text:
What makes us all different and similar to some extent?
It is said that genes define how we look physically and psychologically; so for example if a male human sperm carries a certain number of genes, say x, and a female carries y, then mathematically there would be m genes from the male and n from the female, and a finite total available. Could there be people identical in appearance if the same genetic combinations recur?
Also we find similar-looking people with perhaps similar behaviour accross diferent geographic locations; does this means that they have similar genetic make-up, up to some percentage?
Please correct my biology and share the possiblity of having genetically identical people across different geographic locations.

Please see this question and answer (http://biology.stackexchange.com/questions/10474/on-average-how-many-genes-alleles-do-people-share/17292#17292)

For ease of explanation let me first tell you that the "genetic makeup" is called "genotype" and that "how we look physically and psychologically" is known as "phenotype". These are not complete definitions of the terms but this should help you understand what we're talking about. I also apologise for the lack of detail or inaccuracies which many fellow contributors may find aggravating, but the question calls for keeping things down to the most important aspects :)
Do genes define how we look?
Genotype defines to some extent the human phenotype, but we don't know exactly to what extent regarding most aspects of the phenotype. This is called the "nature vs. nurture" debate and is concerned with the effects of genotype itself on phenotype vs. the effects of non-genetic influences after fertilisation (such as chemical surroundings during embryonal growth, experiences at young age etc).
Numbers of genes from males and females
Another misunderstanding is that a sperm carries a certain number of genes which it combines with a number of genes from the egg. While this is strictly true, the number isn't what matters because we all carry the same number of genes (*). The genotype doesn't depend on the number of genes, but rather, almost all genes exist in several variants within the human population. So the genotype is actually about which variants an individual carries, not about the number of genes. In biology, we use the term "allele" to refer to variants in this context. So in other words, each gene can have different alleles.
People with identical appearance
If two people have identical alleles for all genes (i.e. identical genotype), then they can indeed look almost identical. However, because of the vast number of genes and alleles present in the human population, it is practically impossible for the same alleles to come together in two humans. With only one exception: if two individuals result from the same combination of sperm and egg cell, they will be identical, and this is exactly what happens in monozygotic twins.
Similarities by geographical region
However, the total number of genes and alleles is limited (**). This concept is what people call the "gene pool" and is the reason why humans are still always humans and share certain similarities. In particular, for most of human history our geographical movement has been limited (most of the time), creating geographical "sub-gene pools" (to keep it simple). This is why people from the same geographical region are more likely to look similar; they have a higher chance to share the same alleles of genes that determine appearance. In terms of behaviour - to whatever degree genotype influences behaviour, peopel from the same geographical region will be more likely to be similar in these regards than people from different geographical regions. However, you can now hopefully understand why this "degree of similarity" is next to impossible to quantify (lack of knowledge: which genes determine what, how many alleles exist of them, how many people have which allele, how much and how far do people travel,...).

(*) Ok, not quite - it is possible for an individual to have the odd gene actually completely missing, but for the sake of simplicity we all have the same number.
(**) Again, not strictly, because new alleles and possibly even entire genes can result from mutation, but this is relatively rare and on the large scale you can work on the assumption that they are limited in number.

It is said that genes define how we look physically and psychologically

I would be skeptical of anyone saying this. Nature vs. nurture is far from settled, especially in psychology. The trend seems to be that many behavioral traits have a large heritable component, but are far from being determined only by heritable traits.

if a male human sperm carries a certain number of genes, say x, and a female carries y, then mathematically there would be m genes from the male and n from the female

I think you are confused. If a sperm carries $x$ genes and an egg carries $y$ genes, the resulting zygote will have $x+y$ genes. If the male had $m$ and the female had $n$ genes, $x+y\approx m+n$ and $m \approx 2x$, $n \approx 2y$.

Could there be people identical in appearance if they end up with identical combinations of genes?

Yes, we call these people identical twins. It could also occur by chance in unrelated individuals (well, everyone is somewhat related...) but this is extremely rare. There is just that too much variation in the human genome. There are literally tens of millions of points in the genome where some people have one version and others have another, and this person would have to happen to have the exact same version at each one as you do. This is an order of $10^{-8}$, if we consider humanity completely homogenous (and it isn't, so the probability is even lower).

we find similar-looking people with perhaps similar behaviour accross diferent geographic locations; does this means that they have similar genetic make-up, up to some percentage?

The genes may be different and still lead to the same phenotype. Say one person has the set of genes that result in red hair, another one has the set that results in brown hair. They are both albinos. They'd look the same, but have different genes.
Also, genes are not the only thing that determines how people look or behave.
So the fact that two people are phenotypically identical does not imply they are genetically identical. You can come up with a Bayesian probability that says they are more likely to have similar genes if they look similar, but how do you calculate the priors? Worse, how are you even going to measure how "similar" people look, or behave?


text:
Sequence alignment scoring
The following table is from Deonier's text Computational Gene Analysis at p. 152.
This is an exercise in global sequence alignment and scoring of alternative sequences.
The text proposed a solution (in parentheses). Setting aside the upper left hand portion of the table it seems there may be a better path.
It's more likely I  misunderstand the idea than that there is a typo.
$$\begin{array}{c | c | c | c | c | c | c |}- & -& T & G & G & T & G\\ \hline  - & (0 ) & -2 & -4 & -6  &-8  & -10 \\ \hline
A &(-2)  & -1 & -3 & -5 & -7 & -9 \\ \hline
T &-4 & (-1)  & -2 & -4 & -4 & -6  \\ \hline
C &-6 & -3  & (-2)  & -3 & -5 & -5  \\ \hline
G &-8 & -5 & -2 & (-1) & -3 & -4 \\ \hline
T &-10 & -7 & -4 &-3 & (0)  & (-2 )\\ \hline  \end{array}$$
Just looking at the upper left corner,
$$\begin{array}{c | c | c |} (0) & -2 & -4...\\ \hline -2 & (-1) & -3...\\ \hline  -4 & (-1) & -2...\\ \hline  -6 & -3 & (-2)...\\ \hline  \end{array}$$
which seems to give -7 versus -8 for the book's path. Below are the book's alignment and the one corresponding to my scoring, which may reveal my error.
$$\begin{array}{c | c | c | c | c | c | c |} A: & A & T & C & G & T & - \\ \hline
B: & - & T & G & G & T & G  \\ \hline
\end{array}$$
$$\begin{array}{c | c | c | c | c | c | c |}
A: & A & T & C & G & T & - \\ \hline
B: & T &  - & G & G & T & G  \\ \hline
 \end{array}$$
I had no trouble constructing the matrix just scoring it. it's a small point but I don't like to move on without understanding it.  Thanks for any assistance.
Edit: Both current answer seem clear on this but just for completeness: a match = 1; mismatch = -1; indel = -2.

The problem is that you are using the T twice. Let's build the alignment manually, we have two sequences:
>seq1
ATCGT
>seq2
TGGTG

So, to build the alignment using your approach, we would take the first nt of seq1, the A and choose the highest scoring nt from seq2 to align it against. In your example, that would be the T (-1) which produces:
A
T

OK, now we move to the next nt of seq1, the T. Now, in your table, the highest score is indeed for TT but we have already used the T from seq2, we can't use it again! In your alignment, you used a -. The score for T- at position 2 is -4. This means that your alignment:
ATCGT-
T-GGTG

Has a score of:
$(AT)_{pos1} + (T-)_{pos2} + (CG)_{pos3} + (GG)_{pos4} + (TT)_{pos5} + (-G)_{pos6}$
Which is:
$-1-4-2-1-10 = -18 $
While the book's alignment is:
$(A-)_{pos1} + (TT)_{pos2} + (CG)_{pos3} + (GG)_{pos4} + (TT)_{pos5} + (-G)_{pos6}$
Which is:
$-2 -1 -2 -1 -10 = -16 $

@daniel in which case it is probably mistaken (my approach, not your text). Taking what you show out of context, I am simply using the score for each position. So, since T- has a score of -10 in your table, I am using that.

We agree about the alignments. Why is the second score -4 in my alignment? That might clarify for me.

If you are saying the -4 in my score is because it's -2 in the 2d position, then why isn't -1 in the 4th position -4? This might clarify.

@daniel the -4 in your score is because a T in seq1 aligned to a - in seq2 has a score of -4 in the table. The -1 is because TT has a score of -1 in the table. However, while I have actually worked with this kind of thing, I have never worked with it in depth and it was a few years ago now, I may well be wrong.

If I am myself not mistaken, the table shows the paths of least resistance. There are many paths through this table and all of them are not shown only the ones that cost the least. You need to understand that a mismatch between the letters costs -1 (eg - AT), but an empty square  costs -2 (-A or -T). So your solution would cost = -1-3-4-3-2-4 which sums up too -17.
This is a full alignment table. The top value is going diagonal, the second value is going down and the third value is going right.

Could you explain how you get that -17? A gap costs between -2 and -10 depending on which one in the table in the OP. The score of the mismatch also changes. Where are your numbers coming from?

