Science topics: Biological Science
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Biological Science - Science topic

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Questions related to Biological Science
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I want to learn graphic design related to biological science. Please recommend me a course or software.
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It all depends on what you want the tools to do for you. If you are working with statistics and want to build charts, for example, Adobe Illustrator is a solid program. I have an ecologist friend who uses it in his research. Of course, there are other programs that will do the same, like Microsoft Excel. As far as online learning platforms, you can probably take a good quick class on Udemy or Skillshare.
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Component: Pure water, Bsm buffer, Bsm polymerase, primer, MgCl2, dNTP, DNA Salmonella
Heat 60 Celcius 1h and 80 Celcius inactivation 10min
Sometimes the results from gel electrophoresis appeared DNA bands but sometimes less band intensity. What happen? Not suitable primer or expired chemical?
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@Chayanit Thairat, Thanks for the protocol. I wanted to know if your are following a published protocol, then you may be able to compare your results with the reported observations. If you are optimizing your protocol, some parameters may have to be adjusted to get the desired gel profile
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When run a LAMP reaction, sometimes false positive appeared in agarose gel electrophoresis. What are factors to create contaminations to false positives? What contaminations do in LAMP?
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Are you sure that you did not have any smpling problem such as insufficient amount of primer or different sources of genome! If not, you might optimiza the amount of enzyme, temperature and Incubation time. Also, i highly reccommend you in order to observe better amplification in LAMP assay do not forget using betain and MgCl2, I used it, it works😊
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Do you have any experience or opinion about the accuracy of scientific information? The paper describes the accuracy of Wikipedia. I am experiencing resistance from wiki-bot/automatic response that prevents me from correcting the wrong knowledge. Thank you.
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I share the concerns of Ehtisham Lodhi that Wikipedia is insufficient and unreliable. I would have no hesitation to think if I needed reliable information (such as for quoting for a reference for my own paper), I would go to a search of peer reviewed literature or even (if the style is old fashioned or the Lecturer is) try a textbook.
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Dear scientific community,
What is your view on adopting the Blockchain and Non-Fungible Token (NFT) technologies in Biological Sciences? and how it can transform the genome storage or genome bank (governments of many countries are planning)?
Also, how this technique can be adapted to the local level or, say at the hospital level, to store any particular portion of human DNA in the worst-case scenarios like accidents or any disasters.
Also is it possible to donate blood can be stored in the hospitals and it can be connected through the NFT and once the owner wants to sell it can (Anyhow the blood business is unethical but if it can be tokenised people might move more towards donating it, also the hospitals are making money out of taking blood freely)
Also, you can suggest on your behalf, what are the latest area (with respect to biological sciences) where these techniques can be applied.
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The discussion is about how the NFT and blockchain can be applied to the said area.
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What software do you use automated meta-analysis? I am interested in AI-based software but other suggestions will be welcomed. Thank you.
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#MachineLearning Hello researchers, I was wondering that what are the most remarkable applications of machine learning algorithms in Biological sciences? My naive thoughts are: DeepMind by Google: Protein Structure predictions #Epitope predictions by DTU - Technical University of Denmark in Immunology Predicting tumor entities by DKFZ German Cancer Research Center for Central Nervous System. Please add to this list, looking forward for an interactive discussion. #structuralbiology #bioinformatics #research #immunology #cancerresearch
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https://www.nature.com/articles/s41592-021-01380-4 Deep Learning based approaches for protein structure prediction have sent shock waves through the structural biology community. We anticipate far-reaching and long-lasting impact.
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In the last three decades, the number of biological data has diversified and grown. This growing increase has resulted in the development of computer applications to ensure better handling of biological data. In the midst of this situation, for some, it is essential to develop programming skills and use professional software in undergraduate teaching in Biological Sciences careers. However, another group thinks that training in biostatistics specialists is the key to guaranteeing the proper use and handling of biological data. Faced with this problem, the following questions arise that I would like to invite you to debate:
1. Would success lie in including programming courses in the curricula of life sciences majors?
2. What will be the best programming language to teach, R or Python?
Should biological data management skills training be developed in graduate education?
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I confess I have struggled with this question myself.
