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How valid are Koestler’s criticism of evolutionary theory?
I recently read Arthur Koestler's 1967 book The Ghost in the Machine. In it, Koestler criticises the neo-Darwinian theory of evolution—beneficial random mutations preserved by natural seleciton—as insufficient to explain the formation of complex forms like eyes and eggs. The issues Koestler has with the theory are ones that I've been trying to wrap my head around since before I read the book, but I'm aware that:
a) the book is half a century old;
b) Koestler was not a biologist or scientist; and
c) neo-Darwinian theory/the modern synthesis seems to have stood the test of time
so I'm wondering how accurate Koestler's account of the theory is, and if he is wrong what the retorts to his claims are. Here are two examples he gives of complex forms:

[The giant panda] has on its forelimbs an added sixth finger, which comes in very ‘handy’ for manipulating the bamboo-shoots which are its principal food [but] that added finger would be a useless appendage without the proper muscles and nerves [and t]he chances that among all possible mutations those which produced the additional bones, muscles and nerves should have occurred independently are of course infinitesimally small.

and

The decisive novelty of the reptiles was that, unlike amphibians, they laid their eggs on dry land...[b]ut the unborn reptile inside the egg still needed an aquatic environment...[i]t also needed a lot of food...[s]o the reptilian egg had to be provided with a large mass of yolk for food, and also with albumen—the white of egg—to provide the water. Neither the yolk by itself, nor the egg-white itself, would have had any selective value...[e]ach change, taken in isolation, would be harmful, and work against survival.

Instead of random mutations and external selection, he suggests that ‘internal selection’ works at all levels, from chemical upwards, to correct ‘misprints’ long before the developed organism is exposed to any sort of external selection. The implication that there must therefore be some plan towards which embryonic development works is supported by two examples:

the growing eye-bud of the embryo is an autonomous holon, which, if part of its tissue is taken away, will nevertheless develop into a normal eye

and

[the fruit fly has a recessive gene that when paired with another in a fertilised egg will produce an eyeless fly.] If now a pure stock of eyeless flies is made to inbreed, then the whole stock will have only the ‘eyeless’ mutant gene, because no normal gene can enter the stock to bring light into their darkness...within a few generations, flies appear in the inbred ‘eyeless’ stock with eyes that are perfectly normal.

His other main point is that evolution takes a zig-zag path, evolving down until reaching an evolutionary dead-ends before retracting to ‘an earlier or more primitive, but also more plastic and less committed stage—followed by a sudden advance in a new direction’. For example:

[A]mphibian...ancestry...goes back to the most primitive type of lung-breathing fish; whereas the apparently more successful later lines of highly specialised gill-breathing fishes all came to a dead end.

and

...the human adult resembles more the embryo of an ape than an adult ape

Is Koestler's science just faulty, or are these valid criticisms that've been resolved since?

I am entirely unfamiliar with Koestler, but based on the excerpts you posted it sounds like he just making assertions to justify his own hypothesis. Does he make reference to any actual experiments?

Regarding the panda example: polydactyly occurs in many mammals often as the result of a single mutation. This example is commonly used in teaching developmental biology as it shows the effects that single mutations can have on tissue patterning during embryogenesis. You can read the Wikipedia article for a primer on this. If such a mutation happens to have a selective benefit for pandas, it is entirely plausible that it could take hold in a population.

Regarding the reptile example: I don't have any specific information on this, but evolutionary theory does not say that deleterious mutations cannot become established in a population (assuming for the sake of argument the mutations leading to reptilian eggs were in fact deleterious). It depends on the strength of selection against them, among other factors such as genetic hitchhiking or heterozygote advantage.

@canadianer For the zig-zag theory of evolutionary progress he cites Garstang, for the embryonic tissue reformation Weiss.

Regarding the fruit fly example: It is difficult to comment without knowing the details of the actual experiment. A well studied gene in fruit flies is called eyeless (actually the Pax6 transcription factor with homologs in all sighted animals studied) because mutations to it can prevent eye development. In such mutants, it is hypothetically possible for back mutations to restore the original phenotype (I'm not aware if this has actually been observed, but I'm not aware of a lot of literature on fruit flies).

Maybe both. Certainly his understanding of limb developement doesn't match modern understanding. The quote you provide seems to indicate that he thought the appearance of an additional digit would require a multitude of coordinated mutations. Our current understanding seems to indicate that it's all about changes in the regulation of genes. For example in fruit flies mutations in the antennapedia gene can cause antenna to grow where legs should be or visa versa. Another example is polydactyly(extra toes) in cats which be be caused by mutations to a single regulatory region.

within a few generations, flies appear in the inbred ‘eyeless’ stock
  with eyes that are perfectly normal.

I'm not a fruit fly expert, but this seems highly dubious to me. There is a well studied eyeless mutation, but it's dominant, not recessive. Furthermore getting two copies of this mutant eyeless gene is lethal at the embryonic stage. This means that a colony of adult eyeless flys are necessarily all heterozygous. That is, they have one copy of the mutated eyeless gene, and one copy of the normal eyeless gene. By Mendel's laws, a quarter of the offspring from the completely eyeless generation are going to have two copies of the normal eyeless gene, and so will have normal eyes. I wouldn't be surprised if the flies with normal eyes outcompete the flies without eyes, so eventually the eyeless flies will disappear from the colony. I can't tell you whether Koestler has mis-characterized this gene, or is talking about some other gene all together. Citation needed.

Koestler's entire argument can be summed up is an argument of irreducible complexity, which always stems from a lack of understanding of the biological systems. All his arguments stem from a lack of knowledge about the things he is describing. Lets handle them in order.

Panda thumb. lack of understanding. The panda thumbs does not move, it is just a spur of bone. but becasue it is a wrist bone it still has muscles on it so the argument is wrong in two ways.

Reptile eggs. Amphibian eggs have yolks and albumen. so this again is just a lack of knowledge.

Internal selection is again based on a lack of knowledge, the "plan" embryonic development works from are called HOX genes, which regulate development. And there are  organisms without them and indeed behave just like you would expect. Eyeless fruit flies do not lack the genes to make eyes they have a mutation in the HOX genes that trigger eye development, (lake a "make eye here" on a blueprint) and just as single mutation can prevent the gene from functioning, another can make it functional again, we can can even trigger eye development in the wrong place, say on the legs.

Is just confusing, It sounds like he thinks there needs to be some overarching plan to evolution instead of the chaotic whatever works mess that actually happens. In which case he does not even understand what evolution is, so his arguments against it make even less sense. I certainly can't imagine why he would claim teleost fish are dead ends when they are the most numerous vertebrate on the planet.

Time — i.e. the advances in our knowledge of molecular genetics — has clearly disposed of Koestler’s arguments, as it has of many of those of people who cannot see the wood for the apparently diseased tree.
Other answers provide chapter and verse, but what I wish to contribute in this answer is something about the intellectual bias that influenced Koestler’s views. Most of us will be aware that many anti-evolutionary arguments are made from religious conviction, rather than from disinterested scientific rationalism, but the poster and the younger members of this list may not be aware of a different kind of intellectual bias.
Although Koestler is most famous for his book “Darkness at Noon” in which he attacked the evils of Stalinism, after which he rejected the Communist party, this did not change the (in many respects admirable¶) socialist principles that had lead to his joining the party in the first place.
So, what does this imply? It does not imply a rejection by Koestler of Darwin’s theory of evolution, but a rejection of the idea of a genetic mechanism in which man is subject to the dice of random mutation. He still clings to a doctrinal belief in Lamarckism in which man evolves by the incorporation of characteristics acquired by his own efforts†. It is ironic that despite repudiating Stalin, he hung on to Stalin’s dogmatism that led to Lysenko and the consequent murder of Soviet geneticists as well as the death by starvation of untold thousands of Russians.
And the moral for today? There are several. But it is politic to restrict myself to suggesting one should question the motives of those who cry “epigenetics” when they haven’t the first idea of what they are talking about.

¶ In my opinion. (Not particularly relevant, but to show I am not criticizing him from a right-wing standpoint.)
† The actual context at the time he wrote it was different — a rejection of social Darwinism. I personally regard the latter as having nothing to do with genetics or biology, but in order to repudiate the one, he seems to have returned to his repudiation of neo-Darwinism.


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Do ribosomes read mRNA?
So I understand that tRNA bonds to a codon (with an anticodon) in the translation process. I read in my biology textbook that the ribosomes "read" the mRNA strand.
Why do the ribosomes need to read the mRNA strand? Are the ribosomes able to intepret the message and bring the correct anticodon to it? Or is the main function of the ribosomes just to join amino acids to make polypeptides? I'm just confused why the ribosomes read the mRNA strand when it seems like there is no need to.

Welcome to SE Biology. As your question appears to be just a misunderstanding of rather loose language I am giving a brief response in a comment and pointing you to an online source where you can find more detail. Yes, it is the anticodon of the tRNA that decodes the codons in the mRNA, so strictly speaking it is the tRNA that reads the mRNA (no need for the word "strand"). However the ribosome is required for this complex process, and it is where the tRNA, mRNA and other components bind, so the author is expressing this idea loosely

Since ribosomes act as a catalyst I would assume the reaction could happen without them but is would be many orders of magnitude slower, and likely to produce erroneous results of fail halfway. Its not a bad question but it could be worded clearer. "can it occur without ribosomes" would be a good foundation question.

@John — Protein synthesis is not a single reaction. Whereas peptide bond formation could occur at a slow rate without ribosomes, the other requirement to hydrogen bond to the mRNA at the same time makes that kinetically very difficult, and then you have to start at a particular place on the mRNA and continue. Yes it must have evolved from a simpler system, but no, it's very different from a simple catalyst. And don't encourage people to ask "could" questions — they generally yield subjective answers — we need "can" questions that are answerable.

