text:
Where is energy stored in a molecule of ATP?
Where is energy stored in a molecule of ATP?
How is energy released from a molecule of ATP? What specific bond needs to break
What is the difference between ATP and ADP?

Define pigment

a.  What pigments are found in plants?
b.  What colors of the Visible Spectrum do chlorophyll pigments absorb? Not absorb?
c.  What would you expect to happen if a plant was grown under a green light? Blue or red light?

Label and define the following:

a.  Granum:
b.  Thylakoid:
c.  Stroma:
4a-3 Explain how photosynthetic organisms use the processes of photosynthesis – Ch. 8-3

Define autotroph, give an example
Define heterotroph, give an example
Define photosynthesis and write out the equation for photosynthesis (both the word equation and the chemical equation – you need to be able to recognize the chemical equation)
What are the three factors that affect the rate of photosynthesis, and how does their absence or presence affect the rate?

The rate at which a plant carries out photosynthesis depends in part on its environment. Plants that grow in the shade, for example, carry out photosynthesis at low levels of light. Plants that grow in the sun, such as desert plants, typically carry out photosynthesis at much higher levels of light.
The graph below compares the rates of photosynthesis between plants that grow in the shade and plants that grow in the sun. It shows how the rate of photosynthesis changes with the number of micromoles of photons per square meter per second (μmol photons/m2/s), a standard unit of light intensity.

a.
When light intensity is below 200 μmol photons/m2/s, do sun plants or shade plants have a higher rate of photosynthesis?
b.  Does the relationship in question 1 change when light intensity increases above 400 μmol photons/m2/s? Explain your answer.
c.  The average light intensity in the Sonoran Desert is about 400 μmol photons/m2/s. According to the graph, what would be the approximate rate of photosynthesis for sun plants that grow in this environment?
d.  Suppose you transplant a sun plant to a shaded forest floor that receives about 100 μmol photons/m2/s. Do you think this plant will grow and thrive? Why or why not? How does the graph help you answer this question?
4a-4 Describe the light-dependent and light-independent reactions of photosynthesis (comparison of products in each) – Ch. 8-3

Answer the following questions regarding the Light Dependent reactions:

a.  Where does the energy for the light dependent reactions come from?
b.  Where within the chloroplast do the light dependent reactions take place?
c.  What pigment is contained within this structure?
d.  Define photosystem
e.  The light dependent reactions start in which photosystem?
f.  What are the products of the light dependent reactions?

Homework questions and trivial questions about basic biological concepts are off-topic on Biology unless you have shown your attempt at an answer. For more information see our homework policy.

So you just decided to copy-and-paste your test here without even trying to answer any of the questions? Lovely...

As far as I know the polyphosphate stores the energy, and the nucleoside is just a flag to know where it delivers the energy to.

It's fine to ask us to answer your homework, under two conditions. One, explain what you have done so far to answer it. Two, expose one task per question only.

The energy is "stored" in every bond. The primary bonds that break are either the first and second phosphate or the second and third phosphate creating AMP or ADP.
The middle letter stands for Mono, Di or Tri (meaning 1, 2 or 3 phosphates).

Please read our homework policy before answering questions like this.


text:
Is evolution a fact?
Richard Dawkins in one of his videos says that Evolution is a fact and not just a theory.
He goes on to say that man and chimpanzees both evolve from apes.
Is this correct (Is evolution a fact and did humans & chimps evolve from apes)?

Yes. But Dawkins talks like this because of a cultural context, which is the struggle between science and some religions over the proper method for belief formation.  A minority of religious believers wish prescientific texts to have authority over scientific evidence.  Historically, when science has challenged religious authority, it has often been violently suppressed.  Nowadays, attempts to overrule science more often rely on bad methods, poor understanding, and misleading rhetoric.  Dawkins's statements of our scientific knowledge often lack nuance but help immunize the credulous masses.

@ShirgillFarhanAnsari: Lots of interesting and important things cannot be duplicated in a laboratory. However, you can extend laboratory-gained knowledge and apply it to things observed in the real world - e.g. dating objects using timings from decay of radioactive isotopes. Science is not limited to lab experiments, although knowledge from them can be considered more robust due to repeatability etc.

Don't confuse "evolution" with the "Theory of Evolution". "Evolution" is a fact. But the "Theory of Evolution" is an attempt to describe/explain how "evolution" happens in life. "Evolution" is fairly simple and it's easy to demonstrate its existence. But the details of how it works across all life forms in nature are many, complex and varied. Some of the details have possible variations, so some of the details are disputed. It is irrelevant to the fact of "evolution" that the complete "Theory of Evolution" is not finished. The theory is still a work-in-progress; the simple fact is not.

This question and its answers is mainly dealing with how you translate between scientific statements and common-language statements, and how the same words are used differently in the two domains. Therefore, this is mostly a question about semantics and the philosophy of science (at least until the words used by the OP is better defined), not about biology, and I vote to close. There is basically no hope of an Answer to this Q without clearer language, which the disagreements in the answers and comments show quite clearly.

The question has the default of improperly using the terms fact and theory and their definitions is a question of philosophy and not of biology. However, I think we should keep this question. The excitement it provoked probably shows the need for a declared position on our community. I also think that such post may come handy for future reference on Biology.SE even though the main answer is not trying to demonstrate a point but only to clearly explain the position of the scientific community.

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I've edited this to make it less about the is evolution a fact or theory? component (which will illicit opinionated answers) and focus more on the how do we show that humans and chimpanzees have a common ape ancestor? side of things (which should be able to get solid, fact based answers)

Minor point compared to the others, but you understand humans and chimpanzees are apes, right? Homo sapiens is literally the type species for the Hominoidea (apes). Saying we've evolved from apes implies we're not apes any more; it's a strange way to put it.

its the only origin of species that cannot be proven false, and is proven true in every test it has gone, geologically, DNA, physiology, berhaviouraly, and other tests all test know to man have confirmed evolution.

Humans and chimpanzees are both species of apes that evolved from another species of ape.