The score of a mismatch is always -2, only if you use more than one gap then it increases by -2 with every gap. That is why the top row is -2 (one gap); -4 (two gaps); -6 (three gaps) and so on.
I did explain how I got -17 = - 1 - 3 - 4 - 3 - 2 - 4. You just need to add the values of each place.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
Can we really 'discover' 85% of mammalian viruses?
This virology [blog] discusses estimates of the number of mammalian viruses and the costs of 'discovering' 85% of them.
My question is whether this is not a forlorn hope. The ".632 rule" in statistics says roughly that as we approach n random samples from a large population of size n we will see only about 62.3 per cent of the population. After a point we would begin to see the same viruses again and again. This argument is probably stronger with respect to marine viruses, as they may be even more numerous and sampling at depths could be difficult.
I wonder if someone with experience sampling small organisms from large populations or familiarity with the literature has an idea about the plausibility of seeing 85% of a large population, such as mammalian viruses, by sampling?
If the samples are really random (in some sense) and the population is large, a few computer simulations reveal the power of this rule of thumb.
Edit in response to comment/question:
Like any such estimate, the blog's estimate of 3.6 million is a guess. I am not reproducing the calculation here because it's just speculation.
Having said that, if 3.6 million were correct, we would have to draw about 6.8 million samples to find 85% of the existing viruses, 8.2 million to find 90%, and so on. As the blog notes, the PCR approach detects viruses similar to those we know, so the sampling is worse than random. If we look at the difficulty of finding/using a method that has a reasonable chance of capturing any of the extant viruses, the number 3.6 million looks very big.

How did they know/estimate the total no. of viruses ?

Is there an article you could refer me to for the .623 rule? I was very interested and would like to know more and also could you elaborate how you made the calculations in your edit. Thanks

@Bez: If you go to the Cross Validated site, problem 96739, user603 gives a really good short description of the calculations. He also gives some pseudocode to implement the calculation but you can to it fast by solving $1-(1-1/n)^x = .632$ etc. using the program of your choice. $n$ in this case was 3.6 M and so solving for x we get 3.6 M. If we insert 0.85 instead of .632 we get 6.8M. And so on.

Excellent page, I found the R code on the page very helpful. Many thanks

Regarding the question, I guess it is possible to reach the %85 based on the formula however I think there are two major problems that could affect the percentage. First most of the viruses collected for analysis is probably not collected/sampled at random as (unfortunately) samples are collected when they are of interest e.g disease causing viruses etc. Second is that there are perhaps many places, which have not yet been sampled due to inaccessibility etc. So in short I think it is possible but there are barriers but these are just my thoughts and I could be totally wrong!

@Bez: Yes I think this is all true. And maybe the biggest barrier is the numbers. How to do 7 million random samples. I don't think we're allowed to group results from disparate studies unless they are all following some common procedure.

For some statistical models, see e.g. The Mathematics of Biodiversity (Part 1) by John Baez.
However, in terms of new species, such statistical methods may not suffice - usually also our tools for discovering change. So it might be more accurate to extrapolate number of some kind species we know as a function of time.
For extrapolations (though not for viruses) see e.g.:

Camilo Mora et al., How Many Species Are There on Earth and in the Ocean?, PLOS Biology (2011).

In any case, for viruses (and many other fast-multiplying asexual creatures) defining number of species can be anywhere from tricky to impossible (for fundamental reasons, not only - practical). At best you can try to estimate their time to the last common ancestor. See also links in this discussion on Azimuth.

@daniel Fixed, thanks (sometimes I have issues with copy-paste). BTW: AFAIK OP means 'Original Poster' (i.e. you, in this context), not 'Original Post'.

@daniel I feel overnerded by you (and thanks, it is always good to know). In any case, in the context of Stack Exchange (unlike fora, separating Q from A), I see people using OP when they mean Original Poster (as it is easy to refer to question as 'the question', or Q).

I was thinking about 'outnerded' (it sounds right), but decided to go for 'overnerded' (compare: 'outpowered' vs 'overpowered'). But you are an expert on words here.

OK, here goes. Using MathSE because it's bigger--questions 8623,513239,774176 Poster; questions 708644,272591,350485 Post. I think most refer to poster because it's a service-oriented group. But...

Let us continue this discussion in chat.

Can't--I'm off to the salt mines...

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Protoporphyrinogen (IX) formation in heme synthesis

This picture shows one of the steps of heme synthesis. In this step two propanoate groups of coproporphyrinogen III are decarboxylated to form protoporphyrinogen IX. The enzyme that catalyses this step is an oxidase. Oxidase enzymes catalyze the removal of hydrogen  in the presence of oxygen to form water or hydrogen peroxdide.
So, will a water molecule form in this step? 2H+ will come from the two carboxylate groups and oxygen will combine with it to form water. Will a water molecule form in this way?

Oxidase enzymes catalyze the removal of hydrogen (addition of oxygen).. Oxidases don't add oxygen; they use oxygen as a cofactor or electron acceptor. Oxygenases are the ones that add oxygen. And all oxidases give rise to either $H_2O$ or $H_2O_2$

Nonetheless, your title and the diagram is not really related to your actual question. Please clarify what exactly you want to ask.

@WYSIWYG, I have edited the question.

so, will a water molecule form here?

Seemingly the enzyme uses molecular oxygen in the reaction and one of the end products is water.
This reaction scheme is more detailed and presumably accurate.
http://www.hmdb.ca/reactions/3063
In addition there is also a set of papers detailing coproporphyrinogen oxidase which was also on the website, hopefully one goes into more detail on the reaction.
http://www.hmdb.ca/proteins/HMDBP00251


text:
Is there a human form of estrus?
Now I just learn that estrus is a trait in all mammals except Humans. So does it occur significantly in Humans? Of course I'm aware of the cliched "horny", "aroused" etc., but is it a biological function in Humans too? and if so, when and what is it called?

By 'human estrus', I take it to mean that the female shows some increased desire when they are fertile.
At the height of fertility, which coincides with estrus, female behavior changes a stronger interest in sexual activity is exhibited.  In many primates in general, the female may give of a strong scent or even physically show color or swelling that indicates even to observers of other species that they are fertile, also engendering sexual behavior in the males.
For instance, baboons are well known for reddening of the female's rump and they also emit a strong scent.  Non - primates also show estrus - most of us know how dogs and cats can change their behavior.
Human signs of Estrus is of great interest to primatologists, evolutionary biologists and psychologists as it influences the biology and the social nature of people.  It has been proposed that humans do not exhibit estrus and this is still an influential idea. Certainly its difficult to look at a woman and tell whether she is ovulating and most women themselves cannot tell when that is happening.
Still, examination of behavior and appearance have shown that womens appearance does change over their monthly fertility cycle.  Women's faces may become thinner at higher fertility and this and other cues make them more desirable on the average.  While their sexual desire is not clearly higher, female perception of men's faces changes too.
While this is quite different than the typical definition of estrus, the biochemical cycle of fertility does affect human social behavior and preferences, perceptions.  The evolutionary reasons for these changes are probably adapted to the highly social nature of human existence and the fact that offspring are such a large investment.


text:
Why some neurons are tetraploid
Why are some neurons tetraploid, and how does this result from it's ancestor cell ?

Please don't ask multiple questions in a single post. Break them up into separate questions.

I have removed the second part of your  question. If you wish to ask it please make a separate question.

where did you see tetraploid neurons? provide the link to the source.

I didn't know that - interesting question!

Neurons are tetraploid in pathological situations like Alzheimer disease:

Neurons that duplicate their DNA are rarely observed to undergo mitosis, and they remain for long time as tetraploid cells, in accordance with the chronic course of the disease. We have recently shown that cell cycle re-entry and somatic tetraploidization occurs during normal development in a subpopulation of RGCs (retinal ganglion cells), giving rise to enlarged neurons with extensive dendritic trees. Tetraploization in these neurons occurs in response to the activation of the neurotrophin receptor p75NTR by an endogenous source of NGF (nerve growth factor).

Source: Frade JM, López-Sánchez N. A novel hypothesis for Alzheimer disease based on neuronal tetraploidy induced by p75NTR. Cell Cycle 2010; 9:1934 - 1941; PMID: 20436277; http://dx.doi.org/10.4161/cc.9.10.11582

These neurons are generated in response to nerve growth factor (NGF) acting through the neurotrophin receptor p75 (p75NTR), which induces E2F1 activity and cell cycle re-entry in migrating RGC neuroblasts lacking retinoblastoma (Rb) protein. We have also showed that brain-derived neurotrophic factor (BDNF) prevents G2/M transition in the tetraploid RGCs, thus being crucial for the maintenance of the tetraploid status as well as the survival of these neurons. The realization that tetraploid neurons can be readily observed in the vertebrate nervous system has important physiological consequences.
Several eukaryotes are known to undergo endoreduplicative cycles leading to somatic polyploidy, thus increasing cell size in specific tissues. Examples of polyploidy in neurons are known in some invertebrates.

Source: José María Frade. Somatic tetraploidy in vertebrate neurons - Implications in physiology and pathology. Commun Integr Biol. 2010 Mar-Apr; 3(2): 201–203. PMCID: PMC2889987

It's not all pathological. From the same second article cited:

Modern techniques such as flow cytometry, fluorescent in situ
  hybridization (FISH), slide-based cytometry (SBC) and quantitative PCR
  analysis of DNA from isolated nuclei can all reliably quantify the
  amount of nuclear DNA in neurons.11 By using SBC, flow cytometry and
  FISH, we have recently demonstrated that tetraploid neurons exist in
  the normal vertebrate retina, representing a subpopulation of RGCs
  that, in the chick, innervate lamina F in the
  stratum-griseum-et-fibrosum-superficiale of the tectal cortex.12 These
  neurons are generated during the early stages of retinal development,
  soon after they acquire neuronal markers. Indeed, a subset of
  migrating RGCs expressing the transcription factor E2F1, and lacking
  Rb protein, was observed to undergo S-phase and remain in a permanent
  G2-like state. Therefore, endoreduplication, but not alternative
  mechanisms such as aneuploidy or cell fusion,13,14 represents the
  mechanism generating tetraploid RGCs in the vertebrate nervous system.

Can you add what article you quoted this from (either a link to it, or reference to the book or journal where it could be found).