@David Hence my statement that the question could be reworded as can the reaction occur without ribosomes. Which should be established before the above questions. Also I never implied ribosomes were not important, just that exploring how the system could function without them would be a better way to answer the OP's unfocused questions. For instance one thing we know for instance is that many mismatches in mRNA codon binding is because the RNA molecules are not rigid and can distort to form a wider range of binding, one function of ribosomes may be to limit such distortion.

@John — OK. But I think the poster can answer his question by reading a better account of ribosomal protein synthesis. I neglected to mention that your question is answered in a way by non-ribosomal synthesis of cyclic peptides by certain bacteria. Any new question would need checking that it hadn't been covered previously.

The first two sentences of the Wikipedia Ribosome article say:

The ribosome... serves as the site of biological protein synthesis (translation). Ribosomes link amino acids together in the order specified by messenger RNA (mRNA) molecules.

Slightly later, in the Overview section it says:

Ribosomes can bind to a messenger RNA chain and use its sequence for determining the correct sequence of amino acids for generating a given protein. Amino acids are selected, collected, and carried to the ribosome by transfer RNA (tRNA) molecules, which enter one part of the ribosome and bind to the messenger RNA chain. It is during this binding that the correct translation of nucleic acid sequence to amino acid sequence occurs.

And it then tells us "The attached amino acids are then linked together by another part of the ribosome."
So, the function of the ribosome is to make sure each codon of the mRNA is matched up with the correct tRNA, and then to catalyze the linkage of the associated amino acid to the growing chain of the protein being built.

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Calculating PCR Cycles
I have a problem understanding a PCR exercise, it says to calculate the number of cycles to get 1µg of the DNA fragment, starting from 10ng and then from 500ng, I know about 2^n, and the exercise even gave the answers:
For 10ng, we need 29 cycles
and for 500ng, we need 24 cycles
But I don't know how they did it, I tried with 2^n and ended up with something totally different. I would be grateful if someone explained it to me. Thank you.

With every round of PCR, your sample doubles (ideally) and you are right when using $2^n$ for calculating the amount of DNA produced.
The formula would basically be like this:
$$X_{n} = X_0 2^n \\[1em] n=\log_2(X_n/X_0)$$
Just substitute the values of $X_0$ and $X_n$ — 10ng and 1000ng. The answer would be ~6.64 cycles.
The 500ng case is easier to imagine. The amount is doubled between 1µg and 500ng. So it is just one cycle of PCR.
If this was your answer then you are right. If book says otherwise then it is wrong or you could have read the question wrong.

Thank you, i got exactly that, 6,64 and 1 cycle, but i was so confused.... there probably was a mistake in the book, thank you again, i appreciate it ^^

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Why are market squid attracted to fishing lights but also avoid naturally lit surface waters during daytime/full moons?
Squid fishermen use really bright lights (which can be seen from space!) to attract squid to the surface at night, but a lot of squid also naturally avoid surface waters that are lit during the day (by the sun) and at night (by full moon). As far as squid are concerned, what is the difference between the bright artificial lights and diffuse light that naturally occurs?

Great question...I don't know the answer but I look forward to hearing from someone who does!

Despite many sources stating that the lights attract the squids, the explanation given here is much more logical. Squids feed of small fish, crabs and shrimp, which in turn feed on plankton. Zooplankton is known to migrate vertically during the day (up at night, down during the day), which has also been reported for squids, probably following their prey.
The reason for this migration is that zooplankton feeds on phytoplankton, which can be found at the sea surface, where it gets most of the sunlight. During the day the zooplankton stays in deeper waters, because at the surface its easier to be spotted by predators. It's safer to move up during the night to feed. Other predators feeding on zooplankton follow, including the squids.
The vertical migration might be coordinated by an internal clock rather than light. It would therefore not be inhibited by the bright fishing lights. The squids don't seem to respond to the light, but rather to their prey.
Therefore, rather than attracting the squids directly, the fishing lights will attract phytoplankton, which attracts zooplankton and small fishes, which attract squids.


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Circadian clocks in enzymes
I'm aware of the existence of circadian clocks, but I don't understand exactly how circadian clocks regulate other circadian mechanisms. For example, if an enzyme is found to have a circadian rythm, how is this rhythm produced? Is it because of one or more clock genes?

If i am right, i think that all circadiam mechanisms regulations by circadiem clocks is highly discuss theme in chronobiology. So i dont think that you will get sufficient answer. Anyway can you be more specific about what kind of enzymes would you like to know because still it is too broad.

I think more details about what you're interested in would be helpful here. You seem to have two questions: 1) how the biomolecular clocks generate rythms, ie the fundamental nature of the biological oscillators, and 2) how they transmit that information to other biological elements like genes etc.

Molecular feedback mechanisms create rhythmic patterns. The circadian rhythm is driven by a handful of genes, which in turn can regulate a number of downstream factors.
Here is a very nice explanation of the Drosophila circadian clock, which gives you an idea how this works. The video shows the same animation adding more factors every time to guide you through how the system works on the genetic/protein level.
A brief summary: The genes period and timeless are transcribed over night. Their proteins stabilize each other and build up in the cell. At the same time they block their own transcription, limiting the amount of proteins.
Other factors destabilize the proteins and evoke their degradation. One of them is the light activated protein Cryptochrome. This helps entraining the clock and results in the removal of Period and Timeless protein during the day. The negative feedback of their blockage is removed and transcription starts anew at night, when Cryptochrome is inactive.
These clock genes do not only regulate themselves but can also activate or deactivate other factors resulting in daytime-dependent transcription of genes or protein activity.
The whole picture is of course a bit more complicated and involves a lot of additional factors. But also in humans and other mammals you find very similar mechanisms.


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Is this formula for calulating the energy requirements of pets applicable to all animals?
This website gives the formula: 70M3/4 = Resting Energy Requirement for pets in calories/day, where M is the mass in kilograms. Is this formula correct and accurate, and will it work for rabbits, mice, and guinea pigs?

There's a lot to talk about here, have you started with something like https://en.wikipedia.org/wiki/Kleiber%27s_law to guide you a bit? Is anything still unclear to you after you read that page?

No, because the exponent "3/4" is more important than the "70"; "70" depends on among other things the units you use - your question has lots of subquestions though, and most of them are answered there; your title is about Kleiber's law.

No, I would not use this formula for rodents. The "3/4-law" is usually used only for mammals with a mass of m>10 kg and was derived by Kleiber from limited empirical data sets.
For mammals with a bodymass below 10 kg the prefered exponent seems to be 2/3 which was derived from the relationship of volume and surface of the body and heat energy as the main source of metabolic rate. See here.
Either way this are only approximate calculations I would not trust too much as exceptions occure frequently and also the age and/or physical state can make a difference.


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Is this plant lantana camara? If not what is it?
I was in a botanical garden recently and wasn't able to find the tag on this plant. The diameter of the entire flower tended to be around 5cm.
Google seems to suggest its lantana camara but I'm not 100% convinced yet.

When rubbed, its leaves produced a minty aroma

It does seem very similar. Why do you doubt?

It is Lantana camara you are correct.  There are many hybrids out there as well.

It is Lantana camara, you can check here: https://en.wikipedia.org/wiki/Lantana_camara

Someone (not me), downvoted your answer. If this can be helpful for you, the reason might be that you do not give enough details in the answer itself. You should probably give more information such as key criteria that allow the confirmation of the identification of this plant.


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What is the population limit that makes consanguinity an issue?
A recent incident brought in the news one of the last uncontacted people - the Sentinelese:

the Sentinelese appear to have consistently refused any interaction
  with the outside world.
There is significant uncertainty as to the group's size, with
  estimates ranging between 40 and 500 individual

If I understood correctly, the Sentinelese have a rather small population for dozens if not hundreds of generations and I am wondering if consanguinity is not issue (e.g. serious childhood effects) for them.
Question: What is the population limit (lower bound) that makes consanguinity an issue?

Yes, inbreeding depression can be a big problem for very small populations (It's also a big problem for conservation efforts of critically endangered species, such as the Kakapo). Unfortunately, I can't really answer your specific question regarding lower bound.

I don't have a great knowledge in population genetics but I think your question can be answered by the relationship between loss of heterozygosity and the effective population size.
For an ideal asexually reproducing genetically diploid population, the heterozygosity is lost with increasing generations according to this equation:
$$H_t=\left(1-\frac{1}{2N}\right)^t H_0$$
where $H_t$ is the heterozygosity at the generation $t$, $H_0$ is the heterozygosity of initial population and $N$ is the population size.
If you analyse this equation then you'll note that heterozygosity exponentially reduces at rate inversely proportional to the population size.
For real populations you have to replace the population size with effective population size. Effective population size for a sexually reproducing population would be:
$$\frac{1}{N_e} = \frac{1}{4N_m} + \frac{1}{4N_f}$$
Where $N_e$ is effective population size, $N_m$ is number of males and $N_f$ is number of females.
You can find the derivation of these formulas in Principles of Population Genetics by Hartl and Clark.
Other than that, the probability of extinction is also higher, the smaller the population is.
When would consanguinity be an issue depends on other factors too such as initial heterozygosity, presence of deleterious alleles in the gene pool and other environmental factors. I don't think there is some kind of mathematical/practical lower bound. The minimum viable population is approximated using simulations.


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Brownian motion : Understanding the output of mvBM function.?
To fit the brownian motion for independent evolution of traits i used below code:
rownames(carni)<-gsub("_",".",rownames(carni))  #Renaming to match the tip of tree
#Independent Evolution
brown_indepen <- mvBM(carni_tree,carni,param=list(constraint="diagonal"))

mvBM is the function from mvMORPH package. It seems by giving constraint="diagonal" would fit the model for traits to be evolved independently. I would like to know the idea behind it. Also, i got the below output after running the code. I would also like to know what below output means.
LogLikelihood:   -589.2373
AIC:     1186.475
AICc:    1186.771
4 parameters

Estimated rate matrix
______________________
      size    range
size  73.70335  0.00000
range  0.00000 13.54524

Estimated root state
______________________
       size    range
theta: 38.43947 13.78439

Size and range were the two traits.

