texts: Does the human body metabolize what it smells, even in trace amounts?

texts:
I conjectured to a friend that some small amount of anything we smell is likely metabolized by the body. He disagreed. My thinking is that, if you are smelling something, some portion of molecules are being sensed by the olfactory tissue and some portion is taken into the lungs. Of the portion taken into the lungs, some portion is exhaled and some portion remains. I didn't propose a mechanism for the part that "remains" at the time, but it seems reasonable that some of it gets caught in mucus, some of which is then swallowed.

Obviously, a very, very small portion of whatever we're smelling would go through this process if my conjecture is even correct. For context, we were discussing people who have elected to restrict their diets for ethical or similar reasons. I was comparing what I proposed to when food products are labeled with "may contain trace amounts" due to "shared equipment".

So I guess my questions are these: was I right in my guess, and if so, was the mechanism correct or not?


texts: Is there any survival benefit in humans that can be obtained from chronic exposure to low dose radiation, or is any dose of radiation a potential harm?  Has any research been done into this?


texts: Do two hormones have the same effect on a cell if the second messenger is the same?

texts:
There are so many hormones/cytokines/neurotransmitters and receptors, all of which act through about 4-5 second-messenger systems. So if one particular cell has receptors for say, two different hormones which act via the same second messenger, is there any way that the cell can distinguish the two stimuli? I’m guessing there must be some distinguish between the two, otherwise, wouldn’t the effect of both the hormones be the same?

For example, in a hepatocyte, beta-adrenergic receptors and glucagon receptors both act via Gs-coupled receptors, downstream of which, cAMP is increased. Since the cAMP is the same, the changes it would make are also the same. So does it to the hepatocyte, make no difference if the first messenger was epinephrine or glucagon?

I’m assuming the receptors would make a difference, but aren’t the coupled G-proteins (Gs) also the same? Is there a difference of amplitude?

Note: I understand that it is not necessary for the hormones to produce an exclusively different effect. I also understand that systemic effects can be different because of differential distribution of receptors. My question pertains to the effects on a single cell.


texts: The Na+/K+ ATPase pump exports 3 Na+ for every 2 Ka+ imported. This process is ATP dependent, but I have not been able to find how many ATPs are required in each translocation. What is the stoichiometric ATP cost of this reaction?


texts: What is the name of the plant with the down-falling light purple leaves?

texts:
I've seen this flower in Scotland in August 2015:

What is the name of that flower?

To help people google it:

The plant has light purple leaves with some white spots. On those white spots are dark purple points. It is sometimes quite high (about 1.70m I guess). The bloom points downwards.


texts: When looking at skulls from early hominids, how do we know their language creation abilities?

texts: If there are no vocal chords left, how do scientists deduce what sounds the specimen was able to create?


texts:
Edit: just to clarify, I am asking what, if anything, the literature says can be gleaned about evolution by studying cancer, especially relating to how multicellularity evolved and the traits used to force cells under control of the organism.

Most of the original question details I had added were just my own thoughts on the topic.

Original question

Is there a sense in which cancer can be considered as a return to the unicellular "origin" of a cell?

It has always seemed to me like cancer is almost inevitable by the structure of the cell (its poor "design", essentially). The only thing standing in the way are the cellular controls: senescence/apoptosis (e.g. p53 pathway), immunosuppression (e.g. cytotoxic T lymphocytes), telomeres, etc...

So it seems like multi-cellularity did not evolve "ground-up", but was instead generated by slowly differentiating the functions of the various cells, while developing "top-down"controls against errant cellular behaviour.
Thus, cancer, which occurs when these protections fail, is in some sense merely a return to an ancient evolutionary root.

I suppose some arguments against this include the fact that modern cells are vastly different than their ancient ancestors (or even modern archaea/bacteria).
So the best we can perhaps say is that the core of the cell has been sufficiently preserved (ribosomes are still mostly RNA, are they not? :] ).
Further, it is hard to call some of the "micro-evolutions" of cancer (e.g. interleukin-8 production) as returns to primitive behaviour.
In these cases, I tend to see them as necessary occurrences to remove the "top-down" controls, rather than as integral to the destructive out-of-control growth characterizing oncogenesis.
But, debatably, perhaps not all of them are (e.g. extravasation in metastasis).

Obviously this seems very simplistic, but is there any literature thinking about it this way? Or directly debunking it?


texts:
I have noticed that if you look directly at tubelight (I have only white ones in my home) and close your eyes little, you see little random shaped colourless things sometimes with slow speed and sometimes with falling down.

They are shaped like circles with something in between and in chains of random length.

My father has also seen them. So, I am sure I am not imagining things. What the hell are they?


texts:
Can anyone identify the species of this fish carcass?

This photo was taken in Brooklyn, NY. The fish would have presumably been in Gravesend Bay.


texts: Where do I get an annotation file for yeast genome with ENSEMBL ids?

texts:
Even the annotation files hosted on  the Ensembl site have systematic names (starting with Y..) instead of ENSEMBL ids (starting with EN..).

I bet there would be a place where I can get an annotation file (GFF3 preferably). Please let me know if you know such.


texts: Are all functions of a human cell known?

texts:
Please bear with me as I'm intruding into your world from a computer science background.

In programming, once you have created a program, you know all functions of that program. Thus, 100% knowledge is achieved.

My question is, in the field of Biology, how much do we think we currently know about the human cell? Are all functions known (eg. 100%)? Are most functions known (60%)? Or do we know a miniscule proportion (1%~5%) of functions of a cell.

The reason I ask is I'm interested in the concept of simulating cells via computer. If we know about a given biological function of a cell, we could convert it into a mathematical function for use within a simulation. With simulations, you could simulate the cell's reactions to drugs, viruses, cell garbage cleanup, etc, based on it's defined functions. And the more functions we know about human cells, the better the simulation.

Thanks in advance.


texts: If animals aren't getting tooth decay because they don't eat processed foods, could similar work for humans?

texts:
In previous question here on stackexchange biology I read that animals don't get dental caries because they aren't exposed to refined carbohydrates like sugars. My question is: in theory, could a human be completely dental caries-free if he followed the diet of not eating any processed food? :))

And also, are fruits like apple or orange 'safe' against dental caries? (since they're not 'processed' sugars?) Thank you kindly for answers.


texts:
In physics, "almost everything is already discovered, and all that remains is to fill a few unimportant holes." (See Jolly.) Therefore, on Physics SE, people are veering off into different directions: biology, for example.

Thus, it happens that a question about bicycles generates some discussion about evolution in biology and animals with wheels.

Three explanations are offered for the apparent lack of wheely animals (also on Wikipedia, where, by the way, most Physics SE questions are answered perfectly).

Evolutionary constraints: "[A] complex structure or system will not evolve if its incomplete form provides no benefit to an organism."
Developmental and anatomical constraints.
Wheels have significant disadvantages (e.g., when not on roads).

Now, I suggest that all three can be "solved".

With time.
With a symbiotic relationship between a wheel-like animal and a "driver"-like animal, although this gets awfully close to a "driver"-animal to jump onto an actual (man-made) wheel. (So, perhaps, you can suggest a better loophole around this constraint.)
Roads are presumably not the only ecological niche where animals with wheels could thrive. I'm thinking of frozen lakes, although there skates would be better than wheels.

What, therefore, is the explanation for there not being any wheeled animals?
Please consider, in your answer, the counterfactual: What assumption of yours would be falsified once a wheely animal is discovered?


texts: What makes phenol an antiseptic, is it because of its acidity which may increase the proton concentration at cell membrane? I am unable to figure out the exact mechanism.


texts: Why are adenoviral vector vaccines safe in terms of insertion mutagenesis due to genome integration and E4 region's proteins effects?

texts:
Disclaimer: I'm neither a genetics professional nor an anti-vax fanatic, I just tried to compare COVID-19 vaccine types currently available on the market and got some questions that I'd like to answer rationally.
Some of the vaccines that are being actively used now are based on adenoviral vectors, such as ChAdOx1, Ad26, or Ad5. These vectors are replication-defective, usually due to removed E1/E3 regions.
I looked for existing information about adenoviral vectors and found some facts that may relate to safety, but I can't conclude if they are rational or not for vaccine applications, since most studies are made for gene therapy or animal models.
Proteins activity
Wild-type adenoviruses are considered to be able to lead to tumors in rodents (Wiki: DNA oncoviruses), mostly due to E1 region activity, but E4 also adds to its oncogenic effect
(Cell transformation by the adenovirus oncogenes E1 and E4), and may affect DSB repair (Expression of the adenovirus E4 34k oncoprotein inhibits repair of double-strand breaks). That may be related to the “hit-and-run” mutagenesis theory.
For Ad9, E4 alone can show that effect, E1 is dispensable (Adenovirus type 9 E4 open reading frame 1 encodes a transforming protein required for the production of mammary tumors in rats)
Genome integration
It's thought that adenoviruses do not integrate into the host genome, since they don't have a tool for that, but occasionally it happens with low probability (10^-3 .. 10^-7 per cell), particularly in cells where the virus can't replicate and lysis doesn't happen, which is always the case for replication-defective vectors (Chromosomal Integration of Adenoviral Vector DNA In Vivo, Frequency and Stability of Chromosomal Integration of Adenovirus Vectors, Insertion vectors for gene therapy, Illegitimate DNA integration in mammalian cells, Viral Vectors: The Road to Reducing Genotoxicity, Viral Epigenetics).
That raises questions about the possibility of insertional mutagenesis. As I see, such questions are often discussed in the context of DNA vaccines, but extremely rarely for adenoviral vectors which also deliver DNA into cells.
Finally, the question itself:
Should risks of insertional mutagenesis due to viral genome integration and E4 region's proteins activity be considered and discussed or they are not important / do not exists at all for adenoviral vector vaccines? Have I missed any studies about these topics?
Can these risks be estimated in numbers and compared with similar natural events?


texts: What does conditional analysis of a SNP in a GWA study entail?

texts: I am familiar with the use of tag-SNPs in genome-wide association studies to identify gene loci involved in complex traits, but I keep seeing the term "conditional analysis" used without any explanation. Is it some sort of mathematical manipulation in which the significance of a tag-SNP is reduced to zero, to see if other SNPs are directly associated to the phenotype in question?


texts:
When we see something, how and where in the brain do we remember it and are able to recognize it later?

