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Why is one phase of a plant dominant (Alternation of generation)?
In plants, there is the alternation of generation.
In nearly all land plants, one phase of the two possible phases is dominant--namely the sporophyte.
The "dominance" over the other phase can be seen in the following ways:

The gametophyte organism depends on its sporophyte progenitor, while the sporophyte organism is fine without the other.
The sporophytes are more structurally complex, larger and longer lived.
The sporophytes carry out more activities/functions and receives more subjective attention.

I want to know if there is an evolutionary reason why alternation of generation, one phase is dominant. Here are some guesses:

Zipf's law: as one of the two phases got more complex (start doing more complex jobs) It became more convenient and more likely for that phase to acquire other functions, causing the complexity of that phase to increase with a sort of positive-feed-back-loop, while it became more beneficial for the other phase to depend on the other more and more, to reduce its complexity.
Chromosomal difference: the sporophytes of plants are diploid while the gametophytes are haploid, perhaps one of the two configurations is more efficient?
The sporophyte generation "reproduce" asexually, perhaps this allows it to have a little "head-start" in accumulating non-sexually reproductive functions and became more complex as explained in 1.

Short answer:
Many of the evolutionary developments in plants developed in the sporophyte life stage. Because increased fitness of these increasingly sporophyte-"dominant" plants would result in a greater survival and reproductive success, these plants became more dominant than the more-limited gametophyte-dominant early plants.

In other words, natural selection of the fittest plants (which happen to have sporophyte traits increasingly adapated for living on land) likely led to the dominance in the sporophyte life stage.

Long Answer:
I would suspect this is due to the evolutionary advantages that are associated with the sporophyte life stage in land plants. Multiple advantages developed in the sporophyte stage of plants as they evolved from simple gametophyte-dominant bryophyte ancestors to the vast array of much more successful and dominant ferns, gymnosperms, and angiosperms.

 Shift from gametophyte-dominated life cycle (in bryophytes) to sporophyte-dominated life cycle. Source: Cengage Learning (2016)
Evolutionary developments that have occurred across almost 500 million years in land plants include the development of stomata, true leaves, pollen and seeds, and flowers and fruits. Each of these developments occurred in the sporophyte life stage.

Each of these evolutionary traits had significant effect on the success of the various plant types that possess them, as can be inferred from the increasing success and dominance of increasingly more evolved plant Divisions.
Each of these sporophyte-focused evolutionary traits increased the reproductive success of plants (therefore swaying increasing advantage toward plants possessing increasingly sporophyte-dominant life cycles) due to their ability to increase plant size, growth, and success living in arid (i.e., terrestrial) environments.

stomata allow for increased gas exchange with more limited water loss (note: these were necessary with the development of cuticles in sporophytes of early bryophytes as well)
vascular tissue2 allow plants to grow taller/bigger/more complex while still receiving water and nutrients from the soil
true leaves allow for greater energy capture and growth (and therefore increased competitive advantages)
pollen and seeds allow for greater dispersal and removes/limits the constraints of aridity on fertilization
flowers and fruits increase pollination and seed dispersal

Reducing the gametophyte stage to small cells within larger sporophyte plants allows this otherwise water-necessary process to occur in the dry conditions of living on land. As such, the pollen-bearing plants (i.e., gymnosperms and angiosperms) have been very successful in colonizing vast terrestrial ecosystems.
Another evolutionary advantage proposed, (e.g., see Bernstein et al. (1981)1 and Michod & Gayley (1992)3) is that the diploidy of the sporophyte stage allows masking of the expression of deleterious mutations through genetic complementation. From Wikipedia:

Thus if one of the parental genomes in the diploid cells contains mutations leading to defects in one or more gene products, these deficiencies could be compensated for by the other parental genome (which nevertheless may have its own defects in other genes). As the diploid phase was becoming predominant, the masking effect likely allowed genome size, and hence information content, to increase without the constraint of having to improve accuracy of replication. The opportunity to increase information content at low cost is advantageous because it permits new adaptations to be encoded.

However, this proposal has been more recently challenged by Szövényi *et al. (2013)4 because evidence suggests that selection isn't more effective in haploid vs. diploid lifecycle phases of mosses and angiosperms.

For further reading:

"Evolutionary history of plants" [Wikipedia]
"Evolution of Seed Plants" [Lumen Learning]
"Evolution of Seed Plants" [OpenStaxCollege]

 Citations
1  Bernstein, H; Byers, GS; Michod, RE (1981). Evolution of sexual reproduction: Importance of DNA repair, complementation, and variation. The American Naturalist. 117 (4):537–549. doi:10.1086/283734
2  Lucas, W.J., Groover, A., Lichtenberger, R., Furuta, K., Yadav, S.R., Helariutta, Y., He, X.Q., Fukuda, H., Kang, J., Brady, S.M. and Patrick, J.W., 2013. The plant vascular system: evolution, development and functions F. Journal of integrative plant biology, 55(4):294-388.
3  Michod, RE; Gayley, TW (1992). Masking of mutations and the evolution of sex. The American Naturalist. 139 (4):706–734. doi:10.1086/285354
4  Szövényi, Péter; Ricca, Mariana; Hock, Zsófia; Shaw, Jonathan A.; Shimizu, Kentaro K. & Wagner, Andreas (2013). Selection is no more efficient in haploid than in diploid life stages of an angiosperm and a moss. Molecular Biology and Evolution. 30 (8): 1929–39. doi:10.1093/molbev/mst095

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Is lumen space of a thylakoid completely separate from the intermembrane chloroplast space?
The question I have is whether thylakoids form actually completely independent "vacuoles" (i.e. independent membrane enclosed spaces) or whether the lumen space is connected to the intermembrane space of the chloroplast. I have this question because electron photographs that show slices can be sometimes misleading and connected structures may appear to look independent on photographs of slices.

This is an excellent question because in all textbook-diagram (yet I've seen) of mature chloroplasts, all the stroma-thylakoids and grana-thylakoids are drawn as detached-from the periplastidial space, but no-where I've read any text-mention of it.

I've also thought at earlier-classes, why chloroplast is not being called a "3-membrane bound" organelle.

Maybe a detachment-step take place in plastid-development, otherwise the compartmentalization would be poor, and the proton-gradient and other-sorts of chemical-difference would become weak

source: Stack Exchange

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Two sets of chromosome and the sequencing output
Humans have two sets of chromosomes that are not connected in each cell. Am I correct?
I assume while sequencing DNA both of these sets have to be sequenced and the output have to be provided in some order - i.e., paternal set followed by maternal or vice versa, though it may not be possible to know which is paternal and which is maternal.
(I know there are different types of sequencing techniques and output may differ depending on the technique. Here I am speaking of the general case). I tried clarify this question myself. But may be this is such a basic thing that no one seems to touch upon this aspect.

Note for observers: previous question as referred to.

For many biological research questions it is not important to know, if the sequence comes from the paternal or maternal chromosome. - However - as you pointed out - there are different approaches of obtaining the sequences. Some of them would allow to distinguish different chromosomes (see https://en.wikipedia.org/wiki/Contig  ).   In practice: if you would like to know if a variant of a gene comes from the father or mother it is easier / cheaper to sequence them (or do some other faster/ cheaper test on them).

If an answer given to a question is unclear, you can do two things: Either write a comment or adapt your question. Showing the kind of attitude you do "I don't understand the current answer and don't care to do so" is actually insulting towards the people which invest time to write an answer. Actually not the best idea.

I believe the question boils down to simply: How are heterozygous results reported from the sequence alignment process?

This is very similar to your previous questions, but apparently you are not understanding the explanations we are giving, so I'll try again, by giving a (hopefully not-too-technical) explanation of how next-generation genomic sequencing works. To avoid confusion, we'll assume we're working with human samples.
First, many individual cells are collected (the number depends on the application, it can range from 1 cell to millions or more), and their DNA is collected. This process destroys the cells, and all of the copies of all of the chromosomes are mixed together. As mentioned in your other question, there is no possible way to determine which chromosomal sequence is maternal, and which is paternal. Scientists typically don't even think about this.
Next, the collected DNA sample is purified and broken down into small pieces, then ligated to certain adapters to label them for the sequencing reaction. The sample is then amplified in a standard PCR to create starting material that is many times more plentiful than before. This is the DNA library.
Finally, the sample is ready for sequencing. What exactly happens next depends on which sequencer you're using - Illumina, Ion Torrent, 454, or SOLiD are the most frequently-used instrument brands. Within each brand, Illumina for example, there are multiple different kinds of sequencing.
However, we'll just gloss over all that and get right to the output - the instrument produces a file consisting of "reads" from the reaction. These reads are DNA sequences consisting of As, Ts, Gs, and Cs - the "letters" (also known as "bases") of DNA. The lengths of the reads vary by technology and instrument, generally in the range of 100 to 700 bases. One machine, though - the PacBio RS II, can produce high-quality reads up to 14,000 bases, although to my knowledge it is not in widespread use.
Here is where the computers come in. The individual reads overlap each other to varying degrees, depending on the quality of information you're seeking and whether or not you're looking for rare events, such as a small population of mutated cells taken from a heterogeneous tumor. For our purposes, we'll say our sequencing run resulted in a 25-fold overlap, meaning each base in the original DNA sequence of the sample donor was sequenced an average of 25 different times. The computers can then "align" the sequences, either just among themselves, without a template, or, more commonly, to a pre-existing sequence template, such as a reference genome. Eventually, the computer will spit out two sequences - the forward and the reverse strand (although typically you'd just pick one strand, and use the reverse strand for error-checking). This sequence is the average sequence of the chromosome, or other region of DNA being targeted.