This seems appropriate for the biology forum, but consider posting/migrating to statistics or bioinformatics--they may be more familiar with mvMORPH


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How does zoo and laboratory animal feeding work?
What steps are taken to ensure those animals are fed adequately? When dealing with larger populations of animals, how is it ensured that all of those animals received food during a certain time period, and not fed multiple times by different people working different shifts? Is there a procedure in place for identifying and treating animals with over and under nutrition?

sorry you guys I keep  making adjustments to the original question, I might have to divide this post into a separate thread.

I volunteered for 3 years at a large mammal laboratory where we diligently tracked the weight and caloric intake of each of our animals. Diets were weighed out each morning and total calories could be calculated based on the known caloric value of the particular food item.
We fed our animals during training sessions and would adjust the individual's food intake based on their appetite/motivation (i.e. if an animal was full, they'd drop the piece of food they earned or leave the session). This would indicate that we could decrease the individual's diet in small increments.
The animals were also weighed each week. Weight and caloric intake were recorded in daily logs using FileMaker Pro. This allowed us to view fluctuations of each throughout the year and compare to previous years. If an animal's weight was a bit lower at a certain time of year than it typically was in past years, we could increase their diet.
Diet items were selected based off of the animals' natural diet.

In our university, this is regulated by Institutional Animal Care and Use Committee
This organization provides guidance for humane and responsible management of laboratory animals. These protocols were established, and still modified, to enable optimal well-being of animals, as researchers extremely interested in robust and stable conditions for their subjects.
On the practical note, (we work with fish) we monitor such parameters as:
 - efficiency of laying eggs
 - average size and time to adulthood (sexual maturity)
 - life span
 - rate of malformation or illnesses
The food is monitored and regulated to make these optimal, but we change these things gradually, and usually use some smaller population to test changes, before applying to whole colony.


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prokaryotes and Evolution
I have a question that I did not find an answer to online and maybe anyone here could help.
Why are there still prokaryotes today? Why didn't they all evolove?

You are very deeply misunderstanding evolution. Prokaryotes are still evolving and will continue to evolve. Prokaryotes on the whole are extremely successful organisms (i.e. are very far from extinction), so the whole lineage did not need to abandon 'prokaryote-ness'. I am honestly and wholeheartedly afraid a more technical answer will be beyond your understanding. A simple google search will provide you with a million varied, concise responses. Conclusion: evolution is not teleological, i.e. evolution has no end goal in mind.

They did evolve, and they keep evolving every single day, like all other organisms.
Let's take an example. Prokaryotes acquire antibiotic tolerance in hospitals, and have evolved resistance to pretty much every antibiotic available, within a few years of their discovery.
More fundamentally, what is evolution (in a classic Darwinian definition)? Evolution is 1) the random apparition of new traits and 2) the selection of some of these traits because they provide some kind of advantage - antibiotic resistance is a perfect example.
Prokaryotes mutate much, much more than larger organisms like us, so they constantly try new biological strategies, and because their generation time is short, selection occurs much faster. So prokaryotes actually evolve faster than most eukaryotes!
I think you are confusing "evolving" with "becoming more complex", and then "becoming more complex" with "being larger and multicellular". Both of these are incorrect.
Prokaryotes live everywhere on the planet, even in places where animals and plants struggle to survive. They can live in water, in air, in the cold or in extreme heat, in acid, in pure brine... When you think about it, micro-organisms really rock! They can adapt to conditions much harsher than what we can tolerate. This ability to adapt is pretty much the definition of successful evolution.
I'll conclude with a bad analogy: what do you think is the most "advanced": an iPhone, or a big gaming desktop computer? They're both recent, they can do lots of things (some identical, some different) but one if not per se better than the other, they simply have different ways of being awesome, in different contexts.


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Design rules for DNA linkers
I want to use double stranded DNA linkers to physically bind two "things" together, by grafting ssDNA on each one of them and using DNA hybridization as the locking mechanism.
I do not expect the nature of the two things to be important for this question, but if it is, let's say I want to link a solid surface and a protein.
Let's say that my only constraint is that I want this crosslinking to be stable at 37°C.
There is a gazillion ways I could design the sequences, and pretty much anything above 20bp without massive self complementarities should work, in theory. But I don't like to pick bases randomly. So my question is this: is there anything I can look for, except for the two constraints above, to design a good linker sequence?
For example, if the melting temperature is 50°C vs. 65°C, I would expect the structure to be stable (infinitesimal dissociation constants in both cases). Would there be any reason to choose one over the other, except for maybe oligo synthesis price? For a given melting temerature, is there any difference between a long AT rich sequence and a short GC rich sequence?

You might want to pick something that has little or no homology with anything that exists in any organism in the databases, just in case.
Gut feeling says to go for balanced oligos in the middle between AT-rich and GC-rich, and not have repeats or homopolymers.  If you go for AT-rich, then your complementary will be GC-rich, and vice versa. I'm pretty sure there would then be a differential in the mechanical properties of the two oligos - maybe this would be something useful to have for other reasons though?
It seems like most of the design principles might be constraints (do nots) rather then goals (dos), so you could do worse than have a generator churn out random sequences, and score each one against the various constraints.  Random seems OK, if you are then checking each randomly chosen pair against some strong rules.  Then pick ten or so pairs that all score well, get them synthesised and see whether any work...


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Ways creatures evolove
I can't find the right answers to my questions online .
are there other ways creatures evolove apart form nsatural selection?
Thank you

Artificial selection, to name one

Yes, there are a number of processes that affect evolution of populations.
The classification of these processes can be open to some philosophical discussion. For example, most authors, don't really consider natural and artificial selection as being different. Also, most authors tend to consider sexual selection as being a subset of natural selection. At the end of the day, the details classification does not really matter to science as long as we have clearly defined (mathematical) models of these processes. I will just list concepts below ignoring potential issue of classification:

Natural selection
Artificial selection
Sexual selection
Genetic drift (incl. population bottleneck and other demographic elements)
Gene flow, interbreeding and hybridization
Linked selection (genetic hitchhiking, background selection)

For more information about what evolution is and what are the processes that affect evolution of populations, you might want to have a look at a short very introductory course to evolutionary biology such as for example evo101 by UC Berkeley.


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Quantify Protein Denaturation with Change in Solubility
I plan to run a lab which compares the impacts of ethanol and methanol, in varying concentrations, on the denaturation of whey protein.
Change in water solubility is a good indicator of the degree of denaturation in a protein, but online research doesn't seem to be showing any exceedingly simple method of quantifying a change in solubility. Can protein precipitation be used to measure solubility? If so, I have access to a centrifuge, ammonium sulfate and just about any other chemical compound. Are there any better methods, altogether?
Is change in solubility the only factor which may reflect denaturation?
Thank you

How do you plan to actually measure the protein?

By mass scale. I need a way to find the solubility of the protein solution, as in solution of saturation.

How pure is your sample?

I’m varying the samples by solution of ethanol or methanol (Ex 1:1 ethanol/water ratio).

Mass of protein is kept as a constant, as well as volume of solution

To answer your question though, the whey protein I’m using is 95% pure.

There are many ways to assess protein denaturation. Keep in mind that denaturation and precipitation are not necessarily coupled. For instance, detergents can denature proteins and yet make them quite soluble. It seems that you are asking two separate questions here. If you decide that protein solubility is what you want to measure, we can suggest some simple protocols.

I have decided to simply separate the formed precipitate from the solution with a centrifuge, filter the precipitate with filter paper, determine the mass of the precipitate, and find a ratio between that mass and the full mass of the utilized protein sample. Is that a good way to assess the degree to which the protein was denatured? It seems to me like my best option...


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Equation relating probability of fixation and number of generations
I am trying to find an equation that relates the variables of probability of fixation and generations. Or, how does number of generations affect the probability a gene will fix, if population size doesn't significantly decrease or increase.

You may want to have a look at the notion of Moran process, that's pretty much what these models are designed for.

From Hartl and Clark's 'Principles of Population Genetics' Third Edition chapter 7: Kimura and Ohta (1969) showed that the mean time in generations until the allele of frequency p is fixed (ignoring cases where the allele is lost) is:
$$t_1(p) = -4N[(1-p)log(1-p)]/p$$
The mean time to loss of the allele is:
$$t_0(p) = -4N[p \cdot log(p)]/(1-p)$$
Thus the mean persistence time of an allele is:
$$t(p) = -4N[p \cdot log(p)+(1-p)log(1-p)]$$
Hopefully I didn't make any typos there, but I reccommend this book to learn all the ins and outs of popgen. There is a PDF of the third edition online in an archive. For more book recommendations, please have a look at the post Books on population or evolutionary genetics?
You can also find these equations in the original article: Kimura and Otha (1968)

By wrapping your equations in dollar signs, you can use LaTex type of formatting. For example $\frac{1}{\sqrt{2}}$ becomes $\frac{1}{\sqrt{2}}$. See your answer edited for more info. I also added the original article and a link to more book recommendations.

It seems like answer to your question can be related to effective population size and idealized population. One of the models to to consider is Wright-Fisher model:
$$\frac{(2N)!}{k!(2N-k)!)}p^{k}q(2N-k))$$
where N is individuals, so there are 2N copies of each gene, k is number of copies of an allele that had frequency p.


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Why is Turner syndrome a problem?
Turner syndrome is a chromosomal disorder where one of the X chromosomes is missing. For more details visit the Wikipedia page
I don't understand why missing one X chromosome would be harmful. In normal females one of the two X chromosomes is inactivated at an early embryonic stage to a Barr body. For more details visit the Wikipedia page on this.
This X chromosome inactivation can be beneficial. For example, women are less prone to sex-linked genetic disorders due to this X chromosome inactivation.
My questions are:

If only one copy of an X chromosome is active in normal human females, why would having only one copy of an X chromosome cause a disorder?
What does it mean to deactivate parts of a chromosome
Why would it be essential to have two copies of a gene, as only the dominant one is expressed?