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
how is the plasma membrane repaired after endocytosis?
When the vesicle is swallowed of course the lipid layer internalizes. My question is how will the top segment of membrane will bind back together when that vesicle took the membrane with it inside cytoplasm. Will the plasma of the cell decrease or they will repair back and how does the membrane know that a certain substance is outside and i have to internalize myself in order to swallow. The same thing with exocytosis: How does the membrane open itself and repair back and what will happen to the membrane of the vesicle which went out?

You have one misconception about the endocytosis: In the process no hole in the membrane is generated. It works in principle like in the figure below (it is of course more complicated, but this should explain it):

The membrane forms a vesicle around the particle which shall be integrated until it is completely surrounded by a membrane. At this point the vesicle is detached from the cell membrane and inside the cell. To accomplish internalization, the particle binds to certain receptors which regulate this process. See the Wikipedia for more details.
Exocytosis works in principle the other way round. Here are the visicles detached from the Golgi apparatus (mostly at least) and are directed to the cell membrane. Here the fuse with the membrane and form a pit which has its opening to the outside, releasing what was in the vesicle. It works like this (image from here):

In this process you have to differentiate between permanent unregulated exocytosis and regulated endocytosis (for example for the release of hormones) which are regulated by signal transduction pathways.


text:
Pharmacology: Drug Administration
Why is the enteral route seem by far the most common way to administer a drug to the body?

Who says it is the safest route?

Question seems valid to me. It appears difficult to deny that the oral route is the most common administration route. However, it is true that any answer given to this question will be partly opinion-based...

Let's review drug administration routes, and see for yourself:

transdermal/ionophoric: expensive, unreliable release concentrations (which makes it expensive because of the extensive research needed for controlled release), noticeable to others ("why do you have that skin patch, mom?" Er...)
Sublingual: quite similar to oral route, however absence of first pass hepatic metabolism can result in completely different blood concentrations between the two routes. Impairs speech. Could cause mouth irritation (quite disabling). Requires patient compliance.
intravenous: quite unpractical in outpatient settings. Invasive measure.
intramuscular/intradermal: hurts. As all things using a needle. Usable, but impractical in the outpatient setting. Can lead to skin lesions (insulin injection in diabetes, for example)
rectal: culturally unacceptable to some, unreliable release.
vaginal: similar to rectal, but only for women obviously
spinal/epidural: very invasive, only in inpatient settings.
topical: usually only acts locally, can cause discomfort (eyes)
oral/enteral: well known pharmacokinetics, mostly invisible to others, practical in the outpatient setting, requires limited patient compliance, well known excipients. Of course there can be secondary effects, but that is the case for all administration routes. Most common side effects are abdominal discomfort and nausea, but no one can see you in the water closet. Plus people are used to see pills as medication, something which might not be the case for other routes, depending on the cultural background of the patient.

This answer is of course somewhat subjective, however the importance of the patient's perception and his/her view of what the administration route implies socially cannot be overemphasized.

Also IM (Intramuscular).


text:
pfu Turbo DNA polymerase AD
What is the duration (Life") of pfu turbo DNA polymerase AD. I am trying o Amplification a 3.3kb fragment and the PCR schedule is 6 hours long. The manufacturers notes just specify that its activity remains 94-99% in 1 hour at 95, nothing more.

I don't know the exact half-life of this special Pfu polymerase, but generally Pfu polymerases are pretty stable. This source gives a half life of 18-25 hours at 95°C, meaning you keep the enzyme at 95°C for the whole time a you still have 50% activity after that time. Since you don't do that, I wouldn't worry too much about the activity. To be safe, you can add an extra long (probably 10-15 minutes) single amplification step before cooling down.


text:
Pancretic Acinar Cell - ATP, calcium concentration data
I need to find a decent source of data for concentration of ATP and calcium in the pancreatic acinar cell.
So far all I can find is ATP or calcium 'levels' based on fluorescence , which are not accompanied by a value of concentration in moles/molar.
Is it possible to find this information in a specific book or website, to avoid trawling though vast amounts of literature?

Have you tried asking on Biology as well? I'll have a look to see if there's anything around in the literature that I can find too.

See http://www.pancreapedia.org/tools/methods/measurement-of-intracellular-calcium-concentration-in-pancreatic-acini

In this study, even though they have used fluorescence based method, they have reported concentrations.

When we studied basal intracellular calcium concentrations in acini from control rats they were in the low nanomolar range (140 ± 5 nmol).

For ATP concentrations you can see here.

Is it possible to find this information in a specific book or website, to avoid trawling though vast amounts of literature?

There is the human metabolome database. However, it doesn't have data for all cell types. Either more studies are required or the database needs updation.
Similarly there is the yeast metabolome database (you may not require it for your query but just another piece of information that I thought is worth adding).


text:
Where can I find the tissue-specific protein expression levels for hTERT (telomerase subunit)?
I find a number of contradictory sources regarding the tissues in which hTERT - the protein - is expressed. Does anybody know some resource that authoritatively (as authoritative or widely-accepted as is possible) lists the various tissues and hTERT's protein expression levels?
Any similar resource for gene expression of hTERT?

I have found that biogps.org has all expression data I need:
https://biogps.org
https://biogps.org/#goto=genereport&id=7015

not heard of this before - just had a bit of a play and it does seem like a great tool!

Thanks but this is only gene expression. I'm talking of protein expression, which by no means correlates to gene expression. It's often assayed by immunohistochemistry with scaling up achieved with tissue microarrays


text:
Fish "coming back to life" after being frozen
I've encountered a clip on Youtube showing a goldfish thrown in liquid nitrogen and immediately after to normal water and swimming normally. In the explanation to the clip it says:

For everyone that is worried about the goldfish, it survived and was perfectly fine until we fed him and a few of his friends to our turtles. (Which is what they were bought for in the first place!)

I am wondering now as to several issues.
If the goldfish wasn't fed to the turtles and was allowed to live out its life, would it suffer any long term damages from the act?
Is time an issue here, if the fish was kept frozen for a longer time, would it suffer more damage and would it be able to be revived?
Is the size and nature of the fish's body a factor? Would a larger animal or an animal with better resistance to frost that would take more time to completely freeze have damage due to gradual freezing of body and systems?
Does the fact that fish have cold blood affect the result of the experiment?

Well, as and you can see the fish just "froze" for max 2 seconds. It is normal to live because it didnt die from cold.

I have no idea what's the real reason for the survival of the poor fish, but I would guess this is all in the timing. I know for certain ;-) that one can submerge a hand in liquid nitrogen for a short time or in general one can pour liquid nitrogen on the skin with no harm done whatsoever.
The reason is that the difference in temperature that interface (-180 deg C or so for liquid nitrogen and 20-30 for the skin surface) is so large that nitrogen vaporizes instantly and does not penetrate/affect the tissue. The demonstrator could have pulled the fish with bare hands.
I think that for the goldfish the time was too short and while it was cooled/shocked a bit, it might have been too short to do any serious damage. But -
As a scientist, I can't help but notice that we don't really know the condition of the fish before or after the liquid nitrogen 'treatment'. We only see it flapping for a few seconds when back in water. I wonder what happened to the eyes and the mouth, both quite sensitive tissues for such a shock. Also, the water the fish was in was a factor probably, providing additional buffer between the fish and the liquid nitrogen.
Last but not least, the ethical committee quite certainly did not approve that demonstration.

Of course we do not really know whether liquid nitrogen was really in the other pot... we just see smoke


text:
Is it possible to create an experiment in house conditions to prove the existence of germs?
I realise that the best way to prove the existence of germs or single-celled organisms is by looking at them through a microscope.
But I don't have a microscope at my home, how can I design an experiment in a normal house environment to show the existence of germs (or other single-celled organisms) without spending too much money?
By "house environment" I mean that I have access to normal stores and the internet. If it's something that can be bought in a "normal" store or on-line without getting me into trouble, and doesn't cost a lot then I can have access to it. I don't have access to lab grade equipment or conditions, so no sterile rooms or special growth environment.

I thought about the following experiment, inspired by the mythbusters pyramid power episode. In the episode they cut an apple in half and put one half under a pyramid and the other not under a pyramid. In the first attempt one of the halfs rotted quicker than the other, they concluded that it happened because the saw they used to cut the apples wasn't sterile.
So I thought about taking 3 apples, contaminating a knife (by rubbing human saliva on it). Cutting one apple with the contaminated knife, one apple with a sterile knife (using rubbing alcohol to sterilize it) and one apple by a knife that has 1 contaminated side and one sterile, which is a contaminated knife, that had only 1 side sterilized with rubbing alcohol. Then leaving the 6 halves in separated sealed containers (some tupperware) for a few days and then looking examining the rott. The expected result is that the "contaminated apple" will have a lot of rot on both halves, the "sterile" apple will have no (or close to no) rot, and the half and half apple will have one rotten side and one not rotten side, and the sides will coincide to the contaminated/sterile sides of the knife touching them.
Will this experiment work?

Do you have access to growth media (agar plates)?

I have access to normal stores and the internet. If it's something that can be bought in a "normal" store or on-line without getting me to trouble, then I have access to it.

Is proving existence of fungi relevant ? If so, you could wet a bread with water and keep it in a hot and humid place. You will see moulds growing after 2-3 days.

@biogirllajja, what is the control group? how do I prove that those are microorganism and not just a property of the bread?

@IlyaMelamed You could keep the bread in a refrigerator where the fungi will not grow.

We can see the moulds growing with naked eyes but you could see them better with a good magnifying glass.

@biogirllajja, what you describe is an experiment on best environment for fungi growth, what I'm looking for is to take 2 (or more) exact environments and show that by introducing bacteria to one of them I create a difference. A wet and hot bread is not the same environment as a refrigerated bread.

