text:
How would you effect bulk DNA gene therapy for a human?
Let's imagine  that we understood DNA programming and our genome very well and realized that there were some significant flaws (we die, we need sleep, etc.) And let's imagine that we understand how to make our genome do what we want, but it's a major refactor.  We're going to have adjust 10-15% of our DNA. (Note this is just a contrived example to suggest why we would want to make such a drastic change - our ability to actually know what changes to make is unimportant for the question.)
How would we replace/or modify this much of our DNA?  It seems the problem is very similar to gene therapy, but on a larger scale.
A few possibilities come to mind.  We could make a virus that would modify our DNA.  Or perhaps we could generate the new genome and inject it into some cells which would then just outlive the others (eg because these cells won't have a Hayflick limit) or will be able to generate lots of new adult stems cells with the "refactored" DNA?

I don't think replacing that much DNA would be possible in anything larger than a zygote.

Why is this opinion based?  It's not a question like "what is your favorite codon".  I'm asking a serious question about the ability to replace DNA in a complex organism.

Any statement of the form "Is X possible" where X is a completely speculative and untested concept is opinion-based here.

@MarchHo - I reworded the question. I fully expect that an approach is possible, eventually.  I just don't know what approach would work.  I suggest two.  Perhaps the virus approach is untenable because virii are small and replacing that much DNA would not be possible even with a complex DNA.  http://en.wikipedia.org/wiki/Gene_therapy is basically this same concept at a much smaller level.

I think the bigger problem is replacing the DNA in every cell of an adult. Gene therapy will probably be most successful in cases were you only need to deliver a small amount of DNA to a certain set of cells. There are enough problems getting a 5000 bp plasmid into tissues, trying to get entire chromosomes into cells would be much harder.

"cells which would then just outlive the others (eg because these cells won't have a Hayflick limit or will be able to generate lots of new adult stems cells"
You're describing cancer cells, unfortunately. A major challenge is that all cells accumulate mutations with time, and with rounds of cell division - so a major "upgrade" would be improved genome maintenance. This would be a challenging thing - the machinery and systems maintaining our genomes are complex!

The replacement of whole chromosomes with ones designed de novo is possible now: http://www.sciencemag.org/content/344/6179/55

@Yehosef I like your question, and think of similar things, in the context of doing business in the intersection of tech and genomics. Have you any thoughts on that? Would love to Skype, if you are interested.

@tyrex - I've thought about it.  You can contact me at gmail.com

@Yehosef Thanks, I wrote an email. If it didnt reach you, let me know, and I will give an email address here.

Let's imagine that we understood DNA programming and our genome very well and >realized that there were some significant flaws (we die, we need sleep, etc.) And >let's imagine that we understand how to make our genome do what we want, but it's a >major refactor. We're going to have adjust 10-15% of our DNA.

I think we both recognise that this is a very naive view of biology and the nature of how organismal properties emerge (through multiple levels of systems) ultimately from the genetic code, the information in the genome, and the developmental process.
It is more pertinent and promising to think about treating genetic diseases.
Some genetic diseases are caused by mutations to single basepairs (e.g. the HgbS variant of the haemoglobin beta chain, which causes sickle-cell anaemia).
Other genetic diseases are caused by rearrangements of large segments of chromosomes, and the gene dosage imbalances that arise from this (e.g. Charcot-Marie-Tooth syndrome 1A). Finally, some genetic diseases are caused by a major gene-dosage imbalance caused by having an unusual set of chromosomes, "aneuploidy" (e.g. down syndrome, where chromosome 21 is present in 3 copies).
'Large-scale' gene therapy could be something useful for aneuploidy. Recently, the mechanism for inactivating one X-chromosome in female somatic cells has been applied to silencing the surplus chromosome 21 of Down Syndrome.
In yeast, a 'designer chromosome' has been chemically synthesised, and has been used to replace the corresponding native chromosome in yeast cells.
So although I think the premise of your question is basically science-fiction and naive, it is becoming possible to silence or replace whole chromosomes. More realistically than making our species immortal and ever-awake, this technology could possibly translate to therapies for some genetic diseases. But of course, the problem of retrospectively getting your therapy in to many somatic cells is still there. Engineering zygotes is feasible but has ethical problems - also, where pre-implantation screening is permitted, IVF can simply include genetic selection rather than genetic engineering!

Thanks for the answer!  I don't recognize it as a naive view of biology b/c I really know very little about biology.  But I understand computers and programming and my understanding of DNA/biology is that they are very complex biological machines/computers.  Even though our understanding of these mechanisms is only in its infancy, I don't see any reason we won't eventually understand it at a level that we can program whatever we want (see http://en.wikipedia.org/wiki/Synthetic_biology)  Maybe that's naive - but I'm not convinced.

The problem is that the kinds of properties of living things you can readily see and care about (you list needing to sleep, mortality - these are especially tough cookies!) are emergent, and very far abstracted from the genetic information. Abstracted through multiple layers of extremely complex non-linear dynamic systems, such as genetic regulation, patterning in development, tissue interactions.
Also, these properties have emerged from evolution by natural selection, and this 'blind' optimisation process often leads species down dead-ends, often compensating its past wild excursions...

Evolution by natural selection doesn't have foresight, and so while it is busy selecting 'fit' individuals under the circumstances du jour, over long time-spans it can be raising dependencies and fragilities. The panda bear is a great example, along with the swathes of extinct forms.
Maybe for a computer scientist you could think about digging down into treacherous local minima...?
But your question is a super-interesting one, and it turns out people are working both on replacing large chunks, and replacing all instances of a short 'word'.

I understand that it's not always as simple as finding the "need sleep" gene. Genes cause proteins which cause lots of interesting thing. But I expect that within the next few hundred years (at least) the growth of our understanding of biology combined with growth in computer simulations/modeling will provide us with tools far beyond our ability to even grasp them today.  We have computers today which are creating simulation of the formation of the universe - how many more years before we have reasonably accurate models of human biological systems?  I don't expect that many.

Yeah the future is exciting, let's hope we live long enough to see some interesting stuff. We're currently at the stage where (rather) small proteins and some solvent can be simulated as a system of atoms under relevant physical forces, for long enough for the protein to fold up in to a reasonable structure. But this is the top of the top and isn't really giving an insight in to biology yet (it will!!)
Meanwhile we're trying to predict folded protein structures from sequence data as a short-cut. It's slow progress....

A major drawback and problem with your idea is that some genetic problems are developmental and have no effect if applied on adults. For example, a gene known to cause crooked teeth would have to be fixed before permanent teeth grow in - no point in patching it after that, except if you also want to patch in infinite tooth replacement.
Retroactively fixing developmental problems through DNA is a pain. In the worst case, you have to clear out the defective piece, then regenerate it after the patch. Bioactive machine parts or cybernetics might be preferable. If you have the tech to fix DNA like that, you probably have the means to produce the needed machine parts.
"Modifying the DNA" isn't a magic solution either. There are all sorts of ways that genes can be deactivated or suppressed - and there's a field of study around such mechanisms known as epigenetics. You could waste billions on patching a gene only to find that your patch has no effect because you failed to consider these.
The most promising applications of gene treatments for adults are mainly in cases where a faulty gene generates a malfunctioning product that is normally constantly needed. An example is genetic insulin deficiency (where a person is unable to produce insulin, effectively causing diabetes.) If the gene is corrected, insulin can be properly produced.


text:
Are mitochondria alive?
I'm working on an assignment for my IB biology class and some assistance would be highly appreciated. I've read several articles and I still haven't quite gotten the answer I'm looking for. I have to write a one page summary on whether or not Mitochondrion are alive or not.

Think about the definition of a living organism... Does it reproduce, or some kind of growth? Can it live by itself?

Mitochondria are symbionts that are no longer free living. Some of there essential genes have been incorporated into the hosts genome and some remain within the mitochondria themselves. After billions of years of coevolution, they have, for the most part become organelles, and are considered to be organelles. You could not lyse a Eukaryotic cell and grow mitochondria. But Eukaryotic cells need mitochondria to function efficiently.

The definition is a matter of philosophy and not everybody agree. And typically "can it live by itself?" would be a pretty misleading question given that it would exclude all parasite from the realm of living things. If you push the concept of ecological interdependence a little further it would even yield any living individual to be excluded from the realm of living things. A wolf for example is not a living thing just because it depends on its preys and on the plant that is producing its oxygen (and other species with which it has a relationship).

@TanMath, you have just given a 50-50 scenario. They can reproduce, as that is how the cell gets new mitochondria, but they cannot live by themselves as some of their key genes have been transferred into the host genome, so vital proteins can no longer be synthesized but the mitochondria.

@Remi.b. Free living in this case implies having a complete genome. Mycoplasmas have extremely small genomes, but they have all of the genes that they need to function. Humans cannot synthesize all 20 amino acids and need oxygen and other things from our environment, but our genome allows us to interact and survive within that environment. Mitochondria have transferred many of their genes to the host genome. They do not have the genes they would need to produce the essential gene products that they would need to survive in say an enucleated cell, such as an RBC.

@AMR I was reacting to Can it live by itself? in TanMath's comment, not to free living in your comment

Welcome to Biology.SE
Fields of interest
The assignment you have to write has a little bit to do with Biology and a little bit to do with Philosophy! The question of what is alive and what is not depends on the very definition of what is a living thing and this question is not of interest to biologists but only to philosopher.
How to nail this assignment
Therefore, for your assignment you will need to understand what a mitochondrion is (the Biology part) and to understand how do the different definitions of life apply to the mitochondrion (Philosophy part although you will need some knowledge in Biology to understand the relevance of these definitions).
What is a mitochondrion?
This question is too broad and cannot be answered here. Make sure to have a look at the wikipedia page. In short:

mitochondrion contain DNA
mitochondrion is the result of a bacteria that has somehow been internalized into a bigger cell (it is a symbiont). This is why today mitochondrion contain DNA. It is therefore not exactly an organelle like others. Note that plants, in addition to having mitochondrion, they have plasmids that are also consequences of a similar process of internalizing other form of life.
mitochondrion DNA evolve (of course)
mitochondrion are basically the energy factory of the cell.
mitochondrion are not able to live by themselves outside a living cell (to my knowledge).