I've edited your question to improve the spelling, grammar, and style. Feel free to roll back or make further edits if you'd like. I'd note, it is best if you ask only one question at a time. I think @AliceD and my answers have addressed your main question (if X inactivation happens anyway, why is Turner syndrome a problem?). I've very briefly addressed what X inactivation is. If you have more questions about it, I would recommend asking another question. If you would like to know more about what having two copies of a gene accomplishes, that should probably be its own question as well.

If I do that people downvote and mark it as duplicate

Duplicates aren't bad. they mean you have asked a good question and we already have an answer for you. If a duplicate doesn't actually answer your question, you just need to articulate the difference between the duplicate and your question.

Short answer
Some genes on the X chromosome escape X-inactivation. Two copies of these genes are needed for normal development. These genes are also present on the Y chromosome. Hence, healthy males and females both have two copies of these genes. In Turner's, the SHOX gene seems to be one of the culprits, which is needed for normal skeletal development.
Background
It appears that both of the X chromosomes are needed for normal development in females, as some genes on the X chromosome escape X-inactivation. Many of these genes are located at the ends of each arm of the X chromosome in areas known as the pseudoautosomal regions. Although many genes are unique to the X chromosome, genes in the pseudoautosomal regions are present on both sex chromosomes. As a result, men and women each have two functional copies of these genes. Many of these genes are essential for normal development (source: Genetics Home Reference).
Which genes on the X chromosome are responsible is not yet known, but a gene called SHOX seems to be involved, which is important for bone development and growth. The loss of one copy of this gene likely causes short stature and skeletal abnormalities in women with Turner syndrome (source: NIH), see Fig. 1.
SHOX is a transcription factor of the homeobox family. It acts during early embryonic development to control the formation of the development of the skeleton. It plays an important role in the growth and maturation of bones in the arms and legs source: NIH).

Fig. 1. Some developmental malformations seen in Turner's syndrome. source: University of Chicago
FYI - I wrote an answer before checking for duplicates. I think my answer does add additional information (the SHOX gene is not mentioned in the linked question's answer

Rudimentary ovaries may be caused by wrong genome imprinting cause XI did not happen. We know that much better in 2022.

@AliceD's answer is excellent, but I thought it would be helpful to include an additional perspective.
The issue here isn't that monosomy X shouldn't be a problem because the majority of one X chromosome is inactivated. It is that monosomy X isn't as big a problem as any other monosomy because the majority of one X chromosome is inactivated. Monosomies generally lead to embryonic or fetal loss. There are a number of other disorders and reports that are described as monosomies, but they are partial monosomies (e.g., monosomy 10, monosomy 22). Monosomy X is the only complete monosomy that regularly produces a viable fetus, occuring in about 1 in 4000 live female births. It is believed to be present in 1-2% of all conceptuses.
There is an excellent overview of this topic in Chapter 5 of Thompson & Thompson Genetics in Medicine, with a particular discussion of Turner syndrome in Chapter 6.  There is also a review of the process of X inactivation, which involves usual strategies of silencing genes (conversion of a section of a chromosome to heterochromatin by covalent modifications of histone and DNA). It is just used more broadly on the X chromosome.

authors: Валерий Заподовников


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Barr body. How does it work?
Barr's body is a spiral X chromosome. If I'm not mistaken, one random chromosome (a healthy woman) is inactivated in each cell. Which X chromosome is inactivated in a given cell is random. I've heard the example of a tricolor cat. The patched coloring is caused by the fact that  cells responsible for the color of each patch contain another inactivated X chromosome.
But what if a girl is a carrier of the Daltonism gene, why isn't she sick if a chromosome with this gene can be inactivated in some cells?

Hi silly school girl. There are 5 question marks in the question, that's about 4 too many. Try to post a targeted, clear question instead of stacking up a bunch of questions.

Thank you for your comment, I'll take it into account.

Get better? It was necessary to reduce a question a little. Thank you for your friendly attitude to young and naive students.

Like you said the sexual X chromosome inactivation is random in each different cell, this means women have some cells with the maternal x chromosome active and others with the paternal x chromosome active. Now if a woman carries the daltonism gene mutation (heterozygous for color blindness) she can actually manifest signs of the disease if the retinal cells randomly silenced the healthy x chromosome instead of the mutated one in more cells compared to the opposite pattern of silencing (meaning she can present daltonism out of pure bad luck).
It is worth mentioning that the magnitude of this disease will never be as strong as it presents itself in males since women (even the unlucky ones who present signs of daltonism) will always have the protection of a certain percentage of retinal cells with the healthy x chromosome active. The only way a woman could have classic daltonism to the same extent as a male is if she presents the color-blindness gene mutation in combination with Turner syndrome.
In conclusion recessive X-linked diseases aren't "everything or nothing" since woman could present signs in function to the number of cells that randomly inactivated the healthy X chromosome. They will fully express themselves in males all the time though.
References:
Scitable by nature education - Q&A
X chromosome inactivation - Nature education


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I want to extract genes from genomes
I m a student at computer science and I'm working in a project called Plant Breeding and for moment I need to extract genes from a file with genomes.
I know that the start sequence of a gene is ATG and the stop sequences of a gene is TAA,TGA or TAG.Should I know about inside more apart of the fact that inside I will find only A,T,G,C and inside are exons and introns?

I would highly recommend you to look into the detailed descriptions (or even papers) of how gene prediction and genome annotation is done.
This is a very complicated problem and you seem to missing knowledge of many details that need to be considered, but also there is a lot known about how to do this right, so you don't have to solve this by yourself.
A few very important details, that you either haven't stated or are misunderstanding:

The the ATG codon is the start site of translation, but not the start of a gene. A gene encompasses a promoter (which are very hard to define/predict), 5' & 3' UTRs (untranslated regions) in addition to the open reading frame, which is marked by start & stop codons.
In addition the genomic (i.e. DNA) sequence will contain introns, which are usually much larger than the exons coding for the proteins, and may contain any sequences, so you can not look for codons there.
If you are working with species for which the genome sequence is already known (which is a big number of species), at least a 'rudimentary' gene prediction has very likely already been done. You can find the annotation of all identified features (like genes) in the genome annotation files corresponding to the genome, however this gets very detailed and complicated very fast.
If you are working with a newly sequenced species, where this has not yet been done you need to be aware whether you have genome and/or transcriptome sequences (the latter are important to find gene locations with high quality).

Can you tell me someyhing about introns and exons?
The rules to split them.

And something about the size of the genes for Brassica napus oleifera and Brassica rapa oleifera.

I agree with Nicolai's second point - has your species been sequenced and assembled previously? If yes, then search online for the genome annotation (https://www.ncbi.nlm.nih.gov might be a good starting point).
If your species has not been assembled and annotated, then you might want to look into de novo gene prediction software. This page has a list covering some of the various kinds https://en.wikipedia.org/wiki/List_of_gene_prediction_software


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What is difference between Incest and Inbreeding?
Are they the same? As both are related to sexual activity between close relatives.

Welcome. What have you found so far? I think copying and pasting the question title in google will deliver a result in no time.

Incest is a human concept defined by law and social conventions. For example, see a definition of the word: "sexual intercourse between persons so closely related that they are forbidden by law to marry".
A person who was adopted may have siblings who are genetically more different from them than other people they could legally have romantic relationships with. In many countries you may marry your cousin, but not your foster brother/sister born on the other side of the world.
Anthropologist Claude Lévi-Strauss pioneered the study of the universality of the notion of incest; romantic relationships with family members is culturally forbidden in pretty much all cultures around the globe. But why? One of the explanations is linked to the notion of inbreeding.
Inbreeding (mating between genetically closely related individuals) favors homozygosity, and as a consequence a certain genetic homogeneity in which there is often not a "functional" allele to compensate for the "broken" one - the consequences on physiology and mental cognitive abilities are often dramatic (see Roberts, BMJ, 1967 or this article from Stanford @ the Tech, for example); it is hypothesized that this is the reason why evolution selected behaviors that avoid the risks linked to inbreeding.

Incest and inbreeding are different concepts. Incest involves crossbreeding between close relatives. Inbreeding is a broader concept. It can be a connection between relatives or self-pollination.
UPD: This is certainly not a journal article, but..... https://en.wikipedia.org/wiki/Inbreeding

Hi, the silly girl again! We expect answers to be backed up by credible sources, preferably journal papers. In addition, the answer isn't clear - the last sentence doesn't make clear why it's different.


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Can a dividing cell that skipped DNA replication become cancerous?
Let's assume that a cell fails to replicate its DNA during the S Phase of the cell cycle. Let's also assume that the appropriate CDKs are inactive (perhaps due to mutation or lack of cyclin proteins etc.) and the G2-M checkpoint fails.
2 questions:

Will the Spindle Checkpoint fail due to not having duplicated DNA, or can mitosis complete and form aneuploid daughter cells?

More to the point, if mitosis can complete after a cell fails to replicate its DNA (irrespective of the answer to question 1), can the resulting cell (if viable) lead to a neoplasm or cancer?

My thought is no because the odds of having subsequent generations of cells experience similar losses of DNA via mitosis of un-replicated cells would eventually lead to mostly non-viable next-generation cells and the "uncontrolled" division would cease.

Though, admittedly, this assumption is dependent on the assumption that the original cell has a heritable issue that "disables" the appropriate checkpoints (vs some random fluke event) allowing the uncontrolled cell line to continue duplicating with un-replicated genomes.

I'm also not sure how ultrafine anaphase bridges (see Moreno et al. 2016) can be informative for this question.

I found a paper (Deshpande et al. 2005) that discusses cyclins and cdks in development and cancer, but their paper focuses on the transition from G1 to the S phase and stops short of discussing mitosis of un-replicated cells

Note: this might sound like a homework question, but I'M the one writing the assignment! In fact, it's an exam, and I'm trying to cover my bases for the answers I provide for a different cancer-related question to ensure there are not multiple correct answers.