I fully endorse comments by Jochen Wilhelm , but I'm not sure that the solution is to make undergraduate students learn programming in R or Python or Julia. Long ago, as a Masters student, my professor made the class calculate Regression, t-tests, and ANOVA with a simple calculator and pencil and paper. Most of us still came away with the illusion that "statistical significance" is the same as "important".
My point is that understanding abstract ideas such as data variability, relationships, differences, error in estimation, and causality are not the same as understanding formulae, or ability to apply a formula on paper or in a computer program.
The two tasks can be done together: there are many resources for "learning statistics with R", for example. But learning statistics and learning to program are still two different tasks.
Another question that could be asked is whether we should expect undergraduates to become researchers? To what extent should undergraduates be able to gather and analyse data themselves? Most graduates with biology and life-sciences degrees become field officers, lab-technicians, school teachers, etc..
If the majority are not expected to become researchers, then perhaps they need only to understand the purposes of (and flaws in) various statistical tests with sufficient competence to read and understand a scholarly paper.
Personally, I'm a big fan of R, but I also like using Orange Data Miner for ad-hoc analyses.
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I read this report that 3% (v/v) Ethanol increases recombinant protein expression in Escherichia coli. The SDS PAGE gels seem pretty convincing (1).
However, assuming I get great expression of recombinant protein with 3% (v/v) Ethanol, how am I supposed to decontaminate the biohazardous cell waste from the experiment?
Bleach decontamination isn't a good idea because bleach would react with the ethanol.
Autoclave decontamination isn't a good idea because ethanol is flammable.
Is safety just not a priority?
Source:
1) Chhetri G, Kalita P, Tripathi T. An efficient protocol to enhance recombinant protein expression using ethanol in Escherichia coli. MethodsX. 2015;2:385-391. Published 2015 Oct 8. doi:10.1016/j.mex.2015.09.005
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Hi Adron Ung . The reactions of bleach and ethanol I have seen contain at least 70% ethanol. I'm skeptical that 3% ethanol + bleach could cause significant production of dangerous chemicals.
But you can always keep the 3% ethanol + bleach waste in a fume hood overnight just to be on the safe side.
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bioRxiv is an open access preprint repository for biological science papers starting in November 2013 and hosted by the Cold Spring Harbor Laboratory. How important, useful and informative are these preprints, which are not peer-reviewed, but are screened and checked against plagiarism?
bioRxiv seems to fill an important need based upon the number of submitted papers. Do you submit preprints to this server? Do you think it help or harms research communications?
If so, how much are your bioRXiv papers read and cited verses the typical journals you would send to for a given paper? How much do you read and cite bioRXiv papers compared to other journals?
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One of my friends was accused of plagiarism; do you know why?
After about three months, his research paper was rejected because of plagiarism. When he checked the journal report, he found that his paper was accused of plagiarism and with a 61% percentage. The reason is that his manuscript was previously uploaded as a preprint. It took him another two months to solve the problem and removing the manuscript from the database of the preprint.
So, in order to solve such this type of issues, it may take several months of following up to remove the manuscript from the database of the preprint. Anyhow, If there were accusations of plagiarism, it is not well for any researcher's reputation, in any meaning.
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I'm sorry if we are supposed to ask only about specific research topics, but lately, I've been wanting to learn a new language that could also help me on my research field.
I'm not sure which one should I pick because I'm interested in Reproductive Toxicology (hopefully I can apply that knowledge on wildlife and conservation), but I haven't been able to find any trustworthy link that could guide me to the job and research offer on this fields worldwide.
Even though there are some sites that talk about it, they are either old publications or emphasize more on the "diplomatic and corporate" side of language learning.
If someone could please guide me at least a little bit to have a better understanding on the Biological Sciences opportunities attached to different languages, I would really appreciate it.
Thanks in advance!
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From vaccines to medical devices that provide a better quality of life, the United States has long been a global leader in medical research. Yet new investments by other countries, particularly China, threaten that standing.
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Hello everyone. Can someone please tell me, is there any database of research projects from where I may get details of various ongoing or completed projects?
Thank you very much!
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There has been many occasions where people do not expect to be answered in terms of engineering, especially in biological sciences. However, it is more common to find the answer in terms of an engineering only in biological sciences. We have reached a point where it is impossible to separate, the engineering from the biological discipline.
The most common one is genetic engineering. How many more engineerings are there and can anyone explain the differences and what they are?