Definitions of life
It is important to understand that the definition of life has absolutely no impact on biology and is nothing but a question of nomenclature.
There are a lot of definitions and I can't cover all of them here. You might want to have a look at this wiki page. The previous link lists the most common properties we think about when thinking about the definition of life.

Homeostasis: Regulation of the internal environment to maintain a constant state; for example, sweating to reduce temperature.
Organization: Being structurally composed of one or more cells — the basic units of life.
Metabolism: Transformation of energy by converting chemicals and energy into cellular components (anabolism) and decomposing organic matter (catabolism). Living things require energy to maintain internal organization (homeostasis) and to produce the other phenomena associated with life.[49]
Growth: Maintenance of a higher rate of anabolism than catabolism. A growing organism increases in size in all of its parts, rather than simply accumulating matter.
Adaptation: The ability to change over time in response to the environment. This ability is fundamental to the process of evolution and is determined by the organism's heredity, diet, and external factors.
Response to stimuli: A response can take many forms, from the contraction of a unicellular organism to external chemicals, to complex reactions involving all the senses of multicellular organisms. A response is often expressed by motion; for example, the leaves of a plant turning toward the sun (phototropism), and chemotaxis.
Reproduction: The ability to produce new individual organisms, either asexually from a single parent organism, or sexually from two parent organisms,"with an error rate below the sustainability threshold."

Related questions
The question of whether viruses are alive is a very common one. Here are two Biology.SE posts on the subject:

why-isnt-a-virus-alive
changing-the-definition-of-life

source: Stack Exchange

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

sort: votes


text:
Photosynthesis Equation
The equation for photosynthesis is
$\ce{6CO2 + 6H2O + Energy -> C6H12O6 + 6O2}$
My confusion rests in the following: during the photolysis (water-splitting) step of the light reactions that occur in Photosystem II, water gets split into 2 H+ ions, 2 electrons (which enter the photosystem), and one Oxygen ion. But if Oxygen ($O_2$) is comprised of two oxygen ions covalently bonded to each other, doesn't this mean that
$\ce{6H2O -> 3O2}$  ?
Could someone please clarify this for me?

There are 12 oxygen atoms in CO2 and 6 in H2O giving you a total of 18 Oxygens on the reactants side of the equation. On the products side, you have 6 Oxygen atoms in glucose and 12 in gaseous oxygen for a total of 18. The reactants and products balance. You are forgetting about CO2.

These representative reactions are a bit misleading. CO₂ fixation is not directly coupled with production of oxygen. This may not be an answer to your question but my suggestion would be to just dump these oversimplified explanations in the trash can and have a look at the actual stoichiometries in the Hill reactions.

Equation you have mentioned is balanced chemical equation. In reality these are series of Redox reactions, major two as follows,
Oxidation of oxygen from water in presence of light (energy from photon),
$ 2H_2O  \xrightarrow{Photons} O_2 + 4H^*$
Ions produced from above reaction reduces carbon dioxide ,
$4H^* + CO_2 \rightarrow (CH_2O) + H_2O$
So both equations combined, we can write general form as
$nCO_2 + nH_2O \xrightarrow{Photons} (CH_2O)n + nO_2$
In simple words to answer your doubt, in final equation 2 oxygen molecule coming from per 2 $H_2O$ molecules and 1 coming from per $CO_2$ molecule. Hence final balanced equation is
$6CO_2 + 6H_2O \xrightarrow{Photons} 6(CH_2O) + 6O_2$

Reactions 3 and 4 do not use photons. It is a crude representation of the Calvin-Benson cycle.

Reaction 3 is general form to represent complete reaction (1+2)

But it is as misleading as the OP's reaction. It is an extreme oversimplification as you know very well. These reactions are not even directly coupled. I think you should address this point.

Are you sure we should add that detail here ? It might confuse OP more, considering OP is concern about where is extra oxygen coming from. If so, you can convert this to community wiki and edit answer.

I think the "representative reaction" is the source of all confusion. People have to realize that it is incorrect. In reality these are not coupled reactions and therefore the stoichiometry cannot be exactly balanced. The approximate stoichiometries can be obtained from analysis of the metabolic flux.

It's still a bit confusing, but that's okay (this is only for an AP Bio course and I just wanted to get things straight in my mind). Thank you Dexter and WYSIWYG

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


text:
Does evolution only give rise to traits that confer fitness?
Does evolution only give rise to traits that confer fitness? In other words, does the existence of a trait imply it's conferring of fitness? If not, what are some counter examples?

I think there's a very important sense in which your question is exactly backwards.  "Fitness" is not really something that is a priori measurable.  Instead, it's measured by an organism surviving to pass on its genes to future generations.  So everything which lives to reproduce is, by definition, "fit".

Rephrasing the question

Does evolution only give rise to traits that confer fitness?

The phrasing is actually a little nonsensical, but it is easy to understand what you mean. The reason is that "fitness" is not a characteristic of individuals but a measure (a variable if you wish) of a characteristic. Imagine you are talking about Shaquille O'Neal and you say "He is height!" instead of "He is tall!". Allow me to rephrase the question correctly. Note that because "high fitness" is a statement relative to the fitness of the others (just like being tall is relative to the average height), I highlighted in my rephrasing of the question this relativity.

Does evolution only give rise to trait variants that are associated with higher fitness than other variants?

Short answer
No!
Examples
Very simple examples include all the genetic diseases.
Reasons
In short, evolution is much more than natural selection. All of the following are reasons for why there are low fitness variants in nature.

genetic drift (incl. bottleneck or founder effect),
spatial variation in the environment and gene flow (hence migration load)
changing environment (incl. the biotic environment and the social environment) and non-equilibrium conditions in general
local peaks in fitness (and the concept of pseudo-species; fitness landscape)
trade-offs
genomic conflicts

and many others...
For more information on the "why" part of the question, you should start with an intro course to evolutionary biology such as Understanding Evolution by UC Berkeley for example.

I saw you posted this as I was typing my own answer; since I already had the bit about beating @Remi.b in my answer I decided to submit it even though it's basically identical to yours.

Thanks, the counter example of genetic diseases is brilliant.

Just a follow up question: why was my phrasing incorrect, i.e. what is the difference between "trait variants that are associated with higher fitness than other variants" than "traits that confer fitness"? Thank you!

@HuiWang Good follow-up question. I edited my post to add more info. Let me know if this clear things up for you.

I'll try to beat @Remi.b to the suggestion that you review Understanding Evolution as a general overview of evolutionary topics.
For a quick answer: no.
Sometimes people confuse the great importance of natural selection in evolution with an equivalency between natural selection and evolution. However, there are many many contributors to evolution, many of which do not involve fitness.
I'll list just a couple examples:
Genetic drift is random change in allele frequency because of random sampling of reproductive organisms.
Founder effect is a somewhat related concept, referring to the change in allele frequency in a population that becomes isolated from the rest of the individuals of a species: that population has a selection of traits that might differ from the species as a whole, and lead to future speciation.
There are many more.


text:
Are there toxins that cause heart attack and/or stroke in multiple individuals in short time frames?
Are there any known environmental factors that would cause more than one person to have a heart attack or stroke within a short period of time (e.g. 2-3 months) of one another? I'm particularly looking for causes that are likely to be found around the home (e.g., chronic low-dose CO poisoning), as opposed to industrial sites.

Could you give us some more details or narrow down your question? I'm afraid right now it reads to me like a request for an entire section of a toxicology text. Many, many substances could lead to a heart attack or stroke. It sounds like you have something specific in mind. What's the context here?

Candidly, I'm not certain how to be more clear, but maybe that's because I lack expertise in this area. I'm looking for a toxic substance that could reasonably be expected to be found in a house, and that could make the house's occupants likely to have a heart attack or stroke over the course of several weeks or months of exposure. I'd be inclined to exclude things like smoking, as the exposure needed in that case is on the order of years or decades. Does that help?

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


text:
Abnormally fast nerve conduction
Is there any neurological condition or disease where nerve conduction becomes abnormally fast?
We know that myelinated neurons conduct impulses much more rapidly than non-myelinated ones as the myelin ensures that the ions carrying the signals don't leak while flowing through the axons, acting as an insulating material. In demyelinating diseases, the myelin sheath gets lost, affecting the conduction velocity leading to abnormal nerve conduction, which can be rescued by certain therapies such as introducing NPCs that differentiate into oligodendrocytes promoting remyelination.
So I was wondering whether there is any form of disease or at least some theoretical possibility where the nodes of Ranvier are at abnormally long distances from each other leading to conduction velocities much greater than normal.

Welcome to Bio.SE! What attempts to answer this question have you already taken? We ask that all question posters here attempt to search for an answer to their own question and explicitly indicate what research they've already done, what they learned, and what is still confusing or unknown to them. Our goal is not to simply be an answer site, but rather a site that promotes self-learning with some expert help along the way :). Please take a moment to edit your post with this additional detail, and it will likely be received more positively by our community. Thanks!

Action potential amplitude decays between nodes of Ranvier, which is why they exist and are spaced the way they are: to boost the signal at appropriate intervals.
Demyelinating disorders reduce the distance at which the propagated signal can extend without being 'boosted' at a node of Ranvier, leading to conduction failures. See another Q&A here:
Why does damage to myelin sheath in multiple sclerosis lead to a decrease in information reaching the brain from sensory receptors?
If you separated nodes of Ranvier too far apart, the same thing would happen: you might increase conduction velocity a bit, but you'd also cause propagation failures.
It's not really possible to prove a negative, so while it would be possible to provide a reference if there was a "neurological condition or disease where nerve conduction becomes abnormally fast?", it's not really possible to give a reference if the answer is "no", but at least it would not work the way you propose.
You might describe some forms of epilepsy as involving "too much neural activity" (as a simplification), but not "abnormally fast".
Speed of transmission is a function of the diameter of nerve fibers, so obtaining faster conduction would be at the expense of reducing space for the number of fibers in the PNS, or additionally the number of neurons in the CNS.