From Wikimedia Commons: Mapping Reads.png
However, one can pretty easily detect mutations, such as single nucleotide polymorphisms (SNPs), deletions, insertions, etc. In the case of a SNP (pronounced "snip"), one allele of a gene has one sequence on one chromosome (lets say ATTCGTAAC) while another allele of a gene on the other chromosome has a single-base change (ATTCTTAAC, for example, where the G was changed to a T).
The point, directly relating to your question, is this: The final sequence that eventually comes out after all the computer wrangling is a single sequence with certain areas that may differ from chromosome to chromosome, or cell to cell in the original sample. There is no way to determine if the G in our example above was on the maternal or paternal chromosome. There is also no way to tell if, 20,000 bases down the line, another mutation is on the same chromosome as the G, because no single read can (currently) span that entire length. You might have a pretty good chance of determining that if the other mutation is, for example, 300 bases away, because many technologies can perform high-quality reads longer than that, so you'd just have to find the individual ones that contain both positions.
I know this was a little long-winded, but hopefully I was able to answer your question.

Matt, if the guy didn't understand first time, why did you give such a long and technical answer second time? It would be enough to say what's in your final paragraph that he'll probably never get to. i.e. The result is a mixture of both chromosomes, so we only know if the sequence at any point is the same for both or different. (And because of crossing over there's no such thing as a maternal or paternal.)

@David I had to try - the answers to the previous question weren't that great, and while the OP said s/he didn't care about the details of sequencing, I figured that actually explaining how sequencing works in general terms would help them understand why there is no "order" of which chromosome comes first. And, I had some free time, so it wasn't that big of a deal.

@David regarding crossing over: that happens during meiosis in the parent, when germ cells are being formed. The egg is haploid, as is the sperm, but after they join the chromosomes do not cross over again.

Whoops. Shows how little I know about classical biology.

@MattDMo Could you please explain the last paragraph of your answer? You said (in your example) that we can't determine the G in our sequence was on the maternal or paternal chromosome. Won't both the alleles on the homologous chromosomes be sequenced? If yes, do we have sequences of both the chromosome (be it or be it not distinguished) in the final sequence? I don't know the intricate details on this subject, but it occurred to me whether or not we have a single allele of a gene in the final sequence or both the alleles (in case of diploid) and how does this happen for both the cases?

@Ramil All DNA fragments in the sample are (theoretically) sequenced, so both alleles of a particular gene will be sequenced, but unless we already have the paternal and maternal sequences as a reference, there is no way to know if the G came from the mother or father. The whole point of my answer (and the last full paragraph) is that the final product is a single sequence, with electronic "pointers" indicating areas of heterozygosity, such as the G→T difference. However, we can't tell which original chromosome the G was on vs. the T.

@MattDMo If both the alleles of the genes are sequenced, how do we get a single sequence for each gene? And the heterozygosity you mentioned, is it with respect to the reference genome?

@Ramil Differences between alleles are generally very slight when it comes to the DNA sequence - perhaps a few or only a single base difference. I already explained how these differences are detected and reported in the final sequence. Depending on the read length of the instrument, you may not be able to show that multiple differences are in the same allele - you'd need a different technology such as RNA-Seq for that. I used the term heterozygosity to refer to the difference between the two alleles possibly present in the sample.

@MattDMo You mean the forward and the reverse strand that you mentioned gives the difference and the final sequence is the average?

@Ramil No, the forward and reverse strand have nothing to do with determining variations between alleles, they are only used to add more confidence to reads, as they are perfect complements of each other. The final sequence uses this code, so in our example instance the base would be reported as a K (either G or T). With a high enough confidence in this call, one can assume that both G and T are present at that locus, meaning two alleles. You can also go back to the original reads and see that ~50% are G and 50% T.

@MattDMo Ohh! Thanks a lot. Makes sense to me now.

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How can you stabilize enzymes in pellets made from microcrystalline cellulose?
I want to make pellets consisting of mainly the following:

microcrystalline cellulose
saccharose
rice starch
ascorbic acid
glycerin

and an enzyme as active component.
Is it furthermore necessary to add protease inhibitors or other stabilizers to remain the activity of the enzymes for a periode of at least one year OR is the dry environment conservation enough?
The enzyme is called histaminase and is extracted from kidney cortex through a series of centrifugation, filtration and dialysation. To be more precise, it is a liquid protein extract containing small amounts of this enzyme. No buffer etc. is added to the protein extract so far. The whole purification process is done at 4°C. I don't know how long the enzyme is stable without further preparation. Probably not that long because some proteases should remain in the natural homogenate from porcine kidney cortex. The other components of the pellets are of pharmaceutical quality. The aim of this experiment is to feed the pellets to dogs with digestive complaints. For this purpose the pellets will get a enteric coating to survive acid environment of the stomach.

So you're trying to make pills?

Other questions: what is the enzyme? How is it purified, and how pure is it? Has it been lyophilized? What storage condition requirements do you have - room temp? +4? -20? -80? What is the stability of your prepared enzyme, without putting it into pill form? Does it have BSA or other carrier proteins with it? If so, at what concentration? Are your other materials sterile? Have they been tested for protein content? As you can see, a lot of factors go into determining the stability of a protein. Please use the [edit] link to add all of the requested information into your question.

@MattDMo hope the added informations help

As you can probably guess from my comment, there are a lot of factors to take into account when thinking about protein stability. Here's what I would recommend you do.
First, make sure your extract is in a neutral buffer, like PBS, HEPES, or something similar. This is a fairly standard procedure when working with proteins. Next, since this is a kidney extract, there are likely to be gobs of proteases around, so I would strongly recommend adding broad-spectrum protease inhibitors, and keeping the extract as cold as possible to inhibit any enzyme activity. I would also add BSA at 10 mg/ml, both to stabilize the proteins and keep them from precipitating while in solution, and to lessen the chances that any proteases present will attack your enzyme of interest.
Once you have your solution stabilized, I would aliquot it and lyophilize it. Proteases are most active in solution, so once dried you'll reduce their activity even more. You can now add the inert ingredients (microcrystalline cellulose, etc.), mix thoroughly, press your tablets, and add the enteric coating. Finally, once everything is prepared, I would store the final product at as cold a temperature as is convenient. Again, this will inhibit any enzyme activity and prevent degradation.
I don't know if you have a functional assay to determine activity of the enzyme of interest, but if you don't I'd highly recommend developing one if at all possible. This way, you can test the activity of the fresh preparation of extract and compare it to various stages of processing into tablets, especially the finished goods, to ensure that you haven't lost much activity. I would also test random tablets throughout the year to make sure they haven't lost activity in storage, otherwise you won't be able to compare your experimental results.

I don't want to press tablets. I plan to use pellets like those ones. So I don't have to lyophilize the extract because the process works with a moist compound. But I asked myself if the dogs could get in troubles because of bacteria etc. I centrifugalize at max. 50000g. So cells shouldn't remain in the liquid but what's with viruses?!

Furthermore I read that most of the proteases like PMSF or AEBSF are toxic for cells. So is there a solution for the case of feeding dogs with the pellets?

@Luke I apologize, I misunderstood the type of pill you were making. The reason I suggested lyophilization was not to just dry out your extract, but to preserve it and help protect it against proteases and other degradation, so even through you're making capsules, I'd try to keep everything as dry as possible. As far as the bacteria/virus question, you'll have to decide that for yourself. We (and dogs) don't eat sterile food, everything has various microorganisms in it. Dogs are able to tolerate a wide variety of them, what with the anal licking and eating food off the ground and whatnot.

@Luke as with all potential toxins, the dose makes the poison. Figure out how much of those inhibitors you'd like to add, as well as compounds like leupeptin and aprotinin, look up their LD50 or toxic dose, then calculate out milligrams of inhibitor (or micrograms, whatever) per kilogram of canine, and consult with a toxicologist if necessary. Search around, you may be able to find safer inhibitors. However, throughout all of this, an enzymatic functional assay is vitally important for making decisions about dose and stability - it may turn out you need few or no inhibitors at all.

I know this question was some while ago, but maybe you could help me out again ;-) After the centrifugation I want to make a ammoniumsulfate precipitation with the supernant. Do you think that I have to do a dialysis to remove the ammoniumsulfate OR  could I use the homogenate direct without any further preparation in my pellets?


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Alleles always occur on the same locus
My book says "alleles of the same gene always occur at the same locus, but on a pair of homologous chromosome"
Please how is it possible since genes of particular character always occur on the same chromosome? When we know that alleles combine to form a gene, how comes then do they occur on homologous chromosome?

An allele is a "version" of a gene - you don't combine alleles to make a gene. I strongly suggest you do some more research on your own, perhaps starting here.