@IlyaMelamed I think keeping a bread dry and another wet but keeping them in the same environment should also work. (Not sure though)

You might be interested in the BBC documentary "Afterlife: The Strange Science of Decay", which can be found on youtube. In the experiment, a full apartment + garden enclosed in glass was left to decay. Very interesting to watch, and might give you some ideas for possible home experiments.

You could use Jell-O for growing bacteria if you don't have access to agar ! (I have never tried this but I think it should be possible because the gelatin in Jell-O is like agar.)
You should first sterilize a small knife on a gas stove or with alcohol and then gently rub it on any surface (where you think bacteria are likely to be found ) and then rub it on Jell-O taken in a dish. You should then place it in an environment similar to the one from where you isolated the bacteria. After one or 2 days the bacteria should grow.
For control : You could simply put a plate of Jell-O in the same place but without inoculation of bacteria.
Disclaimer : I am not a microbiologist and I am not sure this would work but you could give it a try as it will not be really expensive :)

Agar is easily available online (~5 euros for 100 g on eBay). For how to make the plates, and a sample experiment see here

I see no reason to restrict yourself to jello or buy agar (its not expensive tho).
Every piece of rotting leftover in the fridge pretty much proves that bacteria and fungi exist....
You can always sterilize any food by boiling it (like jello).   A pressure cooker is better than just boiling it. You will have to boil the dishes you are using too.
Then expose one dish  to something that contains germs and compare it to a sealed sterile container of the food.   Breathe on it or put your finger in it - that should be enough.
Seal the exposed container up good after exposure tho - it can get messy!
Fruit and even coffee will grow the junk you want pretty quick.  Leave it at room temperature for faster results.

Good point. We always tend to think to complicated. The above example with the bread works as well....


text:
What are the internal surfaces of body cavities actually made of?
In Ross's book of histology it says that the mesothelium that includes all body cavities is made of simple squamous epithelium but in other places it says that in the gastrointestinal tract it is made of simple columnar epithelium. Is it that the trachea and the the gastrointestinal tract are not classed as cavities?

It is correct to say that the trachea and GI tract are not classed as cavities, yes.

The peritoneum, the pleura, the pericardium, the tunica vaginalis testis and the tunica serosa uteri are made of mesothelium (simple squamous epithelium) [1].
The GI tube is made of a specialized tissue composed from four layers: mucosa, submucosa, muscularis externa and adventitia. The innermost layer (mucosa) has an epithelium that is stratified, squamous and non-keratinising, for protective purposes. The internal organs in the peritoneal cavity are covered with the visceral sheet of peritoneum which is the adventita layer [2].
Trachea is made of respiratory epithelium, which serves to moisten and protect the airways. It is lined with pseudostratified columnar epithelium with goblet cells that produce mucus [3].
Trachea, stomach and intestines are considered cavitary organs as opposed to parenchymatous organs (lung, kidney, liver).
References:

Wikipedia contributors, "Mesothelium," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Mesothelium&oldid=598055771 (accessed June 26, 2014).
Wikipedia contributors, "Gastrointestinal wall," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Gastrointestinal_wall&oldid=598338180 (accessed June 26, 2014).
Wikipedia contributors, "Trachea," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Trachea&oldid=613017631 (accessed June 26, 2014).


text:
Where might I find a list of all recorded instincts by species?
Where might I find a list of all recorded instincts (possibly with all other attributes) by species?
Thanks,
Chenz

What instincts are you talking about?


text:
Can the sulphur content of biological material be reliably calculated from fat, fibre and protein contents (Weender Analysis)?
An often-used analysis of feedstocks for lifestocks is the Weender analysis, which basically divides the volatile solid content into fats, fibre and protein, as well as N-free matter. I found no English language article on the process.
The individual values and how they are arrived at are:

Fat: anything dissolvable in organic solvents;
Fibre: anything not dissolvable in acids or bases;
Protein: N-content times 6,25 or 6,38 for plants or protein (and the N-content in protein is most of the times close to 16%);
N-free: the rest (sugars, starch, pectines, organic acids ...).

This data is often more readily available than a full chemical analysis.
I want to know the sulphur content - can I reliably say fats contain v mass-% sulphur, proteins x mass-% ... and so on?
If yes, would this be applicable to manure also?

I would say theoretically yes, if you know lots of other information, but practically no, because of all the unknowns.
According to this paper cysteine content and therefore sulfur content of proteins vary depending on what kind of organism your organic material is coming from. Animals have more, bacteria tend to have less.
The sulfur content as a fraction of protein content in a given animal or plant is constant or nearly constant across the entire animal/plant. If a sample's protein content is 50:50 corn protein:sheep protein it's possible to estimate the sulfur content of the protein fraction from the sulfur contents of the sources of the protein.
In addition the sulfur content can be affected by fermentation and sulfur/sulfate-reducing bacteria, many but not all of which are anaerobes. So figures for whatever the source of the feedstock is (as far as cysteine content) can be affected by whatever happens to it afterwards. Chicken waste with a high sulfur content allowed to ferment may give off fairly large amounts of hydrogen sulfide, lowing the sulfur content without necessarily affecting the bulk protein content. The reverse might also happen, where protein is digested and sulfur is released as sulfates but kept in the mixture.
Even if you know for certain the sources of all of the protein(and that no further biological activity has changed them), the unknown amount of organic acids is going to throw off your sulfur estimates if there are sulfur-containing organic acids in the N-free fraction.


text:
how cells make other macro molecules?
We know that the nucleus of the cell is the White House of the cell and its DNA is the president and it commands to make protein. So my question when DNA only codes for protein and enzymes,after the birth of a new cell where does the cell get lipids and carbohydrates to make membranes, organelles, water, ions, plasma membrane etc ...?

Molecules like complex lipids and carbohydrates are all synthesized by a special class of proteins that catalyze chemical reactions, called enzymes. Since the information of these proteins is coded for in the nucleus, you can imagine that ultimately the synthesis of these molecules does boil down to the genome.
The basic building blocks that the enzymes use to synthesize complicated molecules come from things you eat. Of course, we eat things that were once alive, and so the molecules that we get have been built up through enzymatic processes in the organisms we eat.
Ultimately, the "pre-organism" source of most of our molecules is CO2 from the air. Plants and photosynthetic algae have proteins that allow them to use the energy of the sun to reduce the carbon, making useful compounds such as glucose.

so imagine the first cell of the universe the begining of the world where the cells got there other molecules??

Looks like in the beginning of the world there were a lot of organic molecules available (since there wasn't bacteria to eat them). The cells only began building them after a long process of natural selection. http://en.wikipedia.org/wiki/Abiogenesis


text:
How does a fertilized egg form 23 pairs of chromosomes?
I am always confused about this...so when one cell which has 23 pairs of chromosomes undergoes the two meiotic divisions it produces four cells containing 1 chromatid of every chromosome pair so when this fertilizes the opposite gamete (of course it has also one chromatid of each chromosome pair) when they are fertilized they make one 23 chromosomes because 23 chromatid from one and 23 from other and they will form 23 chromosomes not 23 pairs of it, so my question is how they form 23 pair of it or to make it homologue..please clarify with some pics??...tnx

you've almost got me confused as well! 23 chromatids in each gamete: 23 + 23 = 23 pairs, no? the gamete chromosomes do not fuse or recombine in fertilization or anything like this.

I was confused by this for the longest time too...it's confusing how a both a single chromatid and a pair of chromatids can both be referred to as a chromosome.

After fertilisation the zygote has two copies of each of the chromosomes (not worrying about sex chromosomes). When each of these is replicated the cells will have chromosome pairs, which will then divide in mitosis.
The classical chromosome image of pairs of X-shaped chromosomes relates to the situation at mitotic metaphase when each of the chromosomes has replicated and consists of two sister chromatids. As anaphase proceeds the splitting of the centromeres means that each of the sister chromatids becomes a chromosome, and each cell ends up with a pair of each chromosome type, just like a zygote.


text:
Why doesn't the cytosol dissolve the polar structures?
we know that cytoplasm of cells are filled with water molecules and other hydrophilic molecules so my question is why the water of cytosol doesn't dissolve the ionic part of the lipid bilayer or why it doesn't dissolve the proteins and enzymes which are most polar and ionic and they still form structures,organelle and function and suspended in water?

Many cell components are not simply hydrophobic or hydrophilic, but have dual affinities. Proteins typically have structures which result in the interior of the protein being hydrophobic and the exterior, which is exposed to the water in the cytosol, being hydrophilic. Thus, differences in polarity between different regions allow proteins to be dissolved in the cytosol while still maintaining a stable structure.
Similarly, the lipid bilayer is composed of phospholipids, which can be described as "tails" of hydrophobic carbon chains connected to hydrophilic phosphate "heads". The phospholipid bilayer is organized so that the phosphate heads are on the surface of each side of the bilayer, with the carbon chains from each side of the bilayer intertwined with each other in the interior.