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


text:
Do quantum mechanical effects such as uncertainty, tunnelling and entanglement play role in the electron transport system of respiration?
The electron transport system of aerobic respiration involves an extensive pathway of electron and proton transfer from one centre to another. Now, since they are quantum mechanical particles, shouldn't they exhibit quantum behaviours such as uncertainty, quantum superposition, quantum coherence, or maybe in some cases even tunnelling or entanglement? Do these behaviours have any definitive role to play in the entire process? And how exactly does the biological system deal with these quantum mechanical behaviours? What about the wave-like property of the electrons? Is there any "more quantum-mechanical model" of respiration?

Why electron transport rather than any other chemical reaction? They all involve movement of electrons. You could ask this question on SE Chemistry, where it would be more appropriate, but if you are looking for anything "suprachemical" to explain biological chemistry because it is biological, then you will be joining a long line of disappointed physicists starting with Max Delbrück.

I would suggest you look into the field of quantum biology. This TED talk (https://www.youtube.com/watch?v=bLeEsYDlXJk) is a good place to start.

Check out work of Judith Klinman, in particular Hydrogen Tunneling Links Protein Dynamics to Enzyme Catalysis (freely available Annual Review article)  and Hydrogen tunneling in biology and (an interesting wrt NAD(P)-linked enzymes) Tunneling and dynamics in enzymatic hydride transfer. I wouldn't even think of doing just to the work of JK in an answer here: you will need to ask a specific question

Very good evidence for quantum-mechanical tunneling comes from the magnitude of the isotope effect in hydride and deuteride transfer reactions (The magnitude of the effect is often much greater than that predicted from  'classical' isotope effect theory, especially for primary isotope effects. See here, for example). The mass dependence of QM tunneling makes it more likely to occur in electron transfer reactions but it can also occur, in, say, an NADP-linked enzymic hydride transfer. All in the free Klinman article cited above –


text:
Why are Barr Bodies usually seen along the edge of the nucleus under the light microscope?
We do a typical class exercise of aceto-orsein staining of buccal epithelial cells from female students to visualize Barr bodies under the light microscope. All the illustrations and pictures in the books depict a Barr body located on the edge of the nucleus, but that is not always the case in the students' samples. Given that the cell is a 3D structure, I couldn't explain why the Barr body would localize itself to the edge of the nucleus with respect to the viewer's 2D perspective.
In this article's introduction, a statement is found saying:

"In interphase, the inactive X chromosome (Xi) is found as a condensed
  heterochromatic Barr body, usually positioned at the nuclear or
  nucleolar periphery (1-4)."

By "usually", does it mean that it is pure luck? Is there any explanation as to why we would have a tendency to see it localized to the edge from our perspective, exactly on the rim of the nucleus, and not just somewhere random?


text:
How much does biomagnification affect human beings?
It is known that the effect of biological magnification increases with higher trophic levels. Since, we are at the top of the food chain, how much are we affected by it? Is there any proof of humans affected by biomagnification? And should we be worried?
Thank you, for your attention!
Edit: Before posting here I had searched on Google Scholar about 'effect of biological magnification on humans'. Not only I couldn't find anything specifically about humans, whatever I found were too complex for me to comprehend. (I'm not a student of Biology). Yet, some of those which I understood stated that, accumulation of substances upto hazardous levels poses health risk. What I am trying to know is that, have there been cases where we know biomagnification to have hurt humans?
Thank you again!

Short answer: yes. What has made you think otherwise? Your question suggests that you don't fully understand the concept of biomagnification -- the magnification takes place as you move up trophic levels . Being at or near the top would suggest we are strongly impacted by this phenomenon.

For an example, see warning labels about mercury in seafood.  (Seen recently on packages at the US Whole Foods grocery chain.)

@theforestecologist I understand the concept and I know it to be real. Neither am I thinking otherwise. Only I want to know should we be worried about it?

@TheDude What would you differently if you were worried about it?

@BryanKrause Honestly, I was curious and just wanted to know. But after seeing your question, I guess, depending on its level of impact, I may tell my family and friends to become vegetarians (so as to stay in a lower trophic level and be less exposed to it).

What is biomagnification?

Biomagnification is the process by which chemical contaminants increase at a far greater rate than thermodynamics would predict. Specifically looking at organic / lipid soluble compounds. A very basic explanation is that as food is digested and the lipids are absorbed, chemical concentration (see Fugacity) within the food increases as it travels along the gastro-intestinal tract. As we consume more of the contaminated food it accumulates in our bodies, and if a threshold is passed can result in negative physical effects in our bodies.

Have humans been affected?

Agent Orange - the US sprayed a significant amount of Vietnam with agent Orange, which contained dioxin. The persistent nature of the compound caused it to accumulate in the soil and vegetation, and eventually the contaminated vegetation was either consumed directly by the people, or by wildlife which in turn, could be eaten. The result was that even though the compound itself was relatively harmless to humans, as it travelled up the food web, the concentration increased via the mechanism described above. The same mechanism is what resulted in pesticides like DDT being banned in the 1970’s.

Should we be worried? (Opinion)

Of course it is something that we should be aware of, and there are some guidelines with eating seafood / fish. Aquatic and marine systems typically can support a higher number of trophic levels and as such we should pay much more attention to seafood. For example, around where I live we have Fish Consumption Guidelines ) that encourage people to limit the number of fish meals per month, especially for women who are or planning to get pregnant. This allows time for our bodies to remove the accumulating compounds before reaching dangerous levels. Therefore, you do not need to eliminate higher trophic organisms from your diet, just enjoy them in moderation and not excess. Knowing where your food comes from also helps in making these decisions.

Your wiki link mentions both the negative human impacts as well as biomagnification, but it doesn't explain in what way biomagnification of agent orange has impacted people. Please consider finding a source that supports your claim more directly. Thanks.

@theforestecologist - there is an entire section regarding health effects on the Vietnamese people. Are you asking for a more mechanistic approach?

Yes. Most people know (and your link provides evidence) that people are negatively impacted by agent orange. But we're also harmed by nuclear bombs and malaria. How exactly does biomagnification play a role in the harm that agent orange causes humans? I did not see anything from your article that explicitly made that link.

Minamata disease is another. https://en.wikipedia.org/wiki/Minamata_disease?wprov=sfla1


text:
What´s the origin of junk DNA?
Most eukaryotes posses a certain amount of junk DNA in their cell nuclei. What is (are) the origin(s) of this junk DNA, And is it realy junk (superfluous)?

There is nothing like junk DNA. Originally we thought this would make about 90% of our genome, but since then we learned a lot of functions for it: Regulatory, miRNA genes, etc. Carrying so much "junk" around would pose a massive evolutionary disadvantage.

You wrote that "all organisms...in their nuclei". Two of the three kingdoms of organisms do not have nuclei, so I have edited your question. I am also unsure whether all eukaryotes have junk DNA. I would advise you to think carefull before writeing "all" in relation to biology.

@chris - You're flat-out wrong.  Many functions have been ascribed to regions once believed to be "junk", that's true.  But if you add up all those now-functional regions, you're still left with about 90% of the genome being junk, because each of those new functions is only a tiny fraction of the genome.  Don't read media reports, and don't even read the press releases from the teams who find functions -- go and actually do the math, and it still turns out that 90% of genomes are junk

@iayork Not junk - non-coding. That's a big difference.

@iayork You are voicing very strong opinions here. Try to replace "junk" with "of unknown function" in your statements and you'll realize why the term junk DNA is so misleading and is very rarely used by scientists (as opposed to journalists).

Most scientists are virtually ignorant of the whole field of junk DNA.  There are people who actually do study junk DNA, and they call it, yes, junk.  The less people know about the field, the more absolutely confident they are in their claims about it; and that includes scientists in unrelated fields, who rarely other to read the literature of the specialists.

"Junk DNA" is more aptly named noncoding DNA. This is defined as any DNA region that does not encode for a gene or more precisely is not within an open reading frame. In the human genome over 98% consists of noncoding DNA. However the more we learn about molecular biology the more we understand the biological function and importance of noncoding DNA. Examples for important functions are:

Regulatory regions that control the expression of a gene
Regions coding for regulatory RNA
Regions where epigenetic regulation takes place

However, there are also regions which likely do not have beneficial biological function, which may rightfully be called junk:

Transposons are genetic regions that can copy themselves (either by an enzymatically active RNA or by encoding for the protein transposase). They are believed to have evolved as "selfish genes" and several known defense mechanisms against rogue transposons exist (siRNA, RNAi). Transposons and the defense mechanisms have now become powerful tools in molecular biology research.
Endogenous retrovirus sequences which are remainders of retroviruses which have inserted themselves into the germ line and become inactive through mutation.

However, even these "junk" regions are believed to have important evolutionary functions such as protection from mutation through retroviruses: Because there are large DNA regions where the precise order and function is not important, a retrovirus that inserts itself at random positions of the genome is less likely to cause permanent damage.

"Junk DNA" is more aptly named noncoding DNA.  I don't agree with this. Much non-coding DNA is functional, and there is no reason in principle that non-functional DNA couldn't produce at least a (non-functional) transcript - as ENCODE showed directly.  Trying to make "non-coding" synonymous with "junk" confuses the issue.

@iayork Did you read beyond the first sentence? I am saying exactly what you are saying. The reason I open with this particular sentence is that most people do use junk DNA and noncoding DNA synonymous. In fact, if you search google or wikipedia for junk DNA, the first hits you find are all about noncoding DNA.

Since you agree that junk DNA is not non-coding DNA, why confuse the issue by saying the junk DNA is "more aptly called" non-coding DNA? The two are very different in concept and practice.

@iayork Sorry pal, but your definition of junk DNA is just different from how most people understand the term. Therefore this discussion will lead nowhere. I am just going to say that I will stick to using junk DNA and noncoding DNA synonymously since that is what most people do (as you can see if you look at the top 10 hits for "junk DNA" from google).

@Thawn I liked your description , you can refer to this paper as an example http://www.nature.com/nrg/journal/v6/n12/full/nrg1756.html

@Learner That is indeed a good article describing the evolutionary role of non-coding DNA. However, unfortunately, nature does not offer that article free of charge which means most people will not be able to read it. Therefore, I will not add the link to my answer.