Homologous chromosomes refers to the "twin" chromosomes in your cells (one from your mother and one from your father). Each somatic cell has at least one nucleus containing all your chromosomes*2. Having two sets of all chromosomes is referred to as diploid. On a chromosome, genes are encoded through different nucleotide sequences in DNA, and thus have a specific spot on the chromosome. The spot where a gene is located is called the locus, and because you have two chromosomes in your cells that contain the same genes (though maybe different alleles!), the genes will be in the same locus (same spot) on the both of the chromosomes.
The alleles do not actually combine to form a gene. An allele is simply one variant of a gene, and there can be many alleles for one gene. If a person has the same allele on both chromosomes they are considered homozygous for that allele and if they have different alleles they are considered heterozygous for it. Genes can also be considered either dominant or recessive. If they are dominant, they can be expressed with just one copy in the cell, but if they are recessive the same allele must be present on each chromosome. The alleles do not "combine to form a gene", they are simply separate copies of the same gene with possible variations on them. Homologous chromosome simply means the other copy (e.g. a gene on the 3rd chromosome of your mother will be present on the 3rd chromosome from your father although it could be a different allele due to a variation in nucleotide sequence). I hope this helps, although I would suggest doing some more research on your own, perhaps through https://www.khanacademy.org/science/biology. Their videos tend to be very descriptive.

@Shirouh If this answer addressed your problem, please consider accepting it by clicking on the check mark/tick to the left of the answer, turning it green. This marks the question as resolved to your satisfaction, and awards reputation both to you and the person who answered.


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Effect of sleep deprivation on pupils and pupillary responses
What is the effect, if any, of sleep deprivation on pupils? Specifically:

Are pupils more dilated/constricted?
Is the pupillary response to light any different?
Anything else?

Are you referring to pupil measurements in passive subjects, or when engaged in cognitively demanding tasks? In other words, are you talking about pupil size as such, or to pupil responses during task performance?

Both, if possible. I was talking about effect on pupil size, and pupillary response to light, but if there is any other effect of sleep deprivation on pupils, such as a change in pupil responses during task performance, I would be grateful if I could know about that, too.

It's always best to ask specific questions. Broad inquiries like this question as it stands tend to result in open ended discussions.

Okay then, I am referring to pupil measurements in passive subjects.


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Biological data source of trees
I need some biological data for many types of trees, but I can not find good source of this on internet.
Where can I find following type of biological data of any tree:

Biological Profile
Taxonomy
Distribution
Cultivation
Edible Medicinal Parts
Phenology

Wikipedia: Vascular Plant

All trees are either gymosperms or angiosperms

Wikipedia: tree

Wikipedia: Medicinal plants

The Ecological Data Wiki search for Woody Plants is a good start for some nice datasets. There is also the USDA Plants Database which has information for every plant in the U.S. Woody species are well represented with lots of species specific info. These can be downloaded handily with an R package.
Looking for occurrences? Put the species name into GBIF to get historical records of where and when a species was found. This has an R package as well.
Want distribution maps for all trees in North America? Someone has done that for you here.
Phenology? The National Phenology Network.
Edibility? I've never come across a specific data source for this. But the best reference I've used is the Handbook of Edible and Poisonous Plants of Western North America. It's an amazing book with years of research put into it. It does not have any pictures nor a key to identify plants, but it does have information on pretty much every plant in the Western U.S. at least at the genus level.


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Relative roles of ATP and NADPH in anabolic and other processes
Chemistry isn’t my strong point, but I’m trying to understand why NADPH is said to be the main agent necessary for anabolic reactions, and if NADPH is used for anabolic reactions what is ATP used for? Movement?
An example of what I'm wondering: When skin cells are exposed to sunlight, to synthesize melanin is the free energy of ATP hydrolysis sufficient? For example by catabolizing some protein in the cell and using the amino acids to synthesize melanin? Or is NADPH always necessary?
I have not been able to find an explanation on-line that addresses this, so suggestions of a suitable book would be appreciated.

Welcome to SE Biology. Your question is based on a misconception, so I am using this comment to put you on the right track before suggesting the question be removed. ATP is not a reducing agent, it is "the universal currency of free energy in biological systems and you can read about it in section 14.1.2 of Berg et al.. You are correct in relation to NADPH, but the contrast that you should be making is with NADH, an important use of which is to generate ATP — see Berg et al. 14.2.

I see, thank you, it's a little more clear now.

Hmm. Are you sure? After posting I started to wonder whether you were thinking about some anabolic process that required both NADPH and ATP, such as fatty acid synthesis; or had read that reactions of both of these effectively supplied energy. You may not be "good at chemistry", but understanding metabolism involves only a few chemical principles. However these are fundamental. Do you understand the idea of free energy changes in a reaction, and are you clear what reduction is? If there is a particular area of metabolism that provoked your question, we might use that to clarify things.

I guess so, more or less
a reductant is an elecron donor
an oxidant is an electron acceptor
Reduction means gain of electrons
Spontaneous reactions "generate free energy"
What is getting difficult to understand for me is how this energy will be used.
I'm trying to translate it to everyday life of an organism
What i "think" i understand is:
NADH and oxidative phosphorylation get us mostly free energy without a change of mass as we'll be exhaling carbon dioxide and urinating water.
while NADPH get us both free energy and mass.

An example of what i'm wondering:
Skin cells are exposed to sunlight, to synthetize melanin is the free energy of ATP hydrolysis sufficient? For example by catabolizing some protein in the cell and using the amino acids to synthetize melanin?
Or is NADPH always necessary?

OK. What I propose is later today to change your question slightly to something like "Relative roles of ATP and NADPH in anabolic and other processes" using your clarification and example, and then provide an answer (rather than a comment). You can modify the question if it's not quite on the spot.

Preamble
I don’t know where you read the statement “NADPH is... the main agent necessary for anabolic reactions”, but  out of context it is very misleading, and it is difficult to envisage circumstances in which it would be helpful for students of metabolism.
Put simply, NAPH is only used in anabolic pathways which involve chemical reduction.
You ask for a suitable book, but the book I’m going to quote from (Berg et al., Biochemistry) would overwhelm you (and any other student — it is grossly overweight). However an old edition is available on-line, and by citing specific sections you can read what is relevant (and spare me breaking up my answer with pirated diagrams).
ATP and NADPH: energetic similarities and differences
ATP and NADPH can both be regarded as ‘energy-rich’ in the sense that they can undergo reactions that have a high negative change in Gibbs Free Energy (which is what determines whether a reaction proceeds) and that this can be linked to certain other reactions with a positive free-energy change — including, but not exclusively, those in biosynthesis — to drive an overall reaction. (Incidentally both these compounds are synthesized in reactions powered by solar energy during photosynthesis.) However the nature of this linkage or coupling to other reactions differs between NADPH and ATP, and this difference determines the roles that they can play.
The oxidation of NADPH to NADP+ has a standard redox potential of +0.32V , which is an effective a negative standard free-energy change, but it can only occur in conjunction with another redox ‘half-reaction’ with a redox potential that will result in an overall negative free-energy change. Berg et al., section 18.2.1, presents a calculation to show how NADH (essentially similar to NADPH in this respect) can reduce pyruvate to lactate. The key point is that this overall reaction is a chemical reduction, so that the ‘energy’ of NADPH is only of use in reductive synthesis.
The ‘energy’ of ATP (more properly its group transfer potential) is in fact the negative free energy of the hydrolysis of ATP to ADP (and orthophosphate), or to AMP (and pyrophosphate). If an enzyme can couple this reaction to another with positive free energy of hydrolysis then it can drive the second reaction. This important point is dealt with in Berg et al. section 14.1.3 and it is also worth reading the preceding section. ATP is not a reducing agent so is not limited to oxido-reduction reactions. (The hydrolysis of ATP can also be used to provide e.g. mechanical or electrical or light energy, which is why Berg et al refer to it in section 14.1.2 as “…the Universal Currency of Free Energy in Biological Systems”.)  In synthetic processes ATP (or other nucleotide triphosphates derived from it) is often used in reactions forming bonds (C–C, peptide, glycosidic, phophodiester). In some of these cases the hydrolysis of the ATP is used to generate an activated form of the basic component, which allows it to form the bond in a subsequent reaction.
Example of a synthetic pathway using both NADPH and ATP
In Fatty acid synthesis NADPH is used for two reduction reactions — ketone to alcohol, unsaturated C=C to saturated C–C bond — whereas ATP hydrolysis is coupled to the formation of the C–C bond of the condensing unit, malonyl CoA. This is shown in Figure 22.22 of Berg et al..
Example of synthetic pathways using ATP but not NADPH
The synthesis of the peptide bonds of proteins requires condensation of the carboxylic acid group of one amino acid with the amino group of another. This is not a reductive process and NADPH is not involved. ATP hydrolysis ‘activates’ each amino acid by attaching it to the ribose of a transfer-RNA in a bond that has a high enough free energy of hydrolysis to ‘drive’ peptide bond formation to the growing polypeptide chain at the peptidyl transferase centre of the ribosome.
Melanin synthesis?
This is an area in which I am profoundly ignorant, but from Googling it would appear that the first phase of melanin synthesis is the conversion of tyrosine to DOPA and then to indoles. These reactions are oxidative (using molecular oxygen) rather than reductive, so do not use NADPH, and the bond formation is cyclization to form the pyrole ring. This seems to proceed without ATP — presumably it is energetically favourable overall. There is a Wikipedia entry for the key tyrosinase oxidation reaction.
I suppose the anabolic phase is the polymerization of the aromatic units to form the crosslinked polymeric structure of melanin. This appears to be poorly understood, but there is certainly no indication that NADPH is involved, and it would appear to depend on chemical features of the environment of the melanosome, rather than on ATP. (There is a recent short review in this area by VJ Hearing).
You mention the role of sunlight in this process. Although sunlight in itself can provide the energy for one stage of the synthesis of Vitamin D in the skin, this is a ring-splitting step. A direct role in the polymerization of melanin doesn’t seem to be suggested.