What happens in the brain that makes this possible?


texts: Is there a cheap and easy way to check for potentially unsafe UV exposure?

texts: My lab has an older large Fotodyne tabletop UV transilluminator for visualizing gels.  It has a UV blocking cover that hopefully reduces UV that passes through, but I've always been suspcious as to how effective it is.  Obviously this part can be replaced with a new one, but short of guessing on the recommended 50 hr lifetime, how would one know the level of UV passsing through?  I considered simply placing a gel on top, but that is far from quantitative.  I am really just curious if there is an easy to make and/or obtain sensor that could be used to know when UV expose could be considered dangerous.


texts: Can anybody recognize this cardiac waveform?


texts: Does caffeine actually enhance cognition?

texts:
I have heard, respectively:

Caffeine measurably enhances cognitive function.
Caffeine does not measurably enhance cognitive function in any significant way.
Caffeine enhances cognitive function, but only indirectly, in that it counteracts the effects of fatigue.
Caffeine enhances cognitive function, but only indirectly, in that it counteracts the effects of caffeine withdrawal.
Caffeine has no physical effect on cognitive function, but has a psychological effect.

What is the actual behavior of caffeine in relation to cognition?  (I'm particularly interested to know if any research addresses the claim that it only counteracts the effects of caffeine withdrawal)


texts:
Edit: Large carnivores require lots of territory. What about bears? They're omnivores. How much does that count?

Is there anywhere I could find weight/territory ratios for mammals, depending on diet? Does necessary territory matter so much depending on the diet of a large mammal?

Thanks


texts:
So, clearly, the endosperm would be a fusion of the polar nuclei and one male gamete. Does this mean that each male gamete would have a T allele on it?

I can't seem to figure out a way to predict the allele distribution between the 2 polar nuclei since the flower has a Tt genotype.

Along the same lines, how can I predict what alleles the haploid egg would have? T or t? So, in that case, there would be a 50% chance of the embryo being TT and 50% chance of it being Tt (I didn't understand what the plus sign signifies).

The correct option is D, but I can't figure out how to get to that answer with absolute certainty.


texts: Philosophy of Science question permitted here?

texts: Clarified my question re vernacular - science codependency, shortly after it was put on hold. Also, 'Philosophy of Science' IS a topic in biology stack exchange  Please explain why my post's still on hold?


texts:
I recently read "What a Fish Knows: The Inner Lives of Our Underwater Cousins" by Jonathan Balcombe. The first part was the best where the author explained how fish are very advanced creatures because they have been around a lot longer than other vetebrates.

Are there any other books out there similar to this one? There seem to be tons of bird research books. Of course, birds are relatively easier to study than fish. (Their size and ability to fly makes them difficult to track. But, at least they are not underwater and sometimes stay in one area for awhile. Fish are pretty much constantly on the move.)

I am not really looking for a text book unless you know of one that is interesting to read and not just a list of facts...unless a text book would be a good place to start.

I have read Colin Tudge's books on trees and birds. I wish he would write one on fish.


texts: How to do manual Saccharomyces tetrad separation with minimal equipment?

texts: I would like to separate the four ascospores from individual asci by manual microscopic manipulation without at micro-manipulator and a basic dissecting microscope capable of 600X total magnification and a fine needle. Is this possible? My guess is that human hands would not be steady enough. But what did they do before micro-manipulators were commonplace?


texts: Why darwins, a measure of evolutionary change, is calculated on the log scale?

texts:
In a famous paper, Haldane is describing the idea of rate of changes in "darwins". Here below is the excerpt where he introduces the math about the concept.

Haldane, J. B. S. 1949. Suggestions as to quantitative measurement of rates of evolution. Evolution 3:51–56.

  Now suppose that in time $t$ the mean length of a structure has
  increased from $x_1$ cm to $x_2$ cm, the mean value of the
  proportional rate of change

  $\frac{1}{x}\frac{dx}{dt}$ or $\frac{d}{dt} (\text{log}_ex)$ is

  $\frac{\text{log}_ex_2-\text{log}_ex_1}{t}$

I don't understand why he is arguing that the difference should be logged. Why can't you just use:

$\frac{x_2-x_1}{t}$?

What justifies this line below?

  $\frac{1}{x}\frac{dx}{dt}$ or $\frac{d}{dt} (\text{log}_ex)$

Why not just using:
$x\frac{d}{dt}$?


texts: what is “a group of living things that can interbreed and produce full interfertile offspring”?

texts:
lets call this term "collection" Example: group of humans.

what is not a "collection" horses and donkey: can't produce full interfertile offspring, lions and tigers: can't produce full interfertile offspring, Camels and Lama: can't produce full interfertile offspring.

And no this is not "species". Polar bear is a species grizzly bear is a species they can produce interfertile offspring, they are of the same "collection"
Two species can belong to the same "collection". Two different "collections" can't be of the same species.

And no this is not a homework question.

Why is this not defined in biology?

Why is this down-voted? I know what ring species is. First and last generation do not interbreed naturally. But it does not say they can not interbreed at all or can not produce full interfertile offspring.
The question is about having the ability of intebreeding and producing full interfertile offspring.

I will add more details:
The term species is a fuzzy term and makes a lot of confusion. I'm not asking about it.
There is a clean cut for all living things that intebreed and produce. For a given group of living things they either can intebreed and produce full interfertile offspring or not. There are many example.
Why is this clean cut not have a term in biology?

Again. This is not a "species" and from my point of view the term species should not be used in biology. Anything is a species... Homo sapiens, Neanderthals two different species although they had interbred and produced full interfertile offspring.....

Different dogs "races" are sometimes called different speices although they can intebreed and produce full interfertile offspring.

I already know about the fly experiment where the author claims that he got two different "species" of flies after some year of combination of sexual isolation and interbreeding. But no, all flies during the whole experiment of the same "collection" even if the author says they are different "species". The author did not make sure that they intebreed, he let them naturally decided whether they want to interbreed or not. They did not because they are not attacted to each other, but this does not mean they can not interbreed and produce full interfertile offspring.


texts: How to study the effect on tau protein isoforms on microtubule based transport?

texts: From what I read, A-beta plaques inhibit microtubule based transport of mitochondria when tau protein is present in the cell. How would I be able to do a test to see if one isoform of tau is more effective at conferring this A-beta sensitivity than another isofrom?


texts: How exactly do mosquitoes navigate directly on target?

texts:
There is a question on mosquito orientation in darkness, however the answer does not address it very specifically and I'm more interested in mosquito ability to lock on target than general navigation.

I know that they use their antennae to detect CO2 and lactic acid. However smell alone doesn't seem good enough for precise landing.

They do have eyes, however they can operate in complete darkness which means the eyes are redundant system for the attack.

They can sense heat, but they do not seem to attack non-fire based heat sources.

So how exactly does a mosquito succeed to land on piece of uncovered skin? Does this tell us anything about interfering with their navigation system?


texts:
We have 2 cats, aptly named "Fatty" and "Tiny".

"Fatty" is a 6 year old house cat that hasn't seen the outside world in years.

"Tiny" is a cat we rescued about 45 days ago and she's roughly 2.5 months old.

Tiny came in with what looked like an eye infection, a million fleas and intestinal worms.
We kept the cats isolated until Tiny could be seen by a veterinary doctor. She had treatment to kill fleas and worms and we just washed her eye and it cleared quickly.

Soon after Fatty started to develop a cough; the doctor at the clinic said it was some cat flu, probably brought over by Tiny and she got some antibiotics.

If the flu is a virus, I question the antibiotics.. but we went through anyways.

Now we're a month and a half later and Fatty has completely lost her voice and she articulates sounds that are like 'krr'; she is unable to make any normal cat sounds anymore.

The doctor said it may be cat herpes that was introduced by Tiny; if this is the case, she'll never 'speak' again. In the meantime, Tiny is doing very well.

The most striking change is in her behavior; at first she didn't accept Tiny, now they are friends, but she has become slow, uninterested in any form of play, doesn't really purr anymore, doesn't come close to us and walks away when we pet her.

So, my question is: if she had the herpes virus, which is very common in stray cats where we live, can it have any effect on her brain that would explain a huge change in behavior? (her blood test is normal)


texts: How to know which residues belong to the variable or constant regions of a Fab (fragment antibody)?

texts:
I have a fragment of antibody (Fab) structure, and I know its amino acid sequences of its heavy chain and light chain. As each chain of Fab can be divided into variable and constant regions, how can I know which residues belong to the variable or constant regions?

I can of course look at its 3-D structure in pymol, but it is difficult to know the belonging of residues between the variable and constant regions.

This link clearly shows how to identify the CDR regions based on its amino acid sequence. Is there a similar way to differentiate variable and constant regions?


texts: Ways to measure effectiveness of a gene therapy trial?

texts:
I understand that Fluorescence in situ hybridisation  can be used to measure the effectiveness of a gene therapy experiment/trial.

But what are some other genetics techniques to measure the effectiveness of a gene therapy clinical trial. Would blotting (northern/southern) and PCR be a way to tell if a new genome have been integrated into existing cells.

Thanks


texts:
I've been doing some light reading on DNA damage theory of aging. One of the main ideas from that theory that I got is that the accumulation of damage in our DNA is one of the biggest causes of why we age, which is quite intuitive for a non-biology major like me. Furthermore, there has been research on DNA damage repair pathways and ways on how nanotech can help repair DNA. The technicalities are beyond me. My question is

  If accurate DNA repair is such a difficult mechanism to sustain over a
  lifespan, then why not catabolize DNA and replace it with a new one?

It seems very feasible to synthesize human DNA (please inform my ignorance, if I'm wrong. lol.) and it looks very promising after reading this: https://www.wired.com/story/live-forever-synthetic-human-genome/.