Briefly, we know of many mechanisms by which genomes can get larger.  Tetrapods had at least two complete genome doublings in their history; transposons expand; retroviruses insert; partial duplications lead to pseudogenes.  And these expansion mechanisms can be fast -- full genome duplications double size in a single generation.
But we know of very few mechanisms by which genomes can get smaller, and most of those are very slow, and very few are targeted.
From an mechanistic viewpoint, it's very difficult to imagine a targeted way to remove useless but harmless DNA quickly, and with 100% accuracy.  If accuracy is not 100%, then the pathway would be more harmful than the DNA it seeks to remove.
The key is that if extra DNA is either harmless, or nearly harmless, there's no reason to eliminate it, and there are reasons (errors in removal) to not try to remove it.
So the short and simple answer is that genomes can accumulate useless DNA much more readily than they can get rid of it. It's just common sense, which matches 30 years of experimentation.

This is a good explanation why evolution tends to favour "bloated" over "streamlined" genomes. However, this is only true for higher, multicellular organsims, where fast replication is not key to survival (in multicellular organisms, most of the cells are not replicating throughout large portions of the organism's life). For single celled organisms this is definitely not true and they quickly loose genes unless there is selective pressure to keep them.

@Thrawn Agreed that the genomic dynamics change in different groups.  The theoretical arguments are the same, but the "cost" even of non-functional DNA becomes higher.  A trivial cost for multicellular organisms, that's not sufficient to select for genome shrinkage, may be a significant evolutionary cost for others.

You know, for someone who so vociferously and adamantly claims to know what the "true scientists of junk DNA" are doing and saying, there is a rather obvious lack of citations in your answer.

@MattDMo which part don't you understand? Most of this is pretty basic stuff.  As I say, it's just common sense.


text:
Why does the affinity of haemoglobin for oxygen increase at higher elevations?
Why does the affinity of haemoglobin for oxygen increase if an organism lives at a higher elevation where the oxygen pressure is lower?
Wouldn’t its affinity for oxygen decrease because the acidity of the body would increase with the lack of oxygen? The textbook said otherwise though and I don't understand.

There is a subsequent related question with answers here.

Possible duplicate of Why does the affinity of haemoglobin's for oxygen decrease at high altitudes?

@tchrist — The problem is that this is the earlier questio, and has an answer with votes. Could it be merged with the later one? I only flagged the link to the later question because I am trying to tidy up the questions on oxygen binding curves (there was another recently) so that anyone asking about this or searching is shown links to them all. (I had to add the haemoglobin tag to some of them.) It seems to me there are three types of question so far — Bohr effect, high altitude/2,3-BPG, and the interaction of the two. (No question about foetal haemoglobin yet.)

The question seems to be based on the idea that there would be physiological adaptation to low oxygen, possibly through the Bohr effect. In fact the usual mechanism of adaptation is through genetic change.
There are a lot of examples of animals which live (or fly) at high altitude and which have a haemoglobin with a higher oxygen affinity. Examples which spring to mind are the bar-headed goose and the camelids of South America (llamas, alpacas etc.)
Haemoglobin has evolved as an efficient oxygen-delivery protein by having a variable affinity for oxygen: low affinity at low oxygen concentration, high affinity at high oxygen concentration. This is achieved through co-operative binding (allostery), and it ensures that the protein loads up with oxygen in the pulmonary circulation but releases oxygen in the peripheral tissues.
At high altitude, where the partial pressure of oxygen is lower, the haemoglobin of humans, for example, will not be fully saturated, impairing the delivery of oxygen to the body. Haemoglobin variants with an increase in the overall affinity for oxygen can achieve full loading at the expense of slightly less release in the tissues - overall a better oxygen delivery function. This is what happens in the camelids, but there is no such adaptation in humans living at high altitudes.

Instead humans have more red blood cells when living in higher altitudes. This is why athletes train at high altitudes.

@Chris, in fact this isn't the case. It is true that if a sea-level dweller goes to high altitude the red blood cell count goes up (ertythrocytosis), and this is exploited by athletes. However this increases the blood's viscosity and can lead to unwanted complications. Tibetans have an adaptation which prevents this increase taking place in the first place.

Interesting. There are limits for a maximum hematocrit for athletes, if they go over it (this is mostly due to EPO doping) then they are not allowed to participate.


text:
Why do red blood cells maintain Iron in the Haem group in the +2 (ferrous) oxidation state?
A lot of sources tell me that RBCs contain a number of enzymes, and that these serve multiple functions from maintaining the structure and elasticity of the corpuscle wall, to preventing the oxidation of iron (ferrous) in Haemoglobin to the +3 Ferric state.
But what none of them say, is what problems (if any) arise when the iron is oxidised. Hence the question, why avoid the Ferric state?
I'm still a high-schooler and from what I've learnt, is that the higher the oxidation state of the cation, the higher its polarising power (Fajan's Rules) hence stronger the bond. So wouldn't iron in the Ferric state be able to bind with oxygen better, and isn't that desirable? ( Or is oxygen release to tissues going to be problematic? )
If the Ferric state is desirable, then why do RBCs have mechanisms (the enzymes mentioned earlier) in place to prevent the oxidation of the Ferrous to the Ferric state?
Thanks!

Q. “What problems (if any) arise when the iron is oxidised?”
A. Haemoglobin will be converted to methaemoglobin which cannot bind oxygen.

To quote from the article on Methaemoglobin in Wikipedia:

Methemoglobin (English: methaemoglobin) (pronounced "met-hemoglobin") is a form of the oxygen-carrying metalloprotein hemoglobin, in which the iron in the heme group is in the Fe3+ (ferric) state, not the Fe2+ (ferrous) of normal hemoglobin. Methemoglobin cannot bind oxygen, unlike oxyhemoglobin. It is bluish chocolate-brown in color. In human blood a trace amount of methemoglobin is normally produced spontaneously, but when present in excess the blood becomes abnormally dark bluish brown. The NADH-dependent enzyme methemoglobin reductase (diaphorase I) is responsible for converting methemoglobin back to hemoglobin.

The question also asks:

“…the higher the oxidation state of the cation, the higher its
  polarising power… hence stronger the bond.So wouldn't
  iron in the Ferric state be able to bind with oxygen better…”

which can be transformed into:

“Why can‘t methaemoglobin bind oxygen?”

The answer is chemically rather complex, but one thing you should be aware of is that in haemoglobin (and myoglobin) the oxygen Fe(II) is five-coordinated (as shown in the diagram below where Fe is black) and binds oxygen in the sixth position (to the right).

In simple terms, the electronic change in oxidation to Fe(III) causes a change in the geometry of the haem pocket such that oxygen no longer can bind (although now water can). This page elaborates the point, without providing a full chemical answer.
Footnote: Fe(II) or Fe2+ ?
Some readers may be wondering why I have referred to the ferrous state of Fe in haem as Fe(II) and not Fe2+ (which the Wikipedia entry uses). This is to avoid implying that there is an overall charge of 2+ on haem groups in haemglobin and myoglobin. Inspection of the structure of haem (above) will show that the formation of two covalent bonds to imidazole nitrogens has left haem with a zero net charge.

I have added a section to address in a more chemical/structural manner the question I previously ignored — why Fe(III) cannot bind oxygen.

I have added a footnote about oxidation state nomenclature of Fe and the actual net charge on haem, provided a diagram and annotated the diagram of the haem pocket.

what problems (if any) arise when the iron is oxidised:
  Nothing.

It's part of the transfer job :)
Hemoglobin from RBCs is responsible for oxygen transfer through your blood vessels all around your body and oxygen molecules attach the heme(Fe) group of hemoglobin protein. In fact the special physical form of this molecule which is ferrous (Fe2+) allow it to transfer oxygen molecules. When an oxygen molecule binds to hemoglobin it temporarily transfers to the ferric form (Fe3+). So when a hemoglobin oxidizes to the ferric form there will be no place for oxygen to bond with.

I think you should withdraw your conclusion of "nothing". The question asks about systems for reoxidiizing haemoglobin. These do exist, and deal with haemoglobin that has the Fe(II) irreversibly oxidized to Fe(III) in methaemoglobin, with oxygen concomitantly reduced. You are talking about the oxidiation state of Fe in the deoxy-haemoglobin complex which is thought to be nearer to III than to II. Fair enough, but you should make that clear and admit that you are not addressing the main concerns of the question.

To state it simply:
Hemoglobin is the oxygen transporter in the body.  The oxygen binds to the iron in ferrous state in the hemoglobin molecule.
Hemoglobin takes up O2 from the lungs and transports it to the peripheral tissues for their respiratory needs.
True, that according to the rules of chemical bonding oxygen would form a stronger bond with ferric than with ferrous.
And this would sure be desirable if we were to only consider oxygen uptake.
The oxygen loaded onto hemoglobin also needs to be unloaded in the tissues for their usage, which would be difficult with ferric iron.
Hence oxyhemoblogin (Hb[Fe2+]+O2) transports oxygen While methemoglobin, oxidised hemoglobin, doesn’t. It’s rather bad for our body to have it more than it’s usual level i.e, 1% of total hemoglobin. And erythrocytes(RBC) have mechanisms to regulate the same.
Hope this helps.

Because RBC'S contain certain enzymes which prevent the Oxidation of ferrus to ferric.
Other reason is that ferrus is only capable of binding oxygen and not the ferric iron.That's why iron is present in ferrus form and not in ferric form.

Welcome to Biology.SE! It isn't clear that this adds anything to the existing answers. 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. Thanks!


text:
Why is Capsaicin injection not used instead of nerve surgeries for pain?
High concentration capsaicin kills c & a-delta nerve fibers permanently or at least long term.
This has been known for 30 years.
But capsaicin is only used in creams and patches, and not for injecting direcly into nerves, and people resort to nerve surgeries like nerve blocks, razor-damaging nerves, or rhizotomy to cut the nerve partially or fully. All of these options affect not just pain functions, but overall sensory functions.
On the other hand, capsaicin destroying c & a-delta fibers just affects pain.
So why is no one interested in capsaicin injection as an option before cutting nerves?