Wow, thank you so much for such a detailed explanation, i'll also surely check the book out.


text:
Why are chromatophore in phaeyophycae chloroplasts integrated within the endoplasmic reticulum?
Why are chromatophore in phaeyophycae chloroplast integrated within the endoplasmic reticulum? While reading about phaeyophycae I came across this point, but couldn't figure out why and what could be the evolutionary basis for this?

Secondary endosymbiosis.

@ always confused can u give an elaborate answer please

I'll take time.

I've posted one answer.

Before explaining it, you need to know 2 things.
Fact 1:  a cell of an Eukaryotic organism; such as a higher-plant, an animal, or a fungus, is actually not a single cell, but mixture of cells from different distant taxa.
taxon-1. The main, host cell (probably came from an archaebacteria (archaea) ), whose 'own' genetic material is in its nucleus.
taxon-2. mitochondria (probably derived from an eubacteria (only 'bacteria' of modern use) allied to proteobacteria)
(found normally in all eukaryote, except a few )
taxon-3. Plastid (whose most-important form is chloroplast) (probably derived from an eubacteria, allied to cyanobacteria , i.e. blue green algae) (Found in higher plants, and so-called 'algae' ).
It is now very well-established that mitochondria and plastids are 'cell'-s, with their own genetic machinery (including DNA, whose sequence match not-with host-nucleus, but match to bacteria!! However, some of DNA was probably got mixed with host-DNA, via DNA-transfer). They are partially autonomous because they can synthesize some proteins (metabolic-machines) from their own genes. And such an organelle can arise from pre-existing such-organelle, and can-Not appear de-novo from host cell.
Plausibly, many-many-million-years ago,  the precursor of eukaryote , certain organism allied to archaebacteria, 'ate' (phagocyzed) these eubacteria , and instead digesting them, they involved in a mutually beneficial symbiosis. Gradually they get converted into some 'organelles' through millions of years.
This concept is known as 'Endosymbiotic theory of origin of eukaryotes' .
 Image from Gerald Karp.
(Initially it was unknown,and it was thought that chloroplast and mitochondria evolved by gradual complication of the main cell.  when Harry Margulis gave this as hypothesis, it was rejected because it was unbelievable. Later-on it was established as true)
However, this-type of endosymbiosis is also called 'Primary endosymbiosis', where a purely-single cell engulf another purely-single cell.
Fact 2: The group 'algae', named in a very early-stage of science, was a horribly 'hotchpotch' group (extremely polyphyletic or artificial). This group is a set of organisms which can perform oxygenic photosynthesis. But some of them are similar to plants (green algae), some are highly similar to some protozoan ('primitive animals'), for say, some euglenoid and dinoflagellate algae. There are lots of such close-related protozoans that can't photosynthesize and don't contain any chloroplast. Whereas, Blue-green algae (cyanophytes) (with a highly similar photosynthetic mechanism), is a bacteria.
It was an enigma for the scientists. How  a few members from separate groups can contain plastid? Could they separately evolved the same structure? Is it possible to coincide so-much convergent evolution? or if the common-ancestor of all of them, contained the plastid, then why that structure disappeared in so-many members?
This enigma was quite drastically cleared up after discovery of this past endosymbiotic mechanism.
It was then found-out that, the finest classification (excluding the chloroplast), which was showing the different groups under algae are highly unrelated; is true. Actually members from far-distant taxonomic groups, 'ate' some unrelated photosynthetic primary-endosymbiotic associations, and formed another association. Thus they all got the very-similar photosynthetic apparatus; though the hosts were unrelated. This was something very new-to science.
these 'another-association's, i.e symbiosis between impure cells, is known as secondary endosymbiosis.
It is assumed that, the trace of these secondary endosymbioses; left some remains as the plastid-coves' structure.

Here is a classification of algae, taken from Robert Edward Lee, Phycology, 4th edition, in a simplified diagram. 4 basic types of photosynthetic structure is found in algae, according-which the classification has been done.
 .classification of algae, by Lee.
(Representation concept courtesy- a note shared to  me by a college- friend several-years ago).

Now, How these structures exactly developed?

Each cell contains so-many membranes, that , practically we have poor way to determine from which-of the membrane of which symbiont; certain ultimate membrane came. There are controversies. Such as according to Lee (already mentioned book) and diagram used by Hans Walter Heldt, Plant biochemistry, (3rd edition, Academic press- Elsevier), the outer membrane of chloroplast came from the cell-membrane of host-cell (phagocytic vesicle's boundary). like
 (redrawn from Heldt)
Whereas some other source tells that, the outer cover of chloroplast came from "outer membrane" of cyanobacteria , (Since it is  a gram-negative eubacteria, so carries 2 membrane). (Wikipedia tells "The two innermost lipid-bilayer membranes that surround all chloroplasts correspond to the outer and inner membranes of the ancestral cyanobacterium's gram negative cell wall, and not the phagosomal membrane from the host, which was probably lost." https://en.wikipedia.org/w/index.php?title=Chloroplast&oldid=737014760#Primary_endosymbiosis).

However in my answer I've followed Lee (4th edn).

Answer:

step 1 : Origin of chloroplast, the primary endosymbiosis.

 Diagram from Lee.
(already discussed).
This step's product found in group 2 algae. (Glaucophyta, Rhodophyta, Chlorophyta) Higher-plants probably evolved from Chlorophyta (green algae) and they also contains this-sort of chloroplast.

Step 2:

Probable sequence of evolutionary events that led to a chloroplast being surrounded by a single membrane of chloroplast endoplasmic reticulum. Initially an isolated chloroplast was taken up by a phagocytotic protozoan into a food
vesicle, with the food vesicle membrane eventually evolving into the single membrane of chloroplast endoplasmic reticulum surrounding the chloroplast.
Diagram from Lee.
Products of this step found in Group-3 algae.

Step 3. Another event of secondary endosymbiosis.

The sequence of events that led to the evolution of algae with two membranes of   chloroplast endoplasmic reticulum.
Products of this-step found in group-4.
Diagram from Lee.

by the way, all these steps are assumptions by scientists.

There is another concept called tertiary endosymbiosis. When in certain step of  secondary endosymbiosis, a chloroplast (from certain-one cell out of 2) lost, it is called tertiary endosymbiosis.

Reference:

Phycology/ Robert Edward Lee/ 4th edition/ Cambridge University Press.
Plant Biochemistry/ 3rd Edition, English translation/ Hans Walter Heldt/ Academic Press - Elsevier.
Cell and molecular biology - concepts and experiments / 6 th Edition / Gerald Karp / Wiley.


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How to get started in bioinformatics
I'm a second year bachelor electrical engineering student and self-taught programmer. I've always had a interest for biology, but never got into it (besides two year biology in secondary school and some basic biochemistry in chemistry class).
I'm especially fascinated by the interplay between computer science and biology, both computer science used for biology and computer science concepts inspired by biology. Think of things like the human genome project, genetic algorithms, deep learning, protein structure prediction etc etc. I think many of this things (the computer science used for biology things) are - as far as I know - part of bioinformatics.
I've done challenges on Rosalind and although they are nice, it feels more like training/reinventing the wheel. Althrough it may be too much to ask, I'm want to do something "real" which could actually be used. Not that I want to start straight away without learning, but I don't have a picture in mind of what I can do after learning some theory.
I'm looking for an overview of the field of bioinformatics and some guide on how to get started. Some examples on what I can work on. Maybe there are some power intensive algorithm I can start designing chips (ASICs) for, in order to speed up the process. This just one example.
I hope you can help me, thanks in advance.

Welcome to Bilogy.SE! I am unsure whether you are more interested in Bioinformatics, Computational Biology or Biological Computation. The distinction between these fields is sometimes unclear and may differ depending who you may ask but I think worth it to take some time to read their definitions.

A first step to Bioinformatics or computational biology is probably to understand the basics of molecular biology (Here is a khan academy link that may help)

Thank you. :) To my knowledge bioinformatics and computational biology are really close to each other. Bioinformatics slightly more focusing on (theoretical) computer science, while computational biology focuses slightly more on the mathematics. (Again, this is my idea of it.) For biological computation I see a bigger difference, cause it's the other way around (computers using biology instead of biology using computers). I have some basic knowledge of molecular biology (or biochemistry, I think that's more or less the same). (continue...)

I know for example how you can translate a string of DNA into RNA into aminoacids or identify (some simple) mutations. But (of course) I really don't know how I would predict the 3D structure of a protein. So it's a little bit hard to me to know where I should begin. If I look at how I got into coding, I wanted to build a website so I looked up a tutorial. When I wanted something new, I searched how to do it and learnt it on the way. For bioinformatics it's harder for me. I don't really have a goal in my mind like making that website, if you understand what I mean. (continue...)

And that's because I don't really know what I will be doing with it (bioinformatics knowledge). Anyway, really appreciating your help.