A tiny bit of terminology
Fact

In popular culture, the term fact means "something that is true". I would consider a theory as being the closest concept in science to what is called a fact in the population culture.
In natural sciences, the term fact is rarely used but would have the same meaning than the one in popular culture. The reason we are not often using this concept is that in science (nor in any other field of knowledge) one can never definitely know the truth. We can only have evidence that are congruent with a hypothesis or body of statements. In such case we talk about theory (see below).

Theory

In popular culture, "theory" is used to mean what the natural sciences call a "hypothesis."
In the natural sciences, a theory is a body of thoughts/statements that is very well supported by loads of evidence. In science, a theory is not a hypothesis. For example: Theory of evolution, Theory of general relativity, transition state theory, etc. Note by the way that various definitions of theory are in use (ref.). The below answer respects the definition that I gave above.

The scientific terminology presented above is actually a matter of philosophy and not science. If you need more information about the definitions of "theory", "fact" and other related terms, you may want to ask on Philosophy.SE. Stephen Jay Gould summarized the concepts of theory and facts nicely when saying

[..] facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts.

In the answer below, I am using the scientific terminology.
Your questions

Is evolution true?

Evolution is what is called a theory in natural science (The Theory of Evolution a.k.a. modern evolutionary synthesis), and it is extremely well-supported. Evolution is NOT a hypothesis. In other words, we have a lot of supporting evidence that living beings have evolved and are evolving.

Did both humans and chimpanzees evolve from apes?

Humans and chimpanzees are apes (great apes to be more accurate). Both humans and chimpanzees evolved (and are still evolving) from a common ancestor who already was a great ape. We have a lot of evidence to support this common ancestry.
What does the theory of evolution say?
Understanding Evolution (by UC Berkeley) is a short and introductory course to evolutionary biology. Of course, there exist other good sources of information online such as Evolution and the tree of life by Khan Academy.
We have a number of posts providing book recommendations for

General biology (Books for beginners and Introductory biology text for an outsider)
Intro to evolutionary biology (Text Book Recommendation: Organic Evolution and Introductory books about evolution)
Intro to evolutionary genetics (Books on population or evolutionary genetics?)

You will also find a lot of introductory posts on biology.SE such as for examples:

Why do some bad traits evolve, and good ones don't?
Is there a biological mechanism for evolution encoded into our DNA?
Does it make sense to classify all humans in a single species?
Why is a heritability coefficient not an index of how “genetic” something is?
How could humans have interbred with Neanderthals if we're a different species?
If dinosaurs could have feathers, would they still be reptiles?
Why does evolution not make our life longer?
Why don't mammals have more than 4 limbs?
How to define “evolution”?
How did some humans evolve to be white?
Who are humans' closest relatives, after primates?
Did cats evolve from monkeys ? or vice versa?
Why do the ancestors of birds still exist?
How does Natural Selection shape Genetic Variation?

What are the evidence?
Demonstrable and repeatable examples of evolution lists sources that list evidence. There are probably thousands of pieces of evidence listed in total, all explained in lay terms with links to the original article. Of course, this is just a small sample of the evidence we have.
The post Is there any biological evidence that is not suggestive of or seems to disprove evolution? might be of interest too.

Thanks to @CortAmmon's comment for correcting a very poorly phrased sentence.

-1.  If you are going to answer the question of "is evolution true," you should use correct phrases.  We cannot say "We know for sure that populations of living beings evolve," but rather we must say "we have observed data consistent with the theory that populations of living beings evolve."  If we're going to answer one of the most contentious questions in science with "science is right," we are obliged to be very careful with our words.  Jumping from "evolution is well supported by evidence" to "evolution is true" is a tremendous faux pas.

Because my degree is in mathematics, and also by observation of how the word is used in science, I think this definition of "theory" in the natural sciences is completely incorrect. A theory is a description of some aspect of the world, complete with explanatory and predictive power. Whether it's correct or incorrect doesn't affect whether it is a theory. Newtonian mechanics remains a theory despite having been disproved. Superstring theories remain theories while awaiting experimental tests. In most cases (but to the dismay of logicians), "theory" could be replaced with "model".

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@WYSIWYG I am not pleased my comment has been removed. That was for others to see to place this answer into perspective. It was not a discussion, but a pointer for 'blind' upvoters only seeing the upvote score. Not appreciated to remove that. Biology.SE should pursue a high level of answering including citations to the scientific literature.

Thank you for your comments. Following your advice, I made a few edits to clarify my point. I think it is not desirable that I talk further about terminology as the question is not a question of philosophy about this terminology but a question about biology.

@AliceD comments are second class citizens on Stack Exchange by design. Expect them to be removed liberally.

@corsiKa- might be, but here at Bio comments are usually dealt with pretty seriously. They are not just removed. There are meta posts on it in fact. Answers with many upvotes on questions with >1k views draw more attention. The amount of comments should therefore be viewed at in terms of how many folks  are posting. A continued dialogue should be short cut. A series of comments by various posters should be left alone. But this discussion should be done at meta :-)

Evolution is considered a theory rather than a fact because to earn the label "fact" something must be reproducible.  Since evolution is a mechanism of action rather than a specific outcome it is inherently incapable of ever reaching this standard.

I see where you are coming from with this answer, but still think that it's  very misleading. In the middle of the answer you are indirectly implying that all scientific theories are "true", when scientific theories actually have different levels of support (Your argument: evolution = well-supported scientific theory --> evolution = true). You can very well have parallel scientific theories at the same moment in time (sensu Lakatos' Research programmes), and it is relatively meaningless to say that they would all be "true" on the merit of being scientific theories with some level of support.

A scientific theory is a structure of conjecture to explain an observed fact. The theory may be wrong, but that doesn't mean that the observed fact is untrue. Newton's theory of gravitation was a bit wrong, but gravity remained a fact. Darwin's theory of evolution might be a bit wrong, but evolution would remain true, we would just explain it slightly differently.

I don’t believe in deleting comments but the ones by J. C. Leitão and Cort Ammon, and the fact that they are so prolifically upvoted, reflects poorly on the community: They parrot an extremely naïve understanding of Popperian theory of science. People, please, don’t become so reflexively defensive of science that you put the meaning of words on their head. Of course science can prove things, and we can say that things are true. This isn’t “being careless” with words, but rather using words exactly the way everybody understands them. To say that “‘evolution is true’ is a faux pas” is inane.