EDIT: It was pointed out to me in the comments that my question is too broad, please do tell me how to make it more specific, if you agree that's the case here. I'm very happy to accept technical answers, since I can always retrace it to the basics.


texts: What is the convention for log notation in biology?

texts:
I'm reading through some oldish (1980s) papers on length-weight relationships in fish and crustaceans. Many report log-log relationships without specifying whether this is natural log, base 10, etc. In mathematics log is typically assumed to mean natural log, but the results reported in these papers make more sense if you assume "log" means "log base 10".

Is there a convention in biology that I should be aware of?


texts:
I need to download all uniprotIDs of a cancer pathway, say the AKT Signaling. It may be super easy, but I don't know which resource to look at since it is a new field.

How/where do I find these?


texts: What is the earliest point at which one can detect pregnancy?

texts:
Imagine a woman gets pregnant on day X. What is the shortest interval (like a day, a week, a month) after which she can detect she is pregnant?

Example: Let's say that she keeps track of her menstruations and the next one should occur on 2018-05-01. On 2018-04-29 she has sex without protection and she doesn't take birth control pills. On 2018-05-02 she hasn't got her period. Is it reasonable to assume that she is pregnant based on these facts?

Note: I need this information for a fiction book. It doesn't need to be 100 % accurate, just believable.


texts: Why do (many) humans like carbonated drinks?

texts:
Many/most humans like certain types of food/drink because of the psychological/physiological responses we have to consuming them. Some examples:

We like sugar because it is very energy-rich (and is relatively scarce in nature).
We like salt because it is one of the essential building blocks of our cells.

But why do we like drinking carbonated drinks? (Soda drinks like Cola, Fanta, Tonic, Dr. Pepper, etc. but also sparkling wine, cider, champagne) Except in some very rare, special springs, carbonated water does not occur in nature. Why do we like drinking it so much?


texts: Photosynthesis: What Powers the Splitting of Water?

texts:
The splitting of water is an endergonic (non-spontaneous) reaction, and thus would require energy (chemical work to be done) in order to happen.

In Photosystem II, an enzyme catalyzes this splitting, but where does it get the energy from? Does it use ATP?


texts: Are alpha-ketoglutarate and glutamate involved in all transamination reactions?

texts:
Is it true that for all biochemical transamination reactions, that alpha-ketoglutarate and glutamate serve as the amino group acceptor and donor, respectively?

If this is true, then is it safe to assume that alpha-ketoglutarate is necessary for every transamination reaction?


texts: Genetically improved *Leucaena leucocephala* seeds

texts: I am looking for fast growing Leucaena leucocephala seeds. Now, I am cultivating Leucaena leucocephala which can grow 6 meters in a year. But I am looking for a genetically improved seed which can grow up to 10 Meters in a year.


texts: SARS-CoV virus stability at low temperatures

texts:
For SARS-CoV-2 and SARS-CoV1 this study published in NEJM by a NIAID team was done at a temperature of 21-23°C (see the Methods section in their supplemental material).

What's known about virus stability in general and for these two viruses specifically at much lower temperatures? (e.g. 4 °C, fridge temperature).


texts: When streaking microbes on a plate to test growth after uv exposure, does how I streak make a difference?

texts:
I've been working on what I think might be a special strain of E. coli, I've been streaking it on LB agar plate and exposing it to varied times of UVC via the germicidal hood.
I'm wondering if how I streak, as in too heavily, vs very lightly, or diluted culture, etc would make much effect in survival.
If I'm putting too much onto the plate, the e coli could be self-shielding, or some ecoli dying off, but the rest underneath being protected from the light.
I've done several generations of surviving colonies, I'm now comparing to wild type to see if my streaking method results in survival in both.
This test will also rule out if the lamp is failing and my surviving colonies are just the tougher ecoli compared to the growth on the control.
tldr
Should I lightly streak or dilute my culture to ensure all ecoli are being hit with the UVC?


texts: Translation of Poly-U in the Nirenberg and Matthaei experiment

texts: In the Nirenberg and Matthaei experiment the artificial mRNA, polyU, was translated into polyphenylalanine in a cell-free system, establishing that UUU was the codon for Phe. How did this work as the artificial mRNA lacked an AUG initiation codon, which we now know is required for translation of cellular mRNAs?


texts:
Campbell Biology 10e, in discussing the functions of introns, writes:

  The presence of introns in a gene may facilitate the evolution of new and potentially beneficial proteins as a result of a process known as exon shuffling. Introns increase the probability of crossing over between the exons of alleles of a gene—simply by providing more terrain for crossovers without interrupting coding sequences. This might result in new combinations of exons and proteins with altered structure and function. We can also imagine the occasional mixing and matching of exons between completely different (nonallelic) genes. Exon shuffling of either sort could lead to new proteins with novel combinations of functions. While most of the shuffling would result in nonbeneficial changes, occasionally a beneficial variant might arise.

Hitherto, I had perceived crossing over as the shuffling of alleles between two homologous chromosomes, not of parts of alleles. That is, breaks in the DNA during synapsis would occur in between loci, not within them. Am I wrong to think that? My books tell me that, with regards to evolution, sources of genetic variation include mutations and genetic recombination. Genetic recombination includes random fertilization, independent assortment of homologs, and crossing over, yet it is only mutations that can produce new genetic material. If exons were crossed over, then new alleles would be formed, would they not? Is this a type of mutation? (I do not recall studying such a specific case of mutations.)


texts: Finding DNA from Amino Acid sequence problem

texts: My attempt: First I took the single letter AA codes and made them amino acids.  So, the first one is Trp which is 5'-UGG-3'.   From this I got the DNA sequence 3'-CCA-5'.  However, the correct answer (shown in red) doesn't have this sequence.  What did i do wrong?


texts: What are "inactive" cells during Ca2+ imaging of neurons?

texts:
I am reading this paper, and have found the following Figure (Extended Data Figure 5) where they show maps of active cells in the amygdala as imaged with a miniscope and GCaMP6m:

Legend:

Using the spatial filters provided for each neuron by the automated
cell sorting algorithm7,44, maps of all active cells detected in the
BLA on each day of the study were made. Standard methods of image
alignment43 were used to register these maps across the different
days. Approximately 50% of all neurons observed across the entire
experiment were detected as active on individual days. a, Example maps
of active BLA cells from three mice on the first (left), third
(middle), and last (right) day of the 6-day experimental protocol
(Fig. 1c). Circles indicate cells that were active in only one of the
three recordings (grey), on two of the three days (blue), or on all
three days (red). Scale bars, 30 μm. The maximum number of active
cells seen in one session was 192

As can be seen not all cells are active every day.
My questions:

What are "inactive" cells? I am asking as I assume that cells always do have some baseline spontaneous activity which could be recorded with Ca2 imaging. I guess my confusion is that if we define cells as inactive which only have baseline activity, I wonder how we quantify "spontaneous" activity where an animal is for instance just exploring the environment without an experimental stimulus being present (periods of time which would be used typically to determine baseline activity)?

Are "inactive" cells not visible at all during Ca2 imaging (is it not possible to even see the cell's morphology/shape when there is no GcaMP signal)?


texts: It seems that dolphins have (among?) the highest encephalization quotients found outside of humans, higher even than chimpanzees. By the "use it or lose it" principle this indicates that intelligence must be particularly valuable in their niche. Why is that? They are predatory and social, and both of those are associated with intelligence, but why are dolphins smarter than other predatory pack animals? For example, is there something about being an air-breathing organism living in water that makes having a high EQ particularly adaptive?


texts:
I was reading about a viral list of dubious coronavirus tips on The Verge and reached this tip:

  “Even if the virus gets into your mouth, drinking water or other
  liquids will wash them down through your throat and into the stomach.
  Once there, your stomach acid will kill all the virus,” one tip reads.
  Loren Rauch, an emergency room doctor in Los Angeles who has a
  master’s degree in epidemiology, told Mother Jones this advice was
  “totally bogus.”

I asked a friend, who has a PhD. in cell biology, about this and she said that it's true that a virus would be killed by the stomach acid (i.e. due to high acidity, or low pH value, of stomach acid which could easily break the structure of the virus); however, she added that it's NOT true to think that drinking water would wash the virus from your respiratory system (i.e. trachea or lungs) into your stomach, so drinking water regularly does not necessarily help if it's in your respiratory system.

I was a bit confused since the doctor referenced in the article considered the whole advice as totally false; on the other hand, my friend thinks at least part of the advice, i.e. the virus being killed by stomach acid, is true.

Now, my question is not limited to coronavirus and I am not seeking medical advice or treatment here. I just want to  know if my friend is scientifically correct, i.e. whether stomach acid is able to destroy the biological structure of a virus (any virus, and not necessarily coronavirus)? And if so, how does this work biologically?


texts: What's the probability of a non-pathogenic strain becoming pathogenic from plasmids transmitted through the air?

texts:
So the thing is, I was getting a bacterial CRISPR kit for biology class, which is overall pretty simple and I'm just doing this for practice, and my dad was saying he was concerned it would accidentally make the non-pathogenic bacteria I was using pathogenic.  I told him that it was basically impossible for me to accidentally genetically engineer bacteria to be pathogenic because infectious bacteria need a bunch of adhesins to infect the human body.  However, that did make me think, what chances would there be of non-pathogenic bacteria (e coli hme63) becoming pathogenic because of some bacteria in the air getting in the culture and transferring plasmids to become infectious?   Again, I don't think this is likely at all, but I would like to ask those with more knowledge than me.
Edit: it would appear to me that if it was that easy for bacteria to get what they need to be infectious people would be getting sick a lot more than they are.


texts: Why do lychee seeds come in different shapes?

texts:
I've been eating lychee fruits recently and noticed that every once in a while (in about 1 of 10 fruits or so) the seed in the fruit is shriveled, while in other fruits from the same batch the seeds have regular ellipsoid shape:

Top: regular seed, bottom: shriveled seed

The fruits with the shriveled seeds don't look or feel or taste any different from those with the regular seeds.

It seems like a binary trait, i.e. seeds are not more or less shriveled, they are either shriveled or not.

Why are the seeds so different? Do they come from different cultivars, or it's some kind of Mendelian development, or maybe some kind of a plant disease?


texts: Why can't we smell our own bad breath. Is there any way we can do that?


texts: Calculation of saturation of carbon in surface waters

texts:
I've been looking at some journals lately that look at carbon emission from lakes where some lakes act as sources and other act as sinks. The paper that I have been looking at is

http://www3.nd.edu/~underc/east/publications/documents/Cole_94Science.pdf

where they show that lakes are sources of CO2 to the atmosphere. What are the equations that are used to determine the saturation of CO2 in surface waters?