Good that you have these basis. I would recommend to narrow the post down then. For the moment I don't think it is possible to completely address your question as it is too broad. As an example, I am a computational biologist (computational population geneticist to be more accurate; I study various evolutionary processes using individual based simulations and try to develop statistical methods) but I have no idea how to predict the folding of a protein.

If I may ask the question: Why are you in electrical engineering if you are interested about bioinformatics? I don't see much connection. Of course there is no shame (it is quite the opposite actually) to have when working on a subject different from the one your receive through your university training but I am just curious

I'm interested in computers and electronics, that's why I chose it. I feel like electrical engineering really teaches you how they work. Besides that biology (and bioinformatics) have always interested me, so something combining this two should be great.

@Remi.b Also https://www.newscientist.com/article/2082706-bio-coding-language-makes-it-easier-to-hack-living-cells/ shows a nice (and to me really interesting) example.

I am voting to close as too broad. I agree though as @David said that if you can't narrow down your interest, the best for you is probably to contact someone at your own university which research is of interest to you.

I am voting to close because this is opinion based. I know bioinformaticians who started as physicists, biochemists, biologists, computational scientists, mathematicians, MDs etc. and they work on wildly different projects. There is no single-track "best" pathway, or correct niche to get into. Apply for some bioinformatics projects/positions/internships and see if you get them. Good luck.

@Remi.b Also, EEE will have a lot of systems engineering modules, and include proper programming modules (most bio courses have at best a single module on R or Perl that barely introduce you to the idea of a variable), and a tonne of maths. This degree would put you in good stead for a tool building project: The biology you can pick up later!

You will find various bioinformatics tutorials on: https://www.biostars.org/t/Tutorials/
As a computational biologist I would however strongly suggest to attend biology lectures, and read many textbooks that cover topics outside of the favorite topics of today's bioinformatics (Bruce Albert's "Molecular Biology of the Cell" would be a good start):
Technical aspects are easy to solve, and learn (and also to outsource). The difficult part is to find smart problems, and to understand how you can solve some things faster than your competitors by combining bioinformatics with other approaches.
BTW: I really like your idea to approach bioinformatics from the hard-ware side (also see evolvable hardware).

Yes I read about evolvable hardware, it sounds so awesome. Unfortunately I have the feeling it isn't much researched any more, for whatever reason. (Maybe all the more reason to get into it.) And thanks for your advice, I'm going to look for that book.

My advice is to make contact with biologists in your own university.
You say you want real problems, and I applaud this as addressing real problems is the best way to avoid wasting your time (which is an all-too-common fate of forays of this kind). How to make contact? Presumably social media is the way to go. At your age you should know how to use it. You need to aim at PhD students and staff, though, not undergraduates.
Reading books is all very well, but until you know what the problem you're takling is you won't know what to focus on. And biology is too wide and unstructured to master by reading.

I would rather recommend contacting a PI directly then using social media. Many PIs are happy to hire a student who shows interest.

@Remi.b — Sure, whatever works. Would an undergraduate know what PI to contact? Anyway, my point is that a young internet savvy student should use that savvy in his own environment to advertise his willingness to get involved in a project. He should know better than me.

Thanks for your answer. Do you think it is better to contact someone from the bioinformatics department of my university, or to directly contact biologists?

@Kevin I'd definitely go to the bioinformatics dept. They presumably have projects with the biologists already, but if you tell them what your skills are they may well have something you can do. At the very least they can aside you.

Aside from what was suggested in other answers, you should also try to get to know the state-of-the-art in bioinformatics, i.e. read up on what was done in the last few years, have an open eye for new publications in the field and let you inspire by what other people are/have been working on.
This post by Stephen Turner nicely summarises a number of bioinformatics-related journals/RSS feeds, blogs, mailing lists, email alerts/subsriptions and twitter accounts you should assign to or check regularly for staying up-to-date.

I am a Computer Engineer myself and never taken Biology in even my high-school. (Maybe people here would start hitting me but I confess I used to hate Biology to bits - maybe bytes or Megabytes)
In autumn, 2013/14, it was the same Pavel Pavenzer and Philip Compeau of Rosalind, who introduced me to Bioinformatics (I enrolled into that course totally by chance) and Bioinformatics sounded pretty cool. Firstly, since programming was pretty cool as all I had to do was apply string algorithms and later on I was fascinated by beautiful design of Genome by Almighty Allah.
Well here is summary of my experience to share with you:

Buy a good book on Genomics (PS. Verma and V.K. Agarwal is pretty good one - I have found it good enough)
Master yourself in the basic Bioinformatics algorithms (ones you will find on Rosalind)
Check sites like TCGA, ICGC for Gene Expression data. Its in numeric form and you will enjoy applying statistical algos like PCA, Regression etc on them
If you are interested in sequence data classification, then I would suggest you to read String Kernels by C.S. Leslie et al. (I can provide you its implementation using SVM on C++ if you would like)
Most of Bioinformatics courses teach you Sequence-Alignment algorithms or HMMs. They will waste your time. Don't take them too seriously. You will find the reason to reject HMMs in the String Kernel paper (HMMs use Heuristic approach and are very slow and inefficient as compared to SVMs)
There is lot of work yet to be done on Epigenetic data. With little effort, you can contribute to community by publishing your research. I would recommend you to check that aspect as well. But again, take one thing at a time and you are going to start from Nature Scitable (use only this website for first couple of weeks - keep your mind clear and take one task at a time. I have wasted my time by being greedy for learning too much until I came to Nature Scitable and man! It was exactly what I was looking for.)

While bioinformatics presently is a bit heavy on fairly standardized problems involving sequences, you might also consider topics such as computer vision (and to some degree control theory), which are presently seen in many leading computational biology publications.


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Is taking a shower unnecessary if good bacteria surround our skin?
David Whitlock, a scientist, has not taken a shower for 12 years. Instead, he sprays a bacterial mist containing live bacteria to remove odor and maintain the number of good bacteria.
It is because using soap can remove good bacteria on our skin. So he chose not to take a shower but to spray the mist.
This kind of behavior sounds strange to me. But can it be very effective to maintain good bacteria and prevent disease?
I cannot do like him but I am just curious.
Thanks.

the Phrase "good bacteria" doesn't mean it's not gonna be harmful to you . actually they called : normal flora . they are refer not just to bacteria they include all types of microorganisms .
http://www.ncbi.nlm.nih.gov/books/NBK7617/
I give you an example : there is some bacteria in our bowel they help our digestive system to work better . but these bacteria in case of some infectious disease or in the people with Immunodeficiency disease like AIDS turn to be pathogens .
the vision of David Whitlock is not irrelevant in fact in the field of industrial biotechnology we use micro organism to clean and digest environmental pollution like oil spills & ... just like him use bacteria too clean out his body but in fact the thing is he put non pathogens bacteria on his skin so there is no place for other bacteria .
but as a professional view  there amount of normal flora on our skin is 10 times more than our cells so you can not think our skin is a surface and you can just wipe every thing on it just by showering and ... I'm telling you these thing are odd and there is no scientific evidence that support this odd things . maybe in 100 years when we ran out of drinking water we force to make cleaning sprays base on this view . but you know such a crazy but possible thing in theory .

You can read about the guy here: http://www.livescience.com/52719-do-we-need-showers.html He uses soil bacteria from the Nitrosomonas genus, which can break down ammonia and product nitric oxide (NO). According to him horses have these bacteria on their skin. Using soap can destroy these bacteria on our skin and the proper recolonization can take months. So these are really sensitive microbes.
He claims that these bacteria were once part of the human skin microbiome, but was removed when people started to use soap.
I found some circumstantial evidence only:

The groups that'd had more contact with the modern world tended to
  have less microbial diversity, the researchers found. The Yanomami in
  the study had almost double the amount of bacterial diversity as the
  people in the U.S., and about 30 to 40 percent more diversity than the
  Guahibo Amerindians and Malawian participants, said study researcher
  Jose Clemente, an assistant professor of genetic and genomic sciences
  and medicine at the Icahn School of Medicine at Mount Sinai in New
  York City.

http://www.livescience.com/50526-amazon-bacteria-microbiome-diversity.html

This just shows that the biodiversity is much greater on the skin and in the gut of tribe people living in isolation from modern society.
I read a few years ago that tribe people have even soil bacteria on their skin, so it might be true, but I did not find more information about the concrete species living on the skin of these people, so it is inconclusive whether he is right or not. Taking shower is not necessary btw. if you can bear with the odor...


text:
Is there any kind of "unintended consequence" in evolutionary systems?
In the social sciences, unintended consequences is a term used to describe an unexpected positive or negative effect of a particular action. This is obviously the wrong word to use in the context of evolutionary systems but I am looking for something that has a similar concept. It may be related to concepts in dynamical systems theory.
For example, if we look at one trait or a group of traits, we may be able to see how this adaptation benefited a population. However, the mutations that occurred along the way would no doubt alter other systems/properties of the organism. In many cases these effects would be negligible. I am looking for any cases where the effect of one set of adaptation leads to another comparably impactful (either positive or negative) effect for the population.
The following is more theoretical and controversial but I am particularly interested in larger, more complex traits such as behavior (which may be considered the product of many different evolutionary adaptations and molecular changes) and any "unintended consequences" that could occur as a result of such a behavior. For example, empathy may be considered a very complex trait that has an evolutionary advantage (post hoc we might say it evolved because it allows specific kinds of communication in social groups) but it may also cause populations to react incorrectly (with regards to survival) in threatening situations when an empathetic response is not the most optimal response. I realize I am treading in vague territory here and it may be controversial to reduce empathy down to the molecular level as I have done in this example. But if there is any work at least related to this idea on a basic level I would be interested.
In summary, I am looking for either the term that describes this sort of analysis, if it exists, or some major examples that may help me do further research on the topic.