@AliceD The comments are moved to chat and not really removed.

@Remi.b Please flag comments as obsolete if you have addressed the issues raised. As such I feel that this question shouldn't have been alive for so long +26 votes is infinitely more than what it deserves.

It is not the theory of evolution it is the theory of evolution via natural selection, we can directly observe evolution  the theory is the mechanisms behind it, this is why it is called the theory of general relativity not the theory of gravity.

@John It is actually called the modern evolutionary synthesis. Expressions like "theory of evolution via natural selection" would be very misleading given that natural selection is just one of several evolutionary processes.

@remi true, well depending on how you define natural selection, It just annoys me that people use theory of evolution as it it is a complete term, that organisms evolve is not a theory, why it happens is.

I understand your point. That's how theories are usually named though. The theory of gravity does exist. It is not the "theory of gravity by the concepts of inertia and other things, F=ma kind of things"

A scientific fact is something that is true. A fact cannot be proven false. This is no different from the common usage of the word. However, in science, we often do not definitively know what is true. Therefore, scientific facts tend to be observations based on specific evidence.
A scientific theory is a well-supported and rigorously tested explanation of a phenomenon.
These definitions are consistent with those given by the National Academy of Sciences.
In science, we use a body of facts to arrive at a theory. Science is a discipline of likelihoods, confidences, and uncertainties. We gather evidence to improve our confidence and minimize the uncertainty of a theory. This is how we arrive at a very likely explanation, such as the theory of evolution.
But we do not draw facts from theories - we draw theories from facts.

+1 for your answer, specifically the last sentence. Very well put and is one of the key principles we scientists hold sacrosanct (or should at least).

Re, We do not draw facts from theories.  Actually, the best theories predict new phenomena which, if tested, and found to be true, lead to new discoveries and advance our total body of knowledge.  I don't really keep up with evolutionary theories, so I'm sorry to say I can't cite any examples from that field.

@jameslarge precisely. Facts lead to theories which lead to predictions which can be confirmed as fact after experimentation and/or observation. Theories can lead to facts but do not produce them.

Can you give an example of a scientific fact?

@corsiKa An example would be: Say bacteria were experimentally treated with antibiotics. A fact is that 1% of those bacteria survived. Our theory is that those surviving bacteria are resistant to the antibiotics due to genetic mutations which confer a selective advantage. We can then validate and refine this theory by conducting another experiment to generate more facts. Certainly theories help us target further experiments, but the the facts that arise from those experiments are independent of the veracity of the theory.

That is not a fact. That is an observation. By your own definition, a fact cannot be proven false. That observation could indeed be proven false if better methods of detection and analysis are used on the data later. "Wow, before we observed 1% bacterial survival, but upon reexamination of the data collected, it looks like 3% survived!" I would go so far to say "There is no such thing as a scientific fact."

james, that is exactly my point - facts should not be possible to accept or reject. Thus, my statement "There is no such thing as a scientific fact." If we want to use the word fact as the common person does, that's fine. But we should not call it a scientific fact. Being precise with our language is important.

@corsiKa No, the 1% figure was and is true based on my methodology. Your methodology may produce a different number. Both observations are true; however, you may give one more precedence during interpretation, and in refining your theory. You may decide that my fact is inappropriate or irrelevant evidence for the theory, which is perfectly fine.

@corsiKa We can get even deeper than that and cay that 1% figure is a statement (about an observation, made by an observer supposedly using a methodology, ...) - this rabbit hole lead rather deep into philosophy with a sidetrack into psychology and sociology (e.g. if a figure is published there is no way to know if it's about a fact; you can only get your own figure or form a belief). So while you are certainly correct, you are considerably deeper in this hole than vervet seems to be. Probably the OP did not want it that deep or he'd ask on philosophy.se or something.

@EugeneRyabtsev I disagree. The entire discussion hinges on the definition of a fact. The word is used differently in different contexts. That said, I believe we're all saying the same basic things, but we simply have a different threshold for accepting common-usage versus precise scientific usage.

Tl/dr: No, evolution is not a fact (unless your definition of fact defines evolution to be a fact, in which case it is a fact...).  And if that phrase ruffles your feathers, it suggests you should read the rest of this answer.  I usually wouldn't put the Tl/Dr here on this particular topic, but apparently people have been unhappy with my answer being burred in it.
Richard Dawkins is a very loud personality who has demonstrated a consistent interest in silencing dissenting opinions.
Evolution is a theory which seeks to explain the world and predict future events.  It has entered a special class of theories where we have observed so much evidence to suggest that theory accurately models our world that people find that society operates smoother if we pretend that it is 100.00000% true.  In reality it is not.  It could be wrong.  However, we in society have a choice: we can pretend it is 100% true, or we can acknowledge that there is a tiny shred of doubt that must exist due to the nature of the scientific process.  In general, we have found the negative impact of pretending it is "true" is much smaller than the negative impact of people hearing that there's some doubt and presuming there is more doubt than there really is.
In my opinion, what has made evolution so tricky in the political world is that those who understand science well enough to actually understand what is meant by the statistical data captured to support evolution are generally happy "rounding up" evolution to 100% true, because they understand how to use the statistics, and there really hasn't been enough of an advantage to keeping track of the sliver of doubt.  Science always has a sliver of doubt, so they're always watching out for it anyways (no scientist is going to say "you can't be alive" to a new species because it didn't fit the model).  Those who find enough value in that doubt to take the time and energy to call it out by name typically do not have enough of a science and mathematics background to really comprehend what that level of doubt is, or how to manipulate it, so there is a trend of them doing so poorly and coming to very questionable conclusions. Probability is full of such cruel scenarios, such as the prisoner who runs at a wall repeatedly, once every second, and you may be asked to calculate how long it will take for him to have a 50% probability of quantum tunneling through the wall to escape.  Depending on the numbers, that timeframe may be more or less than the heat death of the universe, but the probability is absolutely there, and its never zero! (hint: if you get in prison, try to get out on good behavior... the running at the wall solution isn't the best approach)
In the end, it's all linguistics.  An interesting tangent is the use of "fact" in philosophy.  In philosophy, "fact" doesn't always mean exactly what you may intuitively think it does.  Many philosophers declare that an auditory or visual hallucination is a "fact" because it meets the philosophical definition of "a state of affairs," lending itself to strange phrasings such as "a fact about something which is not real" and other linguistic oddities.