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Intelligence as measured by DNA tests
Suppose a person has an IQ of 130, as measured by a standard IQ test, when he is 18 years old. He then goes on to develop severe mental illness, which reduces his IQ to 100. After this, he takes a DNA-intelligence test, like the one offered by GenePlaza, which claims to measure his intelligence from his DNA. Will this test show an IQ closer to 130 or 100?
Note that mental illness is governed by a combination of genetic and environmental factors.

Note that the "IQ test" on GenePlaza is not meant to be taken seriously: 'The results come with disclaimers saying the results don’t mean much yet, because they predict only about 5 points of IQ. “I hope people are not getting it thinking that this is a true measure of their intelligence,” says Alain Coletta, a bioinformatics scientist and the founder of GenePlaza.'

What are the causes of this severe mental illness in your scenario?

@Remi.b As I said, my understanding is that mental illnesses like schizophrenia are governed by a combination of genetic and environmental factors.

I'm voting to close this question as off-topic because this is a question about intelligence tests, not about biology.

@ David I'm basically asking if a person's true IQ can be accurately predicted from his DNA. How is that not a biology question?

The answer will depend on the data that genetic model was developed from. I would suspect that most research on genetic factors of IQ has been performed in healthy, normal adults, so the model will predict IQ from DNA as if the subject were a healthy, normal adult (whether they are or not). It's unlikely that the DNA-IQ model was developed using a large cohort of mentally ill people, so the model may produce inaccurate results when applied to those people. I would expect the test to produce a score closer to 130 (if it is indeed an accurate model, which I will not discuss here).
Even if there are genetic predictors of the mental illness, it's likely not a 1:1 correspondence between DNA features and the illness, so this effect would be diluted when correlating against a third variable like IQ.


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Why are there so many species of bats?
I read that roughly 20% of all species of mammals are bats. Is there a good explanation for why bats have diversified so much compared to other mammals? Is it because bats' ability to fly allows them to fill niches that are completely out of reach (pun intended) of other mammals? If so, how is this reconciled with the coexistence of bat populations and bird populations?

Indeed, good question. There's tiny bats, large bats, and so many different species of them! A clue can be found in the observation that each bat species is almost always restricted to a small geographical region. With this in mind, it has been shown that an animal lineage's ability to diversify quickly in new environments depends largely on its diet. Bats have an incredible variety of dietary sources. Plant nectar, insects (there's so many different kinds of insects...), blood-feeding, and more! So, as you can imagine, bat species are restricted because they have specialized diets and because they are very good at taking up new diets over evolutionary time. Unfortunately for them, it restricts them to a geographical location much of the time. Geographical restriction is always a good starting point for speciation events, and there have been many in the bat clade. But why bats, specifically, you might ask? Well - it is argued (below) that it is due to the characteristics of their skulls, rather than their wings.
Dumont, E. R., Dávalos, L. M., Goldberg, A., Santana, S. E., Rex, K., & Voigt, C. C. (2012). Morphological innovation, diversification and invasion of a new adaptive zone. Proc. R. Soc. B, 279(1734), 1797-1805.


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How is the activation energy lowered in an enzyme by just orientating the reactants closer to one another?
If the activation energy is lowered, bond strength has decreased. How does purely orientating the reactants closer to one another lower the activation energy in a protein? The only thing I can think of is steric strain.

We welcome new posts to SE Biology, but ask that posters read the advice in the help about posting questions. Your question has problems which can be solved by clearly setting out your assumptions and their basis. You state "if activation energy is lowered bond strength is decreased". You do not say what bonds you are talking about (the transition state?) and your basis for this assumption. Then you say "how does purely orientating…" without saying that you have read (where?) that this is how enzymes works. Please revise carefully.

The activation energy is not only lowered by orientating the substrate but by stabilizing the transition state.
According to the induced fit model many enzymes show a higher binding affinity to the transition state of a substrate.

We welcome new participants to SE Biology, but this is a question and answer site, not a discussion site, so what we expect from an answer is more than the two lines here. First, you need to consider whether this question should be answered at all. It is so poorly constructed that I would say no. However if you must, you need to clarify the question and the false assumptions, porvide more detail, and provide external justification for your answer. Without links or references, how can anyone tell whether or not you are correct?


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Are the bacteria doing the same photosynthesis as plants do?
I mean Plants during photosynthesis produce  oxygen but Do bacteria also produce oxygen during photosynthesis or produce  other gases?
If yes , how do these bacteria process photosynthesis by producing other gases?

There are bacteria that do anoxygenic photosynthesis but, afaik, cyanobacteria (which produce oxygen) are the most important phototrophic bacteria on modern Earth. I suggest you do a bit of reading on Wikipedia.

Photosynthesis is always about using solar energy to oxidize a mineral molecule and reduce an organic molecule, which becomes an energy source for the photosynthetic cell.
Bacteria and plants have different types of photoreceptors. It is not always the same chlorophyll, maybe even no chlorophyll at all ! The different colours in algae come from the different pigments they are using to do photosynthesis.
Plant cells carry out photosynthesis in chloroplasts, which are organites, whereas bacteria carry it out in their plasmic membranes.
Plants do aerobic photosynthesis, which means they reduce dioxygen into water. Some bacteria do anoxic photosynthesis, which means they can reduce hydrogen sulfide into sulfur.


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Cloning a coding gene into a non-expression vector
Does it make any sense to clone a CODING gene into a NON-expression vector?
doing this will only give us multiple copies of the gene, while we could run  PCR instead (Let's say we know the gene sequence)

Welcome to SE Biology. Please take the tour and read how to ask a good question. You need to provide some context to your question as the reasons for cloning genes are numerous, and your quesition is in danger of being considered too wide. You should also indicate what efforts you have already made to answer the question for yourself. Tell us what you found and why it doesn't fulfill your requirements.

In principle, you can amplify any gene with PCR and then clone it into a vector of choice. However, it is often not as easy. Most things can be done with expression vectors, but sometimes it is easier to clone a sequence first and then subclone it.
Some sequences are hard to amplify, especially when they get long or very long. Amplifying 2,5kb can be tricky, digesting and subcloning such a piece might be easier. Additionally yields of PCR can be low, while you get a lot of DNA from a miniprep.
You might want to introduce additional restriction enzyme recognition sites (one can easily be done via PCR, but more again is tricky), linker or additional tags, which are not present in all expression vectors. Then it is easier to simply do a first cloning step into the non-expression vector and then take the complete insert into the expression vector.


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Why is the resting membrane potential of excitable tissue not affected by the extracellular sodium concentration?
I know that the resting membrane potential for excitable tissue (eg, nerve) is primarily determined by the electronegative difference between the inside and the outside of the membrane for potassium ions, as they are most permeate ion by far. And since the membrane is largely impermeable to sodium, it's diffusion potential is insignificant, as such it does not contribute much to the resting membrane potential.
However, is it not correct to think that if the concentration of sodium ions in the extracellular fluid drops, outward diffusion of the positive potassium ions will increase, because the outside of the membrane is now less positive (more negative), subsequently making the diffusion potential of potassium and the resting membrane potential more on the negative side and further from the action potential threshold. I am asking this because my professor was mentioning factors that affect the resting membrane potential, and he mentioned that the ECF concentration of sodium has no effect on the resting membrane potential.

I cannot imagine anyone being able to explain it more clearly than this webpage. Your question is addressed in the middle of the page.
It's easier to split the idea into two separate, but parallel ideas: electrical potential and chemical potential. Both sodium and potassium contribute to resting potential. Sodium affects the voltage (electric potential) across the membrane. However, their chemical potentials (difference-across-membrane) are separate. The key idea is that there is a difference between resting membrane potential and potassium equilibrium potential.
I quote a helpful thing to keep in mind:
In a neuron, the resting membrane potential is closer to the potassium equilibrium potential than it is to the sodium equilibrium potential. That's because the resting membrane is much more permeable to K+ than to Na+.

    If more potassium channels were to open up—making it even easier for K+ to cross the cell membrane—the membrane would hyperpolarize, getting even closer to the potassium equilibrium potential.
    If, on the other hand, additional sodium channels were to open up—making it easier for Na+ to cross the membrane—the cell membrane would depolarize toward the sodium equilibrium potential.

Hey. So if the resting membrane potential is indeed dependent somewhat  on the extracellular sodium ions concentration, wouldn't a drop in that concentration affect the resting membrane potential? If that's true I think the next issue is to only decide on how much of the sodium ion extracellular fluid concentration needs to drop before the resting membrane potential is affected in turn. Please also check my comment on the other answer. Thanks for replying, I really like Khan Academy as well.

This is a common misconception where ion concentrations and charge concentrations get confused.
Although the resting potential makes it sound like there is more "positive charge" outside than inside a cell, that difference is really really tiny, we are talking about a tiny tiny fraction of the number of ions in a cell (see for example Why is it possible to calculate the equilibrium potential of an ion using the Nernst equation from empirical measurements in the cell at rest?). For all intents and purposes, the sum charge of positive and negative ions is neutral both inside and outside the cell, to several decimal points.
If someone says the sodium concentration outside the cell changes they don't really mean just sodium ions, they mean sodium ions plus some equivalent number of negative ions. We can ignore those negative ions if they don't have any membrane permeability (see the Goldman equation: ions with no permeability don't count at all for membrane potential).
So in your question you already identified why extracellular sodium concentration doesn't matter much: its permeability is low and the extracelullar sodium concentration is already high. You should not think about adding extracellular sodium changing the charge of ions outside, you should only think about it as changing the driving force for sodium. The resting membrane potential is then a function of a sum of all those driving forces weighted by their permeabilities and calculated with the Goldman equation.
I won't do the math here, but if you actually were able to dump a bucket of just sodium ions, all with positive charge, in the environment outside the cell without a corresponding negative ion in solution, you would create something like lightning traveling at the speed of light and release enough heat to boil your apparatus.