There is a simple answer to your question: it might cause a massive inflammation-like response and it might also hurt really, really badly.
Capsaicin activates heat receptors which are not only involved in heat reception (that would cause the pain as TRPV1, the receptor, is strongly activated at temperatures higher than 43 degree Celsius - accordingly, it will feel like burning from inside) but also in sensing inflammations within the body. That means that your body will think it has to take strong and immediate action if capsaicin enters tissues directly, flush out a bunch of neuropeptides and actually might start destroying the affected tissues.


text:
Why is glycerol kinase absent from adipocytes but present in the liver?
Why don't adipocytes have the enzyme, glycerol kinase? Wouldn’t it be more efficient for them to utilise glycerol present to synthesize triglycerides than to get it from the liver? So what is the advantage of its absence?

I think it's worth mentioning, in explanatory note to question, that yes indeed lipocytes are being delivered triglycerides by liver - not by LDL though (reminder)  but by VHDL.

The short answer to this question is given in the Wikipedia article on glycerol kinase:

Adipocytes lack glycerol kinase so they cannot metabolize the glycerol produced during triacyl glycerol degradation. This glycerol is instead shuttled to the liver via the blood where it is: phosphorylated by glycerol kinase to glycerol phosphate and/or converted to dihydroxyacetone phosphate which can participate in [glycolysis or] gluconeogenesis.

[My de-emphasis of glycolysis]
To understand this requires one to consider the different functions of liver and adipose tissue and how they should respond to the fed and fasted state. Then one can appreciate that the differences in enzyme complement are one of the ways by which this is achieved. (The other is their differential responses to hormones.)
The role of the adipose tissue is to store fat (triglycerides) in the fed state and make it available for the other tissues in the body in the fasted state.
The role of the liver is to divert metabolism to the synthesis of fat in the fed state (at the appropriate stage) and to ensure that there is a supply of glucose in the fasted state for those tissues that depend on it (brain, erythrocytes) or a supply of ketone bodies for the brain.
The substrates for triglyceride synthesis are L-glycerol phosphate and fatty acids. There are two enzymes that can catalyse its production, glycerokinase (glycerol kinase) in the liver and glycerol 3-phosphate dehydrogenase in both liver and adipose tissue, as shown in my diagram below:

Fed State
The liver has surplus glucose so it can switch to fatty acid production from acetyl CoA (from pyruvate) and generate L-glycerol phosphate from the dihydroxyacetone phosphate intermediate of glycolysis, catalysed by glycerol 3-P dehydrogenase. This allows the synthesis of triglyceride, which is exported as lipoprotein.
When the triglyceride reaches the adipose tissue it is broken down to fatty acids and glycerol by the hormone-sensitive lipase. The glycerol cannot be used by the adipose tissue, but adipose tissue can synthesize L-glycerol phosphate itself in the same way as liver as there is glucose available for glycolysis in the adipose tissue. Hence the triglyceride can be resynthesized and stored.
Fasted State
The hormone of starvation, glucagon, initiates the breakdown of triglyceride in the adipose tissue. As already stated, the glycerol produced cannot be used to synthesize L-glycerol phosphate as the tissue lacks phosphoglycerate kinase. In starvation uptake of glucose is prevented hormonally, so that there is no glucose for glycolysis and hence no hydroxyacetone phosphate as a source of L-glycerol phosphate. Hence the fatty acids cannot be re-esterified and are released into the blood for other tissues, i.e. the response of the adipose tissue to starvation is that required.
The glycerol diffuses to the liver where it can be converted to L-glycerol phosphate because of the presence of glycerol kinase. What is the fate of this? It is not converted into triglyceride, it is converted to dihydroxyacetone phosphate by the reverse of the reaction shown. This is not glycolysed, but converted to glucose by gluconeogenesis, the enzymes for which are present in the liver. The glucose is released into the blood where it can be utilized by the brain, i.e. the response of the liver to starvation is that required.
References
This answer is based on lectures I delivered to undergraduates some years ago, which were drawn from various sources. The problem is that most biochemical texts tend to be organism-agnostic, and any discussion of mammalian tissues tends to be limited. Thus, I can’t find much useful to refer to in Berg et al. on line, except for support in section 16.3 for my assertion that glycerol returned to the liver in starvation is used for gluconeogenesis. I’ll update this later if I find anything more useful.

I think there is a typo in the first line of the paragraph above the diagram. It should be l-glycerol phosphate and fatty acids.

could you answer this please http://biology.stackexchange.com/questions/56029/effect-of-bile-salts-on-pancreatic-lipase-activity

@JM97 — Thanks for pointing out the typo. Fixed now.

@JM97 — Unfortunately I know next to nothing about bile salts. My background is chemical rather than medical, and my research interests were molecular biological. I was obliged to teach metabolism to biochemists, and I also had to mug up on certain medical subjects for lectures to professional students. However the bile never featured.

Refering to the wording of the question, "There are two enzymes that can catalyse its production, glycerokinase (glycerol kinase) in the liver and glycerol 3-phosphate dehydrogenase in both liver and adipose tissue,..." may be considered the gist of the answer? As the question (explanatory text) seems to assume that there is no synthesis of triglycerides in lipocytes at all. There is, though.  Thank you.

Brilliant answer, my voice. "Hence the fatty acids cannot be re-esterified and are released into the blood for other tissues, i.e. the response of the adipose tissue to starvation is that required." Implicit answer to a follow up question that would come from question erroneously assuming that there is no synthesis of triglycerides in lipocytes. Then, question should arise: why do lipocytes then only have that other enzyme.

Every learner surely will be surprised as there is some "prohibition" of using fatty acids for gluconeogenesis. Where do the fatty acids released by lipocytes go to? Surprise.  --- It would be interesting to hear from you - any occasion would do - on role of insuline. Lack of insuline in diabetes might be equivalent to "fasting". Implications for "metabolic syndrome"...

@PeterBernhard — I'll have a look at this when I have a moment. Having written it over four years ago, I will need time to rethink myself into the topic.

Refering to: where do the fatty acids go to? I believe you mentioned that - in starvation muscle need them. Then, in Berg I saw some diagram, where fatty acids apparently released by adipose tissue somehow diffuse freely to the liver (beginner should know: no Lipoprotein transporting fatty acids to liver, correct, in principle..). That was when I first got acquainted with subject. "Over", no answer expected, no need to be  moved to chat, just to let you know.


text:
Do colour-blind people see white?
I know that white colour is perceived on excitation of red, blue and green cones simultaneously.
It is also said that a colour-blind person doesn't see a particular colour and just perceives it as a shade of grey.
If their (for example all red) cones are affected, then how do they perceive white colour?

Clarification: Will a person with defect in red cones perceive white colour when green and blue colour only fall on his retina?
So, basically he will detect RBG and BG both as white.
If not then how will he be able to differentiate?

"People with deuteranomaly and protanomaly are collectively known as red-green colour blind and they generally have difficulty distinguishing between reds, greens, browns and oranges. ... To these people the world appears as generally red, pink, black,white, grey and turquoise." Depends on what type of color blind. http://www.colourblindawareness.org/colour-blindness/types-of-colour-blindness/

If red is absent then how is white colour perceived?

@krythic Why don't you write this as an answer?

@Marzipanherz I don't care about this branch of stack exchange. Why don't you do it? Free points.

I am color blind. I see very bright blues and reds. I nearly never fail to see a red light, a red sign, a blue one, on a different background like a green tree. if you have double genes for it you get it worse. my vision is near perfect for all except color blind tests. only error ive noticed is for blurryness, is one eye sees stars less like pin dots than the other eye. very color blind people have worse color sight, there are many types.

as long as they have rods black white and  greyscale will always be possible.

Question: What kind of vision perception issue is it when the student sees similar intensities/shades of red and white as the same color (that is, red)? (So, red marker on a white board disappears...) What if this person also sees blue as green and yellow and red as orange? Wouldn't it be more than tritanopia? If so, what would this be called?

It's definitely not white or grey generally, it's a mix of other colors, they often have low resolution of a particular color so that it's less visible rather than visible and grey.

Here's a page where you can mouse over a color wheel and see a version in color blind mode:
http://www.archimedes-lab.org/colorblindnesstest.html

The first type of cone is primarily sensitive to short wavelengths (blue), another to medium wavelengths (green) and one to long wavelengths (yellow). The yellow cone is usually referred to as the red cone. While its sensitivity peak lies in the yellow wavelength band, it is also quite sensitive to red. A single cone cannot detect color, as it provides only a scalar number indicating the total light energy it absorbs. For example, the red cone by itself cannot distinguish red from yellow, green or orange. Red is detected by a combination of high activation of the red cone, low activation of the green cone and no activation of the blue cone. This page has a very comprehensive graphs and a first hand account of Tritanomaly
Evolutionary gene mechanisms have a particular knack of varying vitally important organs and functions, arm length, walking gait, hair type, color, and colorblindness is perhaps an expression of high variance to a survival critical and modular organ which animals have a high variance in depending on their habitat and survival requirements.

Thanks. One last query: consider a person who has defect in red cones, now if we put Blue and green light on his retina will he detect it as white? Since red cones are anyhow not functioning in his eyes , will he perceive it as white? If not then by what mechanism will he perceive white colour?

when all the cones are signalling a balanced range across the spectrum he will see it as white. I changed the answer with an extra graph to explain that the cones are not RGB, they have broad reception, with a page to a guy who says how he got used to greens being grey or white and reds being confused with  yellow and orange. None of the cones sense precisely red so there won't be a very narrow reaction to red colors.

Well, we can't see things as colorblind can (I have very strong reason to think  even non-colorblind people don't see colors identically due to veriations between cone cells sensibility). Given page does not give us their perception. Colorblind people can see some impossible colors, for example. For us it is a mystery until a device is made capable of affecting cone cells selectively. And I'm not sure achromatopsia makes people see everything grey. Grey is a composition of all three types of cones being involved. But their cones, I guess, don't work.


text:
What causes bacteria to change their proteins to become resistant to antibiotics?
FMRSA (meticillin-resistant Staphylococcus aureus) became resistant to penicillin by a change in its DD-transpeptidase. What triggered this change? Did it happen by chance or does the bacterium have some sort of response mechanism to cause this change on detecting penicillin?