EDIT
I pose a statistics question to you.  Your answer to this statistics question states how you approach the definition of some very key words, so the answer as to whether evolution is true or not will depend on them.

I flip a coin multiple times.  There's no reason to presume it's a fair coin, so no reason to presume P(heads) = 50% like in so many coin tossing problems.  I flip the coin a million times.  It lands heads every time.
I am about to flip the coin again.  Is the statement "The coin will land heads up" a true statement?

If you answer "no," because the coin flipping problem is in the domain of statistics, and statistically prior observations do not define the results of the next flip (though they obviously suggest at it), then your answer should be "evolution is not necessarily true," There's an extraordinary body of evidence supporting the claim statistically, so we can certainly make the claim "we are quite confident that evolution is true," but we cannot take the leap to declare it is "true" because we are basing our position in the statistics that form the foundation of modern science.
On the other hand, if you answered "yes," then you may state "evolution is true" to your hearts' content.  You have made the presumption that a bunch of evidence is the same as truth.  Of course, you make that statement without the backing of mathematics, so you don't actually have any proof to back your statement.  You are, in fact, making as religious of a statement as the claims that evolution is false made by creationists.  You are declaring something to be true, simply because you believe it to be true.
Why do I make such a big deal about this?  Because claims such as "evolution is true" are making it harder and harder for people who do not believe in science religiously to accept the results of science.  If I can talk to a creationist about evolution, I can get them to understand our POV in about 5 minutes... but it takes 30-50 minutes of battling them to get there.  Why?  Its because they have been told over and over a point of view about what science claims which is not technically accurate and conflicts with their beliefs.  The overstatement of the confidence in evolution from "very confident" to "100% proof positive without a doubt confident" actually gets in the way.
So please, decide which version of the word "true" you wish to use, the mathematical one or otherwise, and make your statements accordingly.  Just know that the mathematical rigor behind the study of evolution is only applicable if you're using mathematic's definition for key concepts like truth.

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Evolution is similar to gravity: we don't yet have complete explanation for either, but it would be pretty stupid to pretend that they are not real physical phenomenon ("fact") with all the supporting experiments humans have done over time.

@MikkoRantalainen The devil is in the details with such linguistic claims.  Gravity is an amusing example.  If I may use a slightly different phrasing than you did, consider the phrase "gravity is an attractive force between two masses." (recognizing that isn't your claim... work with me for a moment)  Such a statement might be deemed a fact until 1915, when General Relativity demonstrated that gravity is not a  force.  One can certainly add a few dozen additional words about phenomenology and human scales to clarify...

...but in the end, a "theory," as defined in science, is really awfully big to just boil it down to its name and say "X is a fact."

None of the answers so far have really provided much evidence, so here is a small sample of the peer-reviewed articles, based on genomic information that provides the facts that we know so far that provides us with the evidence to draw the conclusions that we do.
Morris Goodman, The Genomic Record of Humankind's Evolutionary Roots, The American Journal of Human Genetics, Volume 64, Issue 1, January 1999, Pages 31-39, ISSN 0002-9297, http://dx.doi.org/10.1086/302218.

Provides an overview of the sameness of the Human and Pan (chimpanzee and bonobo) genomes and also goes through other similarities such as extended gestational and postnatal upbringing for humans and Pan. Discusses similarities uncovered through observational studies that "chimpanzees are emotionally complex and intelligent."
It goes on to discuss phylogeny, different classifications and the history of some of the branching of species.

The Chimpanzee Sequencing and Analysis Consortium, Initial sequence of the chimpanzee genome and comparison with the human genome, Nature 437, 69-87 (1 September 2005) | doi:10.1038/nature04072; Received 21 March 2005; Accepted 20 July 2005 Here the abstract probably best defines the contents of the journal article.

Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.

Feng-Chi Chen, Wen-Hsiung Li, Genomic Divergences between Humans and Other Hominoids and the Effective Population Size of the Common Ancestor of Humans and Chimpanzees, The American Journal of Human Genetics, Volume 68, Issue 2, February 2001, Pages 444-456, ISSN 0002-9297, http://dx.doi.org/10.1086/318206. From this paper we are given evidence of the following

To study the genomic divergences among hominoids and to estimate the effective population size of the common ancestor of humans and chimpanzees, we selected 53 autosomal intergenic nonrepetitive DNA segments from the human genome and sequenced them in a human, a chimpanzee, a gorilla, and an orangutan. The average sequence divergence was only 1.24% ± 0.07% for the human-chimpanzee pair, 1.62% ± 0.08% for the human-gorilla pair, and 1.63% ± 0.08% for the chimpanzee-gorilla pair.

The key to this evidence is this; "we selected 53 autosomal intergenic nonrepetitive DNA segments from the human genome and sequenced them in a human, a chimpanzee, a gorilla, and an orangutan."
The significance of this lies in the fact that intergenic non repetitive DNA has very little, if any, selective pressure on it to maintain its sequence. Assuming that random mutations do not significantly alter gene expression, then there is no reason that there should be such high rates of homology, unless we are closely related to these other species on an evolutionary time scale. That being said, if some of those changes do have modest effects on gene expression, whether they are timing of expression in development, levels of expression, or tissue specific expression, then those can result in the differences we witness in the modern versions of the species alive today.
It would not be too surprising to find this level of homology in coding regions of genes across mammals, especially if we looked at the amino acid homology of the proteins encoded by these genes, as mutations in these genes would be under evolutionarily selective pressure. But to see homology this close in DNA in between genes suggests a very close relationship.
Philipp Khaitovich, Wolfgang Enard, Michael Lachmann & Svante Pääbo, Evolution of primate gene expression, Nature Reviews Genetics 7, 693-702 (September 2006) | doi:10.1038/nrg1940
Finally this paper gives an explanation of how gene expression can account for the evolutionary differences seen between Humans and other primates. It is unfortunately behind a pay wall, but here is the abstract of the article to give a sense of what it has to say on the matter.