I would like to add the engineerings I can think of, but I am afraid I am not an expert on these areas, as I still need to give a definition to all of them. I will appreciate if anyone could complete the definitions, and make a list of them.
Is there anything else on these engineerings?
Any contribution is welcome.
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For Much Detail......it may helpful for you
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Please can anyone suggest fast publishing Scopus indexed journals, which can publish research articles in biological science?
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You can also check some MDPI journals apart from Biology, generally they are fast
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Biodiversity is diverse in virtually unlimited degree, which results from the essence of processes of evolution of species, filet lines and entire ecosystems. It is thanks to the millions of years of evolutionary processes on Earth that there are so many different natural and highly diverse ecosystems in which different species of flora, fauna, fungi and microorganisms adapt to life in different and very diverse geographical and climatic environments.
The largest biodiversity of ecosystems and species functions in natural environmental environments in which ecosystems have evolved without human impact through millions of years of climatic and geographical conditions enabling the development of various life forms. These types of high biodiversity sites can be found in unpolluted rainforest ecosystems in tropical forests, in temperate climates and in coral reefs.
Unfortunately, human civilization activity contributes to the successive and accelerating process of biodiversity reduction by dying out species of living organisms. The areas of natural natural ecosystems are decreasing, including those in which the greatest biodiversity is diagnosed, such as the rainforests of the Amazon. The protection of naturalistic ecosystems and thus the protection of the planet's biodiversity is the most important challenge for mankind in the 21st century.
Do you agree with my opinion on this matter?
In view of the above, I am asking you the following question:
What do you think is the importance of biodiversity in natural ecosystems?
Please reply
I invite you to the discussion
Thank you very much
Best wishes
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I agree Danung Nur Adli
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Today we can speak of the existence of a global crisis of specialists taxonomy. However, a little-addressed topic is undergraduate training in this important branch of the biological sciences. How is taxonomy research motivated in Biological Sciences majors? Is the teaching of taxonomy adequately and intentionally approached? Final Degree Projects are done today on topics related to taxonomy?
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Hello Abdiel;
1. Earning tenure requires publishing in high impact journals. Taxonomic papers aren't often published in those journals.
2. Requirements for undergraduate degrees no longer emphasize Organismic biology and so our students aren't often exposed to the subject.
3. Job opportunities in fields where taxonomy is essential aren't well publicized...at least not in the USA.
4. Natural history collections in colleges and universities are badly undervalued and so the raw material of taxonomy is inaccessible.
It's a bleak picture. Best regards, Jim Des Lauriers
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I am not sure if any one study on this topic. It has been observed in certain cases that success-full researchers have poor academic record. These are exceptions, I am interested to know any study on this topic. Please also cite examples that shows negative or positive examples. Ideally there should be high positive correlation, if it is not than why?
I mean if person got good grade/marks or rank at school/university level will be a grate scientist. For example if topper of JEE (top exam in India for getting admission in engineering college) join research, he/she will be best scientist in the world.
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From my long experience of teaching, the researchers who have rich researching CV usually have poor teaching records and vice versa. That is especially true for the universities that haven't a sufficient researching budget. The reason behind that is that researching needs more time at the expense of teaching.
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I read in many articles a statement that best proximity point theory has applications in the field of Economics, game theory, biological science. But I want to see some physical problem that was mathematically modeled and then solved by using best proximity point theory or fixed point theory.
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Please se my recent paper, "Approximation of fixed points and best proximity points of relatively nonexpansive mappings".
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Artificial intelligence application in biotechnology and nanotechnology may solve many problems in biological science.
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(Sep 29, 2020): Artificial intelligence (AI) is having an impact in biotechnology and nanotechnology in the USA. Several big pharmaceutical companies have partnered with AI startups and other large corporations that work in AI (the likes of Google, Microsoft, etc.).
Use of software with AI algorithms in the healthcare marked is a multi-billion dollar business as we speak (in the USA). In short, there is scientific and commercial potential.
Can AI solve many problems in biotechnology or nanotechnology? In my opinion, the answer is nuanced. I can clearly see the value of AI in areas such as diagnostics where diagnostic algorithms can outperform health workers in detecting diseases from medical images. However, this does not require much thinking (it requires better detection!).
