compound. Please can someone show me your calculation for either obtaining a final concentration of 10mM or 1mM (please show calculations for both, as i havent decided which one to make yet), how much DMSO I will need to use. Thank you
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I agree with dr.John Machell,it’s far a away from my speciality.
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I am carrying out a research on science self efficacy and meta variables as correlates of biology achievement among secondary school students
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This thread is for those who want to know how to calculate Research Interest (RI) and participate in this validation study. *** Welcome to the validation study of my formula for Research Interest (RI) on the RG site! Details are in the first reply in this discussion.
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We know that the brain sends and directs meaningful messages to control the patient's cells.
as we know, The brain is affected by factors such as diseases And we know that the brain also controls other organs of the body.nevertheless,Damage to the CELLS is visible on eeg?
Is Cancer Effective In EEG?
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Stomach cancer is cancer that may affect any part of the stomach and extend to the esophagus or small intestine, and it causes the death of nearly one million people annually. It is more prevalent in Korea, Japan, England and South America. It is more prevalent among men than women. It is associated with eating too much salt, smoking, and also low intake of fruits and vegetables. Therefore, it is believed that its spread in countries such as Korea and Japan is due to the consumption of salted fish mainly by Koreans and Japanese, as well as the use of canned food and food preservatives. Mucosal colonization of H. pylori is believed to be the main risk factor in about 80% of stomach cancers
Stomach cancer is diagnosed through an endoscopic examination that allows a biopsy to be extracted from the affected tissue, and then analyzed to confirm the presence of a tumor. Dr. Riccardo Rosati, a specialist in gastroenterology at San Raffaele Hospital in Milan, says, "Before undergoing treatment, the patient needs to do a series of other ultrasound and other examinations to check the areas, glands and organs covered by the disease, in order to determine the degree of its progression.
As a researcher, I believe that stomach cancer cells do not send messages to the brain due to the lack of associated neurons
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I'm doing a research project where we are testing different methods of fluorescent live/dead stains and we need to kill some strawberry and potato roots so we can stain them. The only method we know will work well is boiling them in 70-80 degree water, have any other ideas?
thanks!
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Starting to boil in a waterbath or autoclaving are two options for heat treatment. This is the section of the operation that requires the most improvement. Only 15 minutes of autoclaving (without preceding KOH immersion) is required for greenhouse-grown plant roots that are ~4 weeks old. Adventitious roots that are 1 centimeter in size and ~3 months old must be soaked overnight and autoclaved for 60 minutes. Multiple soakings and more than one hour in the autoclave may be required for some tissues. The time it takes to boil something is usually longer than the time it takes to autoclave it.
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Context: Biology, Anticancer, Cell Signaling, Medicinal Chemistry, Apoptosis
Your answers are highly appreciated! Thank you!
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You can try to check Bioorganic Chemistry and Journal of Medicinal Chemistry. wishing you all the best