The recent IPCC report also mentions that lakes act as sources of CO2 but does not give any indication of the equations used to come up with these values. Presumably, to determine the concentration of carbon in the surface water you need to use other measured variables such as temperature. Can anyone suggest a method for estimating this concentration ?


texts: How much of what we eat ends up in the toilet?

texts:
An awkward question. Bear with me...

In terms of mass, what percentage of the food that we eat do we end up excreting? Of course, it depends on a whole host of factors so lets assume a healthy average build/height male with a balanced diet in his 30s who doesn't drink or smoke.

I ask this because I am quite intrigued by my own bowel movements (typically 2 or 3 days apart and average in size - I have no problem passing them btw they've just never been that regular). I know my bowels are not excercised like most other adult males but what's more intriguing is that when I do finally "go", it looks like and feels like I've hardly eaten over the past few days! Take this weekend for example, it's fair to say I've been overdulging and overeaten but by the end of this week I will probably "see" only 10% of that in the toilet.


texts: How to get Population Genotype Frequency from 1000 genomes Perl API

texts:
Posted a similar question on Biostars but got no response. Not sure if I'm allowed to link to it? Basically I want to pull genotype frequency data for a population group (such as CEU) instead of allele frequency data, via the Perl API for 1000 genomes. I have tabix and perl API installed. This is for 100,000+ SNPs so the solution should hopefully not involve manually downloading genotype and calculating the frequency manually in a for-loop. My understanding also is no solution exists in BioMart (according to the Biostars answer).

Following the instructions here, I can see how to get specific genotypes for all individuals as a list.

Eg: Input -> Some snp, CEU... Output -> G/G 0.87, G/A 0.13 (frequency of some snp for CEU population).

I need to do this for 100,000+ SNPs, so I imagine manually pulling all genotypes for each SNP and calculating the frequency manually in a loop would not be practical.


texts: Estimation of species range fragmentation

texts:
While discussing species distribution patterns along spatial, temporal or functional gradients one often finds a hump shaped species richness pattern.
This is well documented in many taxa and spatial scales and known as the   mid-domain-effect (e.g. Colwell & Lees 2000 ).

These patterns also arise stochastically (depending on the species range frequency distribution). So random distribution of species ranges midpoints are used as null models to test for these mid-domain-effects.

However, these models assume unfragmented species ranges. With a highly fragmented species range the pattern would look quite dissimilar.

So I don't want to start a discussion on the validity of this concept but rather ask:

Given a gradient and known species occurences on that gradient.
Has anyone read an article about (or has an idea) what would be a good/unbiased* estimator for species range fragmentation?

Thanks

*e.g: One that doesn't over- or underestimate fragmentation for rare or abundant species


texts: What measures are commonly used for the complexity of an organism?

texts: I'm aware of measures like number of distinct cell types being used as a measurement of complexity in biology, for example in the G-value paradox. But this doesn't really help for unicellular organisms. Is it possible to define a unit of complexity to make comparisons between different organisms?


texts: When was it determined that Type 1 Diabetes is an autoimmune disease?

texts: I just found out today that type 1 diabetes is an autoimmune disease.  When was this discovered?


texts: Mass change in deamidation from Glutamine to Glutamate

texts:
To detect the deamidation from Glutamine to Glutamate in a protein, normal practise seems to be a mass spec, where it is claimed there is a change of 1 dalton.

EG It is claimed that:

  Deamidation of an Asn to Asp/IsoAsp results in an increase in mass of a single dalton.

But when I look at their table, they are using Glutamic Acid as being 1 Dalton heavier than Glutamate, but at pH 7 the Glutamic Acid will be deprotonated to Glutamate. Do they  put the sample in pH 4 to protonate the Glutamate first? But then you are risking catalysing the hydrolysis of Glutamine anyway, rendering your results useless!

There should be a charge difference though, as you are going from neutral to a negative charge, so that would show up in a change in mass/charge on the mass spec, rather than a mass change.

Any help would be appreciated.


texts: What is the etymology for Pinus halepensis?

texts:
I have a problem of figuring out the etymology of Pinus halepnesis.

An etymonline search with halepensis brought no result.

It is unclear to me from the English wikipedia article and from the English WikiSpecies article what is the source of the name.

It is often called "Aleppo pine" --- maybe this is the source.

In Israeli Hebrew (as in Hebrew Wikipedia) it is called "Jerusalem pine" (אורן ירושלים) which is clearly different than standard.

What is the etymology for Pinus halepnesis?


texts: Different level of toxicity between smoke

texts:
Has there been studies on the difference between the smoke generated from:

cigarette or cigar manufactured by brands which are proven to contain more than a hundred of dangerous additional components
tobacco/marijuana (more or less pure?)/any-plant-dried-leaves made cigarettes.

Apart from the nicotine both contain naturally, are the latter safer to inhale? in which scale?

The other question Effects of smoking tobacco compared to inhaling other smoke, reminds the danger of all source of intoxication, wall paints are also to consider.. and outdoors gas pipes, etc... But I'm doing a fixation on smoked drugs. I've been living in residences, sharing corridors with flats with more or less important smoke concentration, and had developped fumiphobia (but this is out of topic).

This is probably psychological but I'd never stay in the same room than someone smoking, but if someone take some dried leaves out of a plant,.. roll them in paper, fire it and inspire it. It never happened but I wouldn't be as much scared by the generated smoke. But if a study would show that manufactured cigarettes are between 1.5 and 3 times more 'toxic' then I would consider both cases dangerous.


texts: How do trees lift water higher than 10 meters?

texts:
The atmosphere pressure is 10 meters of water (approx). This means that it is impossible to lift water higher than 10 meters with vacuum or сapillary action (on Earth, under normal conditions).

There are trees higher than 10 meters.

How do they lift water to their tops?

UPDATE

In other words: how cohesion-tension theory can be true if it apparently contradicts the laws of physics?

UPDATE 2

Atmospheric pressure helps to rise the water, not resists rising. What is resisting is water weight. When water column is 10 meters high, then atmospheric pressure can't help anymore.

Any adhesion/cohesion mechanism can't help here too, because it acts only in thin molecular layer. To transfer action force further the pressure is required, which is insufficient at 10 meters.

UPDATE 3

If we had capillary small enough to rise water to 10 meters and then we will build smaller capillary which we expect will rise water higher, we will fail. Water column will break and does not climb higher than 10 meters.

Menisci acts like small piston and can't help rising water higher than 10 meters.

UPDATE 4

Common pressure distribution in capillary is follows:

$P_0$ is atmospheric pressure. As you see, right under menisci, the pressure is lowered by $2 \sigma / R$ where $R$ is the radius of menisci and $\sigma$ is surface tension. The entire term is called "Laplace pressure". As you see, it can't supersede atmospheric pressure, because water continuity will be broken in the case.

I.e. no any menisci can rise water higher than 10 meters.

The existence of higher trees PROVES that there are some other significant mechanisms, not adhesion/cohesion, not capillary.

UPDATE 5

Current version, as I understood it, is based on a declaration, that a water, if put into thin capillary, can behave like a solid body. Particularly, it can resist tension up to minus 15 atmospheres.

This is a tensile strength of concrete, so I don't believe that without additional proofs.

I think it is just not hard to make thin tube, put water into it and check, how high it can climb.

Was it done ever?


texts: When someone gets infected with influenza, and gains some immunity, is that immunity just as good as getting it from a vaccine?

texts:
A friend thinks that being infected with a new influenza virus means that little immunity is gained, unless you get a vaccine. But, he is forgetting that new strains can make current vaccines out-dated.
I'm sure the immune system will "remember" that particular strain just as well as getting a vaccine.
When someone gets infected with the influenza, and gains some immunity, is that immunity just as good as getting it from a vaccine?


texts: Do puffin beaks have vertical slits or cracks?

texts: I have seen a photo where puffins seem to have vertical lines on their beaks.  It is uncertain if those are just line or actual slits or cracks in the beaks.  Do puffin beaks have slits or cracks?


texts: When analysing phosphoproteins via Western blot, why is total protein level of the target protein recommended as an internal loading control?

texts:
I am analysing the expression of a protein kinase via Western blots, and it is a phosphoprotein. I have labelled my membrane with antibodies against the phosphorylated form of the protein (using phospho-specific antibodies) and also for total protein (using pan-specific antibodies).
I have read that when studying phosphoproteins, you should normalise the phosphorylated protein signal to the signal for total protein. In this journal paper, it states that the Journal of Biological Chemistry recommends that “signals obtained using antibodies specific for phosphorylated epitopes should be normalized to the total protein level of the target protein”.
I have seen in other journal papers analysing the expression of a phosphoprotein via Western blots that they also normalise the phosphoprotein signal to total protein signal (of the target protein).
However, I am not sure why the total protein level of the target protein can be used as an internal loading control?
I have read in this handbook that internal loading controls are endogenous reference protein(s) that are present in all samples at a stable level and unaffected by the experimental conditions.
I want to compare the expression of my phosphoprotein between samples of different experimental conditions. I know that normally total protein stains such as Ponceau S or housekeeping proteins are used as an internal loading control and for normalisation.
But why is it recommended that you should normalise to total target protein (when looking at phosphoproteins), because one does not know whether the expression of total target protein will be stable between different experimental conditions? Any insights are appreciated.


texts: If phages (bacterium-eating viruses) prowl on bacteria, are there bacteria (or other micro-organisms) that hunt phages for food? They are rich in proteins anyway... Are there studies on this subject? Thanks


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

texts:
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 summarize below from memory. I mentioned this to a colleague who teaches anatomy and physiology, and he said that it sounded not very credible. I told him I'd find the article and send him a link, but I wasn't able to find it again. I'm wondering if anyone can help me find the original scientific paper, or a popularization.

