Questions tagged [literature]

Questions about scientific journal papers, books or other written sources, or for requests for references.

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52 views

Genetic evolution without crossover

Can someone please point me to the origin of the system of coupled differential equations (1) in Section 2 of Shahshahani's book$^\star$? $$ \dot{x}_i = x_i \sum_{j=1}^n m_{ij} \frac{x_j}{|x|} $$ ...
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How does the phosphorylation state of 4E-BPs affect translation of nuclear-encoded mitochondrial transcripts?

A 2020 review paper about mTOR (ref. 1) says: because biomass accumulation demands vast reserves of energetic currency, mTORC1 enhances translation of nuclear-encoded mitochondrial transcripts ...
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1answer
480 views

How to decipher references in natural history works of the late Renaissance and early Modernity?

Old botany books from the 17th, 18th and 19th centuries (and maybe also some later ones ?) enumerating lists of species use to give references to their own sources as abbreviations of one or few ...
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"Free space" volume in the nucleus

Take a mammalian cell, say a HeLa cell for concreteness. If a molecule (e.g. a transcription factor) enters the nucleus, what is the effective volume that it can explore/access there by free diffusion?...
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1answer
209 views

Why did Rivers replace Koch's postulates?

In 1937, Rivers introduced a new set of postulates that were meant to replace those formulated by Koch. However, I couldn't find an article (or other scientific literature) that describes why Koch's ...
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References for historical momentum in asexual species definitions

For sexually reproducing organisms, the scope of a species is somewhat fixed by reproductive compatibility. However, this all collapses for organisms that exclusively reproduce asexually. Here, my ...
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1answer
25 views

Exploring speed of ants

I'm working on developing a model of ant foraging. To do this, I have simulated food morsels distributed randomly within an area, with the minimum distance between morsels being variable. I'm trying ...
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18 views

Soil microbiology reference

I am after some good reference on Soil Microbe Ecology and Biology. I am a biophysicist, and have read the very gentle approach of "Life in the Soil" (James Nardi). Another book I have been ...
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1answer
101 views

What fraction of bacterial proteins are membrane bound?

Almen et al. showed that around 27% of the human coding proteins are membrane bound. How does this compare with bacteria such as E.coli or B.subtilis (or any other bacteria)? Is there a paper out ...
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1answer
87 views

Questions on mid-2019 Covid-19 Spread in Spain

I recently read in the news from Reuters that Covid-19 was already present in the Europe in March 2019 as reported by the study by Chavarria-Miró et al (2020). According to Chavarria-Miró et al they ...
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1answer
459 views

Is it possible to exclude article types in a PubMed search?

I have a question about searching PubMed. I want to search for original research papers while omitting reviews. Is this possible in PubMed? Example If I am interested in the relation between Acute ...
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Specific mechanism behind lethality of yellow coat color in mice

Our high school genetics chapter has some extra information about L.Cuenot. It only covered his research, and the fact that mice homozygous for yellow coat color would die before birth. It was an ...
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Symmetry in Biology

It seems a curious fact to me that all organisms I can think of exhibit some definite symmetry on a large scale (much larger than molecules), and in particular mirror symmetry. Since it is so wide ...
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What is the evolution metaphor about water flowing downhill?

As part of my biology undergrad degree, I took a course on the Origin of Species, where we read Darwin's book and also several other readings about the origins of evolution. I recall that during this ...
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How can I search through literature databases for words containing a * when the asterisk is read as syntax and not part of a query?

I'm exploring the literature on microRNA, where it is common for the less utilised strand of the miRNA duplex to be referred to as the miRNA* strand. However, I am experiencing some issue searching ...
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Exhalation in human breath, through mouth or nose: which is most usual?

Until now I believed that breath exhalation through the mouth is common for most human beings, and this fact is implicit in several technical contexts of which I can think (sports, music, medical ...
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What is the energy required for storing and performing computations in synthetic computational biological cells?