The use of AI in other areas is where real brain power is more important is a “gray” area. For example, as far as I know, no AI-designed drugs have ever been considered for approval in the USA.
There are several reasons why this has not happened. For example, level of trust (AI models are as good as the datasets in which they rely), validation of predictions and clinical trials are expensive, complicated legal issues (not clear who owns who owns the copyright based on the current laws, a human creator or a human who pushes a button and let AI do the job?), etc.
Nevertheless, those that are convinced on the bright future of AI applications will tell you that very soon AI-based approaches will lead to “wonder” drugs which are not conceivable to a human medical expert on the basis of the same (large amount) of information.
In a nutshell, time will be the better judge.
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I would like to draw a figure for nucleic acids strands in pipe-like appearance with some curvatures and colors. I want the figure to be attractive, not just a collection of dull thick lines.
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Do you want a detailed molecular model or a schematic representation? In the latter case, make sure that you draw a right-handed helix, even Science and Nature embarrassingly had left-handed ones on their covers!
There are several programs that can draw molecular models from crystal structures (pdb-files), Pymol has been mentioned, but also DeepView, Rasmol, Chimera and jMol, amongst others. Personally, I use DeepView, but mostly because I have been using it for many years and know exactly how I get the results I want.
For more schematic representations, you can use vector drawing programs like DrawPlus, Illustrator or xFig (the latter one is free). You could also use CAD-applications like AutoCAD or TurboCAD, they can render things in 3D. This could also be done with Blender or POVray. It really depends on what result you want, what software you are comfortable with and what you are prepared to pay for it (an AutoCAD installation goes into thousands of $).
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I found this research article where they did tested the antimicrobial activity of some plant oils using Agar Well Diffusion ( Esmael, A., Hassan, M. G., Amer, M. M., Abdelrahman, S., Hamed, A. M., Abd-raboh Hagar A., & Foda, M. F. (2019). Antimicrobial activity of certain natural-based plant oils against the antibiotic-resistant Acne bacteria. Saudi Journal of Biological Sciences. doi:10.1016/j.sjbs.2019.11.006).
I presume they use parafilm to seal the Petri dish; but how would you prevent the oils from evaporating from the well and settling onto the agar surface?
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The plates should sealed by parafilm with sterile laboratory conditions to avoid evaporation of the agar plates.
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Seeking answers from the experts.
If you had a choice of equipment for your lab, what items do you think would be essential for advanced biological science research? We have a pretty well stocked lab, but I add one piece of equipment every year. We would be looking for something that would last for a minimum of 10 years, be scalable and versatile but still fit in a relatively small lab. Getting access to core facilities is very difficult so we have to plan...
Also, can anyone recommend a couple of good options for a
1. bench top flow cytometer
2. bench top sequencer (is it worth getting a next get sequencer)
3. Any thing else?
Thank you!
Leya
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I would recommend a small lab device called Pipette Genie. It was really helpful when dealing with a lot of samples on 384 well microplate. Here is their website, if it helps.
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Entomology is studying insects and their relationship to humans, the environment, and other living organisms.
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Entomology as a biological science is important for the following reasons: a) study of pollinating insects, b) some insect are vectors of human diseases and plant diseases or they destroy crops, c) the study of parasitoïds enables an effective biological control of insect pests. The study of insects enable scientists to find ecological solutions to control the populations of specific insects.
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Hello,
I'm looking for areas in which high impact journals published results that were the opposite results to other publications by high impact journals.
Thank you in advance
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This is a good approach to finding important research to do. I wish you luck, which I am sure will come your way.
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What are the application of thermodynamics (Physical Chemistry) in Biotechnology ?
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Hello Binoy;
Here are a couple of examples from the perspective of an ecologist
1. The function of brown fat in thermoregulation in mammals.
2. The shape of food pyramids. The biomass of producers exceeds that of primary consumers exceeds that of secondary consumers, etc.
These examples should indicate the path to any number of others.
Best regards, Jim Des Lauriers
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Would appreciate any feedback on the following scenario - especially how to think about it in biological and science related to consciousness studies:
I am an addiction psychiatrist and I have ample time to explore the subjective aspects of addiction - specifically how it starts and is maintained. Many people tell me that the addictive compound they are using no longer has the desired effect, does not treat the target symptom, and may in fact make them slightly ill but they keep taking it any way.