Hey. So I have a couple of questions. 1- Why are should ions be separated from charges? In a biological system, aren't they the same thing. 2- Why can't it be said that the extracellular sodium ions concentration has changed without implying that some number of equivalent negative ions has changed as well? 3- And yes the amount of electrical charges participating in creating the resting membrane potential and action potential is relatively very small to the overall charge in and out, but doesn't that make it particularly sensitive to any change in electrical polarity?

Plus it seems to me that the diffusion potential for potassium is more dependent on the electrical gradient across the cell membrane, considering that at rest, with the potassium channels opens, the intra to extracellular concentration gradient for potassium is 35:1. So in a scenario where the extracellular sodium concentration drops, like in some sort of kidney disease, won't that affect the electrical diffusion potential of potassium, since this must affect the extracellular charge somehow right? even if the membrane is not permeable to sodium.

@Remoun It's really better to not think about charges because the differences in charges are so small: read the answer I linked about how small. The way you should think about resting membrane potential is that you have some ions, and they are all flowing down their concentration gradient according to the difference in concentration inside and out and how much the membrane is permeable to them. So you have some sodium flowing and some potassium. The resting potential is the voltage at which the number of positive ions moving out is the same as moving in.

Because there is more permeability to potassium, if there were no charges more potassium would be flowing out than sodium flowing in. The voltage at which the rate of potassium ions flowing out slows down to equal the number of sodium ions flowing in is the equilibrium potential.

Separating charge takes a TON of energy. You can't just remove a bunch of sodium ions without also removing some equivalent negative ions without creating the equivalent of lightning: a massive flow of charged positive ions away from where you added them rushing every other direction and messing up your lab pretty bad.

@ Bryan. I think that sodium ions as they exist in a fluid, whether in a body or lab, are in a hydrated state, which means every sodium ion is attached to more than one molecule of water through relatively weak hydrogen bonds that are constantly forming and reforming. Since I'm studying medicine, to my knowledge sodium ions can drop in the extracellular fluid either by inadequate intake through diet, or if they are "wasted" when they are not properly reabsorbed from urine by the kidneys (this may not be the only way for such wasting).

In case the sodium ions is wasted from the body, as in the case or some kidney malfunction, they are lost along with their hydration shells, dragging some water along. so I can't imagine a scenario where there is actual separation of charge on the magnitude you've described.

In any of those cases where sodium concentration drops, another negative ion drops as well, trust me. Regardless of being hydrated. This is basic electrochemistry.

Use the Goldman Equation - it's always correct, if you think of something where it doesn't work then you are approaching something wrong.

Re: “For all intents and purposes, the concentration of positive and negative ions are the same inside and outside the cell, to several decimal points.“ Here do you mean charge or ion concentration.

@user237650 I see now the way I worded it was vague. I meant that the ratio of positive:negative ions is 1 outside the cell, and also the ratio of positive:negative ions is 1 inside the cell.


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How does the digestive system determine what to absorb [as nutrients] into the bloodstream?
If you put an egg into a sausage machine it will try to make sausages out of it because that's its job. Does the digestive system attempt to digest everything it receives? Furthermore, does it attempt to derive nutrients from everything it receives? How does the digestive system determine what is nutritious? Can "particles" (e.g., microscopic dirt) pass through to the bloodstream if they are small enough to be absorbed?

Does the digestive system attempt to digest everything and from everything it receives and how it determines what is nutritious?
Human digestive system is genetically determined and can digest only those substances for which it has digestive enzymes and absorb only those that can be absorbed through the specific "channels" in the intestinal lining.
Human digestive system can absorb nutrients "from everything" (not literally, though), for example, sugar from raw sugar cane.
Before absorption, complex nutrients (starch, sucrose, lactose, proteins and triglycerides), need to be broken down by the digestive enzymes into simpler nutrients, but some nutrients need no digestion before absorption. The following nutrients can be absorbed in the small intestine:

Water
Monosaccharides: glucose, fructose, galactose...
Fatty acids
Cholesterol
Amino acids
Minerals: calcium, potassium...
Vitamins
Polyphenols, plant sterols and stanols and various other plant-derived nutrients
Sugar alcohols: erythritol, glycerol
Alcohol

Nutrients that are not absorbed in the small intestine:

Sugar alcohols: isomalt, lactitol, maltitol, mannitol, sorbitol, xylitol
Oligosaccharides: raffinose, fructooligosaccharides, etc.
Certain polysaccharides (soluble fiber): beta-glucan, guar gum, etc.

These nutrients travel to the large intestine, where they are broken down (fermented) by normal intestinal bacteria into absorbable nutrients, mainly short-chain fatty acids (SCFAs), and gases.
Can "particles" (e.g., microscopic dirt) pass through to the bloodstream if they are small enough to be absorbed?
There is a countless list of substances that are not nutrients but can be absorbed:

Medicines and other drugs
Certain food additives (preservatives, dyes...)
Toxins (methanol, cyanide...)
Various random substances ("dirt")

And there is another countless list of substances that cannot be absorbed, for example, insoluble fiber, such as cellulose, and certain artificial sweeteners, such as aspartame and steviol glycosides from stevia.
Sources:

Absorption (Nutrients Review)
Chemical Digestion and Absorption: A Closer Look (Lumen Learning)


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Simple interpretation of effective population size?
I'm looking for alternate ways to explain effective populations size, in more conceptual terms. These need not be perfectly accurate "definitions" but should at least be generally accurate in non-edge cases.
For example, if I have a population with a supposed effective population size of 1000, what (if anything) can I conclude about the amount of genetic diversity present within a single individual sampled at random from the real (census) population?
Like, would it be overly simplistic to say that the sampled individual could be expected to contain ~1/1000 of the population's standing variation? Or to say that a given (observed) nucleotide state has a 0.001 probability of being   fixed?
Again, I'm looking for anything that is not the standard way to explaining Ne
to somehow get a student's head partly into the game without being wholly misleading. Thank you

Like, would it be overly simplistic to say that the sampled individual could be expected to contain ~1/1000 of the population's standing variation?

It is a little unclear what you mean by "variation" here. If you mean "genetic diversity" aka "expected heterozygosity", then it would not just be simplistic, it would be wrong to say that!

Or to say that a given (observed) nucleotide state has a 0.001 probability of being fixed?

Ah that one is pretty good. If the effective population size $N_e = 1000$, then the probability of fixation a a new neutral mutation is $1/2N_e$ (assuming diploidy). The probability you indicate would be correct in a haploid population if you are talking about a new neutral mutation.
Another simple statistic you might want to consider is that, in absence of mutations, the genetic diversity would decrease by a factor $\frac{2N_e - 1}{2N_e}$ at every generation (assuming diploidy again).
You can derive a whole bunch of statistics of interests. For example, the expected genetic diversity in the total population at a locus at which the mutation rate is $\mu$ is $\frac{4N_e\mu + 1 }{4N_e\mu}$. You can derive many other statistics you might be interested in such as the expected number of segregating sites in a sample of size $k$ or the expected coalescent times for examples.
For more information just have a look at an intro course to population genetics. You'll find book recommendation in this post.


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Could you save a species if there were only two remaining?
Let's say an endangered species had only two left (male and female) and they produced 4 children (two male, and 2 female), and those produced? Wouldn't the incest slowly degraded their genes? (Assuming the pair of children created 4 children each, etc)
My main question is could you really save a species with only two?

Incest doesn't degrade genes. Incest increases the chance that alleles with deleterious mutations are paired and therefore expressed. (In other words, inbred offspring are more likely to have homozygous traits associated with deleterious mutations and therefore may experience decreased fitness). Good thing mutations can continue to occur....

"degraded their genes" needs definition

Depends on multiple factors (environment, genetic composition of the parents, the physiology of the species, reproduction rate, etc). I guess it is theoretically possible but the chances of extinction are very high. Therefore as your question stands, it cannot be conclusively answered.

Depends on multiple factors (environment, genetic composition of the parents, the physiology of the species, reproduction rate, etc). I guess it is theoretically possible but the chances of extinction are very high. Therefore as your question stands, it cannot be conclusively answered.


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Gene frequency — database/site
Is there any free database when one can check the gene frequency in a healthy population? For example I would like to check it for genes like BIN1, CLU or CR1. On the English Wikipedia I found a gene frequency for APOE gene (for example: 79% for e4 and 7% for e2), and it was linked to the specific publication. I wonder if one need to look for specific publication when looking for information like that or there is any database with such information available?

I believe SNPedia has frequency information, but I don't know the breadth of their database. Not a biologist.

@MelanieShebel Thanks a lot, gonna check that!

@Mary Are you talking about a specific species?

You can find some, but not all, gene frequencies in a range of populations at The Allele Frequency Net Database - Allele, haplotype and genotype frequencies in Worldwide Populations.
However, your question is broad genes have a lot of variation within them, the most basic being Single Nucleotide Polymorphisms (SNPs) and you've already been pointed to one source of information (SNPedia which is new to me) but you can look at the variation of allele frequency of SNPs in different populations by looking at dbSNP1.  Note they have a subset for variation associated with clinical phenotypes.

1 This may be the source on which at least some of SNPedia is based as dbSNP has been around for a very long time.


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Are all enzymes proteins?
So throughout my education and research career I have been taught that all enzymes are proteins. This makes sense when you consider enzyme denaturing and folding/shape etc. However, I was recently told by a biology professor that in fact, not all enzymes are proteins -- and he alluded to the RNA world hypothesis and rRNA's.
Could someone explain further how exactly an rRNA (or similar) could be (or not be) considered an enzyme, and whether or not all enzymes are proteins etc?
Thank you!

You need to read about ribozymes, and a lot of people were surprised in 1982 when they were discovered. You can find ample information on this wide topic on the web, which is why I am voting to close.

Also about deoxyribozymes (though not naturally-occurring examples are known to exist).