ADDENDUM
Water can disrupt the intramolecular hydrogen bonds by bonding to the donors/acceptors. However, water in many cases can also act like a bridge and stabilize the protein structures. As already pointed out by jarlemag, the hydrophobic residues can push the water out of the pockets where intramolecular hydrogen bonds are to be formed. You may notice that the cores of the proteins are mostly hydrophobic while the surface is hydrophilic. So water plays an important role in the maintenance of the structure. Therefore many proteins need the assistance of chaperones to fold into a stable structure; once folded they maintain their structure while remaining suspended in water (I use the term suspended because proteins don't form true solutions: they form colloidal mixture). Chaotropic agents like urea exert their denaturating effect by disrupting hydrogen bonds as well as by increasing the entropy of the water molecules around the hydrophobic regions and thereby reducing the net hydrophobicity.
(I hope it is clear now)

This answer doesn't add anything to the others, but is an attempt to explain using different language.
"my question is why the water of cytosol doesn't dissolve the ionic part of the lipid bilayer"
In a sense, it does. See my diagram below The bilayer is composed of phospholipids, classic amphiphiles with a polar head group and a nonpolar tail group. The polar head group can interact favourably (in a thermodynamic sense) with the cytosol through hydrogen bonds. In contrast the hydrocarbon tails cannot interact with water through hydrogen bonds. This means that they force a structure on the surrounding water which decreases entropy of the system (unfavourable). The thermodynamic solution to this is for the bilayer to form - this maximises the interactions between the head groups and the aqueous surroundings and minimises the unfavourable interactions between the tail groups and the solvent. A beneficial side effect is tha the close packing of the tail groups maximises van der Waals interactions between them.
On balance the 'ordered' nature of the bilayer is stable because it is paid for by increased disorder of the solvent and favourable interactions between the hydrocarbon tails.
Exactly the same arguments apply to proteins: proteins fold to minimise the exposure of nonpolar amino acid side chains.


text:
What is the function of the RNA primer in DNA replication?
During DNA replication, RNA primase puts an RNA primer in the lagging strand. What is the function of this RNA primer? Why can't the enzymes put DNA fragments directly?

DNA polymerases need a primer oligonucleotide (RNA or DNA) - their substrates are an existing 3'-OH group and a dNTP. The primase however is a typical RNA polymerase, capable of initiating polynucleotide synthesis de novo by positioning a complementary ribonucleoside 5'-triphosphate opposite its complementary DNA base. The primase makes an RNA primer that the DNA polymerase can then use for chain extension. The RNA primer is ultimately degraded and replaced by a DNA polymerase.
The rationale for this difference is that DNA polymerases have an active site that is geared towards proofreading and that primerless initiation would be an error-prone process. By having the primers 'tagged' by virtue of them being RNA, it is possible for the replication machinery to use them but then replace them with a high fidelity DNA copy of the template strand.
Edit in response to OP comment:
Synthesis of the leading strand consists of extending an existing DNA. However the leading strand is also originally initiated, at the ori element, with an RNA primer. Once that first initiation event has taken place the synthesis of the leading strand is simply a process of extending that original primer.
Some viruses employ ingenious variations on this theme such as using tRNA primers , or proteins - see Wikipedia.

so why doesn't DNA polymerase need RNA primer in leading strand?

OK.thanks a lot bro....i really appreciate for giving time to answer..:)

Well, if the answer is useful, you might consider giving it an upvote, or even possibly accepting it. Entirely up to you of course - before accepting might be worth waiting for a day or two in case a better answer comes along.

well i tried many time to vote it..but i need 15 reputations. i have 11 now...so the first i will do when i get 15 reptutations is that i will vote this answer...:)

"but then replace them with a high fidelity DNA copy of the template strand" - I would suggest adding that at the very end of eukaryote (linear) chromosomes, there will not be any way to replace the RNA primer with DNA and it will hence be removed along with the leftover sDNA end to which it was attached - resulting in telomere shortening.

@AlanBoyd Just to add to your answer, the leading strand is synthesised from the primer produced by a primase of the opposite replication fork.

It's known that the RNA primase adds RNA , is this RNA ultimately removed?, Or does it stay there?

In simple terms:
Function of the RNA primer: DNA polymerases need a double-stranded DNA region to which they can attach in order to begin copying the rest of the DNA strand. In order to provide this double-stranded attachment site, RNA primers are added by primase, an RNA polymerase which does not require such an attachment site itself.
When DNA replication starts, one primer is needed at the start of the leading strand. The lagging strand will need new primers regularly, and they mark the start of the stretches known as Okazaki fragments.
Why is RNA used instead of DNA?: Adding primers is an error-prone process, and DNA replication must copy the original strand with as high fidelity as possible. Using RNA for primers and then copying the original using DNA means that there is "memory" of which bits of the new strand were originally primers and hence more likely to contain errors (any RNA in the copy must have been primers). This allows removing them, in order to then replace them with proper high-fidelity DNA copies. When this happens, there is double-stranded DNA around the sites where primers were located, allowing DNA polymerases to attach there and fill in the gaps.
Aside from this, I would guess using RNA for priming may be more energy-efficient as RNA is more reactive than DNA.

Can you elaborate on how the use of RNA primers plays a role in high fidelity?

Presumably, when a polymerase attaches, the first few bases are quite error-prone (wobbly attachment to single-stranded DNA, proofreading at this point would risk the polymerase dropping off the strand). Once the first few bases are added, the resulting double-stranded region can provide more stable attachment and allow proofreading to function properly. When done, it would be better to know which bits of the resulting strand were the first few (error-prone) bases, so that they can be removed and re-done with proofreading. Using a different type of molecule for the primer makes that possible.

So basically, is the need for primer in replication because DNA polymerase  requires double stranded region and this primer being RNA helps distinguish the first few bases added which are error-prone?

Rather: being able to distinguish the first bases is good, and one possibility for this is to use RNA for them and DNA for the rest. To implement that, the easiest is to have two polymerases, one which makes RNA and can attach to single strands, and one which makes DNA but can only attach to existing double-stranded regions.


text:
What's the distinction between a tetrad and a synaptonemal complex in meiosis?
What's the distinction between a tetrad and a synaptonemal complex in meiosis?  Are they synonyms?
I ask because the concepts seem very closely related, but it seems like there may be a subtle distinction.  Unfortunately, none of the sources I've been consulting use both terms.

As far as I can tell there is a distinction.
A tetrad refers to the entire group of four chromatids after they have come together for crossing over in Prophase I (synapses).
A synaptonemal complex as you would expect is formed in synapses.  This is a protein-RNA complex that connects the intervening regions of matched chromosomes in some circumstances - it is not required. Mutated yeast that can not form this complex has still been shown to be able to exchange genetic information.
In other words, you can have a tetrad without a synaptonemal complex, but not vice versa.


text:
Can different strains of Rhizobium share an infection thread or symbiosome?
Rhizobium infection can be triggered at root hairs of legumes, creating infection threads.
Can these infections threads be colonized by more than one type of Rhizobium (e.g. Fixing and non-fixing)?
What about when the infection is inside the plant cells? Can symbiosomes be co-inhabited by different bacteria?


text:
Why are goosebumps so ineffective at keeping us warm?
If the purpose of "goosebumps" is to keep us warm, why is it so ineffective? Or are the changes subtle, but important?

When your brain, the hypothalamic temperature centers in particular, detects that the temperature is too warm or cold, it initiates a number of controls to try and correct this.
Goosebumps appear due to piloerection. This is one of the reactions that occur when the temperature is too low.
This causes hairs to stand on end as a result of contractions in muscles attached to hair follicles called arrector pili.
This particular reflex is not actually important in human beings. However, in animals, this mechanism allows entrapment of a layer of air allowing insulation. This way, the heat loss is greatly reduced.
The other mechanisms are very adept at maintaining temperature in the human body. These include sweating, dilation (vasodilation) and constriction (vasoconstriction) of skin blood vessels and increasing and decreasing the body's heat production.
For example, when it's too hot, dilation of the skin blood vessels can increase heat transfer by up to eight times.
Source: Guyton and Hall. Medical Physiology. 11th ed. Elsevier Saunders.

Cutis anserina (goosebumps) are caused when the sympathetic nervous system induces the arrectores pilorum muscles at the base of each hair cell to contract and raise up the hair.  Zoidberg has posted an answer describing the mechanism as I was writing mine, so I'll move directly onto effectiveness.
The reason that, as you say, the mechanism is not particularly effective in humans is our relatively small amount of body hair.  As mentioned the purpose of the erector muscles causing the hairs to stand up is to allow for air to be trapped at the surface of the skin rather than absorbing heat from the body then taking it quickly away.  Mammals with denser fur/hair are likely to have a much better insulating effect from goosebumps.
Some animals have adapted to use the mechanism for another purpose, however; the porcupine being a prime example.  When threatened, the porcupine uses its arrectores pilorum muscles to elevate all its quills, making it appear larger and more threatening or to actively repel an attacker.  The extra rigidity that they gain from doing this1 also helps to contribute towards making their spines a very effective defence:

Goosebumps have also been reported in humans during periods of stress, anxiety and even sexual arousal.  This is related to the stimulatory effect that adrenaline has on the sympathetic nervous system which, as mentioned above, is responsible for the stimulation of the erector muscles.

1Mechanical design of hedgehog spines and porcupine quills. Journal of Zoology
Volume 210, Issue 1, pages 55–75, September 1986


text:
Correlation between muscle size and absolute strength
Is there a linear connection between muscle size and the power it can produce?
If not, why? And what is the true correlation if any, can it be described with an appropriate function? What other factors modify it? (Red/white fiber for instance?)

The short answer to your question is that the work output from a muscle is a combination of physiological cross-sectional area, length, fiber type, and recruitment (how many motor units are activated).
Read on for more details.
Force output (tension) of a muscle is proportional to its physiological cross sectional area (Fundamental of Medical Physiology), and shortening is proportional to the length of the muscle. Work output (force X length) is a function of both. Power (work / time) involves both force, length change, and the shortening velocity. Shortening velocity is related to muscle fiber types.
There is a complex relationship between force output and length. In the graph below, the x-axis is relative length (1.0 being resting). When muscles operate outside a relatively narrow range (gray box), the cross-bridges are either too close together or too far apart to optimally generate force. When the muscle gets really stretched, force goes up, but only because passive tension (the intramuscular connective tissue is getting stretched) increases.

The force-velocity curve below relates relative force output to how fast the muscle is shortening (which can be negative; i.e., lengthening contraction). The green part of the curve is muscle shortening. As velocity approaches 0, the muscle produces maximal shortening force. When the muscle goes into the red part of the curve, force is even higher. In order for a muscle to shorten very quickly, it can't produce a lot of force (far right).