Example: Patient A is taking very high doses of benzodiazepines for anxiety. He does not notice any anti-anxiety effect but wants to continue taking them anyway. He is seen to taper and discontinue the benzodiazepines and a standard approach is to take gabapentin for this process. He notices a marked antianxiety effect from the gabapentin but not the benzodiazepines. It is not a tolerance effect because he never got any relief from the benzodiazepines and described that to me as "always having a high tolerance".
I have seen the identical phenomenon with opioids and stimulants.
Any ideas about how to conceptualize this in terms of neurobiological substrates?
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What George if there is only one? Addiction? I still see occasionally clients who have experience of such drugs and their effects, and the diminishment of anxiety, for example, comes only at the very beginning but in a somatic fashion. All the effects seem the same.
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We have reared this insect from the leaf galls of Alstonia scholaris. The rearing of insects has been done in the Biological Sciences Laboratory, Department of Biological Sciences, Mahatma Gandhi Chitrakoot Gramodaya Vishwavidyalaya, Chitrakoot., District Satna (MP)India.The image of eggs and adults are attached
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Thank you for the answer given by Dr. Luis Miguel Constantino . I did not aware that Pseudophacopteron tubereculatum (Crawford, 1912), bacame synonym of Pauropsylla tuberculata.
I have recently collected this Gall from Tamilnadu, India. I think this is very common type of gall in Alstonia scholaris
(L.) R. Br..
Thank you Once again.
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What kind of scientific research ( hypothesis ) can I do and complete it in the absence of availability or absence possibilities to do this research. Knowing the research I want to do is related to biological sciences in the specialty (immunology)and medical science. Is it possible to do this and what are the ways or methods to do such researches ?
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agree with@ Ajit kumar Roy
regards
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Current technologies restrict the speed biological research can be conducted. The majority of research requires invasive procedures (time consuming and prone to health risk). The adoption rate of technologies is impeded by the requirement of wearing technology or undergo surgery. Implants or the wearing of devices reduces convenience, is physically limiting, and is viewed as being visually unattractive.
I believe that with the removal of these limitations, the speed of which research is conducted will 'explode' - people will be able to perform their daily functions, with full range of motion, without having to wear any devices or be hooked up to equipment.
DARPA has recognized this, and is pushing magnetic field sensing to a new era with through the “Atomic Magnetometer for Biological Imaging In Earth’s Native Terrain (AMBIIENT) program”. They want to be able to read the magnetic field generated by the body without needing the subject to be shielded from the Earth’s magnetic field.
I am expecting the Darpa initiative to be successful. I am looking to discuss how it might be possible to remotely read biological signals, leveraging our environment.
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I have a couple of idea’s as to how you might induce / extract signals from the human body, leveraging that bio-matter is non-linear and that everyone’s brain signatures and heart beats are unique:
  • use a high-gain or specifically tuned antenna to directly read signals generated by the body
    • broadcast two or more RF signals at the body – this will cause new signals to be generated in the body.  Each new signal will be the difference between each of the signals being broadcast.  Example: if you broadcast one signal at 2,000 Hz and another at 2,100 Hz then a 100 Hz signal will be introduced into the body
    • we currently use magnets to induce signals in the brain – perhaps this could be an alternative?
  • broadcast multiple RF signals on an individual and extract biological signals by receiving those same signals and their harmonics - then compare the differences across them
    • record all of the signals being generated by the body using multiple points of reference - then use mathematics to reconstruct the ‘core signals’ based on the differences between the signals across each point of reference (note that technology like this already exists, but it is not being used on the body)
  • reading bio-photons, or the energy generated during their generation or when they are transmitted
  • electromagnetic coupling with the human body
  • applying the principle that two resonant objects of the same resonant frequency tend to exchange energy efficiently, while interacting weakly with extraneous off-resonant objects - note that in this method, a side band signal would be present, enabling the ability to introduce a secondary signal into the organ
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Hi,
If you could name the most important publications relating to any of the biological sciences over the last 100 years what would those be? Beginning with Francis & Crick's paper on DNA...
Thanks
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Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid J. D. WATSON & F. H. C. CRICK Nature volume 171, pages 737–738 (25 April 1953) | that is most likely the most important paper in the era of biology after Darvin's books.