According to this account, humans have a mutation, not present in other primates, so that when we eat, our glycogen stores are replenished quite a bit faster -- maybe by a factor of 2 or something. Of course digestion is complicated, and the speed of digestion depends on the macronutrient and even on the subtype of that macronutrient (e.g., we probably process maltodextrin faster than whole-wheat bread), but for typical foods I think the idea was that a human would rebuild their liver and muscle glycogen reserves in a few hours, as oppose to twice that for other primates.

The article also said that this evolutionary innovation had a cost associated with it -- that it led to an increased susceptibility to certain types of cardiovascular disease, which our close relatives don't get as easily.


texts: How did the huge dinosaurs cope with gravity and loads on bones, etc.?

texts:
It's very costly to be a huge animal. Your mass grows in cube when you scale up, but you still only have two/four legs to support the same weight. This increases the pressure that your body needs to cope with.(this is easy to see if you compare an ant with an elephant. The elephants legs are much thicker and strudier in comparison to it's body)

Looking at a T-rex for example, speciemns have been found that are believed to weight more than 9 tonnes, compared to an elephants 10 tonnes. T-rex has ofcorse has only two legs. The heaviest dionsaur is believed to have weight 80 tonnes. That is the weight of about 20 cars on each of their feet.

How could they support such massive weights?


texts: Effect of ethanol and detergent on cell membranes problem

texts:
I am currently writing my biology report for an experiment I did on how ethanol and detergent affect the cell membrane. For my ethanol experiment, all went as expected. However, for my detergent experiment, the results seemed quite strange. The absorbency rate was higher for the 20% and 40% detergent than it was for the 100%. It seemed as though the results were backwards. I'm really confused.

What might have happened? Was it just an experimental error or is there a reason behind this? Can you also please explain to me what detergent does to a cell membrane exactly?


texts: Are there ways to genetically increase mutation rate of E.coli?

texts:
Are there ways to increase mutation rate of E.coli using genetic modifications? I know possible ways it can be done without genetic modifications by exposing the cells to stressful conditions like anaerobic and radiation but what are some genetic ways?

Thanks!


texts: 16s rRNA Sequencing From Gut Microbiome (stool)

texts: Do I extract RNA or DNA from gut microbiome (stool samples) if want to do 16s rRNA sequencing?


texts: The relationship between the shape of the bacterial DNA and the blocking of replication machinery

texts:
I was reading a course about tolemers when I arrived to this phrase :

  [...] The ends of a linear DNA molecule cannot be replicated by the cellular replication machinery (which may be one reason why bacterial DNA molecules are circular).

I want to know what is the relationship between the circular shape of the bacterial DNA and the blocking of replication machinery ?


texts: Are CoA and CoAS the same thing in a compound?

texts: Is CoA-S-R the same as CoA-R, and is CH3C(=O)CoA the same as CH3C(=O)SCoA? Eg. Above is the compound on the right just coenzyme A or is it actually another compound and not just notation?


texts: What is the fate of NADH produced in the liver during oxidation of lactic acid?

texts:
NADH (‘reduced NAD’) is produced during the oxidation of blood lactate in the liver. Glycolysis requires NAD+ (‘oxidised NAD’), whereas gluconeogensis requires NADH. However the NADH is apparently not always used for gluconeogenesis (How is NAD+ used in lactic acid fermentation after it is oxidized from NADH?), i.e. the Cori Cycle does not always operate — so what becomes of the NADH in this case?

My best guess is that, along with the pyruvate, it may be transferred in the blood somehow to do to the site where it is needed, and it will then be taken into the electron transport chain, while the pyruvate will be taken into the Krebs cycle.


texts:
To spawn, salmon return to the river in which they were born. Is it because the individuals remember the specific river, or because populations are genetically conditioned to follow specific environmental cues that guide them to the specific river?

In other words, if a salmon is artificially taken to lay eggs in a different, ("wrong") river, will its progeny return, when grown, to the river where they were born, or that where their mother was born?

If salmon that was grown in a fish-farm is taken to the sea, does it return to a river? How does it choose which?


texts: I am using Fermentase First strand cDNA synthesis kit but its buffer is over. I need to work today but I have not access to any sorce currently. I have PCR buffer in the lab. Can I use PCR buffer instead of cDNA synthesis buffer? What are your other suggestions? Thank you


texts: Why does an electrical shock freeze up muscles?

texts:
Why is it when someone comes into contact with an electrical supply that their body freezes up and is unable to move away from the electrical source?

Can someone explain this through a physiological perspective?


texts:
I've been reading a lot about stem cell research and the work on growing artificial organs.

I assume, with sufficient advance in the technology, there is no theoretical reason it would not be possible to grow genital organs (gonads, uterus) in particular?

So my question is: is there any theoretical reason you could not use this process to grow the genital organs of the opposite sex of a stem cell donor?

So then, would an ovary grown from male stem cells potentially ovulate Y-gamete eggs?


texts: Michaelis-Menten equation; how to find the constants from enzyme activity experimental results?

texts:
I was wondering what the constants in the Michaelis-Menten equation actually mean in experimental data of enzymes. How do I process the data to find Km and Kcat?

I did an experiment on catalase and its breakdown of hydrogen peroxide. I used a gas pressure sensor to track how much O2 was produced from the reaction over time. The following is an example raw plot of what I found. Point 0 is when I put the substrate and the reaction started (so I think I can call this the "maximum amount of substrate concentration" - in the Michaelis-Menten plot, it should be on the far right side.)

To find the speed of the reaction at each point, I thought of finding the slopes between each point, which basically equates to finding the derivative. Since the raw plot I found looks like a logarithm function, so I would predict that the derivative would look like a hyperbola (with x > 0). Indeed, this is the (crude) graph of the "derivative" of the previous plot, which looks like a hyperbola:

I believe that Kmax is the y-value of the first point in this graph - the initial velocity when the substrate is mixed with the enzyme. The substrate concentration is at highest at time 0, and the substrate concentration decreases as time increases.

So I thought, to make the Michaelis-Menten graph, I should flip the x-axis so that the substrate concentration is increasing along the x-axis. Yet, my problem was that if I do this, then the graph ends up not looking like the Michaelis curve...

What I would have wanted to find is the Michaelis-Menten curve, so that I can also derive the Km and Kcat values. Does anyone know how to do this? Or am I doing my steps wrong? Thank you very much for helping me!

Michaelis-Menten Curve:


texts: What does the "G" and "V" in penicillin V and penicillin G stand for?

texts: I've been looking for a convincing explanation for the designation penicillin G and V. The answers I've found includes G as in "gold standard" and "V" as in "viscus" but they're not sourced and not especially credible explanations.


texts: Why is half dose of Oxford's vaccine of covid more effective than full dose?

texts:
I recently read in a newspaper that the half dose of the Oxford's vaccine is 90% effective while the full dose is only 62% effective.
Why is this the case ?


texts: What are the limiting factors of pathogen population size in human populations?

texts: I understand that one limiting factor in non-human animal populations is that increased pathogen populations decrease animal populations from killing them, which decreases the density of the animals, which makes it harder for pathogens to infect other animals. However, pathogens, at least in developed nations, don't seem to kill a large enough number of people for this to be the main limiting factor. So what else are the limiting factors?


texts:
Chemotherapy kills cancer cells by targeting rapidly growing cells. That is why patients lose hair as well. Why is chemotherapy-related hair loss temporary?
The doctors say it is because healthy cells are able to repair themselves. But, if that is true, then people should not even lose their hair, as the damaged hair cells would repair themselves before patients lost their hair.


texts: How does a pinched nerve cause pain (at the molecular level)?

texts:
Is this due to pressure differentials in the surrounding tissue? (Is it possible to have a pinched nerve without compression of the surrounding tissues, and does this cause pain?)

What are the molecules/cell types involved in this process? Is the pain dependent on the compression of axons from mechanosensitive or nociceptive neurons?


texts: Has a walrus ever been filmed catching a seal under water?

texts: Walruses have been long thought to be grazing feeders, scooping up clams from the sea floor. However, when walruses bodies have been examined by scientists, frequently the remains of seals are found in their stomachs. This has led to the speculation that walruses hunt seals, however, apparently this behavior has not been observed because it would take place under water, if it occurred. The Wikipedia merely says that the "importance of seals in the walrus diet is under debate". Has anyone ever filmed a walrus hunting, catching and eating a seal under water?


texts: We can see length, and other physical quantities. We can perceive through our other senses like (temperature through thermoreceptors, weight through pressure receptors etc.). But how do we "sense" time?


texts: Explanation of the meaning of high-throughput

texts: Almost all of the papers about bioinformatics, I faced with the high-throughput word, but I could not find any explanation about it (I think it is so easy to understand and that's why anyone explains it but I could not do it ) . Is there anyone who can explain me what do they mean by high-throughput ? Thanks in advance.


texts: Are there any drawbacks to having a fixed-Köhler microscope?

texts: I am considering to buy the Zeiss Primo star microscope. There are two variants: one with so called "Full Köhler" illumination and one with "Fixed-Köhler" illumination. Are there any drawbacks to having it fixed? When I would not want to have Köhler illumination?


texts: Is there any alternative to x-gal white/blue screening for the monitoring of pseudomonas aeruginosa beta-galactosidase activity on agar plate?

texts:
I want to screen a pseudomonas aeruginosa mutant library carrying a lacZ transcriptional fusion for dysregulating mutations. I tried to do it on xgal plates but the accumulation of the blue color makes the screening difficult. I saw that people are using macconkey or endo agar media for two-hybrid beta-gal screening in E. coli for instance. I wonder if it would be something to try even with pseudomonas (which would only possess the lacZ gene, so no permease etc...) and if someone here ever tried it ? Or if other beta-gal substrates could be used for this application ?
thanks
Julian


texts: Phylogenetic method to detect shift in mean of continuous variable

texts:
I am currently working on a project where I study the change of a continuous morphological variable with body size (measured as body weight) across diverse taxa (insects, spiders, lizards, frogs). In order to account for the non-independence of the data, I built an approximate tree based on published phylogenies. I have a reasonable branching pattern down to family or genus level for most taxa, but lack statistically supported branch length.