Muscle fiber type generally relates to both the force output of a muscle fiber and it's shortening velocity. There are different ways to classify muscle fibers (enzyme activity, myosin isoform, or the "classical" method):

SO ("slow oxidative"; the dark meat of a chicken) fibers contract slowly, produce lower force but are fuelled by oxidative reactions and thus have good endurance. At the other end of the spectrum, FG ("fast glycolytic"; the white meat of a chicken) fibers contract quickly with high force, but fatigue easily because they get energy from glucose, which is rapidly depleted. FOG fibers are intermediate between the two.

The muscular fiber cross section and length would be proportional to its strength, but there are also many different kinds of cellular types and structures which can result in muscles which are quicker or stronger, have better endurance etc.
This post from 2009 ago puts forward the hypothesis that chimpanzees, who weigh 70 to 130 lbs (32 to 60 kg) are typically capable of lifting 3-4 times more weight than a human being can. They also put forward that the coordination of the muscle with other muscle fibers makes up the gross difference in strength. Human beings have much better fine motor control for delicate operations than chimps, which might cause the muscles to be less in synch resulting in lower strength despite the fact that we have about the same amount (or less) of muscle tissues in say our arms or legs.

Muscle length doesn't have any effect on force output, only the range of useful shortening distances.


text:
How do large herbivores get enough protein?
The food they eat seem extremely low on protein. Do they need less protein per mass unit than carnivores? Most of them grow quite a lot in the first year, is most of that from the mothers milk?

Most amino acids can be synthesized de novo. The 'essential' amino acids in humans are mostly derived from meat. Those have to be obtained from the diet. I wouldn't be surprised when most herbivores would be able to synthesize all of their amino acids de novo

@AliceD I don't know of any animal that can synthesize all their amino acids. The good thing is that plants can make all of them, and herbivores eat the plants, and the carnivores eat the herbivores.

It boils down to the anatomy.
Herbivores are very good at digesting plant matter, which us monogastrics are not particularly good at. Many herbivores (such as ruminants) have large, highly developed gastrointestinal tracts containing symbiotic bacteria to allow them to digest plant matter. Once the cellulose in the plant cell walls is digested, the animal can then access the nutrients  contained in the plant matter to a degree we cannot. Ruminants (such as cows) are even better able to absorb nutrients in this way than monograstric herbivores (such as horses). Rumen microbes are also an important source in ruminants for production of amino acids.
There's also a reason why the GI tract of these herbivores is so big. In the cow, it's an enormous rumen. In the horse, it's a massive colon for hindgut fermentation. To get all the nutrients they need - such as amino acids - these herbivores have to consume and ferment vast quantities of plant matter. A carnivore can generally get all the nutrients it needs in a much smaller meat meal, meaning it does not need such an extensive GI tract.
Different species, of course, have different metabolic demands and corresponding nutritional needs. Cows and other herbivores cannot synthesize all the amino acids they need, meaning they have to be consumed through the diet. Though it is somewhat dated, an interesting discussion on this subject is Protein and Amino Acid Requirements of Mammals (PDF) by Anthony Albanese (1950). The author goes through in great details the different protein requirements for various species, but I will bring your attention to one interesting table on p 116 as it is pertinent to your last question:

As you can see, the protein content of milk seems to correspond with the time to double birth weight. Cats with a high protein milk grow very quickly, while cows, horses, and humans grow comparitively more slowly (and thus have lower protein milk).
All animals have to get protein or amino acids through the diet, but they just have different methods to satisfy their metabolic requirements. For carnivores, they consume small protein-packed meals. For large herbivores, they have to consume and digest large quantities of plant matter to meet their needs.

Nice, answer, though I wonder how much that table was an example of correlation not being equal to causation. Cat and Dog newborns are very small due to multiple litter mates, and doubling their weight, is less in absolute terms than larger animals. As for humans I wonder how much of the energy load goes to providing energy to brain formation and is less available to adding to muscle, bone, and fat stores.

I wonder if you could add the grass-digesting microbe to the human gut and get the same effect?

The protein RDA of another mammal, the human, is 70g every day, that's about 700g of hay if he can get 100% of the protein from it, that's 4 kilos of grass. So a 700 kilo cow would need about 40 kilos every day, and actually 700kg cows consume about 70kg  of pasture every day.
Probably energy is the most common deficit, and not protein.
Average pasture contains between 11% and 28% protein:
You can read the paragraph on protein:
https://www.teagasc.ie/media/website/animals/dairy/Whats_in_Grass_Todays_Farm_May2014.pdf
The rumen contains many organisms, funghi and yeasts, which can also synthesize their own protein. At about 10^10-10^11 cells per milliliter, ciliate protozoa at about 10^4-10^6 per milliliter, anaerobic fungi at about 10^3-10^5 spores per milliliter and bacteriophages at about 10^8-10^9 per milliliter. It should be noted that many microbes cannot be cultured in labs, so the numbers may actually be higher in reality.
https://microbewiki.kenyon.edu/index.php/Bovine_Rumen#Who_lives_there_.28Microbes_in_Rumen.29.3F
One E. coli cell has a mass of 0.95×10−15 kg, so a gram of rumen can contain 0,00001 kg of animal life, 0,01g 1%? so a 180 liter rumen can contain about 1.8 kilos of bacteria, funghi and yeast. That's a lot, especially if it can double every hour at 37'C.

To paraphrase:
Cattle don't receive their nutrients from what they consume (which, as noted, does not contain much nutrients), but rather from the various bacteria in their guts, which convert the vegetable matter into the numerous amino acids the cattle need.

Welcome to Biology.SE! It isn't clear that this adds anything to the existing answers — unless you have new information to add it would be best to focus on unanswered questions. In addition, answers are much more likely to receive a favorable response if you include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion. ——— Please take the [tour] and then consult the help pages for additional advice on [Answer] effectively on this site and then delete or [edit] your answer accordingly. Thanks!


text:
Why doesn't sugar spoil?
Sugar contains a lot of easily accessible chemical energy. Why seemingly nothing likes to grow on it?

lack of water. even if water is present then 2. high osmotic pressure will cause plasmolysis. Since I don't have a source I am not writing this as an answer.

Ever make bread?  Typically you'll mix a bit of sugar into warm water, add yeast, and wait an hour or to for the yeast to grow.  So the yeast is eating the sugar, but as JM97 says, it needs to be in a dilute solution.

Our food mostly gets spoiled by bacteria and / or fungi. There are 2 main reasons for sugar crystals not getting spoiled.
1- Lack of sufficient amount of water to sustain metabolic processes by microbes.
2- Even if sufficient amount of water is present , then due to high osmolality of the fluid formed, will cause plasmolysis or cell shrinkage.
Some technical data:

Microorganisms differ widely in their ability to resist salt- or sugar-induced reductions of aw. Most disease-causing bacteria do not grow below 0.94 aw (roughly 10 percent sodium chloride concentration), whereas most molds that spoil foods grow at an aw as low as 0.80, corresponding to highly concentrated salt or sugar solutions.

Source: https://www.scientificamerican.com/article/how-do-salt-and-sugar-pre/

Pop-sci reference: "How do salt and sugar prevent microbial spoilage? (from Scientific American)

@fileunderwater thanks a lot for providing source.


text:
Hershey and Chase experiment
http://www.youtube.com/watch?v=3QJ4CjFsflA
This is a link to Hershey and Chase experiment. According to this experiment, we conclude that DNA is the genetic material. But how do we conclude that DNA is the genetic material? They only proved that DNA of virus enters into the bacteria, not the protein coat of virus.
The DNA of the virus later destroys the bacteria because the virus reproduces inside them. Does this demonstrate that DNA is the genetic material?

It is a matter of deduction. We know that:

Viruses entering a cell are capable of making more copies of themselves.
The only part of a virus that actually enters the cell is its DNA (or RNA, depending on the virus in question).

Based on these two facts, we can conclude that the DNA ̣--since it is the only part of the virus to enter the cell-- somehow contains the information necessary to make new copies of the virus and is, therefore, the genetic material of the virus.

@MuhammadRafique, I did not mean to push you to accept my answer (it is often a good idea to wait a while in case a better one comes along), I was just pointing out the etiquette on these sites :). Thank you comments are discouraged.

i was not pushed, don't worry....:)...and i didn't know commnets are discouraged, so bye bye...:p

@alanboyd, ouch,thanks for the edit, durned iphone...

This was an important experiment, but did not convince everyone.
Not even Hershey and Chase claimed this conclusion, although it convinced many.  In most mol bio classes or when reading "The Double Helix" you can see how there were lots of facts pointing to DNA, but doubts lingered.  Some viruses contained RNA only and not DNA, but still replicated.  There was also a school of thought which felt that proteins could be the genetic material.
It was Watson and Crick that finally convinced everyone that DNA was the medium of genetic inheritance.  The reasons for this are varied, one of them is probably that atomic structures are so clearly understandable and seem so uncomplicated compared to a wet lab experiment which is built upon so many other experiments.  Questions keep coming up:  "how do you know you shook the flask long enough?", "What if a small amount of residual viral protein got in?"  For every revelation like Hershey and Chase, there are many cases where someone stopped an incubation too quickly or wrote down an illegible number and was found out after publishing.
And you can see how much the structure gave us in one fell swoop: the structure of DNA inspired a mechanism by which replication of the DNA could be produced with some error correction, the central dogma (DNA -> RNA -> protein).  There were several years more effort to demonstrate that the genetic code existed and then parsing out the exact codons and the fact that they were 3 bases long.  But all of this was predicted when the structure was found.  So much clearer as to what is going on.