It has been suggested that evolutionary changes in gene expression account for most phenotypic differences between species, in particular between humans and apes. What general rules can be described governing expression evolution? We find that a neutral model where negative selection and divergence time are the major factors is a useful null hypothesis for both transcriptome and genome evolution. Two tissues that stand out with regard to gene expression are the testes, where positive selection has exerted a substantial influence in both humans and chimpanzees, and the brain, where gene expression has changed less than in other organs but acceleration might have occurred in human ancestors.

Zoonoses and Host / Viral Pathogen Interactions
I should also add that another way we can gauge evolutionary closeness is through host viral pathogen relationship. Viruses have evolved to have a high degree of specificity in their mode of infection, and what works for a virus in humans may be harmless to dogs or birds or mice because the cell surface proteins that viruses exploit to infect the cells of multicellular organisms have a greater degree of difference the further away species are evolutionarily from the last common ancestor. And while there are cases where there will be intraspecies differences that afford immunity, such as the CXCR4 mutation which provides some level of resistance to HIV-1, for the majority of the species, the virus will be able to infect hosts of that species.
Many zoonoses cannot be transmitted between distantly related species. With that in mind, Chimpanzees can catch most all diseases that humans carry and vice versa. Simian Virus 40 has been implicated in human cancers and research has shown that the Human Immunodeficiency Virus originated in Chimpanzees and is called the Simian Immunodeficiency Virus, though the virus proves to be harmless in Chimpanzees.
In contrast cats have the Feline Leukemia Virus, which is highly contagious and can be passed between cats and cause leukemia, but cannot infect humans. Dogs and cats can be infected with life threatening Parvovirus, but humans are not at risk of this infection.
So if you are skeptical of the genomic evidence, then trust the viruses, because they will tell you how closely related organisms are by how effective they are at infecting different species.

Finally a referenced answer +1

It is easily observed that populations of organisms change over time, both phenotypically and genetically.  With some organisms we can observe this over a few days of observation; with others we can use historical records.  Therefore, evolution is an observed fact.
However, most people, by "evolution", are actually thinking of "the theory of evolution through natural selection", which is a theory. In fact, there are a number of explanations for why and how populations change over time.  These include the theories of natural selection, of neutral and nearly-neutral drift, of sexual selection, and so on.  These are of course theories, albeit (for the ones I list here) enormously well-supported theories.
You can compare to gravity. If I drop an apple, it will fall to the ground; if I watch that, it is an observed fact that the apple fell, just as it is an observed fact that the population of viruses I looked at last week changed their genetic composition (that is, evolved) over that period. Newton's theory of gravity is a theoretical attempt to explain why the apple fell.  Like Darwin's theory of natural selection, Newton's theory was wrong, but useful, and like natural selection, other theories have come along to improve on Newton.  (Unlike Newton, Darwin seems to have been almost entirely right, so that the new theories have supplemented but not replaced his theory.)
So yes, evolution is a fact.

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I am not very happy with most of the answers here as they seem to be too ideologically motivated and not so much about scientific reasoning. So I decided to give it another try.
Is Evolution really a fact and not just a theory?
If this is too long for you, let me just say this:
Evolution is an existing phenomenon. There is variation, there is selection and inheritance of traits. This has been studied and there is no scientific doubt that evolution is a process that is happening now and all the time.
Note that I intentionally bolded the word scientific. The rest of may answer will be mostly about science.

In science just a theory is not meant in a pejorative way. Everything that can be disproved, but scientist have not been able to disprove is a theory. The important part is that it must be possible to disprove theories by scientific methods.
In a way you can think of the principle of gravity also as just a theory. If you happen to find mass that does not get attracted by other mass, you would be able to prove Newton wrong. But the evidence of the existence of gravity is so overwhelming that I would not spend too much energy on that :)
So - from a scientific view evolution is a theory with overwhelming scientific evidence. There is so much evidence that among scientist this debate is settled, just like the theory of gravity. The vast majority of the scientific community accepts the theory of evolution as the theory which is most probable to shape life here on earth.
But the attentive reader may have spotted a problem in the last sentence: There is an unlimited number of theories that can explain how the life shaped to a way that we can admire it today.

Long ago people realized that the most important part of a scientific theory is that it must be somehow possible to disprove it. Of course we can create a theory that contradicts gravity where a green-yellowish rectangular slime pushes objects together. Scientists will be able to disprove as long as it is falsifiable.
But if we now give the slime the sneaky attribute that it escapes human senses, we have a perfectly valid theory that cannot be disproved. So if someone would ask you if it is 100% sure that Newton's theory of gravity is correct, what would you answer? You cannot simply dismiss the theory of the green slime, can you?

Okay back to science. Science basically tells you: You can and you even have to dismiss any theory that is not falsifiable. Theories that cannot be disproved are not valid in a scientific sense. Back to your question:
He goes on to say that man and chimpanzees both evolve from apes. Is he 100 % correct?
Is he 100% correct? - Certainly not, we can make a slimy theory that works as well.
Okay, so let's put it in a different way: Is he 100% correct in a scientific sense - This we cannot answer. There may be many now unknown scientific theories that explain life in its current form equally well. But at the moment we only have evolution.

So why then are scientists so sure? Why does Richard Dawkins tell us all the time that evolution is real?
Well scientists are pretty convinced because of two things: Firstly, a lot of scientific evidence has been collected to support the theory of evolution. There are fossils, there is genetic information, there are experiments that validate certain aspects. But what is even more important: Until now nobody could come up with an experiment disproving the key aspects of the theory of evolution.
There is a second important point here: At the moment we don't have any competing scientific theory. The theory of evolution in science is a little like olympia with just one participant. If someone wants you to bet on the winner, what would you do?