I want to know the energy costs of various computations performed through synthetic biological circuits in terms of ATP. I am primarily interested in storing of bits, addition, and multiplication ...
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1answer
145 views

Factors of infection rate

I refer to J.H. Jones' Notes on R0. Preliminaries The standard SIR model consists of a system of three differential equations $$ds/dt = -\beta s i$$ $$di/dt = \beta s i - \nu i$$ $$dr/dt = \nu i$...
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41 views

Floats of Algae, a house-made conjecture

Background In North of Scotland there are many seaweed types. One is a green algae (chlorophyta). They are full of 'bubbles'. According to web searches one of those bubbles (there are two types you ...
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Recommended books and articles on the origin and evolution of sexual reproduction? [closed]

I'm interested in learning about the origin and evolution of life on Earth. In particular, one topic that puzzles me a lot as a layman is the evolution of sexual reproduction, since the DNA mutations ...
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1answer
123 views

Self-study genetics

I'm new at the field of genomics. I'm a theoretical physicist by training and now we would like to translate some of the ideas to the DNA, possibly in real genomic instances. The concrete example ...
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2answers
194 views

Is the SHC014 chimeric coronavirus "eerily similar" to Covid-19 in anything but a journalistic sense?

Gulf News writes: In the virology community, their project is known as "chimeric coronavirus", eerily similar to COVID-19. This chimera is created in a petridish, reportedly with the "...
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46 views

Best fundamental literature about genetics [closed]

I'm seeking for good genetics literature. I'm not afraid of it's complexity, because I want to have relevant knowledges about molecular genetics. After Wikipedia articles and basic molecular-biology ...
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Are there any studies on the solar latitude limits of different plant species, beyond which they wouldn't thrive even with suitable weather?

Not sure whether this belongs here or in the Gardening & Landscaping StackExchange, but here goes... According to maps provided in the paper Present and future Köppen-Geiger climate ...
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1answer
86 views

How does species diversity vs Earth total biomass relate?

Are there any laws/theoretical foundations about how diversity of species relate with total biomass on Earth? While there is a lot of esoteric sort of talk "humanity dis-balances the live on the ...
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1answer
255 views

What percentage of individuals infected with COVID-19 don't have symptoms?

There are various statistics estimating mortality of COVID-19 infections, based on how many diagnosed people have died. These numbers are used by various media to extrapolate how many people will die ...
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1answer
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Ion-gated ion channels

Today I've heard for the first time of calcium-gated ion channels but find it hard to get an idea how they work, where they are located, and which role they play. I assume calcium-gated ion channels ...
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Is feeding wild pigeons really "weakening the entire species"?

While reading about what foods are healthy for pigeons, I came across the following paragraph: (Source) Human interaction and improper feeding of domestic and wild pigeons is believed to be one of ...
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1answer
88 views

Reference Request: Human visual system takes in $10^7$ bits/sec at the periphery and compresses it down to 50 bits/sec deep inside

In Sparse Components of Images and Optimal Atomic Decompositions by Donoho, 1998, the author claims that The human visual system is thought to do a tremendous job in achieving sparse ...
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20 views

quantification of glucose utilization in different metabolic processes

Glucose is commonly associated with ATP production. However, only a small fraction of glucose is utilized this way. The intermediates of glycolysis, TCA cycle, etc. are precursors to various ...
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1answer
89 views

Original Lotka–Volterra model

I am looking for the articles in which Lotka and Volterra published their original predator prey model. I couldn’t find the model presented in many textbooks in Lotka’s book Elements of Physical ...
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2answers
77 views

Nature versus nurture regarding aggression in specific dog breeds

A week ago I was bitten in my face by a dog that originally came from an asylum. That dog is half Rottweiler. Some people claim that the history of the dog is probably different from what the asylum ...
5
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1answer
108 views

A biological system to measure time

First of all I am a physicist, so I apologise for my non-existent understanding of basic biology. However, I have what I think is an interesting question and this seems like a good place to ask it... ...
5
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1answer
148 views

Human evolutionary innovation for rapidly restoring glycogen, and link to cardiovascular disease?