Disclaimer
I voted to close this question as it struck me that the by giving the poster the magic word ‘ribozyme’ he could easily verify for himself that the answer to the question in his title was “No”. However, as this question received answers that I find incorrect or misleading, I provide my own answer to put the record straight.
History and Terminology
Although I would not necessarily regard entries in Wikipedia as authoritative, scientific dates are not particularly contentious, so I refer the reader to the entries on Enzyme and Protein for the following:

The first enzyme to be discovered is said to have been diastase, in 1833, although the opposition of Pasteur to the idea of metabolic activity outside of living things delayed the acknowledgement of this. The word enzyme was coined in 1877 from the Greek, meaning “in yeast”. The catalytic activity of the enzymes of fermentation was studied intensively in the late 19th and early 20th century, culminating in Buchner’s Nobel Prize in Chemistry in 1907.
Although proteins had been recognized in the 18th century, and named by Berzelius in 1838, their chemistry as polypeptides was not established until 1902, and it was not until 1926 that Sumner established that urease was a protein.

Hence, the word enzyme and the concept of its activity was introduced long before the chemical nature of most enzymes as proteins was established, and therefore the poster is correct in not including protein in the definition of enzyme. It is also correct to talk about the later discovery of enzymes that are RNA rather than protein, despite the fact that the latter confounded a general belief that had held for over a half century. Indeed, RNA enzymes are referred to by a special designation — ribozymes — just as most members of genus Cygnus are referred to as swans, but Cygnus atratus is usually referred to as black swans.
RNA enzymes (ribozymes)
A perfect example of an RNA enzyme would be one that was naturally active in the absence of protein and showed catalytic activity against a distinct substrate. As of 2002, when the topic was reviewed by Thomas Cech — who, together with Sidney Altman, received the Nobel Prize in Chemistry for the discovery of the first ribozyme in 1962 — there were no such natural examples.

The type of catalytic RNA discovered by Cech — the self-splicing introns of Tetrahymena are completely free of protein, but act on the pre-mRNA that contains them.
Another type of catalytic RNA, exemplified by the ribonuclease-P discovered by Altman, is active against a substrate distinct from itself — a precursor tRNA — contains protein as well as RNA. However if the protein is removed from RNase-P under appropriate conditions the RNA component retains catalytic activity.

Despite these limitations — and the fact that the only reactions catalysed are cleavage and ligation of RNA — I would have cited these as clear examples of RNA enzymes if I had been the professor to whom the poster addressed his question. Ribosomal RNA probably has catalytic activity, but is less clear-cut, as I explain below.
The ‘RNA World’ and RNA catalysis of other types of reaction
One of the results of the discovery was catalytic RNA in the early 60s was that it gave flesh to an idea that resolved some of the problems of the early evolution of biochemical processes — especially the interdependence of protein and nucleic acid. This was an ‘RNA World’ in which RNA served both as genetic material (before DNA evolved) and the enzymes for performing biochemical reactions, including that of protein synthesis. However the only reactions catalysed by the contemporary RNA enzymes that had been characterized were the cleavage or ligation of RNA itself.
One could argue that other catalytic reactions were taken over by proteins when they emerged, as they were more efficient etc., however the question remained as to whether RNA had the potential to catalyse such reactions. One step in that direction was to artificially select oligoribonucleotides (aptamers) on the basis of their ability to bind particular small molecules. There have also been reports that a small synthetic RNA can catalyse the amino acylation of AMP-activated tRNA for phe.
The peptidyl transferase activity of rRNA
It is in the context of what I have written above that the possible catalytic activity of rRNA should be viewed.

The reaction involved is that of the peptidyl transferase (below). There are no other examples of RNA catalysing reactions other than RNA hydrolysis and ligation
The implications for the ‘RNA World’ hypothesis (which is not universally accepted) are such that — although I personally favour it (and have lectured to students on it in relation to ribosomes) — one must be very careful not to allow this to cloud one’s scientific judgement.

The evidence for the peptidyl transferase (PT) activity of the large ribosomal RNA (23S rRNA in E.coli, 28S rRNA in H.sapiens) is as follows:

Repeated attempts to associate particular ribosomal proteins with PT activity failed and many individual ribosomal proteins could be deleted from E.coli ribosomes without abolishing the PT activity
Affinity labels of substrates of the PT reaction tended to label RNA rather than protein.
The PT centre has been located in the three-dimensional structure of 23S rRNA by crystalization with analogue of the reaction intermediate. No proteins are in the vicinity of this.

This argues strongly that the PT activity of the ribosome lies in the 23S rRNA — but cannot be regarded as a rigorous proof. Not surprisingly, no protein-free RNA or fragment thereof has been shown to be able to catalyse the PT-reaction between the small substrate analogues that can be used for this.
I happen, myself, to believe that the ribosome is a ribozyme — for the little that it is worth — but I would never put forward the ribosome as an example of a ribozyme, when so much better ones exist.

Until the late 1980's all enzymes* were believed to be proteins, and were often defined as protein catalysts, often in textbooks which are often not perfect representations of science. At that point every macromolecular biological catalyst known was a protein so they thought all macromolecular catalysts were proteins. But the discovery of ribozymes (RNA strands that act as catalysts) changed that. The discovery that one of the most well known enzymes ribosomes had their functional components made of RNA and not protein also played a factor.
NOW enzymes are generally defined as macromolecular biological catalysts and include ribozymes. But older works or outdated textbooks will still refer to enzymes as only proteins but newer works will not. Don't feel despondent I was taught the same thing initially, and it persisted for a several years in college. Part of this is each successive step in education tends to lag behind and/or get over simplified in scientific knowledge. Textbook manufacturers are not overly concerned with poor phrasing or outdated definitions and are rarely writtten by scientists.
*in its object form, originally and for quite a long time enzyme referred to the process not the agent responsible becasue the agent was unknown.

By Definition? What definition? It was almost 50 years after the name enzyme (in yeast) was coined that Sumner (1926) demonstrated that urease was a protein. (as every schoolboy knows). And this answer ignores the way the question was phrased, which implies the poster is talking about a word he regards (quite correctly) as meaning a biological catalyst.

Thanks for reminding me to include the origin of the word. if you believe the OP is making a hidden assumption I did not address, feel free to ask them in comments or post your own answer.

"I have been taught that all enzymes are proteins" This only makes sense in English if one assumes the definition of enzyme does not include its chemical composition.

Actually it works either way, it can mean the definition does not include the chemical composition or that it does included it but it is not "is a protein"

As with @mgkrebbs answer, it would be nice to mention the name of the person who discovered ribozymes: Tom Cech.

Oh, looking for the link, I realized I forgot he shared the prize with Sidney Altman

@DeNovo — Better than mentioning names would be to describe the reactions catalysed by the first ribozymes to be discovered and their total independence on proteins. The case of the peptidyl transferase activity of rRNA is much more complex and even contentious, and needs describing, rather than just asserting. I voted to close this question, but I find the answers unsatisfactory enough that I may have to answer myself. (Sharpen your knives.)

I have been accused of including too much auxiliary information in answers, so  am trying to stick to what is specifically needed to answer and understand the answer to the question.

@David true (better to describe the actual discovery), and also when a question is answered by a nobel prize discovery, I do like to see some mention of the person/history. Especially when it's someone like Cech.

It depends on how you define "enzyme".  Wiktionary says an enzyme is:

A globular protein that catalyses a biological chemical reaction.

Wikipedia says:

Enzymes are macromolecular biological catalysts.

So the first definition excludes anything but proteins and the second also allows other large biological molecules which catalyze reactions.
The important core meaning is that of a biomolecule which catalyzes a reaction, and the restriction to only proteins is somewhat arbitrary.  The expectation for decades was that enzymes (bio-catalysts) were proteins because all the ones that had been discovered were in fact proteins.  Hence the older definition included "protein" as part of the definition.
Once it was discovered that some RNA molecules also have enzymatic action (a discovery awarded a Nobel prize in 1989), many have used the enlarged definition for "enzyme" since the enzymatic action of RNA is important.  When RNA catalysts specifically are referenced, the term "ribozyme" is typically used.
Quite a few ribozymes have now been discovered.  An important and well-known one is rRNA, which forms the core of the ribosome and provides the catalytic sites necessary for translation of mRNA into protein.  Another ribozyme is Ribonuclease P. Group I catalytic introns are a kind of intron which act as a ribozyme whose action is to splice itself out of the RNA transcript of a gene so that a mature mRNA can be formed.

The question was phrased in a way which implies the poster is talking about a word, enzyme, he regards (quite correctly) as meaning a biological catalyst. So if you thought his wording ambiguous, you could have edited it. However the answer does not depend on how "you" or "Wikipedia" define enzyme, it depends on the history of the word and of the science. It was almost 50 years after the name enzyme (in yeast) was coined that Sumner (1926) demonstrated that urease was a protein. (as can be found in sources other than Wikipedia). Black swans anyone?

I do love questions that are answered with a nobel prize. It would be nice to actually mention Tom Cech's name here.


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How do I determine an acceptable $F_0$ value in sterilization?
Here's a sample question:

The sterilization process using moist heat is used to kill B.stearothermophilus by heating to 115 degrees C and holding it for 30 mins.
For B.stearthermophilus, it is given that $D_{115} = 11$minutes and z=10 degrees C.
  Determine the sterilization process equivalent time at 121 degrees C. Is this an acceptable $F_0$ value ?

By using formula $F_0 = \Delta(t) \cdot L$
I found $F_0 = 7.5$minutes.
How do I know what is the acceptable $F_0$ value? I've been told it's 15minutes. Is it 15 mins for ALL sterilization methods or is there a method to calculate this regulatory requirement of $F_0 = 15$ ?


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Identify function of cluster with high identity of genes
Let's say there is a secondary metabolites biosynthesis cluster in fungi A.
and I just found out a gene B(identitiy>=50% with nrps gene located in the cluster) from fungi B and also found that gene B is located in some gene cluster in fungi B genome. My question is, with these two proofs can I say the gene cluster including gene B is doing same function with a secondary metabolites biosynthesis cluster in fungi A?