I find a strong change of the scaling coefficient when using phylogenetic least squares (with a covariance matrix based on my tree) vs a non-corrected least-squares approach, suggesting that most of the change observed in my continuous variable is explained by evolutionary history, rather than by body mass as such. I would now like to investigate how early on in the tree these shifts occur.

Intuitively, I could start collapsing my tree into polytomies down to arbitrary taxonomic levels, eg genus, family, order etc, and re-do my phylogenetic least squares. I would expect a stepwise approximation of the pgls to the uncorrected result (in the extreme case, I would end up with a star phylogeny, which should give an identical result to my uncorrected regression). Such an approach may allow to say something about whether most of the change occurs between genera, families etc, but it requires the use of somewhat arbitrary (and controversial) taxonomic levels. I would be grateful if someone would have an alternative suggestions on how to perform such an analysis, with arbitrary branch length and non-ultrametric trees.

Thanks
Thriceguy


texts:
I understand how DNA is replicated and how it directs the synthesis of proteins from amino acids through RNA polymerase, RNA and ribosomes. Now I want to understand how it works in the big picture.

With my current level of understanding, any protein can be synthesized at any time at any rate, but it looks to chaotic to work at all.

What dictates which protein to synthesize at a given time?


texts: How to convince suspension cells to adhere more tightly?

texts:
I'm developing a cell-based assay in 96-well plates that requires adherent cells, as they need to be washed at least twice during the protocol. I'm using in-house strains of HT1080 cells (some overexpressing a certain protein of interest) that unfortunately have been selected for suspension growth in chemically-defined media (50/50 CD-CHO/CD-293). I can convince them to adhere by culturing in DMEM with 10% FBS and growing them in CELLBind flasks, but they still tend to pull away if there is very much shearing force, such as during the wash steps, or when they're in PBS during the assay wash and incubation steps (maybe 2 hours total for now, I'm still optimizing that).

Unfortunately, the parameters of my experiments don't allow me to keep the cells in serum-containing media during the assay, as it would interfere with the uptake of my drug. Like I've said, when in PBS they start detaching, and I would assume the same in HBSS, which I don't really want to use anyway due to its low buffering capacity in CO2 incubators.

Might DMEM alone (without FBS) provide a little more impetus to stay attached during the assay? What would the effect be of increasing the amount of FBS to say 15 or 20% during culturing - would that promote stronger attachment? I'm a little hesitant to coat the wells with poly-D-lysine, as my readout is on a fluorescent imager, and I'm worried it would substantially increase background. I don't really have enough time to re-select the cells for adherent growth (although if I'd known about these issues from my predecessor 3 or 4 months ago I would have started right away...), so are there any other tricks I can try in the meantime? Are there any media supplements I could use to promote adherin expression or something like that? Any tips or advice at all would be appreciated.


texts: How can I produce milligram quantities of an isotope-labeled DNA oligomer?

texts:
I'd like to produce a specific DNA sequence on a milligram-scale and 13C15N-label it. The sequence is around 35 nucleotides long, so chemical synthesis is out due to the exorbitant costs.

I'm also only interested in the single-stranded DNA, so a method that produces double-stranded DNA without any way to easily separate the strands would also not be useful.

What methods are there to produce labelled DNA that fulfill these requirements?


texts: Is covid vaccine helpful for a covid patient?

texts:
I am not a biology student and this question came in my mind out of nowhere.
I read somewhere that the vaccines contain some denatured or almost dead corona viruses and when these are injected in our body , our immune system remembers them and if the actual (killer) corona virus enters our body , our body recognises it and quickly attacks it.
But if we have a  corona patient his body has already identified the corona virus and so if the vaccine is given the body will not have much changes to do and simply refuses it .
So is it okay to give the covid vaccines to a covid patient ? Can it make the infection even worse ?


texts: In an ant (or bee) colony, what is the very approximate ratio of new breeders to workers?

texts:
For example, out of every 1000 eggs laid, X mature into drones and/or virgin queens.  That seems impossibly precise but it illustrates the kind of number I want well.  I'll accept answers for any species and any number of species, even one, with any amount of precision or lack thereof, because right now I can't even feel confident saying that there are more workers or more breeders, though I obviously suspect more workers.

I would also be ecstatic to have any live count just before the nuptial flight, i.e. for this colony in this study there were X workers, Y drones, and Z virgin queens just before the nuptial flight, or X workers and (Y+Z) breeders, or X% of the colony was breeders, or for this species on average X% are breeders just before the nuptial flight.

Anything.  Any one thing and I can accept it as an answer.

I can find any number of studies that talk about the sex ratio between drones and virgin queens, so I know someone is counting.  Maybe I'm not reading closely enough, but they always seem to slip away from giving all the numbers I need to figure this out for myself.


texts: Does ale give less of a hangover than a lager?

texts:
I got into an argument surrounding beer type and hangover. Apparently there is a opinion that ales give you less hangover than lagers do (considering same alcohol content consumed).

My understanding is that a hangover is nothing more than dehydration caused by alcohol. More alcohol per unit of mass - more dehydration.

Is there any biological evidence to show that the same amount of alcohol consumed (with a different type of yeast) per same body mass would have different effects?


texts: Lambda red recombination without electroporation

texts: All protocols that I found about Lambda red recombination are using Electroporation as a method to introduce (inject) the homologous DNA (usually a PCR products or a linear dsDNA) to the E.coli cell. Can I use chemical method (CalCl2 + PEG) and heat shock method instead ?


texts: What is the technical term for when a clade on a phylogenetic tree does not have an extended branch? (see image)

texts: As we see with ZCA2, ECA2 & XCA2 these branches are compressed and do not extend as TCA does. Is there a technical term for this and what usually causes it?


texts:
I understand that AUG is the "start codon", and, because of this, most proteins begin with methionine as their first amino acid.
However, this ORF problem on Rosalind.info states that "AUGCUGAC... can be translated as ...AUGCUG..., ...UGCUGA..., and ...GCUGAC".  That is, something (the Ribosome?  The GTP cap mentioned here? Something else?) must cause the translation to be shifted by one or two nucleotides in the sequence.
My first question is :  What mechanism(s) cause(s) this shift in translation to another Open Reading Frame (ORF)?
Specifically, I want to know how the start codon, AUG, can have one ("A") or two ("AU") of its bases ignored in the Ribosome during translation.
My second question is : How often does this happen?  That is, what is the percentage of (known) proteins that start with methionine vs. the percentage that start with something else due to this "ignoring" of the bases of the start codon?
I am interested in the answers for both prokaryotes and eukaryotes.


texts: Since Oxygen is produced by photosynthesis, would there be less oxygen in the air in winter, where the trees shed their leaves and the sun generally shines a lot less? If yes, would that be a noticable difference?


texts: Is the lac operon repressed in the presence of both glucose and lactose?

texts:
In the presence of both sugars (glucose and lactose) will there be repression of the lac operon completely?

I know that more glucose means less cAMP --> less CAP --> less positive regulation, and thus less lac operon, but does that mean there will be repression of the lac operon?


texts: How do carrier RNAs increase yield in sequencing experiments?

texts: I would like to know how carrier RNAs increase yield in RNA/DNA sequencing experiments. Is their main function in the precipitation steps of each protocol (i.e. small quantities are difficult to precipitate and the carrier RNAs add material), or do they have a role at other stages in the process as well?


texts: How many SARS-CoV-2 viruses in circulation at the moment? Mass?

texts:
How many SARS-CoV-2 viruses are in circulation at the moment? And what is their total mass?

To clarify: if there are 10 000 viruses on average in an infected human and 100 000 humans are infected the answer would be (if all viruses are in humans, which probably isn't true) 10^4 x 10^5 = 10^9 viruses.

Of course I am only looking for a rough estimate, a number that, when multiplied with 10 or 0,1 (so two magnitudes) or so, is correct.


texts: Could an annual plant be genetically modified to be a perennial?

texts: My chives, asparagus, oregano, and rhubarb come back every year like clockwork.  Suppose I want my bok choy to join the party - is there an "I'll be seeing you next year!" gene that can be modified to be turned on to be like my hardy chives, or is it more complicated than that?


texts:
Background: Lemniscus (Latin lēmniscus, ribbon) is a strap of second order nerve fibres which twist as they ascend to the brainstem.

Why do these these nerve fibres rotate?
 What could be the functional significance of such rotation?

I think that rotation is somewhat less beneficial because firstly it causes increase in length thereby increasing the conduction time , secondly it may decrease structural integrity of such a bundle of axons.


texts:
Most antiandrogens inhibit DHT. DHT is connected to testosterone. [1] shows a beneficial effect on prostate cancer which can be caused by DHT. However, according to [2] garlic also increases testosterone.

What are the effects of garlic on Dihydrotestosterone (DHT) or 5α-dihydrotestosterone? Can it be used as an antiandrogen?

[1] Hsing AW, Chokkalingam AP, Gao YT, et al. Allium vegetables and risk of prostate cancer: A population-based study. Journal of the National Cancer Institute 2002; 94(21):1648–1651.

[2] Oi, Y; Imafuku, M; Shishido, C; Kominato, Y; Nishimura, S; Iwai, K (Aug 2001). "Garlic supplementation increases testicular testosterone and decreases plasma corticosterone in rats fed a high protein diet". The Journal of nutrition 131 (8): 2150–6.


texts: Loss in DNA band size extracted from polyacrylamide gel

texts: I'm using cDNA AFLP teq.. I extracted 670 bp band from polyacrylamide (urea) gel and I have amplified with PCR  but on agarose gel it stops at nearly 350 bp.it happened for most of other bands before. I always extracted the precise bands.  I repeated with both pre and selective primers with the same PCR program before done for amplification of digested cDNA and same size bands observed in agarose gel.I wonder maybe secondary structure causes losses in band size (before running in polyacrylamide samples treated in 94 degree for 5 min), but how I can recognize?  i should notice 350 bp band i mentioned above is very sharp. what other thing I'm wondering is can dye uses in agarose gel alternate the DNA charge and reduces the speed of movement . The big  matter is the rate of losses in band size almost is same for almost all of the bands for one primer. Is it happened for anyone before? can i trust on my extracted bands for doing cloning?


texts: How exactly can dsRNA be introduced to a cell?

texts: Is it just by viruses or are there other means by which it gets into cells, such as plasmid uptake?


texts: How long could Earth's oxygen supply last if no new oxygen were produced?

texts:
I read in an article or heard in some documentary that there's so much oxygen in the atmosphere that even if all photosynthesis stopped, there's already enough to last us a long time.