I'm a physicist, not a biologist, but I'm interested in human evolution and its link to the physiology of endurance sports. Circa August 2019, I read an article in the newspaper whose contents I'll ...
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1answer
134 views

Who invented dN/dS?

I am writing a paper, and I want to refer to the original paper that coined the term dN/dS (or Ka/Ks for that matter). I have found early works on dN and dS (like Miyata and Yasunaga 1980), but cannot ...
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1answer
60 views

Growth rate oscillation in the a population of non-interacting bacteria

I have come across this theoretical paper claiming that if you start a batch culture from a single E. coli cell, the exponential growth rate of the population defined as $$k = \frac1N \frac{dN}{dt}$$ ...
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28 views

Where to look up animal facts concisely

Googling leads to results such as this: DIET Eagles primarily eat fish, carrion, smaller birds and rodents. Eagles are also known to prey on large birds and large fish. POPULATION Bald ...
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23 views

Database of colors mapped to species

I was wondering about the physics of color, and now am interested in finding out if there are any resources (databases, text files, html tables, or pdf listings) of species and their associated colors ...
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2answers
78 views

Are there any non-pathogenic gram-positive bacteria in human gut?

I wish to know if there are any non-pathogenic (not even opportunistic pathogen) gram-positive bacteria in the human gut? Is there any reference that shows there exists a non-pathogenic gram-positive ...
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1answer
19 views

How to get taxonomic tree data

I am looking for taxonomy data of individual species and their classes something like the following format: ...
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0answers
22 views

Reference request: Lipid composition in bacterial, yeast and human membranes

I would like to know about the lipid composition of different kinds of cellular membranes. I remember going through such a table once in a paper, but I am unable to find it anymore. What I am looking ...
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0answers
10 views

Is autoimmune disease associated with self-reactive B cells?

I'm a bit of an amateur, so excuse what may be a very naive question, but I somewhat understand how B cells that are self-reactive (bind to endogenous epitopes) are selected out during development. I ...
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24 views

Clarification of method notation in yeast cultivation method

I'm reading a paper about yeast culture and in the methods, it says: Then $5$ ml of sterile $M/15\ KH_2PO_4$, was added to the slant, What is the meaning of $M/15$?
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1answer
72 views

Why do stem cells injected into muscle become muscle cells?

In this article published in Science Daily, researchers injected teratoma-derived stem cells into mice with muscular dystrophy, and the stem cells regenerated 80% of the lost muscle. But what is the ...
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1answer
191 views

Why is exclusive breastfeeding recommended for 6 months only?

The WHO recommends exclusive breastfeeding for the first 6 months of a child's life. Review of evidence has shown that, on a population basis, exclusive breastfeeding for 6 months is the optimal ...
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What is the status of the "Free Energy Principle" as a theory of living organisms?

The free energy principle states that biological organisms maintain their order by minimizing a function called variational free energy (VFE). While it is the case that the minimum to VFE also ...
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1answer
50 views

What does hypolithial mean

I'm writing a thesis in biology and my supervisor asked me to find literature about beetles living under rocks - specifically she wants me to find something about hypolithial diversity. However Google ...
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1answer
36 views

What is an accessible book about plant evolution for a non-biologist? [closed]

I have an acquaintance interested in learning about the evolution history of plants. This person has a wide knowledge on botanics, from personal reading and taking care of plants, but E is neither a ...
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1answer
66 views

Book on the history of Darwin's discoveries and development of his theory

This question is a book request. I am wondering if there are any books with these elements: Tells the history of Darwin's discoveries. Captures Darwin's changing views of the origins of species, ...
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1answer
27 views

What does $g_0$ mean for a centrifuge?

I'm about to make some Graphene Oxide and in the paper for Tour's Method it uses a centrifuge to isolate the solution. However it requires $319g_0$. What does this mean, and will a centrifuge with ...