There is a lot of text here. I have tried to answer the question "Where has a seemingly beneficial/detrimental evolutionary change had the seemingly opposite affect?"

You have addressed my question correctly. There is a lot of text because I wanted to make sure I was clearly stating what kind of answer I was looking for. Sorry if this made it more confusing.

I get what you are trying to say, but want to point out that the terminology is poor - there are no intended or unintended evolutionary consequences of mutation, evolution is a random process, not driven by intentions

@rg255 I should have been more clear. In my first paragraph I said it was the wrong word to use in the context of evolutionary systems and that is exactly why - it is an undirected or non-teleological process. I'll make an edit when I get a moment to be more specific about that.

The term "exaptation" might be an interesting one for you to look into.

Slightly more tangentially, you might also enjoy reading about the Baldwin effect in this context. In particular, since you mentioned dynamical systems, you might like Geoffrey Hinton's famous model of it. (That's the same Geoffrey Hinton who's now very famous in the field of deep learning.)

There is also a field of research from the 90s called "adaptive dynamics" which gets pretty directly at the kind of thing you're talking about, where an evolutionary response is not the optimal one. In fact they claim that in particular ecological contexts a species can end up at a fitness minimum instead of a maximum, and that this can lead to speciation. Those papers tend to be quite impenetrably mathematical, but if your background is dynamical systems that might not be a problem for you.

@Nathaniel This is is exactly when I was looking for. I was having difficulty finding the right wording which made it challenging for me to explain myself in my question. If you want to turn your comments into a more complete answer I will accept it. But for now, this is great to get me starting and gives me a direction to search further.

Are you referring to tradeoffs; advantage in something causing disadvantage in some other thing?

Preamble
Evolutionary systems do not have these exact terms as far as I'm aware (although I'm not a behavioral expert) This mainly is because generally speaking we must stop thinking about traits in terms of "advantageous" or "intentional consequences" when discussing evolution. However there are countless examples where a seemingly detrimental evolutionary trait flourishes, or when a seemingly beneficial trait can be exploited by other species. Here I point out two simple, well known examples that might be what you're looking for.
Physiological disease trait emerges
The most well known is sickle cell anemia (SCA); a disease that also reduces susceptibility to malaria. In areas of the world with high instances of malaria, there are also high instances of SCA (Piel et al 2010).
Behavioral altruistic trait exploited
For behavioral studies I think humans would be too vague... (okay, I know very little about sociology) But there is one story that springs to mind from another animal. Birds are ideal models for behavioral studies.
The cuckoo and warbler are an endless evolutionary arms race in terms of camouflage and behavior. The cuckoo parasitises the nest of the warbler with a single egg in a clutch of 3 or so warbler eggs. The warbler parents will watch the newly born cuckoo kick the other eggs out of the nest, and then continue to feed the cuckoo chick thinking it is their own. The reason is thought to be because the warblers respond to the feeding call of their chicks (altruistic, albeit from parent to chick), however the cuckoo chick can mimic this call much more intensely than an entire brood of warbler chicks (altruism is exploited)(Davies et al 1998). By the end, the tired parents are feeding a chick three times their size.


text:
How do (marine) cells not lose potassium?
Eukaryotic cells keep a sodium-potassium gradient across their external membrane. The concentration of potassium ions is about 5mM outside the cell. Although the potential gradient keeps most of these ions close to the membrane, won't some of these ions diffuse away from the cell/organism? Over long periods of time, wouldn't cells 'dry' out of potassium? I guess the same sort of question can be asked about phosphate.

Might help to focus your question: which organism (unicellular, multi-celluarl) and water kind of water (sea water vs. fresh water)?

If I understand correctly, all organisms in water would be continuously losing potassium by diffusion. Unicellulars in fresh water more so than thick-skinned multicellulars in sea water.

If cells are in a condition where there is low potassium outside, and some of the inside potassium leaches out via diffusion, then they use mechanisms like the Na-K pump to restore the cellular levels.

I think that answers the question. It follows that cells require a certain minimum concentration of potassium in the surrounding water to survive, or at least must replenish it via roots or food.


text:
Can anyone tell me what tree does this leaf belong to?
I found a lovely tree in my friends yard and we do not have a clue what tree is it. The leaf texture is a but like the ginko biloba, but the shape is different. Can anyone identify it? (It's in Romania, Eastern Europe, but I suspect it's not a local tree)

definitely looks like Liriodendron tulipifera (aka tulip tree, tulip poplar, yellow poplar)

maybe it is from tulip-tree (Liriodendron tulipifera)
use one of this applications to identify plant species:

http://www.plantsnapp.com/#theapp
https://itunes.apple.com/gb/app/id957861141?mt=8
https://itunes.apple.com/gb/app/flowerchecker-plant-identification/id916709270?mt=8
https://play.google.com/store/apps/details?id=cz.thran.flowercheckerplus

and many others here


text:
Is there a word for the assumption that a sufficiently complex and refined organ must be the result of natural selection on a large time scale?
Is there a term for the valid assumption that a sufficiently complex and refined organ must be the result of natural selection on a large time scale?
Example:
A biologist exists in a world where nothing has eyes.  They find a creature with an eye as developed as a modern mammal's in our reality.  Assuming this biologist understood what the eye was able to do as far as limiting and focusing incoming light and sending visual information to the brain, etc - it would go without saying that this was a gradually evolved system.
It would be impossible for a parent from a completely eyeless ancestry to spawn a child that had the equivalent of a fully developed modern mammalian eye, both because of the statistically improbability of that happening, and possibly even because of limitations in the way dna works.
Is there a word for this assumption? e.g. "As per the Axiom of Reliable Intuitive Ancestry Determination for Sufficiently Complex and Refined Traits, we will start our genetic research confident that the eye must be the result of iterative natural selection on a large scale of time."
Preferably a term that acknowledges the validity or reliability of this assumption when it comes to very complex and refined organs or systems, such as the eye, the brain, or the circulatory system.

It's clear to me what you are asking. How can a biologist that exists in a world without eyes know what an eye is? That biologist must not also have eyes.

This is a clunky question. As for as I'm aware, whilst it fluctuates, phenotype changes via natural selection are necessarily gradual (unless this has a technical meaning I'm unaware of). Are you looking for a word to describe the difference between "Eyes were selected for via natural selection" and "Eyes were selected for via laboratory/agricultural intervention"?

@James - it's more like:     "how do you know those bumps on the face weren't a recent addition to this creatures genome?  Did you do any testing?"
"No, I didn't have to.  These bumps actually are actually very complex beneath the surface of the skin and perform a vital and well adapted function.   The complexity and refinement alone are enough to know these must be the result of long gradual selection, even in the absence of other evidence."

I think I've almost grasped the question. Could you say "What is the word for assuming that the phenotype has a genetic underpinning?"

Unless I misunderstand, wouldn't all phenotypes have a genetic underpinning?  From my previous comment, one might say "We can conclude that the bump in the forehead is not just an oddball family trait that neutrally came into play a couple of generations ago." -   "Do you have genetic or fossil evidence?" - "No, but we were able to determine some complex and well developed functions that this bump provides." -  A way to shorten this to "do you know this through genetic evidence, fossil evidence, or [blank]?"  [Blank] being a word or phrase that means the complexity itself is evidence enough.

The 'term' you are looking for is actually gradual change or gradual evolution. If you want to make clear that this is an assumption or a theoretical consideration, you could say assumption of gradual change or theory of gradual change, replacing change with evolution if you like.
The idea comes from Darwin directly and was challenged in the 1970's by biologists like Stephen Jay Gould that suggested that evolution is not driven by gradual accumulation of changes but rather by morphological equilibria disturbed by many rapid adaptations forming new species, a concept called punctuated equilibrium.
It speaks for itself that these concepts are opposing but not mutually exclusive. They are rather two extreme states in a continuum.
Edit: As pointed out in a comment by Daniel Weissmann gradual changes also occur in neutral evolution; this is what we call accumulation of mutations - in fact, it also applies to (at least slightly) deleterious variants, especially in populations with small effective population sizes. This means, that the concept of gradual evolution can be generalised to neutral evolutionary processes. However, it does not mean, that the process involving natural selection cannot also be described by gradual evolution. You just have to specify what you are actually talking about. When talking about obviously complex adaptations, you would assume that they have not evolved neutrally.

Say this new species not only has a complex organ like the eye, but also a large lump on it's forehead. We think the forehead lump may be there to keep dirt off of it's nose.  However, without a close examination to other factors, like parents, environment, dna, etc, we cannot assume gradual change.
It may be very well be an anomalous mutation in this individual or incidental to adaptations elsewhere, or DNA evidence might show it in fact has been gradually evolved.
With the eye we can make this determination with no evidence aside from how well adapted and complex it is.