Do you know about selection pressure?

You are basically asking for a very introductory course to evolutionary biology. Just have a look at any good introductory course. Consider for example evo101. It is free, simple and fast to go through.

Do you mean that the MRSA is continuously changing this transpeptidase and the lucky ones survive or does this transpeptidase only change when it is needed? If so, what triggers it to change or how does this bacteria know when to change?

Can you explain exactly what you mean by "the MSRA"? Please be as absolutely precise and accurate as possible.  your ability to get a clear answer is directly proportional to your ability to ask a clear question, and to clearly and precisely understand the terms you are using.

MRSA stands for methicillin resistant staphylococcus aureus; I'm not sure what is unclear about that or the question.

I have simplified and clarified the question particularly to remove the original anthropomorphic implications. Bacteria do not ‘know’ anything and it encourages loose thinking to write in that manner, even if you spell out the quotation marks when speaking.

The bacteria doesn't know.
When an organism copies its DNA, it sometimes makes mistakes. Different organisms have different rates of making mistakes; the rate of mistakes can be really high in some organisms like bacteria.
DNA copying mistakes (or unintended changes without copying, like due to UV damage) can sometimes be a big problem for multicellular organisms. If some of your cells have different DNA than others, they might function poorly, or they might grow too fast, stealing the space and nutrients from other cells in the organism, causing cancer. Multicellular organisms like humans have a lot of DNA repair mechanisms and methods to detect DNA damage and have cells sometimes suicide when they have been damaged.
For bacteria, DNA copying mistakes aren't as much of a problem, and there are lots and lots of bacteria out in the world. That means a lot of different mistakes. When a mistake is bad for a bacterium, it is more likely to die. Those types of mistakes therefore don't get recopied over and over again.
Sometimes a mistake is accidentally helpful.
Occasionally, a mistake actually makes a positive difference for an organism. If there are trillions of bacteria, just a few of them might have mistakes that make them resistant to a particular antibiotic. Let's say it's 1 out of 1,000,000,000.
In normal conditions, that doesn't matter much. If it doesn't hurt them at all, they will just keep on replicating the mistake, and other bacteria keep on replicating no mistake, and the proportion stays 1 out of 1,000,000,000.
Accidentally helpful mistakes become more common in a population
Now, let's say you expose that population to antibiotics that kill 99% of the bacteria with no mistake, but kills none of the bacteria with the mistake. Now, your 1,000,000,000 bacteria is 10,000,000 bacteria, but you still have 1 with a mistake. Now when those bacteria replicate, 1/10,000,000 will have the mistake. If they grow evenly back to 1,000,000,000 now you have 100/1,000,000,000 bacteria with the mistake. As you repeat this process, eventually you will have lots of bacteria that have the mistake, and that proportion of individuals will be insensitive to the antibiotic.
Biologists call these mistakes "mutations" and they call the increased survival and reproduction of organisms with helpful mutations "natural selection" - over time, natural selection is an important contributing factor to evolution of species.
At no point in this process is any awareness of what's happening necessary! All you need is variation, caused by replication mistakes, and some selection pressure that gives an advantage to individuals with certain mistakes. Making some mistakes in replication is a constant source of variation in biology, and the key process that, along with selection, has led to the vast variety of life around you.


text:
Is the start codon regarded as part of the UTR (untranslated region)?
The Wikipedia entry for Gene contains the statement:

The transcribed pre-mRNA contains untranslated regions at both ends which contain a ribosome binding site, terminator and start and stop codons.

But the page on the Start codon says:

The start codon is often preceded by a 5' untranslated region (5' UTR)

So is the start codon a part of the UTR?

Because the start codon is translated into methionine, it clearly can not be part of the 5'-untranslated region, as @Johnny writes in his answer.
The more contentious question would be for the stop codons and the 3'-untranslated region. Then it really is a question of semantics. One might argue that as no amino acid is inserted in response to these codons, they are not translated. However if one considers the meaning of the word ‘translate’ and its application to the genetic code, a stop codon clearly is translated — it is read and translated into information which initiates the release of the nascent peptide from the ribosome.
And so in the Wikipedia entry on Untranslated Regions it (together with the start codon) is shown in the coding sequence, and not in the untranslated region. The annotations used by GenBank also include start and stop codons in the coding sequence (CDS in their annotations) — see, for example the annotation for this insulin precursor sequence.

The start codon both in prokaryotes and eukaryotes isn't a part of the 5'UTRs, it is present downstream the UTRs.
In prokaryotes the Ribosome binds to the Shine-Dalgarno sequence (AGGAGGU) of 5'UTR. This sequence is found 3-10 base pairs upstream from the initiation codon.
In eukaryotes the  initiator codon is usually the first 5'AUG3' present on kozak consensus sequence (GCCGCCRCCAUGG, where R is adenine or guanine). The ribosome does not bind to this sequence directly but browsing for it from the 5' end it starts synthesis once it reaches the consensus sequence.
This kozak sequence ranges from the terminal portion of 5'UTR to the first few (actually four) nucleotides of translating region.
Sources:

Principles of genetics by Snustard and Simmons
Berg's Biochemistry

That translation starts from the terminal part of the untranslated region seems unsemantic.

I've updated the answer.

This statement is incorrect.

The transcribed pre-mRNA contains untranslated regions at both ends which contain a ribosome binding site, terminator and start and stop codons.

The start codon always encodes for methionine (eukaryotes) or N-Formylmethionine (prokaryotes), thus, seeing that the start codon encodes an amino acid, it would be considered part of the translating region.


text:
How do antibiotics combined with a non-Western diet affect weight loss?
Wikipedia describes a Western diet as:

... higher intakes of red and processed meat, butter, high-fat dairy products, eggs, refined grains, white potatoes, french fries, and high-sugar drinks.

In the following article there is information about research done that suggests mice eating a high-fat diet while taking antibiotics become obese:
Scientific America: How Gut Bacteria Help Make Us Fat and Thin
I was wondering whether there has been any similar study to see what happens to obese mice or humans that take antibiotics while eating a non-western diet such as the Mediterranean diet, which this Guardian article suggests does not cause weight gain?:
The Guardian: High-fat Mediterranean diet does not cause weight gain

The Scientific American article states that food you are referring to was "high in fat and low in fruits, vegetables and fiber" but you refer to fat as the key.  It could be that the reduction of one of the other components is the cause.  For example, fiber is often prebiotic.  It could be the case that a high-fat, high-fiber diet would change the result.

Actually, on second look, your question actually misrepresents the study.  The mice on antibiotics gained much more weight on a normal diet but this effect could be eliminated by putting these mice in the same cage with those not treated with antibiotics.  The change in diet eliminated the cohabitation effect.

https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.6b00942 antibiotics in pigs and effect on plant lignan metabolites.

I don't believe elevated polyunsatured fatty acid consumption falls under the tendencies of the western diet, and may be more reminiscent of the Mediterranean diet, so hopefully this answers your question. This study took mice with elevated blood and tissue omega-3 levels, and were used to identify if high levels of omega-3's could prevent the deleterious effects of excessive antibiotic use on gut microbiota. Regarding microbiota diversity, antibiotics are known to create an imbalance between bacteroidetes (decreased) and firmucutes (increased) - this study evidenced that the omega-3 mice were able to rapidly recover their bacteroidetes composition and reduce the amount of firmucutes present in comparison to the control, which in short is good news, as this also prevented later-life obesity in the omega-3 mice in contrast to the obese controls.
For skeptics of microbiota-influenced weight loss (and I know there's many), there is quite a bit of literature out there describing the relationship between gut microbiota diversity and energy expenditure. The short description is that elevated bacteroidetes (in proportion to firmucutes) is associated with lean phenotypes, that diet is very much capable of modulating gut microbiota over short periods of time, and transplanting microbiota compositions into obese individuals has definitively shown an effect on metabolism. The only problem to a gung ho microbiota therapy is, no one knows the gold standard for microbiota composition.

Maybe what we need to do is go to one of these isolated communities where they still live on hunter gatherer diets and trade something for a turd specimen, preferably polished.

Although evidence of absence is not proof of absence, there are currently no published studies on PubMed which have mice/antibiotics/(Mediterranean diet) or (olive oil) in the abstract. But I guess such a study will be soon published as the question is fairly obvious and of high interest.

It's been well known in the poultry industry that giving birds antibiotics causes 'growth promotion'. Humans are obviously not birds but given that undisputed fact, it seems reasonable to consider that effect this might apply to other species.

There is no reason to think that taking antibotics is going to tweak your gut flora in a way that will make you lose weight for good.

I beg to differ. If antibiotics can increase weight gain through one type of diet, then is it that far off to reason that antibiotics with another type of diet may cause weight loss? The weight gain seems to indicate that antibiotics may help change gut flora.

Agreed with the comment above. Dysbiosis of the gut can radically change how your gut behaves. There are a number of studies now which have shown that antibiotics cause long lasting effects (e.g. https://www.ncbi.nlm.nih.gov/pubmed/29945240). Typically this has been tied to obesity rather than weight loss, but I suspect that's a Western research bias brought about by increased prevalence and relevance of obesity versus malnutrition.


text:
How is the size of a gene defined?
Is there an agreed definition as to how many nucleic acid bases constitute a gene?
If not, why not? I'm not sure I understand how the exact sizes of genes are defined.

@user19099 Surely there's a range though. From XX Mb to XX Mb.

yeah the range is from 76 (tRNA) to 80781 (titin) bp in humans.

In what species? Using what definition of gene? I think what you're really asking is precisely what the definition of a gene is (you may be surprised to learn that it isn't a black and white concept). If that's your question, please clarify.

I have changed the title because it was not the poster's original and whoever changed it previously did so to one which doe not reflect the question's content. The questioner is clearly not asking  what the average size of a gene is — although one of the answers would have wished this. Rather he seems to want to know  the basis of defining the limits of a gene. (Initially I thought he assumed all genes had a specific size, but that would really be too naive. It's surely just limited command of English.)

@David The title of the original post was "what is the average length of an allele". It is not about answerers wishing for this title so that is is probably easier for them to answer. However, because of your edit some answers seem like "not an answer", now. Why not let the OP clarify the question themselves?