I acknowledge that there are non-scientific theories that can explain all aspects of existence equally well, but I want to strongly emphasize that these are NOT scientific theories. You do not have to accept science as an important explanatory system. But if you do, I hope I could convince you that scientific reasoning of scientists regarding evolution makes sense and although there is no way to quantify this believe in 90%, 99%, 99.9% or 100%, there is overwhelming evidence that make people like Richard Dawkins such firm proponents of the theory of evolution.

Evolution is most real. Have a look at this Wicked Cool Phylogenetic Tree from wikipedia:

What it implies is that there is one common ancestor.
EDIT:
I remember my professor telling me that phylogenetic trees work like a cot mobile. During our lectures on phylogenetics he would on occasion pick up the chalk and make crude drawings of three fish of dissimilar sizes on the blackboard. Always three fish. He would then tell us about how the bigger fish eat the smaller fish. The way I interpreted this is that natural selection played a role in what we observe today as protein to protein or gene to gene similarities. That is what this phylogenetic tree represents. I think my professor made the analogy to mobiles not because they go in circles but rather because phylogenetic grouping can be monophyletic where an ancestor with all it's descendants are considered a group, paraphyletic where an ancestor but not all it's descendants are considered a group, or polypheltic where the common ancestor is not taken into account. I pasted this phylogenetic tree with a monophyletic view on the matter.

There are two other great sources to visualize the tree of life: onezoom.org and tolweb.org.

@MakotoKato: I don't think I have said this anywhere, 'Encyclopaedia Britannica is more reliable than Wikipedia'.

@ShirgillFarhanAnsari My point is that it's NOT full of lies and errors.

It is full of arcticles about Transformers toys, though.

This is a circular argument. You cannot use a phylogenetic tree which is created based on the assumption of the evolutionary process as evidence of said process. You could make a good argument if you explained how that tree was made, that it is a map of genomic similarity. As it stands, your answer is not really proving anything, I'm afraid.

@terdon you are right, I added some additional detail

Disproven: https://www.sciencedaily.com/releases/2015/08/150818153509.htm

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Unknown animal - What could it be?
It's the first time I use this website and I really need help
because I'm totally stuck
Now I'm in school, but I'm trying to prepare for the Olympics
During the preparation, I found the issue on the anatomy of the animals, but it's something new for me - I can't even determine what it is!

What kind of animal is it? Could you determine some, the most vital and major of highlighted points? If you can help me to determine the kind of it, i will be able to use more specific books to find out.
I will be very grateful for any help!

Click on edit and insert in your edit all the terms for the numbers.

@SANBIsamples - that's part of the question, it's homework

okay @AliceD what's unhappy with homework?

@SANBIsamples, there's nothing that's unhappy, but by the looks of it you asked for clarification, but OP asks to have the numbers explained. In other words, you re-asked the question.

@AliceD I consider your homework question closed.

I have no idea what animal this is, perhaps a mussel?

Assuming you mean the Biology Olympiad, I would hazard a guess that this is a deshelled snail, judging from the visible helix in the middle and right images.

This looks like a very specific picture taken from a lab or lecture notes. Unless you were in the lab or lecture, or have access to the notes, it will be tough. Comments above suggested snail and mussel, which were also my first two ideas but it's really too tough to tell.

or a turtle fetus?

The animal is very suggestive for Dog whelk-like mollusc removed from its shell.
I try to mark the organs, do not rely on these marks as an absolut.

Testis
Renal vein
Gill
Mantle
Prostate
Osphradium

10 and others - digestive and reproductive systems, cannot mark precisely.

Digestive gland

source for comparing etc

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text:
Woodland outdoor microscopy advice
Let me start by saying I have never used a microscope outdoors, and in general I have never owned a microscope nor used one regularly.
However, I am currently developing and organising some activities for children, to be carried out in a woodland. I thought it would be really interesting to use a microscope to analyse and compare different samples: leaves, insects, etc. In a word, to do some "field microscopy" (I googled that, but doesn't seem to be a popular expression).

Is it possible?
Is it easy?
What type of microscope should I look for? We have quite a bit of funding, so feel free to suggest anything.

Thank you very much.

Worth considering DSLR and Macro lens. Take a look at macro photography samples. Advantage over microscope is that it is way easy to handle outdoors.

Use of pocket microscopes is not only professional; it is antique enough.

1: Yes it is possible
2: It's not as easy as lab conditions because of variable conditions, chances of equipment breaking, especially when small children are involved.
3: You can also look at a Foldscope. Its a small, but powerful microscope made with paper. It was developed by a scientist called Manu Prakash, and although it is still in its beta testing stage, I'm sure you would be able to obtain a few for your students. It is incredibly cheap, very customizable and really user friendly.
P.S.: With the amount I endorse the Foldscope, you would have thought they could have shipped one of the damn things to India for me.

Wow nice information about foldscope.

You could go wild in a forest with a microscope if you had batteries.

Yes
Yes
200X

There are a range of "nature microscopes" you can buy that will do this.
One cool new portable microscope with video storage is the Mustcam.

My suggestion would be to (have the children) construct some pooters (with a clear vessel to allow viewing) to catch small insects with and use magnifying glasses or hand lenses like this one which gives a range of magnifications.
For most of the things you would want to look at you would not need massive magnification (i.e. you wouldn't need a scope). Microscopes also give the issue of how to fix the object (if it's a living mobile thing) to immobilise it, and a magnifying lens is generally more portable and affordable.
A good tip for looking at very small things up close in the field is to look at them the with binoculars but using the binoculars backwards - it allows you to get a good close view.

IMO you don't need more than 20-40x for bugs and leaves. Beyond that it gets hard to find and focus on the sample, and the optics have more obvious aberrations.
"Field microscope" is a good category to look for. You need a light source in the scope -- most have a small LED. I got a couple of these for my 6- and 8-year-old kids and they have surprisingly good optical quality and durability. I linked to Amazon because there is a sample photo in the reviews.  I'm a professional microscopist, so I'm picky about these things, but I was impressed.
With the field scope I mentioned you can pull off the stage (part that holds a slide) and just hold the scope up to the side of a tree or a rock. Super cool.
Also, look for some rotten wood, or an acorn with a hole in it, and break it up to find the insect larvae inside.