Perhaps worth adding this quote from Watson: "the Hershey-Chase experiment had a much broader impact than most confirmatory announcements and made me ever more certain that finding the three-dimensional structure of DNA was biology's next important objective. The finding of the double helix by Francis Crick and me came only 11 months after my receipt of a long Hershey letter describing his blender experiment results."


text:
Cellular components of blood cells
There are different types of blood cells in the human body i.e. red blood cells, neutrophils, basophils, eosinophils, monocytes, T-cells, B-cells.
What are the cellular components of these cells? What are the organelles that are found in these cells? I can't find this information anywhere.

It's pretty straightforward.  White blood cells have all the usual organelles while mature red blood cells are missing most of them.  WBC can have specialized lysosomes depending on their function, as well as granules if they are granulocytes.

I edited to remove a sentence with a dead link that had no attached information to find out what is was.


text:
Do the four cells produced by meiosis each divide into four cells again?
In the beginning of meiosis, there is one cell. During meiosis, 1 cell divides into 4 cells. Does each of these 4 cells divide each into 4 more cells?

In species where an individual can be haploid (for example in haplodiploidy) then cells produced by meiosis do multiply by mitosis in order for the individual to grow.
From a brief scan the Wikipedia article on ploidy nicely summarises the various possibilities.


text:
How do transplanted stem cells find their way to bone marrow?
Miraculously, transplanted stem cells find their way to the bone marrow missing the stem cells. How do they achieve this?

The transplantation is an equivalent of a process that naturally occurs in human body, homing of the hematopoietic stem cells.
Immature hematopoietic stem cells have the ability to pass the bone marrow barrier, and therefore is able to migrate between bones and other organs within an individual. (e.g. thymus, which is how it can produce T cells.) Williams et al. believe that the process, homing, is a complex interaction and is similar to the migration of leukocytes to inflammatory sites. 1
Peripheral stem cell transplantation makes use of this ability. The donor first will be administered with certain drugs to proliferate stem cells in bone marrow and hereby raising the concretion of hematopoietic stem cells in blood. Those stem cells in blood then will be collected and transfused into the recipient. Eventually those cells will find their way home.

similar to migration of leukocytes to inflammatory sites... so you mean it's somehow like chemotaxis?

@GreekFellows I believe so. In fact, a research I found suggests HSC will respond to some factors.


text:
Does isolation have any effect upon mouse behavior?
I work with a lot of mice. I don't do any behavioral analysis, I just inject DNA or RNA and do imaging assays. However, I have noticed some effect of isolation on mouse behavior. Normally, the mice are housed in our university's animal facility with no more than 5 mice to a cage. Sometimes, 1 mouse will be put in a cage by itself. When I go to get these lone mice from their cages, they seem more skittish, harder to grab, and more likely to bite me than mice kept in groups.
Additionally, our Office of Animal Resources, which is responsible for getting in the mouse shipments and putting them into cages, has recently changed how our mice are caged, with a group of 4 mice being normal, any leftover mice are put into cages with other mice, making a 5 mouse cage. This means I haven't seen a single mouse in a cage for a while. So I might not be the only one to have noticed an effect of isolation on the animal's health.
I have heard of studies on monkeys by B.F. Skinner, where he induced very severe depression and other psychological issues by isolating them, so I suspect similar studies have been attempted on mice using far more quantitative methods than I've been able to do.

Yeah, it's not good:

Social isolation (SI) rearing in rodents causes a variety of behavioral changes, including hyperlocomotion, anxiety, impulsivity, aggression, and learning and memory deficits. These behavioral abnormalities in rodents may be related to the symptoms in patients with neuropsychiatric disorders, such as attention-deficit hyperactivity disorder, obsessive-compulsive disorder, autism, schizophrenia and depression...

Also:

Our findings suggest that [social isolation]-induced behavioral abnormality is a psychobehavioral complex relevant to various clinical symptoms observed in neuropsychiatric disorders, including ADHD, schizophrenia and depression, and that SI-reared mice are a useful animal model to study the pathophysiology/pathogenesis of these diseases.

There's this:

In contrast, long-term social isolation is a model to study the behavioral and neurochemical consequences of depriving rodents of social interaction. Many of the symptoms caused by long-term isolation resemble those seen in depression and anxiety disorders. Furthermore, long-term isolation of male mice is known to induce offensive and aggressive behavior, such as attacks.

And this:

These data suggest that long-term isolation may induce functional changes in the sensitivity of alpha 2 receptor in the noradrenergic system...

And this:

In the present study, we found that social isolation elevated the anxiety levels of mice...

Emphasis all my own.
There's a lot more meat in those studies, and especially the paper they cite in their introductions.  Some of them, as well as others also explore the effect of isolation in addition to other substances.  It can absolutely affect your studies, in particular behavioral or expression-based studies.  Your mouse house is good to change their practices.


text:
mRNA with Pseudouridine and 5-methylcytidine?
I am making mRNA by in vitro transcription for transfection purposes. There is a lot of literature about how protein expression is increased and innate immune activation is decreased by substituting uridine for pseudouridine and cytidine for 5-methylcytidine. I decided to try this, but my yield was lower and the mRNA was shorter than when using natural nucleotides. The papers all say they made the mRNA by simply using the new nucleotides in their in vitro transcription kits, but they never mention any further changes to the protocol. Now I would assume that since pseudouridine and 5-methylcytidine are a little different from the normal substrates for RNA polymerase that they might not be incorporated as quickly and the resulting reaction rate would slow down. It might be possible that the Polyadenylate polymerase that adds the polyA tail doesn't recognize the modified mRNA as well. Both a slower reaction rate and less efficient tailing could make a lower yield of shorter mRNA.
Does anyone here have any experience with IVT using modified nucleotides and can suggest something to improve yields?

After a couple months I got this working. I ordered the psuedouridine and 5 methylcytidine from Trilink. I also switched from the mMessage mMachine kit the the Megascript kit. Megascript has all the nucleotides separated while mMessage mMachine has them pooled. You have to dissolve Trilink nucleotides so that the concentration is the same as the natural nucleotides in your IVT kit. Then you just use the non-natural nucleotides instead of UTP and CTP. Let the IVT reaction run 4 hours. Be careful about RNAse contamination.


text:
Did neanderthals need vitamin C from the diet?
Modern humans need to get vitamin c from the diet, because we do not make it ourselves. Did neanderthals produce vitamin c? At what point of evolution exactly was this ability lost?

Humans can't synthesize vitamin C due to a dysfunctional enzyme L-gulonolactone oxidase, or "GULO".
From Wikipedia:

Loss of GULO activity in the primate order occurred about 63 million years ago, at about the time it split into the suborders Haplorhini (which lost the enzyme activity) and Strepsirrhini (which retained it). The haplorhine ("simple-nosed") primates, which cannot make vitamin C enzymatically, include the tarsiers and the simians (apes, monkeys and humans)

All of our relatives under Haplorhini, including monkeys and apes, are unable to synthesize vitamin C; that would certainly include neanderthals.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Identify this large exotic bird spotted in Taipei, Taiwan
A few months ago while backpacking in Taipei I found this very intriguing large bird facing off a curious puppy in a fairly busy pedestrian area.
The bird did not attempt to fly. None of the Taiwanese locals could tell me what it was and attempts to Google it via description all failed.
I'd appreciate learning the species name, common name in English, and/or common name in Chinese:

For me it looks like a Malayan Night Heron, Gorsachius melanolophus.
They seems to be common in this part of Asia, see the distribution.
It looks strange because he probably get scared.

It seems to resemble the birds in this photo online. It's labelled "黑冠麻鷺", which seems to be the Chinese translation for "Malayan night heron".


text:
What's the maximum and minimum temperature a human can survive?
This is a question that has been in my mind since I was a kid. I'm not a doctor, nor even a biology student, just a curious person. What is the minimum and maximum temperature a human body can stand without dying or suffering severe consequences (eg. a burn or a freeze)? While at this subject, how much more global warming will the human body be able to take? Seeing as temperatures keep on rising, I'm just wondering how much longer until the temperature starts having drastic effects.
In my country the temperature is about 35-40-45 degrees Celsius in mid-summer (I live in Romania, eastern Europe, and the climate is supposedly ideal here) which is very unhealthy. Does the human body suffer more and more as the temperatures change?

Better to say climate change. "global warming" implies that eveywhere on Earth will heat up due to increasing atmospheric CO2. This is not necessarily the case. We will see be seeing regional variations some of which may even include localised cooling, greater precipitation etc.

Why would 35-40 degrees in mid-summer be unhealthy? It's way hotter in many part of the world...

@nico, have you even read my post? Have you ever been to Romania? The climate is soposed to be ideal with a maximum of 28 degress in mid-summer. It's in the paranthesis.

@ThePlan: you can say that it is uncommon for Romania, sure, still I don't see how it is unhealthy... are people getting sick because of that?

Yes, what people are describing in these answers are pretty similar. People faint on the streets here in my country, they report heart issues and the enviroment itself suffers, I watched the asphalt melt beneath the wheels of a bus a year ago. It's a very rough place.

@Bugster, are you asking about ambient temperatures surrounding the human, or the internal body temperature ? The way you formulated the question, it sounds like you are asking about ambient temperature.

The problem is not just temperature but the combination of temperature and humidity. A high temperature is survivable as long as the body can use evaporation (sweating) to keep the core temperature below ca 38°. At high humidity, evaporation is inefficient. The key quantity here is the so-called "wet bulb tempeature" which is the lowest temperature that can be achieved by evaporation, it's routinely measured in weather stations. If it is above 38°, you die. In practice, this doesn't happen because hot places (deserts) are typically also dry, so the wet bulb temp is much lower.