@WYSIWYG Be that as it may. The title did not reflect the question — nor did the answers you mention. In particular they do not address the last sentence. I shall be rewriting my own answer to clarify this. As for the questioner giving clarification, I hope he will.

You asked a question, the question has been answered and then you changed the question. Please, just edit back, accept of the current answer and open a new post for your other question.

@terdon Let's concentrate on humans first.

@user19099: The number for the titin gene is not entirely true. TTN (gene coding for titin) itself is about 300 kb long.

In fact, TTN is not even the biggest gene. The biggest I found is CNTNAP2 with approx. 2.3 mb.

@alexdelarge thanks for that info! I didn't actually search for biggest gene, but just looked for size of titin :)

Is there an agreed-upon definition as to how many nucleobases constitute a gene?
If not, why not?

There is no such definition. A gene is a region of the DNA that is transcribed. Typically a gene should have a transcription start site dictated by a promoter and a transcription stop site marked by termination signals (like terminators and poly-A signal etc.)
There are some little RNAs (~18nt) that are produced from TSS of usual genes but are probably products of failed elongation. These are not really considered genes as they are heterogeneous in size and are not marked by any boundary.
There may technically be a minimum cutoff on gene length which could be the length of DNA necessary for the RNA-polymerase to sit and also include the termination signals. As indicated in the comments, the smallest gene may be the tRNA. However, the smallest annotated gene from the GENCODE annotations is TRDD1 (just 7nt long!!!). This is not based on gene prediction; it is manually annotated by the HAVANA team.

What is the average length of a gene?

I just did a rough calculation from the GENCODE human genome annotation file (version 23).
The average transcript length seems to be around: 1.5kb
The average gene length seems to be around: 29kbp
The genes would be longer than (or equal to) their corresponding transcripts because the latter gets shortened due to splicing.
I made a histogram plot of these lengths for convenience:

Transcript length distribution

Gene length distribution

Note the sharp peaks at 100bp. Quite interesting!

Remi has user19099 have mentioned that the longest gene in humans is titin. It seems that it is the longest gene in many other diverse animals. See What's the longest transcript known? for more details.

Methodology (so that limitations can be identified)
To calculate gene length distribution: I parsed the GTF file for "genes" (third field i.e. feature) and subtracted the fifth field (stop) from fourth (start).
To calculate transcript length distribution: Got the transcript fasta file from the annotated locations. Calculated their lengths. Plotted the distribution.

I hesitated to do that but was too lazy! Good job. Note however that your average is twice as high as Strachan and Read (1999) average. Do you know what is causing these different estimates?

@Remi.b Well, one obvious explanation could be that we have more annotated genes now compared to 1999.

...and we disproportionally annotated small genes in 1999. It is possible indeed. Would be interesting to open a post on the subject.

@Remi.b Or possibly the entire genes were not annotated. With better sequencing technology we can map the genes better.

Very informative and especially the spike at 100bp is so interesting.

@Remi.b yeah, remember that the human genome wasn't sequenced in '99, so those estimates could only be on what they had. Also note that WYSIWIG is referring to transcripts and we had even less information on alternative transcripts in '99 than we do today. Finally, consider long, non-coding transcripted regions which might be included in the dataset that WYSIWIG used (I don't know) and which wouldn't, really, be considered "genes" as such. Well, depending on how you define it... :)

Oh..ok that makes more sense now. Thanks for following up on this issue. +1

@WYSIWYG Thank you for this! I am so happy to see a distribution of what constitutes a human "gene".

@WYSIWYG this is really neat. Can you show me the source code for your gene length graph so I may recreate this graph in another model organism?

@Tom I got a vector of lengths from the GTF file. It's fairly easy. Just take a difference of start and stop. For histogram, I used MATLAB. This can be done in R and python too.

How are gene size defined?
DNA is made of 4 nucleotides A,T,C and G. A series of such nucleotide make up any section of the genome including the genes. The number of nucleotide in a gene is what we call the gene size. Of course, one might discuss on the definition of the exact beginning and end (and methods to determine them) of a gene but this is a discussion for another time.
Because, DNA is double stranded, instead of talking about a sequence of 10 nucleotides, we often talk about a sequence of 10 base pairs (bp). When dealing with longer sequence, we can use the prefix "kilo (k)" to indicate one thousands base pairs. For example: 12 kbp = 12,000 bp. For even bigger values, prefix "Mega (M)" is used to indicate one million base pairs. For example: 7 Mbp = 7,000 kbp = 7,000,000 bp.
Average and median gene size in humans
There is a lot of variation in gene size among genes within a species but also among species. So much so, that an average does not convey much information. But here is the average and median gene size in humans:

The average gene size in humans is 10-15 kbp (kilo base pairs) (Strachan and Read 1999)
The median gene size in humans is of 24 kbp (Fuchs et al. 2014).

The extremes in the human genome
As @user19099 said, the longest gene in the human genome is TTN coding for the titin protein. TTN is about 100 kbp long. tRNA are typically very short sequences (76-90 nucleotides) but please not that these sequences will never be translated into proteins.
Book recommendation
The book A Short Guide to the Human Genome by Scherer is very good to give a feeling of what the human genome looks like.

We could also discuss what a gene actually is and if an entity like the gene as we see it even exists. Good answer though!

Thank you! Yes, the mean and median size of a human gene is roughly what I was asking (one of the questions anyway).

Interpretation of the question
You ask two things: 1. the number of nucleic acid bases that constitutes a gene, 2. (implied) how the size of genes are defined. The first question appears strangely naïve, but the second suggests this may be a misunderstanding. I therefore intend to start there.
How are the limits of a gene defined?
Genes are defined in terms of their information content — most obviously to specify proteins which may confer a phenotype, but also in specifying structural and regulatory RNA molecules. The extent of genes, or the length of DNA they occupy, is therefore determined by their information content.
Are genes contained in similar size DNA ‘boxes’?
Your first sentence suggests you think all genes have a fixed number of nucleic acid bases. This idea seems strange as, at the simplest level (e.g. in bacteria), their information content differs in size with the size of their protein or RNA products. However perhaps you have the idea that the genome is divided into similar sized regions with a discrete start and finish into which the information is accommodated (the rest being packing, as it were). This is not the case.
Genes occupy different lengths of DNA
In fact, the lengths of different genes differ within a species and between species. In simple prokaryotes this is mainly because they encode proteins (or RNAs) of different lengths. In eukaryotes (where the genes are generally much larger) this is further complicated because of the varying number and size of their introns, which do not (normally) encode protein.
How are the end-points of a gene determined in practice?
A simple answer to the above (appropriate to the level of your original question) would be that genes extend from the promotor regions, where the RNA polymerase binds for transcription, to the transcription termination point. Thus, at a first approximation, they can therefore be defined in practice by the regions of DNA that specify mRNA (or pre-mRNA) or other RNAs. The modern method for doing this would be RNAseq.
(The situation is more complicated than this in practice because there may be regions of the DNA that affect the expression but are not transcribed. But I wouldn’t worry about that at the moment.)

@ShanZhengYang — I have tried hard to understand what you were asking in your question. If I have not, could you please clarify.

"Your first sentence suggests you think all genes have a fixed number of nucleic acid bases." Sorry, that was not my intention.

Within my question, I asked multiple questions, which has caused some confusion. Thank you, "How are the end-points of a gene determined in practice?" was in fact one of my questions above. We are still researching how parts of the genome give rise to phenotypes, so it wasn't clear to me how we could be so sure of the boundaries of "genes" which result in "phenotypic traits".

"there may be regions of the DNA that affect the expression but are not transcribed"  This hits at the heart of my question. So...how could these boundaries of genes be so clearly defined? RNA-Seq data is not that clean...

@ShanZhengYang — Thanks for your clarification. Apologies if I my answer was too simplistic. As regards the problem of 'fuzzy boundaries' I imagine that people adopt a particular approach that allows quantative comparisons (between species, between genes) which is indicative even if it is not perfect. For bacteria it may be easy to identify promoters and termination signals and use those; for mammalian genes an RNA seq approach with an annotated genome may be most practical. Different assumptions may be made in different cases.


text:
What is the ultimate source of ADP/ATP in humans?
I am teaching myself Cell Biology from the internet. Despite my usually good Googling skills, I'm stuck in a loop with this question.
Q: What is the source of ATP?
A: ADP
Q: What is the source of ADP?
A: ATP
At first I thought that ATP synthase actually created ATP from scratch as intimated here:

ATP synthase is an important enzyme that creates the energy storage
  molecule adenosine triphosphate
  Wikipedia

I then realise that ATP synthase doesn't create ATP so much as convert ADP.
My Question
Can humans synthesise ADP/ATP from scratch. If so, where are these phosphates made and if not what food source provides them and how? Also, where do we get the phosphorus?
Thanks

As the concern expressed by the poster has recurred in an essentially similar question despite the excellent answer by @MattdDMo, I shall provide an additional answer labouring the basic biochemical points.

Inorganic phosphate (the term used to describe the mixture of different phosphate ions present at physiological pH) in animals is derived from the diet.

Biochemical processes exist (substrate-level and oxidative phosphorylation) in which this inorganic phosphate is transferred to adenosine diphosphate (ADP) resulting in adenosine triphosphate (ATP).

This explains how the γ-phosphate (third phosphate) of ATP can derive from inorganic phosphate de novo. It does not explain where the α- and β-phosphates of ADP (and hence ATP) come from.

There is an enzyme, adenylate kinase, that catalyses the formation of ADP from ATP and AMP:
         ATP + AMP ⇔ 2 ADP

This can be regarded as transferring the γ-phosphate of ATP (derived from phosphate) to AMP to provide the β-phosphate of one of the two molecules of ADP produced in the reaction. So that explains how the β-phosphate of ADP can derive from inorganic phosphate, and thus how both β- and γ-phosphates of ATP derive from inorganic phosphate de novo. What about the α-phosphate?