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For many fellowships, postdocs may be given smaller ($10-30,000/year) amounts of independent research funds.
Do you have any tips for how best this money can be spent? What is the most bang-for-your-buck for a young independent researcher? Are there things that can be purchased that might benefit the researcher beyond their postdoc experience?
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Ajit:
Supposing I am doing an ethnographic case study of a group whose language I know. I wish to observe discreetly and perhaps engage in participatory observation, discreet individual interviews with open-ended questions and review of relevant documentations, historical and otherwise. Here is an adequate triangulation. In this case where do the following (your suggestions) fit in?:
1. Recruitment of manpower (not needed)
2. "Procurement for experimental set up" (not sure what this means, but there is no experiment here)
3. Surveys for data collection (this was not part of the triangulation of the case study and administering surveys for an ethnography can provide unnecessary exposure and too much social desirability bias in close-ended questions, especially if the study is culturally sensitive or reflects on personally sensitive aspects of the respondent)
My point is that monetary allocation is contextual to the study and its research design. There cannot be any predetermined listing for all studies as you have provided.
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I want to know about the burning research topic at present in the field of Biological Science
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Although the book has been published 32 years ago, I think you could find useful tips in ‘The problems of biology’' (Oxford University Press, 1986), a classical reference written by the late John Maynard Smith.
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No doubt 'Charles Darwin's Evolution Theory' had tremendous impact on modern biological sciences. To become more science-based rather than religious belief, is it really important to think and rely on evolution theory?
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Felipe's comment is quite good in several respects I think, but it overlooks what I consider to be the fundamental point about the nature of evolution (and one to my mind is generally overlooked by everybody) - that is evolution as a science is a methodology. Science is not belief, even if we produce theories or principles in which we believe. But these views, perspectives, beliefs etc are generated by METHOD (have to emphasize that). Even creationists fail to realize that the science of evolution is about method. Without method there is no discovery. Of course the concept of evolution as methodology does not fit in well with the ideological form of evolution as a 'fact' or some other belief system as usually taught in schools (at least in the US). In many ways creationists and evolutionists participate in a mutually reinforcing notion of competing doctrines. So ironic.
Also, when it comes to method, one of the principal methods that just about everyone overlooks is biogeography. Biogeography was the key that opened up the world of evolution for Darwin. Just see the first words of his Origin of Species. The distribution of animals and plants is the empirical result of evolution just as much as their biological form.
John Grehan
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Hello!!
Is there any free statistical software (besides R), user friendly and used in natural/biological sciences?
Thank you.
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This is a tough one. Without understanding what you really need from the field - the amount of statistical methods in biological sciences is not as narrow as you think - it's not easy to recommend something. I doubt any other statistical programming language comes close to the amount of methods that R has (Python and Julia are close/may be better, though).
Guessing from your request for a user-friendly alternative to R, I would assume that you probably have tried R, and realised that it is a tough interface to learn, or get used to. That is fine - these things take time. (Apologies in advance if I made the wrong assumption.)
I think you can still have the best of both worlds. There is a statistical program that I stumbled upon more than a year ago - jamovi (https://www.jamovi.org/). I never got to use it, but bookmarked it. I believe it was (and still is, probably) targeted to people who want to use R, but can't get over the console-type interface. There is no doubt that it is focused on being user-friendly. It looks nothing like R, but works like R! (Think of it as a "wrapper" around R that hides the coding and replaces that with buttons and input fields.)
Jamovi not as fully featured (for sure), but it can do the following out of the box (taken from the website):
  • Descriptive statistics
  • T-Tests
  • ANOVA
  • Repeated Measures ANOVA
  • ANCOVA
  • MANOVA
  • Non-parametric ANOVA's
  • Correlation
  • Linear regression
  • Binomial logistic regression
  • Multinomial logistic regression
  • Binomial test
  • Goodness of fit
  • Contingency tables
  • Log-linear regression
  • Reliability analysis
  • Principal component analysis (PCA)
  • Exploratory factor analysis (EFA)
  • Confirmatory factor analysis (CFA)
The great thing with jamovi is that it is free, open, and looks like it is frequently updated. This is important! You do not want to use a free program, spend time to master it and find out that it is abandoned. It is also based on R.