I don't think this is what OP is looking for. The assumption of gradual change doesn't really say anything about natural selection -- it's generally taken to apply equally to neutral evolution.

@DanielWeissman: Thanks for your comment. I edited my answer to account for your argument.


text:
layman inquiry into mechanics of evolution
Consider a species. Without some particular mutation, its members have quality A. Suppose that quality B is better for the survival of any individual member of the species. If one member possesses quality B, natural selection could take over.
What if B is preferable to A, but the intermediary stages are not preferable to either A or B? Can a species go from A to B?
Say an organism has 4 legs but having 6 would be advantageous. Could it get to 6 without some disadvantaged intermediate forms? Or is there a way for a single genetic mutation to result in a one step change? Also, if no organism has ever made such a transition then I suppose it can go without explanation. But then maybe something went from 6 legs to 4, or something.
I hope this isn't too rambling. Kindly,

Your general line of inquiry is good, but with the current state of the question, the answer is "maybe". There's not enough details to evaluate or scrutinize the scenario and give a really meaningful answer. There's so many variables that you're leaving open to us that it's unfortunately more of an exercise in imagination than a request for mechanical clarification. Perhaps for the legs scenario I could point you to Hox genes, which, if duplicated, could potentially duplicate a whole leg-pair segment. Try looking up pictures of "fly mutant hox genes".

Thanks for the help. I realize my question was too vague but I'll look into Hox genes, because it seems, after a quick glance, like it will give me some of the insight I was looking for.

Unfortunately, at least to me, the issue isn't four vs. six legs, to borrow your example. The issue is what other number of variables contributed to the emergence of the 4-legged archetype besides the fitness of # of legs?

Maybe also take a look at my answer to this question. The concepts of gradual evolution and punctuated equilibrium might be of interest for gaining a deeper understanding of macroevolution.

I think it'd be great to make a community post that describe concept of fitness landscape and fitness valley and then to talk about shifting balance theory and the role of phenotypic plasticity and of large effect mutations to explain the transition over a potential fitness valley. There are so many layman that have question on this subject.

@Jozurcrunch You might want to have a look at Understanding Evolution by UC Berkeley. It is  a short and very introductory course to evolutionary biology

There are a lot of exciting ideas here. I really appreciate the guidance.

The question is a very deep one, and the answer is 'it depends'. Organisms can in general only evolve by taking rather short steps through genome space, where each step is better than the last. This could mean one or two nearby basepairs change, or one or two segments of DNA get duplicated, inverted, deleted, etc. It's the DNA that evolution acts on, not the organism's 'qualities', or as we call them, it's phenotype.
In your example, there might be a single piece of DNA which when duplicated, causes the organism's number of legs to go from 4 to 6. In this case the mutation can happen and be selected for and extra legs can evolve. If however the evolution of new legs requires a lot of mutations, non of which are individually useful, then the trait won't arise before the intermediate mutations are selected away.
What may happen instead is something more complicated. E.g. the many mutations for the new legs could initially arise because they are doing something different, and then gradually get selected for other purposes.
In general though the problem of how organisms' move from one peak in the 'fitness landscape' to another is an ongoing topic of research.

Part of the challenge of the legs analogy was that it seemed so complex that it would've required a symphony of mutations to produce in one generation to avoid disadvantaged intermediate forms. I thought it very unlikely, more still if the advantage was only slight, or if it required such a mutation in not just one but a subset of the original population. I guess my initial question is impossible to answer and that I need specific states A and B, for which evidence of the transition from A to B exists, otherwise it is disingenuous to demand an explanation from evolution.

I think the example is actually confusing the issue. As others have pointed out, there might very well be a single mutation separating the four-legged type from the six-legged type, so there would be no intermediate type.
But the basic question stands:

What if B is preferable to A, but the intermediary stages are not preferable to either A or B? Can a species go from A to B?

I did my thesis on this! The answer is a qualified "yes" under certain conditions:

There are no more than a few necessary intermediate steps.
The intermediate types are only slightly less fit than the original type.
The population is large.
There is not too much recombination among the underlying genes. (A little recombination actually makes it easier.)

For details, see here and here. (Sorry, they're pretty technical. I've been "almost done" with a review non-specialists for years now...)

This is interesting. Is your work a model based on the assumptions you've stated and using simulated data? And given those assumptions, a species can go from its current state A to some preferable state B?


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Merge NCBI and Ensembl data
Apologies if this is a really naive question, but I cannot figure out how to do this easily. Here is a related post regarding the best method to find orthologous genes of a species.

Let's say I have a protein alignment downloaded from Ensembl (coming, for instance, from this Ensembl tree).
This gene is present in some other "NCBI species" that I would like to include in my tree (for instance, Stegastes partitus, with available genome and present in the NCBI database but NOT in the Ensembl database). Indeed, if I manually blastp asip protein sequence of D. rerio (extracted from my Ensembl multifasta protein alignment) onto nr database parsed for S. partitus, I find this sequence, corresponding to the first blast hit. Perfect! And I can manually append it to my initial protein tree.
Where the problem starts is that I don't have one gene and one NCBI species but many of them (let's say p genes and n NCBI species). I already have an Ensembl protein multifasta file for each of my p genes.
My question is: is there an easy way to append to each of my p multifasta files the corresponding homologous protein sequence(s) for the n "NCBI species"?
Thanks for any insight!


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How to interpret Glimmer scores?
I am trying to find orfs with Glimmer. At the end, Glimmer gives me a .predict file with the orfs and a corresponding raw score.
When I look at the documentation, it says about the score, "This is 100 times the per-base log-odds ratio of the in-frame coding ICM score to the independent (i.e., non-coding) model score. It gives a rough quantification to how well an orf scores that can be compared between any two orfs." You can look here for the documentation-
https://ccb.jhu.edu/software/glimmer/glim302notes.pdf
But what does the score really mean in an absolute manner? How do I realize for an orf, if the score is significant or not?

The score is the log odds ratio, times 100, that the ORF that you input is a coding region. For example, if Glimmer thinks the log odds are 10 to 1 that your region is coding, then your score will be 10x100 = 10000. Log odds of 10:1 imply more than a million to one certainty.

Thanks. But the documentation says log-odds ratio. But even then, my question is what is a good odds ratio absolutely. More abstractly, when can I be confident that this orf is really a coding region.

You can't really be sure without experimentation and research, because glimmer can screw up. But a score of 300 or more suggests better than 90% odds that it is a coding region according to Glimmer. 10000+ implies a million to one odds.


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What's the difference between the *types* of tissue dissociation enzymes?
I'm trying to dissociate a tumor, and most protocols like NCI/NIH recommend a 10X triple enzyme digestion stock consisting of: collagenase type IV, DNase I type IV and hyaluronidase type V in HBSS. This goes all the way back to the 90s, and the recipe varies between papers (dispase, papain, neutral protease, elastases, etc.). The so-called official recipe that I've been tasked to use is composed of the above, however, mostly from Sigma-Aldrich (C5138, D5025, H6254)
I can't really find anything that says what the real differences are between these types of enzyme are, however. Or why for example type IV DNase works better than type II, and so forth. Is it perhaps that the recipe just happened to stick?

It’s years since I looked at a Sigma catalogue (before it became Sigma-Aldrich) but as I remember, these designations are arbitrary proprietary ones used by Sigma to distinguish different sources — the key point being that Sigma didn’t generally manufacture all of these themselves, but obtained the from third parties.
The other point to note is that these enzyme preparations were/are generally impure,  but to differing extents, so the type designations allowed you to re-order a particular preparation that worked, and also to specify the actual grade you used when you published so that other people could repeat your work. More expensive grades would, no doubt, also work in the sort of crude application you describe, but they would be a waste of money.
I thought the catalogues used to give you some information (organism/tissue at least), but, as I said, it’s been a long time (although be careful with your “way back to the ’90s”, young man).

Regardless of your age, 17 years is a fairly significant amount of time. Old fart.

This is kind of what im getting out of their catalog. I saw one source that said something like DNase IV works better on DNA containing lots of repeats, but I couldn't find anything else to back that up. Cost vs. activity/purity seems to be the case.

And to be fair, reading "Cancer Research 54" circa 1994 is a bit like reading a history book about T cell-based therapies.

But there's some stuff of that vintage and earlier that has hardly been added to since, especially in very chemical areas. I was trying to find info (for a SE Biology question) on sugar ring conformation in different helices and had to walk over to the library to get a book published in the 80s.


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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!


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How dissimilar are the fingerprints of identical twins?
It is a very well-known fact, stated multiple times even in this Stack Exchange, that identical twins have different fingerprints. However, to what specific extents, and in what specific ways, do the sets of fingerprints of identical twins typically differ? Are the differences usually very minor (e.g., just a few stray loops and whorls here and there)? Are they perceptibly different but still fairly similar, with the similarities most likely stemming from heredity and/or cultural ties? Or does the determination of fingerprint patterns behave similarly to a uniformly weighted random number generator, with the fingerprint sets of twins being just as different as those of two people born on opposite sides of the world?
Obviously, due to the random/probabilistic nature of this feature, there may be no single answer to this question — there may be cases where one pair of twins has fingerprints that are more similar than those of another pair. But does anyone know what typical similarities and differences are present between the fingerprint sets of identical twins, and, if possible, the biological causes of such similarities and differences?