Welcome to SE Biology. Take the tour and read the help on asking questions. 1. Your "let's say" suggests that this is a homework question. Is it? 2. you need to set out the information (evidence, not proof in English) clearly, point by point. What does "nrps gene" mean? When you say there is a gene cluster in gene B, what is your evidence this is a "cluster"? You only mention geneB, which I presume is related to one of the genes in fungus A (fungi is plural). Do you know anything about the other genes in fungus B? 3. without demonstration of function you can only talk abut likelihood.


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Can we spike with a different enzyme to a SYBR Green Master Mix?
I followed the standard SYBR Green Protocol for doing a qPCR. For which I used

10 uL of 1X SYBR Green Master Mix
Forward Primer and Reverse Primer (each at a final conc. = 8.5 uM)
Template (unknown concentration from an aptamer selection)
Made to 20 uL with water.

Performed the PCR amplification using

95 C Initial denaturation
95, 68, 72 - cycled 35 times.

But, one set of sample from my aptamer selection (probably high GC content) did not amplify at all. I checked on an agarose gel too.
Important Notes:

My primer conc. is intentionally high - I have always amplified with such concentrations and it works perfectly using Vent Polymerase.

My annealing temperature is also high at 68 C because my aptamer sequences tend to be GC Rich.

Using Vent polymerase my amplification is very strong

On reading notes from vendors, I found out that the polymerase in the mastermix to be some variant of Taq Polymerase[1][3] (varies from vendor to vendor) and also it is known to poorly amplify GC Rich Sequences[2].

https://www.thermofisher.com/order/catalog/product/4309155

https://www.thermofisher.com/order/catalog/product/N8080241

https://www.fishersci.co.uk/shop/products/powerup-sybr-green-master-mix/15366158

Hence, I wanted a suggestion from anyone working with aptamers, or if you have experience working with GC rich sequences on how I could amplify my sequences.
Much appreciated if I could have an answer before next week.
Thanks a lot for your help!!!

Can anyone help with this if you work with GC rich sequences?

I know its too late now, but this is a question well suited to ResearchGate.

I found this following answer in a Stack exchange post and seems to be helpful from the point of view of my question. If it helps anyone the following answers my question that I asked initially:
https://biology.stackexchange.com/q/46649/33379


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Do we know how dangerous six-eyed sand spiders are?
The Sicariidae family contains the well-known and dangerous Loxosceles spp. (fiddle-backs, violin spiders).
The family's other two genera, Sicarius and Hexophthalma (six-eyed sand spiders) have reputedly exceptionally cytotoxic venom, although they live in sandy deserts and rarely come into contact with humans.
Quite common in the exotic pet trade is Sicarius thomisoides (formerly terrosus).  I would be particularly interested in how dangerous this species is likely to be - many are now claiming that research has shown it to be minimally dangerous.  I'm not sure what work this is based on - perhaps this paper? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2767091/


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What is the difference between a signal peptide and a transit peptide?
From what I know, the two names are used interchangeably and I haven't found any resource which says otherwise either. Is there at all any difference, is there a transit peptide that is not a signal peptide or vice versa?

Signal peptides are typically located at the N terminus of a protein. The signal peptides are processed by the translocon machinery and are cleaved off after sorting through the membranes of organelles in the secretory system:

endoplasmic reticulum
Golgi apparatus
ER-Golgi transition vesicles
plasma membrane
lysosomes

Transit peptides target the protein to other subcellular organelles such as (from UniProt):

Mitochondrion
Apicoplast
Chromoplast
Chloroplast
Cyanelle
Thylakoid
Amyloplast
Peroxisome
Glyoxysome
Hydrogenosome

N-terminal transit peptides are quite rare. C-terminal transit peptide motifs are much more common. UniProt holds transit peptides as a discrete controlled vocabulary, separate from signal peptides.


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Organisms that use more than the 20+2 commonly occurring amino acids?
I know scientists have created synthetic bacteria, with a genetic code containing 6 letters instead of 4, with the aim of creating more complex proteins (using amino acids outside of the standard 20+2, the +2 being selanocysteine and pyrrolysine).
Are there any examples of already-known organisms that use more than the 20+2 commonly occurring amino acids, when translating from RNA codons to amino acid sequences using the ribosome? Post-translational modifications would not count, as the ribosome would not be directly responsible for the incorporation of the amino acid into the protein through that method.
Source: 22 proteinogenic amino acids
https://en.wikipedia.org/wiki/Proteinogenic_amino_acid

Are you asking only about proteinogenic amino acids?

Yeah, I'm asking about proteinogenic amino acids. But if an amino acid is used (beyond the scope of the 22+2 common ones), that amino acid by definition should be "proteinogenic", right?

No, there are natural amino acids that are not used to build proteins. Ornithine, for example.

New contributors are welcomed to SE Biology. Good questions aim for clarity, but inadvertant ambiguity is normal. Comments can suggest ways the poster can edit to remove such ambiguity: 1. State that the +2 refers to selanocysteine and pyrrolysine. 2. Reference, e.g. the Wikipedia page on the Genetic Code. 3. State, if that is what you mean by proteinogenic, that you are refering to amino acids incorporated into protein on the ribosome, and are not talking about post-translational modifications. (The answer is that no others are yet known — as your research should have indicated.)

Thanks @David, I've edited my post to reflect your suggestions. How should I mark this question as answered?

I suggest you answer your own question and accept it. (If I do it for you I'll appear to be soliciting points.) You can just say something like "After searching for papers more recent than those quoted in the Wikipedia article, at the time of writing (Dec. 2018) I cannot find mention of any additional amino acids. For example there is an extensive review in Ann Rev Genetics 2017 which only mentions selanocysteine and pyrrololysine."

At this point in time it appears that no known organisms use amino acids beyond the standard repertoire of the 20+2 common amino acids (the +2 being selanocysteine and pyrrolysine) to construct proteins directly from the ribosome. The extensive review provided by Ann Rev Genetics 2017 mentions only selanocysteine and pyrrolysine, and no other amino acids beyond that.

Some methanogenic Archaea incorporate pyrrolysine in some of their proteins (methyltransferases).
Selenocysteine is another non-standard amino acid; proteins with selenocysteine are called selenoproteins. Both prokaryotes and eukaryotes produce selenoproteins.
Both these amino acids are incorporated at a reassigned UGA codon.

But aren't these the +2 of the question?

@David I thought the +2 are hydroxyproline and hydroxylysine but they are not considered proteinogenic because they are result due to PTM.

No. There are a host of post-translational modifications of amino acids. Those two are the ones coded by stop codons in certain contexts and — especially selenocysteine — have been well characterised, as you mention.


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Do sharks fart?
My son is 5 and I'm encouraging him to be curious and ask questions of the world around him.
He asked if sharks fart and how does it smell?  He feels that it would smell of fish and be disgusting.
He was also asking how anyone would know or be able to check. I don't know the answers and am teaching him how to research.

Nice first question, welcome! What have you tried to asnwer that question?

https://www.thenakedscientists.com/articles/questions/do-fish-fart

Thank you very much, had much hilarity explaining the answer    he is particularly  taken by thr idea of herfing communicating by farting!

@Cameron Well done for encouraging your son. If I were you, I'd try to get him to think about how we sense the qualities that constitute a fart and what mechanisms create the fart. A fish may well fart but will we hear it? Will we smell it through the water? Linking back to the creation of the fart (production of gases in the intestinal tract), would we see a new effect like a bubbling in the water?

I thought that anaerobic decomposition will definitely cause methane in any animal which has an intestine. Why isn't that so for all species?

Excellent question. Via Southern Fried Science: According to Daniella Rabaiotti, a postdoctoral researcher at the Zoological Society of London, sand tiger sharks are the only shark known to fart.
They gulp in air at the surface, store it, and when at depth let the air our in the form of a fart to alter their buoyancy. Air lets them float instead of sink, so when they want to sink, that's when they release the air. Shark fart source
There is also a book of species known to fart, confirmed by scientists.
Book of farting animals on Amazon


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If the body continuously produces new sperm, how is there room for it?
If you never ejaculated, how is there room for the constantly generated new sperm? I mean, is there always room for more?

Your testes are a sort of waiting room where sperm hang out, and if ejaculation does not occur, they eventually die, just like red blood cells (or any of your body's cells). Once cells in your body die, they are broken down, and your body uses the components and nutrients to create new cells.
So it's a continual cycle of replacement and death.
Read more here

Hi @J.W., Welcome to Bio.SE, and thanks for the post! You would receive much better response (i.e., more upvotes) if you wrote a more substantial answer. It's great to link to a resource, but providing a bit more info here would make this a stronger answer. It's also great to use very accessible language in your answer (e.g., "waiting room" and "hang out"), but following this language up with more biologically appropriate terminology helps provide a greater sense of credibility to your answer. Please consider revising and adding more detail to your answer. Thanks!


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Exporting RNA in extracellular vesicles (exosomes)?
I'm interested in how much is know about the process by which RNA is secreted from cells into extracellular vesicles.
Where is a good place to start reading about this?
How much is known about this pathway?
Can the pathway be engineered?

Perhaps you should start by searching google scholar for some good review articles (Nature Reviews and Annual Reviews are quite elaborate). A broad question like this is not suitable for the stackexchange format. If you can narrow down your question you can prevent it from being put on hold.

How can I make it more specific? Should I specify an organism?

No, specifying an organism would not help much. If your question was about specific points about the process of exosome formation then you can be directed to suitable paper. However, one can only suggest you to read a review on exosomal RNA. Your question about how much is known is also subjective. The third question: again, one can engineer anything but it may or may not be useful/productive. First, you are asking multiple questions and your questions are, moreover, too broad.

I just want to know if its possible for cells to be (genetically) engineered to produce a signal every time an mRNA is transcribed and have that signal exported into the extracellular environment.