A cool feature that is has is that you can point-and-click your way to analyse the data, and when you have the results, you can switch to "syntax mode" and reveal all the R code used to analyse your data. A self-learning user interface, if you will. Also, a great "insurance" to master a programming language that will most likely persist for decades... should jamovi itself lose support in the future.
Sorry for the long post.
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Bioinformatics question
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In my opinion, in silico work helps a great deal in planning and designing experiments. The predictions of unbiased and stringent in silico studies can be true in most cases. However, proper validation of the predictions through experiments is essential to authenticate the findings. All in all, in silico tools can give direction for your studies and save a lot of your time that you would be otherwise spending if you were to work on it through lab experiments.
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There are many definitions of model-based sciences, which have a different philosophical meaning. This is due to the fact that the signification of the term ‘model’ is ambiguous: some of these theories may be based only on one kind of models and are unable to integrate in their field the other ones. I will give here two examples of model-based theories, but you can find many other ones.
The semantic theory of models, more recently called a ‘model-based’ view of science attacked the empirical explanatory models, which dominated the philosophy of science before the 1960’s, and promoted formal explanatory models during the following decade. Even if various versions of this approach differ (Patrick Suppes, Frederick Suppe, Bas van Fraassen, etc.), it continues to be developed nowadays. In this approach models, as abstract representations of some portion of the world which are different from empirical laws, are the central element of scientific knowledge. For 21st century researcher, computer modelling will permit the statement, manipulation, and evaluation of more and more complex theoretical models, as Thomas Burch (2017) said. But how in this case identify the relations between the theoretical model and the empirical observations, and test the fit of a simulation model? There is a real danger to construct theoretical models without any relationship with observed data and no way to verify this relationship.
The mechanistic view, which had been mainly developed for biological sciences during the 1990’s, is also considered as a model-based science. Again various versions of this approach differ (William Bechtel, Carl Carver, Stuart Glennan, etc.), but its development nowadays is increasing not only for biological sciences but for social sciences. A more recent version of this view is given by Robert Franck (2002) as the functional-mechanistic approach. As the semantic view the mechanistic theory of models rejects the empirical explanatory approach, and may appear as similar. But, while for the semantic approach a theory is a formal system empty of any empirical content, the mechanistic one infers, from the sustained observation of some property of nature, its functional structure –in classical terms the axiom, form, principle or law- which rules the process generating this property, and without which this property could not come about as it does. By focusing on the mechanism, generating a social property, the functional structure is treated independently of the causal structure, and may be generalized. We used this approach, with other researchers, in a recent paper on model-based demography (2017).
Under this question, I would like to discuss here the different model-based theories, their main aims, and the use of the term model.
References
Burch T. (2017). Model-based demography. Springer.
Courgeau D., Bijak J., Franck T., Silverman E. (2017). Model-based demography: towards a research agenda. In Agent-based modelling in Population Studies, Grow A., van Bavel J. eds., Springer.
Franck R. ed. (2001). The explanatory power of models. Kluwer Academic Publishers.
Mäki U. (2001). Models: philosophical aspects. In International Encyclopedia of the Social & Behavioral Sciences, Smelser N.J., Baltes P.B. eds., Elsevier Ltd.
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I think that model-based theories are ideas which substitute realities. This could have interest in theoretical exploratory research but less interest for real and objetive research.
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Hello everyone, 
with my immense pleasure, the college where I teach asked me to deliver a course of statistics for animal science/marine science/bioscience students (2nd and 3rd year of Bachelor's degree).
Can you suggest a good book I can use for the course, ideally tailored for animal/biological sciences?
Many thanks,
Andrea
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Hi Andrea,
you can find books of statistical methods by N G Das 
Regards
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I have read a lot of papers from neuroscience ... psychology ... Biological sciences... they talk about the roles of astrocytes in synaptic plasticity? Is there any evidence to consider astrocytes as the main player of plasticity not the neurons?..is it possible that the plasticity definition based on changing of astrocytic strength by synapses, as well as altering synaptic strength by asrtrocytes? 
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Dear Bassam:
"Neural" includes neurons and glia.
The concept of "plasticity" as the strengthening of synapses apply only to neurons, because the astroglial network does not have synapses (astrocytes communicate by means of gap junctions). 