Identical twin fingerprints are different, but generally more similar than to random people.  For example:

Fingerprint recognition with identical twins is a challenging task due to the closest genetics-based relationship existing in the identical twins ... Srihari et al. [6] analyzed the similarity between twins' fingerprints in a study using fingerprint images from 298 pairs of twins. The authors analyzed this similarity using two-level features. With the features of level 1, they found that twins' fingers are much more likely (55%) to have the same pattern type than non-twins' fingers (32%). With the features of level 2, they concluded that the similarity between the fingerprints from twin fingers is higher than from two arbitrary fingers.

Fingerprint Recognition with Identical Twin Fingerprints

Dermatoglyphic asymmetry and diversity traits from a large number of twins (MZ and DZ) were analyzed based on principal factors to evaluate genetic effects and common familial environmental influences on twin data by the use of maximum likelihood-based Variance decomposition analysis. ... The present results are similar with the earlier results of finger ridge count diversity in twin data, which suggested that finger ridge count diversity is under genetic control.

--Inheritance of dermatoglyphic asymmetry and diversity traits in twins based on factor: variance decomposition analysis

Upvoted especially for the use of the word "dermatoglyphic", whose plural is the longest word in the English language with no repeated letters.


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Origin of enzyme names
Sometimes I get confused about why this or that enzyme was named in this or that particular way.
1) TCA: Why was not isocitrate dehydrogenase named isocitrate decarboxylase?
Wouldn't it have been at least as accurate to name the enzyme in question isocitrate decarboxylase as to call it isocitrate dehydrogenase? It does remove the -COOH, doesn't it?
2) Glycolysis: PEP (phosphoenolpyruvate) carboxykinase. Why isn't it oxaloacetate carboxykinase? Isn't it agreed upon that enzyme substrate be used in the name of enzyme?
3) Why name enzymes by reverse reactions (especially when the reaction is irreversible)? Pyruvatekinase makes pyruvate from PEP. Why not use another name, PEP phosphatase, for example?
I understand that this is the way the enzymes were named and I just have to accept it. But I would also like to understand the logic behind these names.

I don't have a proof for this right now, but since the enzymes usually work in both directions (although under physiological conditions only one direction usually is happening), it is possible that the (for the physiological pathway) reverse reaction was classified and analyzed first.

Sonic Hedgehog, and his arch nemesis, robotnikinin.

As @Chris commented, when assayed in vitro with a single substrate (which may not even be the physiological one) most enzymes can catalyse a reaction in either direction. And enzymes such as pyruvate kinase were discovered before the pathways they are constituents of were worked out in full. Furthermore, the ways of naming enzymes only became more sophisticated as more were discovered and characterized. (Try googling for ‘old yellow enzyme’.)
Let us take pyruvate kinase as an example. The name kinase is clearly not chemically descriptive but was applied to any reaction using ATP. But, never mind, go to the Wikipedia page for pyruvate kinase and click on the EC (Enzyme Commission) number — 2.7.1.40 — in the box on the right. You will come to a page where you will see that, like TS Eliot’s cat, the enzyme has three different names:
Accepted Name: pyruvate kinase
(because that’s what everyone uses and is in all the text books)
Other names: phosphoenolpyruvate kinase; phosphoenol transphosphorylase
pyruvate kinase (phosphorylating); fluorokinase; fluorokinase (phosphorylating); pyruvic kinase; pyruvate phosphotransferase
(note these include naming it for the reverse reaction)
Systematic name  ATP:pyruvate 2-O-phosphotransferase
So why is that the systematic name? If you click back from this page to the group EC 2.7.1 to which this belongs, you will find that this group is of ‘Phosphotransferases with an Alcohol Group as Acceptor’, itself a subgroup of phosphotransferases.
So, to summarize, there is a systematic name that have been arrived at after long and careful deliberation and appears in the introductory paragraphs of scientific publications. Thereafter the common name is used, which although sometimes now recognized as a misnomer, seemed most appropriate at the time.


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How far does your center of mass move from stance to stance?
When the human body is perfectly centered, the center of mass is on the centerline around the belly button.  However, the human body is not always in this rigid posture.  We have many postures that we use.  How much does the center of mass shift, left to right, if we look at different stances.  I'm not so much interested in dynamic motions like walking, but rather static positions like:

At attention (obviously the center of mass will be very centered)
Weight shifted to one leg
A S-Curve, like from the traditional Greek statues

Obviously the center of mass will shift with respect to the ground, staying between the feet, but what I'm interested in is how it shifts with respect to the torso's centerline.

I'm voting to close this question as off-topic because although the question involves living things, it's not a biological question. This is a physics/mechanical engineering question.

@James While the calculation is pure physics, the numbers that would be needed can only be determined empirically based on how human beings carry themselves.  The only source I can think of to acquire such numbers would be biology.

This question is the field of biomechanics (video here). There is of course overlap. However, the simulations and measurements carried out in order to answer this question will be way more at the mechanical engineering end of the spectrum.

You can find the relevant math here:
http://hypertextbook.com/facts/2006/centerofmass.shtml
The key factors are the body mass distribution, height, standing center of mass, heartbeat, clothing, etc. You can approximate the center of mass for a given stance as:

In order to determine the center of mass of a person, we used the formula for torque:

$\Sigma\tau = r \times F$

The torques due to the weight on each end of the person were set equal to each other. The displayed weight on the scale was the force, and there are two different radii. The first radius is the distance to the center of mass from the person's feet, and the second radius is the length of the board minus the distance to the center of mass from the person's feet. The net torque of the system is zero and therefore the torques on the opposite sides of the boards must be equal:

$w_1\times x = w_2\times (l~-~x)$

where w1 is equal to the weight at the person's feet, x is equal to the distance from the person's feet to his/her center of mass, w2is equal to the weight at the head, and l is equal to the length of the beams. The resulting formula, when solved for the distance to the center of mass from the person's feet (radius one) is:

$x = \underline {~~~w_2\times l~~~}$
$\hspace {11mm}w_1~+~w_2$

After determining the location of each person's center of mass, the ratio of the center of mass to the height of each person was calculated using the formula:

$x/h$

where x is the location of the person's center of mass and h is the person's height.

That article had plenty of discussion of the center of mass from head to foot, but no content on left to right.  Part of this is because the study was done laying down, rather than in a standing position.

Its the same math. Just treat right as "head" and left as "foot". The fundamental problem is balancing two loads around a center of mass.

Its the same math, but different data.  I suppose that if nobody has ever done this study before, I can go gather my own data with this method.

COM moves both horizontally and vertically during gait. However, the displacement is much more higher in up-down than left-right shift


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Is a Linker sequence mandatory in primers for PCR Cloning?
I have designed the primers for PCR cloning, but i was not getting any colonies after the ligation. One of our colleagues said, that the restriction digestion might not be working as there is no linker sequence before/after the restriction site in the primer. What measures should I take to be successful in the cloning?

You can add the restriction recognition site directly next to your sequence, this is not a problem. However, a lot of restriction enzymes have a lower or no activity, if the restriction site is directly at the end of a DNA strand and require some additional bases here.

i was using bamhI and hindIII for digestion ... do i need to order a new primer set ... and is there any specific linker sequence for respective restriction enzymes?

This is the website you need, and yes, most of the time it's better to have several extra bases at the start of your primer.
https://www.neb.com/tools-and-resources/usage-guidelines/cleavage-close-to-the-end-of-dna-fragments


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Are the arrows in this diagram of ATP synthase correct?
I have a question about this image below.
Do you think that the pink arrow is actually going in the right direction?
I would suggest a LTO sequence and not LOT, since it is in the T state that ADP + Pi is converted in ATP.

I found this diagram in the book: Alison M. Smith, George Coupland, Liam Dolan, Nicholas Harberd, Jonathan Jones, Cathie Martin, Robert Sablowski, Abigail Amey, Plant biology, first edition                                           There is said that the pink arrow show how the protons rotate the complex, but to me the sequences of the three states are wrong anyway

here is an animation on it. http://www.sumanasinc.com/webcontent/animations/content/atpsynthase.html

Yes, the arrows are correct. However, it's not immediately clear what they're trying to show.
ATP synthase
ATP synthase can act as a generator or a motor. Interactions cause rotation of the F0 subunit and the  subunit's axle has a kink in it which deforms the stationary F1 subunits (the axle can turn either way to act as a generator or a motor). Read more at PDB's ATP synthase 101.

What The Asker's Diagram is Trying to Show
The black arrows in the asker's diagram are implying the movement of ADP or ATP (generation) in and out of the catalytic site. The pink line implies the movement of the axle kink and not the transition of ADP+pi->ATP.
Let's focus on the left-hand subunit across the subfigures and it makes more sense (ADP and Pi go in, protein "closes" and ATP is formed, ATP is released). Meanwhile, the "kink" completes a full rotation.

If the complex move clockwise, due to the H+ movement, (as the pink arrow should show) then the synthesis of ATP should not be clockwise too?

F0 rotates, F1 should not. Only the  subunit's axle is rotating in this figure. L/T/O are referring to different states of each (stationary) subunit.

Ok. If it does not move it makes sense. Just a last question: are these 3 states found for both alpha and beta subunits?

Yup: wiki

I found a good animation clarifying it. http://www.sumanasinc.com/webcontent/animations/content/atpsynthase.html