The α-phosphate in the purine monophosphate AMP derives from one of its precursors, ribose 5-phosphate. The relative points of the pathway of purine synthesis that can be found in detail in biochemical texts such as Berg et al.:
ribose-5P →→→→→→ inosine monophosphate →→ AMP

And the phosphate in the ribose 5-phosphate derives from the γ-phosphate of ATP in the phosphorylation of glucose in the hexokinase reaction of glycolysis, followed by the reactions of the pentose phosphate pathway. In outline:
ATP + glucose → ADP + glucose 6-P →→ ribulose 5-P → ribose 5-P

In summary, the incorporation of inorganic phosphate (ultimately maintained by dietary intake) into the γ-phosphate position of ATP enables its incorporation into the α- and β- positions during purine monophosphate synthesis and subsequent reactions.

Phosphorus is a very common nutrient, found in high levels in proteins, which are in such foods as milk and milk products, meat, beans, lentils, nuts, and grains, especially whole grains. Phosphorus is found in smaller amounts in vegetables and fruit, as well. Adenosine can be found in many of the same foods, both as free ATP/ADP/AMP, and as part of the DNA found in all animal and plant-based foods (are there any other kinds?).
Adenine (the nucleotide base before the addition of ribose creates adenosine) is synthesized via the purine synthesis pathway, whose ultimate product is IMP, or inosine monophosphate. IMP is then converted to adenylosuccinate, then to AMP, which is then phosphorylated to ATP. It should be noted that, as is the case in most biosynthetic pathways, this one requires ATP to power it along, meaning it takes ATP to make ATP.

Would the downvoter care to comment so I can improve my answer? What's wrong with it?

I can't imagine why this was downvoted (+1 from me). Maybe because a quick look at the wiki link obviously requires ADP/ATP in its own production and someone thought it was a circular answer? That's my best guess.

@anongoodnurse The question isn't "Where did the first molecule of ATP come from?", but I guess that's as good a guess as any. I just wish people would leave comments when there's nothing obviously wrong with an answer, like another answer directly contradicting it or something. Oh well, it's not like the rep is a big deal or anything. I just want to be loved! :)

Not my downvote but the only correction I would make is the phosphorous content of grains. They are very rich in phosphate but most of it is locked up in phytate which most mammals can't digest. If you go on a high grain vegetarian diet your phosphorous intake actually decreases. See: https://www.ncbi.nlm.nih.gov/pubmed/21183586

@mimat Thanks for the feedback. Do you know how much is available from proteins and nucleic acids in whole grains as compared to the other foods I listed? That was kind of what I was getting at, not just the total phosphate levels regardless of bioavailability. Also, is phytate broken down by cooking, such that, for example, whole-grain bread has more bioavailable phosphorus than raw grains?


text:
What is meant by "catalytic amount of a hormone"?
This textbook says:

In the classic definition, hormones are secretory products of the ductless glands, which are released in catalytic amounts into the blood stream and transported to specific target cells (or organs), where they elicit physiologic, morphologic and biochemical responses.

What is meant by catalytic amount? Does it mean that amount required for catalysis? I know only renin which is catalytic and act as an enzyme, and many other hormones are non enzymatic so why the term catalytic is used in general sense?

In my opinion it isn't a very good phrase for a textbook because it doesn't have much meaning, but I believe what they are trying to convey is that they are released in small quantities, like is typical of enzymes - you don't need a lot because they work over and over again. By contrast, there are a lot of proteins in the blood that are expressed in fairly high quantities, like those involved in coagulation, to the point that they make up a non-negligible component of the blood.

@BryanKrause - I think they mean simply enough hormone to get the desired response. It can be alot or a little.

@anongoodnurse Perhaps, I guess that's why it really isn't clear. When a recipe for a chemical reaction says "catalytic amount" of something they usually mean a very small amount compared to the actual amount of reactants...like a "catalytic amount of platinum" - it just seems really strange to apply that terminology to hormones. This looks like one of the English textbooks written by a non-native speaker that we see a lot of questions about - sometimes the answer is just that a non-native speaker used a phrase they learned in a different context in a flawed way.

@BryanKrause - I too think it odd phrasing and unclear. I think of a catalyst as something that facilitates a chemical reaction. A "catalytic amount" of insulin depends on how many glucose molecules are in the bloodstream...

The writer obviously means “small amount”, and has chosen his words badly as hormones do not themselves catalyse reactions.
The idea he is probably trying to convey is that a few molecules of hormone binding to their receptor can cause changes to many molecules within the target cell. This often (generally?) involves catalysis within the cell produced by the receptor activating an enzyme, so one can understand the line of thought leading to the misuse of this term.


text:
Visualizing the effect of selection on a population with a fitness landscape in R
I am trying to write a script to demonstrate the effect of selection in a population. The problem that I have is that it is not realistic in the sense that not only the mean would change for directional selection, but the Skewness of the distribution would change as well. How would that be possible to code that and show the movement of the population going toward the maximum fitness peak?
# Define the normal distribution
slect <- function(x,mu,sigma,constant) {
  temp = exp(constant*((x-mu)/sigma)^2)
  return(temp)
}

# Multiply 2 functions
Multiply=function(a,b){
  force(a)
  force(b)
  function(x){a(x)*b(x)}
}
# Set some parameters
ylim = c(0,2)
# X limits
from = -4
to = 7
# Sequence of X
x = seq(from,to,length.out=100)
# Means
muinit = 1
mu1=muinit
mu2=3
# Number of generations
n.gen = 10
# Variance
sigma.0 = 1.1
sigma = sigma.0

# Initialize population
init0 = function(x)slect(x,mu = muinit,sigma = sigma.0,constant = -.5)
# How the population will move because of selection
popmov = function(x)slect(x,mu = mu1,sigma = sigma,constant = -.5)
# Final fitness function
finl = function(x)slect(x,mu = mu2,sigma = sigma,constant = -.5)

# Empty data
data.all = NULL
gen = 1
for(gen in 1:n.gen){
  # system("sleep .2")
  # png(paste0("Desktop/fittest/test",gen,".png"))
  int1 = curve(expr = init0,from = from, to = to, col = "red",
               ylab = "Fitness", xlab = "Phenotype", ylim = ylim, main = paste("Fitness result gen:",gen))

  if (gen ==1) {
    # Result of the first generation
    h0 = Multiply(init0,finl)
    h1 = curve(expr = h0,from = from, to = to, col = "black", lty = 3, add = TRUE)
    finl1 = curve(expr = finl,from = from, to = to, col = "black", lty = 2,lwd = 2, add = TRUE)
    mu1=mean(c(mu1,mu2))
    popmov1 = curve(expr = popmov,from = from, to = to, col = "red",lwd = 2,add = TRUE)
    h = h0
  }
  if (gen>1) {
    mu1 = mean(c(mu1,mu2))
    popmov1 = curve(expr = popmov,from = from, to = to, col = "red",lwd = 2,add = TRUE)
    h = Multiply(h,finl)
    h1 = curve(expr = h,from = from, to = to, col = "black", lty = 3, add = TRUE)
    finl1 = curve(expr = finl,from = from, to = to, col = "black", lty = 2,lwd = 2, add = TRUE)
  }

  popmov1$type = "popmovement"
  finl1$type = "final"
  h1$type = "movement"
  int1$type = "initial"
  popmov1$it = gen
  int1$it = gen
  finl1$it = gen
  h1$it = gen
  df1 = as.data.frame.list(int1)
  df1.1 = as.data.frame.list(popmov1)
  df2 = as.data.frame.list(finl1)
  df3 = as.data.frame.list(h1)
  df4 = rbind(df1,df1.1,df2,df3)
  data.all =c(data.all,list(df4))
  # dev.off()
}

Someone here may be able to answer your question, but if not I would try SE Bioinformatics, which might have been a better bet in the first place.

Modeling for a single genotype parameter or a single phenotype parameter is (IMHO) very unrealistic. I know that doesn't address your question, but it may be relevant to your goal.

@S.McGrew You are right! But my goal here is to have a "simple" case to be visualized (adding traits would start making the thing in 3d and further make it even harder to visualize). But as a first approximation, I wonder how to "show" the effect of a fitness landscape on the population. Therefore, I'm pretty sure that not only the mean is changing, but also the skew of the distribution. This is the core of my question.

If your selective "force" works equally on all parts of the population, you will keep the shape of the original distribution.  In real life, though, the "leading edge" of the population will procreate faster than the "trailing edge".  Account for that and I'm pretty sure you will get the skew you're looking for.

@S.McGrew, This is it, but how to 'account for that' is my question! I don't know how to simulate this part. Now I'm only modifying the mean of the distribution (the     mu1=mean(c(mu1,mu2)) in the script). But there should be something modifying the shape and skew of the distribution (and Kurtosis if the actual density of the population changes) as well.

My suggestion is that instead of representing the data purely in terms of summary statistics, that you actually simulate populations of individuals.
This allows you to plot phenotype values across all of your individuals, and gives you an actual distribution rather than just a defined mu/sigma.
I have no idea if the parameterization is at all relevant to what you're trying to do, but a long time ago I wrote a conceptually similar simulation. Caveat emptor, I was pretty new to coding.
This is in addition to the sensible suggestions from S. McGrew.

There are at least several different approaches that can work.  Without examining your code, it seems that the population is described as a distribution of phenotypes.  You need a way to allow that distribution to change in a fairly complicated way.  So if you define a function to describe the change something like this, you should get results closer to what you're expecting:

define distribution as N(p), where (p) is phenotypic distance from the original peak of the distribution, and N is the number of population members at that distance p.
Define D(pf-p) as the distance from the new fitness landscape peak to a point in the distribution that change.
Define a forcing function that depends on D. This function will either decrease or increase the number of population members at each point along the phenotype distribution, depending on D.  If you want to get fancy, it can also depend on the number of population members in the previous iteration at that point in the distribution.
If you want the population size to stay constant, you should make sure the forcing function adds and subtracts the same number of members from the population.
I would suggest using a forcing function that gets stronger as the phenotype gets closer to the new fitness landscape peak, and make sure the phenotype distribution is nowhere zero when you begin.

The above function should in effect move population members toward the new fitness peak, though may tend to sharpen the population peak.  To fix that you can introduce another function that "blurs" the distribution, like randomly moving members to nearby phenotype values.