Is this correct? Why or why not? If so, how long is this 'long time', roughly? I've seen estimates between 15,000 to 150,000 years.


texts: Acoustic characteristics of thoracic diaphragm

texts:
I am looking for any kind of information about the acoustic characteristics of the thoracic diaphragm. In particular, I'm looking for characteristics which will allow to differentiate it from other muscles using ultrasound, MRI, CT, etc.

References to the literature are especially welcome.


texts:
Often when I sneeze, I smell flowers for a few seconds afterwards.

I've done some searching on the internet, and apparently it's something that is at least not entirely uncommon, although the exact smell description seems to differ. It's sometimes also referred to as a 'honey sneeze'.

Just to be clear, there are no flowers anywhere in sight when I sneeze.

Biology has never been a field of study of mine, but the scientist in me finds it fascinating. I've yet to come across any real explanation for this phenomenon, only guesses.

Does anyone know what causes this, or can you at least give a somewhat likely explanation?

Edit:
When I sneeze through my mouth, I do not get the same smell sensation.


texts:
Assume we are given approx. 80,000 dsDNA fragments of 40 bps length each.
I would like to amplify of each of the 80,000 fragments just one particular strand, such that I obtain amplified 80,000 ssDNA fragments of just 40 bps.

Also beforehand if could be helpful to amplify the 80,000 dsDNA fragments, so where the amplified fragments stay double-stranded.

If you could help me for both amplification steps, particularly the first one, I would be very delighted!

Many thanks in advance!


texts: Protein binds to DNA and just stays there, what will happen next?

texts: If I hypothetically make an inactive version of Cas9 or ZFN (that will bind to the DNA but does not apply the cleavage reaction). What will happen after the protein bound to DNA? Will it be stuck in there forever and disrupt the transcription/translation process? Or will it be self-unbound after a while?


texts: How do I download entire human genome for local blast formatting and searching?

texts:
I'm trying to make a copy of the entire human genome for local blast queries on my machine.  I understand that I need to download it from the NCBI FTP server here...

ftp://ftp.ncbi.nih.gov/genomes/Homo_sapiens

After downloading it I need to format it into a database that blast can search.  I do this using NCBI's makeformatdb command.  It is run like this...

makeblastdb -in entire_human_genome.fasta -dbtype nucl -title human_genome -out human_genome.db

My question is...  Where do I get the fasta file containing the entire human genome?  Do I download the fasta files for all 22 chromosomes, the X chromosome, and then the Y chromosome and concatenate them?  Is there a fasta file on the site containing the entire genome?  A fasta file that is not partitioned by chromosome?


texts: I know that sodium azide and 2,4-DNPH inhibit proton pumps. The azide is called an inhibitor and 2,4-DNP is called uncoupler. I want to know what's the difference between the mechanisms of action of sodium azide and 2,4-DNPH in proton pumps. Why is one called an inhibitor and the other an uncoupler?


texts: What does "cellular" mean in this context?

texts:
I came across a confusing word when I was reading a Scientific American story, “Controversial Spewed Iron Experiment Succeeds as Carbon Sink” (by David Biello). It goes like this:

  “One key to the whole experiment’s success turns out to be the
  specific diatoms involved, which use silicon to make their shells and
  tend to form long strands of cellular slime after their demise that
  falls quickly to the seafloor.”

I'm wondering what “cellular” means in this context. Does it mean “of (diatom) cells” or “porous”?

Could someone kindly enlighten me on this?


texts: Is callus (in the context of plant tissue culture) totipotent or pluripotent? As I understand, the difference between totipotency and pluripotency is an ability to differentiate into extraembryonic cells. So, I stuck on the question: what is extraembryonic plant cells and could callus cells differentiate into it?


texts: Can anybody identify this kind of plant?

texts: Location: Low Tatras, Slovakia, elevation: 1800 m. Can anybody identify this plant from Slovakia mountains?


texts: Why some tissues like small intestine epithelium are able to be replaced so often, yet they are not one of the most common cancers?

texts:
My small intestine epithelium cells are replaced thousands times more than my prostate. Yet I'm much more likely of getting a prostate cancer than cancer on my intestine epithelium. Is there a known cause for this?

Does our body have better DNA-repairing mechanisms or something like that for those tissues ?


texts: I am taking my students to collect water samples from different bodies of water. These bodies of water include the local river, a park pond, and water accumulation from recent rain. Once we gather the samples students will be analyzing the samples under standard light microscopes. I was wondering what is the best way to preserve any life that may be found in the samples in case there is no immediate opportunity to analyze the samples under the microscopes? Is there a specific time frame to analyze the samples before they have to be replaced? Also if they are kept in a bottle/jar does the container have to be unsealed or with perforations to allow air flow? Thank you.


texts:
I'm trying to do spectroscopy readings on plants where I shoot electromagnetic waves and look at their signature/profile.
I want to be able to do this at a distance, in the field and on live plants so that I can modify my rig later to automatically do this on multiple plants daily.

I have no background in spectroscopy, but I heard that waves directed  through leaves can then be received on the other end using something like waveguide spectroscopy. I do not know the frequency range I should be looking at and was wondering how can I identify the range of interest for my plants.
Let's say I want to approximate the chlorophyll content in leaves and see if the leaf is healthy or not and look at its change daily. Some references to learn about this would be very helpful. Thanks!


texts: What gases are needed for humans to breathe?

texts: I will be beginning a science project about sustaining life on space stations. I already know that pure oxygen is harmful for humans but would $O_2$ + $CO_2$ be enough for humans to breathe in or do humans need other gases as well?


texts: What is this unusual structure inside this banana?

texts:
I was eating a banana, and I found this strange biological structure inside of it.

It was a bit tougher than the banana, and ran inside of the body through most of the length. To be clear, I peeled back banana with my fingers to reveal it; it was enveloped inside. It was accompanied by a small void.

No idea what this is, never seen anything like it. It didn't taste good. I'm thinking it might be a mutation. Anyone know what this is?


texts: Term for a prey animal's recognition that something potentially threatening is looking at it?

texts:
On my daily walks I frequently see individual or small groups of cattle egrets. At first I would try to photograph them but they would fly away. This vexed me because they ignored everyone else walking by as well as bicycles or loud vehicles in areas where there were roads.
I took it personally until I realized it wasn't me or my clothes, but the act of looking at them and taking an interest in them that spooked them.
This even happened at distances approaching 100 meters in open spaces, so I am not sure they could resolve my eyes and determine if my gaze was fixed on them. However, a few non-scientific tests suggested that they seemed to get nervous when I turned my head and looked at them, even though I kept moving. But even if I didn't look at them but instead continued to look forward, simply stopping and standing in place to take out my phone to snap a photo was enough to trigger them to fly away.
Question: Is there a term for this phenomenon in birds or other animals, not the flying away or fleeing part, but the recognition that something or someone potentially threatening is looking at them and/or may have taken an interest in them? Are there separate terms for responses to motion and responses to a gaze based on eyes or perceived face orientation?
Note: I have noticed a similar phenomenon with Malayan Night Herons as shown in What kind of big bird is this seen walking around Taipei? The individuals I see are more acclimated to people, but I still have to act at least disinterested when photographing them.


texts: Can proteins from different viruses be gathered in one virus?

texts:
There is a biology project I must do with some of my classmates and we're facing a problem.
We would like to choose proteins from different viruses that seem interesting to us (for example one protein from a negative-strand ARN virus and the other one from a DNA virus) and gather them (theory) together through this process called "directed mutagenesis". Is it possible ? If no, isn't there another mechanism that allows the gathering ?

Thank you !
(PS: Sorry for the english)


texts: How large an expression boost is typical from codon optimization?

texts:
There are lots of different codon optimization approaches out there, and a lot of different qualitative reasons to want optimization (e.g., organism codon bias, GC content, avoiding secondary structure).
One may also want to avoid optimization, however, in order to increase reusability of a component, comparability with prior results, or opportunities for error.
I'd like to know how much I'm likely giving up if I decide not to codon optimize. For example, in my typical work giving up 10% is likely to be lost in the noise, but giving up 2x is worth thinking carefully about, and giving up 10x means it's a must-have.
I know "it depends", and there's a lot of qualitative information out there, but is there any way to get a good rough-order-of-magnitude estimate of the typical expression boost from codon optimization?


texts: Why do we grow so much hair on our heads compared to our bodies?

texts:
I've been wondering about head hair, facial hair in particular. Human males can grow very extensive beards should they choose to not shave - however you do not really see this in our chimpanzee cousins! Yes, they have little pseudo-beards, but the difference being that they do not shave, that is just the length they reach. Whereas in humans we can grow to our hearts content (*this may not be the case, see this question).

I can't really see why this would have been selected, unless it's simply that (evolutionarily speaking) women like men with long beards?

So my question is: why can humans perpetually grow head hair, yet we have lost the majority of our body hair, in comparison to chimpanzees and other ape family members?


texts: Affinity for oxygen and carbon dioxide in animals

texts:
I'm currently reading Treatise on Invertebrate Paleontology (A) and don't understand the following fragment:

  The affinity for oxygen in lower animals is many times that in higher ones, whereas conditions are the reverse with regard to carbon dioxide.

What does it mean by "affinity"? Affinity of hemoglobins (in blood)? Affinity of oxygen-transporting molecules, whatever they are? Something else? The book doesn't provide a source of its claim here.

EDIT: @Will - I'm more interested in what kind of affinity they are speaking about in regards to carbon dioxide (I can't comment due to not having enough reputation yet.)


texts:
Growing in a garden in the philippines

Photo from above notice the unusual leaves

Photo showing bloom... In peak bloom...

Photo showing pod that plant produced at the same time blooms appeared


texts: Is agriculture really a net contributor of greenhouse gases?

texts:
A lot of scientific studies and credible sources indicate that agriculture is one of the major contributors of greenhouse gases. The exact numbers seem to vary a lot, I've seen everything from 8% to 45% of global greenhouse gas emissions.