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Examining milk for presence of harmful bacteria
I am not experienced in diagnostic bacteriology and am interested in understanding more about it in the context of analyzing food purity.
For example, imagine I have a supply of raw milk which might be, for example, a 20 gallon tank. I would like to ensure that listeria, e. coli and salmonella are not present in the milk.
Is it sufficient to take a single drop of the milk and examine it under a microscope or do I have to do more extensive sampling, for example, sampling every inch vertically or something like that?
What is the procedure to make sure my milk is free of the bacteria, or is that impossible?
I am not interested in procedures to kill the bacteria. I know those. I want to understand the diagnostic processes to tell if bacteria is there.

Starting on page 23 are outlined procedures and methods for sampling of milk as required by FDA standards. Of course, individual manufacturers will have internal QA procedures that ensure any state-level testing does not result in penalty to the manufacturer, but since I'm not in the industry, I can't give a more accurate answer. Also, Pasteurization is a method used to make sure microbial counts in the milk are low (not good) or zero (microbes are reintroduced as the milk is opened and used).

As @Kendall says, pasteurization (see here ) is what's generally used to kill pathogenic bacteria in milk. Looking at the milk under a microscope won't help. You'd have to do an ELISA-based assay or PCR... The easiest thing by far is properly carried out pasteurization procedure.

A simple way to know if milk contains any bacterial contaminations is to take ~5 ml of the milk and add a couple of drops of methylene blue to it. If the milk is sterile, it will stay blue. If any bacteria are present they tend to take up the dye, leaving the sample colourless after ~1 hour. A more extensive way would be to plate 3-5 dilutions of the milk sample on LB or nutrient agar.
You don't have to do much extensive sampling. Just make sure that you take a couple of well-stirred samples.

This would seem to only test for any bacteria, not just particular harmful bacteria.

Try to put some references!

@ImprisonedRhesus, if you need to test for particular harmful bacteria, PCR would be the preferrable option as it does not depend on the species and unlike biochemical tests, where you may have to spend more time and run more experiments

@TheMolecularBiologist Okay, if I use PCR I assume I would have to test for particular bacteria. Can I sample anywhere in a vat of milk? In other words does the bacteria spread out so it is present everywhere, or is there the possibility the bacteria would be in just one part of the milk and my sampling could miss it?


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Protocol to dilute DNA step ladder?
I need to run gels that are of not the "most" importance. So I do not want to waste alot of money on step ladder. How do I dilute DNA step ladder? Is there a general procedure, for I have tried googling for one, but I get varying answers, such as a 1:4  dilution, and so on.
This is the information on the Step ladder, by Promega, posted as an image, since copy and pasting would mess up readability.

EDIT:
Even though I awarded the bounty because it gave me the same concept; what I had actually did was to assume I would use $60ul$ of ladder combined with $1$x dye.
Therefore since I started with $1ml$ of $6$x loading dye, $100ul$ of DNA step ladder, and available nuclease free $\ce{H2O}$, and I desired a 5:1 ratio of solution(dye and $\ce{H2O}$)  to ladder.
I would then use $12ul$ of stock to the $60ul$ total.
To make the dye $1$x, I would add $10ul$ of the $6$x dye to make the final concenetration of dye $1$x.
Then I would add up to $38ul$ with nuclease free $\ce{H2O}$.
So, sorry if this was worded redundantly, but It helps me to read, therefore in summary:
$$  +10ul  \text{ of 6x dye}$$
$$  +12ul \text{ of stock 100bp DNA step Ladder}$$
$$+ 38ul  \text{ Nuclease Free } \ce{H2O} $$
$$ \text{__________________________________}$$
$$\sum{60ul} \text{ of ladder & dye} (1 \text{x}) $$
of which total I can aliquot out to my hearts desire.
EDIT2:
The ladder turned out successful.

You'll probably have to titrate it down yourself. You might be able to estimate: The detection limit for ethidium bromide staining is about $1 ng$ per band. The insert says it's at "1 $\mu g/ \mu l$", but that's for all 40 bands and they're clearly not all at the same concentration. Depending on which bands you care about (1600 and below are dim), you might be able to get away with $(\frac{1}{25})^{th}$ their recommended concentration (1 $\mu g / 40$ bands = 25 $ng$) -- but I would titrate a small amount and see what works.

I am trying to visualize the mitochondrial cytochrome b gene of D. melanogaster if that is of any help in this endeavor. I dont think its a larger region according to Flybase.   http://flybase.org/reports/FBgn0013678.html        But to be honest I am a novice.

That gene is ~1 kb, and the ladder is maybe 1/4 as bright in that range compared to the HMW bands. Try diluting around 1:5 (add 4 ul of TE buffer or water per 1 ul of ladder).


text:
Is there any evidence to suggest that exercise reduces the side effects of caffeine?
I heard a friend say:

I'm not drinking coffee this week. My body can only process the caffeine if I run at least 15km a week.

I found this claim fascinating - that exercise temporarily increases the caffeine tolerance of the body.
Caffeine side effects include:

Sleeplessness
Additional grogginess when waking up
Withdrawal headaches
Decreased empathy
A decreased ability to listen to orally spoken detail
A decreased ability to calmly think

My question is: Is there any evidence to suggest that exercise reduces the side effects of caffeine?

What side effects?

There are many things that they could mean, some of which even make sense. Exercise could help lower blood sugar, and so help consume the increased glycogen caffeine triggers. It could also help if the person is getting jittery from increased respiration. Finally, increasing metabolism will flush the stuff faster. Beyond those, I can't think of anything off the top of my head.

Can you please reference where you got your side effects list from.

Hi @AMR - I've referenced it - does that help you out?


text:
Using evolution of bacteria against themselves
We know that mutations happen regularly in bacteria and also that one bacteria might get the mutation and become stronger than the others and thus survive, causing antibiotic resistance as well. Can we deliberately make mutations in bacteria that would harm other bacteria but not humans. This would not only make them stronger and thus let them survive but would reduce the very need of antibiotics as they would be less virulent to humans?