Neuron-astrocyte interactions is a new, integrative field in neuroscience. There are some models attempting to interpret this interacting system. Vera Maura has done a good job of understanding these complex interactions using the retina as a model of the whole brain.
I have built a model in which neurons execute cognitive operations (processing sensory signals, selective attention, memory, motor control), while the astroglial network instantiates feelings (all kinds of feelings - from basic sensations as hunger and thirst to perceptual 'qualia' as the feel of color, sound, taste, smell, also emotional feelings as joy and sadness and social feelings as love and hate).
In this model, neurons induce hydro-ionic waves in brain tissue, having the astroglial network as the master hub that propagates the small waves to the whole system and allow their interferences. For instance, when we are facing dangerous situations the amygdala triggers a wave of fear in brain/body tissue. The feeling of fear is not inside the amygdala, but in the living tissue, having astrocytes as the master hub that broadcasts it to the whole brain and body.
Constructive interferences in the astroglial network produce global waves that instantiate feelings; these waves feed back on the neurons and modulate their activity. The feedback of astrocytes on neurons is part of the neural plasticity phenomenon. According to the model, the wave of feeling reinforce the neuronal patterns that feel good, and depress the patterns that feel bad. There are several well known mechanisms that execute this modulation, for the details please read the paper below.
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Just wondering if anyone has used this extractor and what you think of it? Any tip's or tricks or pitfalls related to it that I should be aware of? 
Do the extraction kits give a good quality yield in your opinion?
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Unfortunately we are not using blood, but stored respiratory samples. We have followed the kit instructions but my main issue is with the internal amplification control for our pcr.
We're having to add a hell of a lot more than our pcr protocol calls for just to get a Cp/Ct of 38.
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I'm taking a survey to identify potential uses of cloud computing in the biological and biomedical sciences. How would or do you use it? For what tasks/methods/questions? What would you like to be able to use cloud computing for?
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of course ...the most secure way is using Software defined cloud networking.
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In cytotoxicity experiment like MTT assay etc. for toxicity reason amount of DMF or DMSO used should be within 0.1 % range. Is there any proper reference that is showing this permissible amount of DMF?
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I think its best to establish safe concentration for the cell lines/cell type you are using instead of using someone else's work. 
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In recent years we have witnessed some breakthroughs in biology with significant progress being made, similar to the progress of physics made in the 19th century. Furthermore, it seems that with the help of new technology, biology can continue its progress towards further glory. What are your views on this? And do you think biology is better equipped to reach an adequate intellectual intensity as physics once was and still is?
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One important part of the evolution of the Chemistry has been part of Physics during the last XX century, and I think its future is going to be more and more joined. The same is going to happen with Biology: its future is in discovering physical laws which can explain its order and this will happen when the Chemistry and Physics can evolve in such direction. For instance, the DNA will be understood when we can explain the physical information kept within it and how can be taken for the rest of the body which nothing more than molecules or atoms.
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Models are abstracts of reality. They also represent prototypes. The need to include modelling and simulation in the Computer Science and Biological Science curriculum of some Universities in different continents, especially in some developing countries, has been an object of debate. They keep asking about the significance of modelling to Computer Science and Biological Sciences.
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Science always proceeds by models . The model is required to test ideas and theories . The more accurate it is , the more it allows you to have correct answers by means of model perturbation. The representation of the model may be different from discipline to discipline, but in the basic sciences (physics, biology, chemistry, etc..) It is essentially mathematical. The mathematical model has the advantage of summarizing, in a precise and concise symbolic language a theory. Obviously, improving the theory, we improve the model. In recent decades, due to the great development of information technology, we can view models through many different graphic visualizations, but there is always the underlying mathematical model. The computational biology (not bioinformatics, which classically is concerned with the storage of data and their analysis) relies heavily on 3D representations of biological models, allowing even their perturbation (and thus obtaining biological predictions), but there is always behind the mathematical model .That's why it is important to include them in the curricula of universities.
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What are the important things other than qualifications, experience and research funding to apply for the academic level position in university. How to prepare for the interview. Suggestions welcome
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Be careful interpreting any answers and advice that you get. There are likely to be great differences depending upon the academic culture of your country and also on the nature of the academic position, such as wether it is teaching, research, both, tenure track or not, etc.