What makes me unsure how to really interpret these numbers is the fact that the process of growing feed to feed livestock, raising livestock, and then eating that livestock, is a cycle. The very same plants that the livestock is eating has during the course of its growth acted as a sink, i.e. absorbing carbon dioxide from the air. This is totally different from pumping oil out of the ground and burning it, which is (in the relevant short term) only production of greenhouse gases, without the sink.

I would assume that any serious study on greenhouse gases would factor in the entire cycle of absorption through animal feed and release back into the atmosphere, yet none of the studies I have seen say exactly how they arrived at the emissions.

Aside from the fact that oil is used in agriculture, when only considering the actual gases released from animal farming vs plant farming, it doesn't really make basic sense to me that there could be a net production of greenhouse gases - where did the surplus come from?


texts: Would Bubling Oxygen Through "Dead Zones" Like A Fish-Tank Make Much Difference?

texts: I am a dilettante when it comes to dead zones. I realize that they vary from fleeting algal blooms to continuous dead zones. For the continuous dead zones it would seem to me that adding a "bubbler" like for fish tanks might help restore the depleted oxygen content, which would increase microbial activity and thereby increase the quantity of nitrogen removed from the water (hopefully) before it reaches the open ocean where the fleeting algal blooms occur. Has this been investigated or could it at least be assessed from a scientific perspective?


texts: Is the "freeze response" really a remain of our reptilian past?

texts:
I'm looking for any reliable sources relating the common-known human reaction on a stressful situation, humans sometimes freeze and can not move. From some materials found on the internet I got that it is supposed to be a remain from the bugs' playing dead. But it doesn't seem to be an advantageous reaction from the point of view of big mammals.

My explanation is that the brain just can't process the new complex signals. Are there any studies about this topic?


texts: What part of the brain controls depth perception?

texts: Specifically the part of the brain that does depth perception based on binocular vision. I have searched all over the web and have turned up nothing. Is it the same part of the brain that processes all images from the retina?


texts: What effect does taking antibiotics unnecessarily have on future bacterial infections?

texts:
I have been told by my biology teacher that you shouldn't take antibiotics unnecessarily because "the body gets used to them" and it reduces the effectiveness of antibiotics against future bacterial infections, which can be dangerous.

I can't understand how the body could "get used to" antibiotics. How does prior use of antibiotics affect their effectiveness against future infections?


texts: Influence of artificial sunlight on the human body

texts:
In a hypothetical scenario, where a large, permanently manned craft is in a continual orbit, and natural sunlight cannot be used as the craft may keep moving and turning, artificial sunlight is used in the form of LED panels.

My question is this: Will the LEDs have any adverse effect on the human body? The LEDs are of the SoLED variety which have very low IR levels and almost nil UV light levels, have any adverse effects on the body? I suppose the lack of UV may cause some disturbance in Vitamin D and melanin levels. Is this valid? Would there be any other problems?


texts: Can we use cancer cells to generate blood vessels?

texts:
Is there any possibility to use cancer cells, which generate blood vessels, to generate our blood vessels when we are wounded or when we have varicose veins in our legs?

Thanks for your answer in advance.


texts: What is the number of synaptic vesicles in an axon terminal?

texts: Is there any research as to the average number of synaptic vesicles per axon terminal in a human neuron's axon? On top of that, what percentage of those vesicles are used in a single action potential cycle i.e. membrane depolarization, hyperpolarization and return to resting potential?


texts:
I quite understand why thymine is present in DNA. So we can mark it out where cytosine undergoes a reaction and is converted to uracil. Then we can repair the DNA.

But how can we make that out in RNA ??


texts: Are there free electrons in muscles, hair, or skin?

texts:
Electric shock occurs upon contact of a (human) body part with any source of electricity that causes a sufficient current through the skin, muscles, or hair.

In metals many electrons are said to be delocalised (i.e, electrons are not bound to any of the atoms). Around one electron per atom is said to be unbound to atom in mettalic lattice. So there will be motion of electrons due to thermal energy, however due to their random motion, there won't be such a significant current produced. When electric field is applied across them there will be motion of electrons in a particular direction, causing significant amount of current. In case of insulators, due to bound electrons we can't expect current through them.

When our body becomes a part of electric circuit, current is said to pass through our skin, muscles, or hair. Does it imply that there are free electrons in skin, hair, or in muscles (like those in metals)?


texts: Is there a season for hummingbird moths (US)?

texts: I have seen hummingbird moths the last few years by accident . Always at dusk , usually on 4 O'clock flowers. This year I have looked for them many times but today ( Aug.24) is the first sighting. Location ,E TX ,garden zone 8. The variety is a sphinx, white lined or gallium (Hyles lineata ). I wonder if I missed them or do they only show up relatively late in the summer (now)?


texts: Help on reconciling seemingly contradictory evidence about fetal experience

texts:
Fetal awareness and especially fetal pain are controversial, political issues. However, I do not wish to get into politics and want to merely stick to the scientific evidence. I have found statements about fetuses in the womb that seem to contradict each other, yet there has been no reference to the opponents in either side.

Some believe that fetuses do not have awareness in the womb and cannot feel pain. Here is an argument along those lines, claiming that fetuses cannot feel pain, even when their nervous systems and brain are developed, because the chemical environment within the womb suppresses awareness and experience that shapes the brain only happens outside the womb.

However, some other evidence seems to claim that fetuses can have experience. Twins can interact with each other in the womb as early as 14 weeks of gestation, as stated here. It is possible to learn in the womb, and newborns, even after they are born, can retain this knowledge, as stated here.

I'm not sure what to think. Are some of these statements, such as the idea fetuses are not aware, just incorrect? Or can interaction and learning occur without awareness somehow? (I know pain is distinct from awareness, interaction, and learning. What seemed particularly strange was the idea that fetuses have no conscious experience whatsoever, especially as no one making that claim, as far as I know, even mentioned the evidence about interaction and learning at all).


texts:
I wonder if all quadrupeds (or, mammals, at least), are edible?

From what I have collected, even down to fish, everything is edible apart from being sick or infected, and, apart from some glands secreting (deliberately, as far as this term makes sense in evolution) poisonous molecules.

This is (if correct), in stark contrast to plants, where frequently many parts of the plant contains poisons. (It has some logic: plants can't run away or mechanically fight back.)

Q: Are all quadrupeds edible?

An additional bonus on: WHY?


texts: Why can we control our breath rate but not our heart rate?

texts: Even though we cannot survive for more than few minutes if we stop breathing or if our heart stops, why is it so that our heart beat is controlled involuntarily while breathing can be voluntarily controlled to a certain extent. I just noticed that blinking of eyes also falls in this category; though we involuntarily blink and our eyelids close involuntarily in bright light, there is still voluntary modulation. What kind of evolutionary changes and natural selection could have led to these kind of voluntary modulations i.e. cortical control over these processes?


texts: Why did evolution make people's skin dark?

texts:
Why do people living in the equator have dark skin?
I know that Melanin acts as a protective biological shield against ultraviolet radiation.

But doesn't black absorb all light in a way making the body more heated than the surroundings ?


texts: Mechanism behind Philadelphia chromosome translocation?

texts:
I was reading up on causative factors of leukemia on medicinenet and I came across the following statement:

  ...an exchange between chromosomes 9 and 22 leads to what is known as the Philadelphia chromosome.

What is the mechanism behind this? Is it purely mechanical? Would the locations on both chromosome’s be equidistance from the end (for lack of biology vocabulary.) In other words, would each segment involved in the swap have to be similarly sized?


texts:
The methods section inside a paper I'm reading make mention of replicate lines.
Example: "We founded 10 replicate lines from a single clone". This is in the context of experimental evolution and artificial selection of Chlamydomonas in a laboratory.

Can you please explain to me what a replicate line is?

Here's a reference to the paper:
Collins, S., Sültemeyer, D., & Bell, G. (2006). Rewinding the tape: selection of algae adapted to high $CO_2$ at current and Pleistocene levels of $CO_2$. Evolution 60, 7, 1392-401. DOI: 10.1111/j.0014-3820.2006.tb01218.x


texts: Possible reasons for DNA getting stuck in well

texts:
I am in the process of Library preparation for Illumina MI-Seq using mtDNA. Using NEB Hotstart LongAmp Polymerase, I was able to obtain upto 10kb amplicons of mtDNA. However, when I switched to a different DNA sample, I am not noticing bands anymore in the gel. Strange thing is that, if I fragment these samples (Diagenode Bioruptor acoustic shearer) I get fragmented smears similar to the ones I expect from fragmenting a 10kb amplicon, even though these are stuck in the well.
Therefore, I dont know if a 10kb amplicon is stuck in the wells and is not migrating (given I see similar results for fragmentation for the samples that got stuck), or I am seeing in the wells what is genomic DNA and no amplification has occurred. Does the 260/230 value affect PCR amplification in any way? (I have a very high 260/230 value ~5 for the new DNA sample I am using)


texts: Are there any epiphytic plants that pull water from the air and supply terrestrial plants with excess?

texts: Do you know of any epiphytic plants that pull water from the air and supply the excess to other terrestrial plants?


texts: Have creatures ever evolved to become less intelligent?

texts:
Inspired by https://worldbuilding.stackexchange.com/questions/58533/is-intelligence-the-natural-product-of-evolution , I'm wondering if creatures have ever become less intelligent as a result of natural selection and evolution.

It seems plausible, because the brain can use a lot of energy, and I've heard of other aspects of an animal atrophying because they're not useful any more, such as vision in the Mexican blind cavefish.

One possible candidate I can think of is the koala: it's described as having a low brain to body mass ratio, doesn't have a great need for intelligence, and may have a need to minimise energy usage.

I'm mainly interested in cases of natural selection, as opposed to artificial breeding - I wouldn't be surprised if we selected animals to be less intelligent.


texts: Melatonin production - requires nighttime, or just full darkness?

texts:
Is melatonin properly produced in daytime sleep in full darkness? Or does it require only nighttime sleep?

Additionally, what other biological implications are there, if any, to daytime sleeping? Melatonin production is the only biological implication I could find so far.