Hypothermia (when the body is too cold) is said to occur when the core body temperature of an individual has dropped below 35° celsius.  Normal core body temperature is 37°C. (1) Hypothermia is then further subdivided into levels of seriousness (2) (although all can be damaging to health if left for an extended period of time)

Mild 35–32 °C: shivering, vasoconstriction, liver failure (which would eventually be fatal) or hypo/hyper-glycemia (problems maintaining healthy blood sugar levels, both of which could eventually be fatal).
Moderate 32–28 °C: pronounced shivering, sufficient vasoconstriction to induce shock, cyanosis in extremities & lips (i.e. they turn blue), muscle mis-coordination becomes more apparent.
Severe 28–20 °C: this is where your body would start to rapidly give up.  Heart rate, respiratory rate and blood pressure fall to dangerous levels (HR of 30bpm would not be uncommon - normally around 70-100).  Multiple organs fail and clinical death (where the heart stops beating and breathing ceases) soon occurs.

However, as with most things in human biology, there is a wide scope for variation between individuals. The Swedish media reports the case of a seven year old girl recovering from hypothermia of 13°C (3) (though children are often more resilient than adults).
Hyperthermia (when the body is too hot - known in its acute form as heatstroke) and is medically defined as a core body temperature from 37.5–38.3 °C (4).  A body temperature of above 40°C is likely to be fatal due to the damage done to enzymes in critical biochemical pathways (e.g. respiratory enzymes).
As you mentioned burns, I will go into these too. Burns are a result of contact with a hot object or through infra-red (heat) radiation. Contact with hot liquid is referred to as a scald rather than a burn. Tests on animals showed that burns from hot objects start to take effect when the object is at least 50°C and the heat applied for over a minute. (5)
Freeze-burn/frostbite, which is harder to heal than heat burns(6) occurs when vaso-constriction progresses to the degree where blood flow to affected areas is virtually nil.  The tissue affected will eventually literally freeze, causing cell destruction. (7)  Similarly to hypothermia, frostbite is divided into four degrees (that can be viewed on Wikipedia).
As to the matter of global warming cooking us to death, I would imagine that it would be more indirect changes that got us first.  If the average temperature had risen  to the necessary 40°C to cause heat-stroke, sea levels would have risen hugely due to the melting of the polar ice caps.  Crops and other food sources would likely be affected too, therefore I don't think that global warming is overly likely to directly kill humans.

Hey, thanks for the answer. That pretty much sums it up.

I don't think this is a good answer. Atmospheric temperature is being confounded with internal (body) temperature here. If the atospheric temperature in Romania is 45 C, you will not die (even given a fatal temperature of 40 C), because your body can thermoregulate (up to a point). Plenty of populations have existed for millennia where temperatures routinely exceed 40 C.

I should clarify that I think this is a good answer to the question: "What is the range of internal body temperatures at which a human can survive?"

I do believe that though temperature above 40°C is alarming many children survive it when they are ill.

Surely these numbers are supposed to be negative, right? I can't imagine how 35°C would result in shivering...

@Mehrdad those numbers refer to the core temperature of a person (how warm they are rather than how warm their environment is.

@RoryM: Ohhhhhhhhh

As Rory explained, internal body temperature needs to be highly regulated.
Sweating is the main built in mechanism for removing excess heat from the human body. According to my biology book, in (100%) humid conditions humans cannot survive in heats of above around 45C, but in a dry environment can survive in heats of over 100C just through sweating.

45C = 113F, 100C = 212F

Some 200 years ago Dr.Charles Blagden, then secretary of Royal Society
  of London, went into  a room that had been heated to a temperature of
  126 degree Celsius ( 260 Fahrenheit) , taking with him a few friends ,
  a small dog in a basket and a steak.The entire group remained there
  for 45 minutes. Dr.Blegden and his friends emerged unaffected.

This shows the power of homeothermy.
Source : Helena Curtis ( 5th edition) Chp. 38

What happened to the dog? (It died because it could not cool down efficiently enough?) I guess the steak was cooked?

@WoJ The dog was ok, one of the steaks was overcooked.
https://publicdomainreview.org/collections/experiments-and-observations-in-a-heated-room-1774/

Yes, we can survive temperatures above 100 F (38 C) but surviving such temperatures requires continuous fluid intake.  Since sweat evaporates quickly in an arid (dry) environment we tend to be unaware of how much water we're losing.  This leads to heat exhaustion, then heat stroke, then death.  Survival time depends on how well hydrated you are and whether or not you can replace the lost fluid.

Can you add a reference to the statement on continuous fluid intake (and in what range it is valid)?


text:
Could an organism theoretically produce a metamaterial-like structure?
I'm curious to know if this is physically feasible because during my reading up on synthetic biology and just general research i realise that life is capable of producing some exquisitely complex materials and biological structures and wondered if they could potentially recreate artficial materials that aren't found in nature well not yet anyway. Could such a structure evolve naturally or would it have to be designed or directed via synthetic biology techniques?
Thank you for your time.

Could you clarify what you mean by 'artficial materials that aren't found in nature'?  Are you talking about chemical production bacteria such as biofuels, or some animal that builds an item such as bone replacements out of coral?

Hi, im talking about materials that have so far only been produced in labs or manufactured using technology and have not to our knowledge been produced or grown by any living thing. I only wanted to know if life could create such complex structured materials.


text:
Forum on synthetic biology and hypothetical biology?
I am interested in synthetic biology, but not a scientist, and would like some advice on where to look for an online forum on synthetic biology and creating fictional species and animals or if someone could suggest the best website to set such a forum up on.
The current research into synthetic biology with biobricks and all the complicated discussion of biochemistry and genetics is too advanced for myself and not what I am interested in. I have fictional ideas of how to create new organisms and symbiotic organisms that are designed and grown for humans to wear and utilise and would like to bounce ideas off other people who may be in to the same area - the potential application of synthetic biology in the far future.
Thank you for any suggestions.

what you ask for is not synthetic biology but science fiction. SF&F-SE would be a suitable forum for this kind of discussion.

Synthetic biology is currently at the level of constructing genetic circuits and modifying bacteria. We still don't fully understand all the details of how single-cell organisms work, so creating new types of animals is pretty far away.

What you want is not a forum on synthetic biology, rather a science fiction site. I recommend visiting the sister website found in https://worldbuilding.stackexchange.com which is a "is a question and answer site for writers, artists and others using science, geography and culture to construct imaginary worlds and settings." I am positive that you will find intriguing discussions on synthetic biology there.

I'm voting to close this question as off-topic because it is not about biology.

Your best bet might be the sub forum on reddit specialized in synthetic biology. Have a look here
Happy science!


text:
Would muscle fatigue still occur if aerobic conditions for a working muscle is maintained?
Put another way if the muscle is given everything it needs to contract and do work will it ever get tired or have a reduction in energy efficiency?
As far as I understand muscles depend upon a blood supply delivering oxygen and nutrients (e.g. glucose and calcium) to effectively contract at its best level of performance. With the ability to work under anaerobic conditions if need be but producing lactic acid as a by-product which reduces the muscles ability to contract and therefore producing fatigue.
I also know that muscles are dependent upon temperature to work efficiently like the rest of the body. So, if the muscles temperature was able to be regulated well enough to maintain efficiency and aerobic conditions are met could fatigue be negated?

I think you need to clarify something. I was going to answer, but then I realized there's a difference between constantly working and operating under stress. Your heart is an example of a muscle that never quits, so it is one example of an answer to your question. However, if you mean when muscles are stressed beyond their normal operating parameters, as the heart rarely is for extended periods of time, then that's a different answer.

ATP is also needed..

thanks for the input. Yeah I was meaning constantly working and/ or under stress in terms of endurance training or activity, I was curious about the limits to how long and far the skeletal muscles can be exposed to. I should have specified the skeletal muscles in regards to the muscles that allow us to run and walk.

It seems that you are asking about activity significantly above basal metabolic rate. If aerobic conditions are maintained (and with appropriate training), muscles can operate more or less continuously for very long durations, days to weeks. In non-humans:

Godwits have been recorded flying over 7000 miles (>11000 km) without stopping for 9 days
Arctic terms migrate 44000 miles (>70000 km), albeit with stopovers
Humpback whales migrate 5000 miles (8000 km). Their muscles are probably operating close to continuously.
Many (most?) species of sharks swim continuously.

There are probably other examples as well (feel free to add). For humans, usually the limit to endurance is sleep. Two forms of racing push human endurance, but the longer races almost always require at least minimal sleep:

Ultramarathons, foot races of 50 mi (80 km), 100 mi (160 km) or more (e.g., 24 hours, multi-day).
Race Across America, Paris-Brest-Paris, and similar endurance bicycle races. The RAAM has a record time of 3107 mi (4971 km) in 8 days, 9 hours for a mean velocity of 15.4 mi/hr (24.6 km/hr).

thanks, I never thought about it from this point of view with examples of animal performance. In regards to the performance of muscles over such long endurance events do you know if they reduce in their energy efficiency, of converting glucose (ATP) muscular contraction, as time passes. I have read in multiple sources the energy efficiency is around 25% for muscles but could find no stats on their performance over time and increase in operating temperature.

If the muscle is provided with adequate food and oxygen, the muscle can theoretically work indefinitely. However, microtearing when a muscle is stressed more than usual can over time damage the muscle. This is the mechanism by which you get larger, stronger muscles. Without rest, it's theoretically possible to simply destroy the muscle faster than it can be repaired.


text:
Loooking for dataset of proteotypic and non-proteotypic peptide
I'm experimenting with peptide prediction using machine learning. I need some data for testing. I already have one dataset, but I need another one or two for verification.
I'm looking for data for a proteotypic peptide and a non-proteotypic peptide.