(1) Not all bacteria are harmful (2) Even if you are able to make such strain, in future, that will also exposed to mutations and you will see new strains coming up with new mechanisms. You must read Red Queen Hypothesis !

We would do that only with the bacteria that harm humans in some or the other way. Yes, even those would go under mutation. So I am concluding that this is not a cure but a short sighted experimental idea?

Maybe. It will depend on your aim/objective of experiment/project.

Mutating Bacteria is a very plausible idea. If you mutate a particular strain of 'helpful' bacteria to become extremely positively selected for in the current environment then it is possible that the rest of the bacteria interacting with your new mutated will face heavy competition and eventually die out.
The major hole in the idea however, is that bacteria regularly undergo horizontal gene transfer which makes this idea extremely, extremely dangerous for humans. (If your mutated bacteria accidentally passes on the mutated gene to, say, a bacteria that causes Tuberculosis, it would initiate a pandemic. It is also equally possible that a dangerous bacteria might transfer its genes to your mutated bacteria.) It is generally accepted that mutating bacteria or other pathogens(most of which mutate at high rates) is generally a bad idea, because once released into the environment, the possibilities of the mutation going haywire are high(other mutations might make them dangerous).
Horizontal Gene Transfer: Transfer of genes due to recombination processes like Transduction, Transformation and Conjugation which can occur between bacteria of same or different strains, species, domains. etc

That's a logical thinking. Thank you. I get a clearer picture now.


text:
Why do workouts cause your muscles to feel heavy?
I know that muscle activity causes your muscles to build up lactic acid. Is this the specific reason that your muscles begin to feel heavy? How does this relate to the healing or inflammation process for muscles, or does it?
Thanks!


text:
Can anyone identify these moths?
Here are two lepidopterans I collected in Oregon (USA). The wingspan of the bigger one (on the left) is ~4 cm. I spent a lot of time browsing this website hoping to find a match, but I didn't have success.

Out of interest, did you find these in the same place at the same time? They have fairly different phenologies...

@theforestecologist approximately at the same place and time. Time period 1 month, place - the same region of a town.

The one on the left is a Lunate Zale Moth (Zale lunata).
See Western Washington University's PNW moths page for more detailed info.

The one on the right is a Forage Looper Moth (Caenurgina erechtea).
See here for an image similar to the one in the question.
And again take a look at Western Washington University's PNW moths page for more detailed info.


text:
Does the modern synthesis theory of evolution deny that acquired characteristics can be inherited?
The following is an wikipedia article on Lamarckism.
https://en.wikipedia.org/wiki/Lamarckism

According to Ernst Mayr, any Lamarckian theory involving the inheritance of acquired characters has been refuted as "DNA does not directly participate in the making of the phenotype and that the phenotype, in turn, does not control the composition of the DNA."[75] Peter J. Bowler has written that although many early scientists took Lamarckism seriously, it was discredited by genetics in the early twentieth century.
The evolutionary biologist T. Ryan Gregory contends that epigenetic inheritance should not be considered Lamarckian.

It seems to me that the assertion that acquired characteristics can be inherited was denied by the modern synthesis theory of evolution.
Is this true?
If yes, what is the reason of the denial?

Where did you hear it?

Answered before searching the site. Might be a duplicate of    http://biology.stackexchange.com/q/884/19650

@Chris Please read my new edit to the question.

Generally, yes, this is not part of theory of evolution as it is generally accepted by most of the scientific community.
For a trait to be subject to natural selection over several generations, it needs to have heritability, meaning it needs to show up in offspring (or their offspring). Generally, what is called an "acquired trait" does not fit that criterion. What's passed on is the genetic material of the parents and that doesn't change when the parent acquires these traits.
For example, bonsai trees are kept small by environmental conditions, as such, their height could be called an acquired trait. Their offspring does not naturally grow as a bonsai tree. Giraffes did not grow longer necks because they stretched them, but because those giraffe ancestors with longer necks (which just happens randomly through mutation - you have varying neck lengths in a population) could reach food more easily and could survive when those with shorter necks didn't. The giraffe example is a classic one that was proposed by Jean-Baptiste Lamarck, whose theory of evolution (called Lamarckism) was superceded by Darwin's.
There are traits where acquired versus genetic traits are hard to differentiate - while a good athlete does not have children who are athletic because their parent did sports, they are often also good athletes. For one thing, the parent might be genetically "suited" for sports and has passed these genes on. Another reason is that they will probably train their children and want them to become more athletic.
I know of one example where something that could be called an acquired trait is passed on to offspring - methylation patterns. Those are modifications of the genetic material that happen during an organism's lifespan and aren't modifications of the actual genetic code - they can be passed on to offspring. Since these patterns influence gene expression, they have an effect on the offspring. However, that's usually not what people mean when they talk about acquired traits.
Lamarckian inheritance

It's worth pointing out that popular conceptions of epigenetic inheritance (methylation patterns) are wildly out of line with the actual science.  Popular media have spread the notion that epigenetic change is much more powerful, long-lasting, and widespread than it actually is; in reality epigenetic inheritance is rare in general, typically has little impact, and even when it does occur generally fades before it can impact evolution significantly.  People who read popular science often believe that Lamarckian evolution has been supported, a view that isn't supported by the actual evidence.

What about the hologenome theory?
The hologenome theory of evolution contains Lamarckian aspects within a Darwinian framework.
http://www.ncbi.nlm.nih.gov/pubmed/19573132


text:
How many mega pixels does the eye have?
What is the number of mega pixels available in the human eye? It seems that newer camera models continuously keep increasing their pixel count. However, they never seem to be capable of reproducing what the eyes can see.

According to calculations done on this it is around 576 MP

There is a similar question on Photography.SE http://photo.stackexchange.com/q/39389

@Ghost A quote from my late answer on that question: "None of these calculations are scientifically accepted." This still stands and the question is purely subjective and speculative.

@GoodGravy - while the subjective conscious perceptual representation of the visual field cannot be expressed in megapixels, the retinal composition of photoreceptors and their relative contributions to the image can be approximated. It is not purely subjective and speculative at the retinal level.

Short answer
The total number of photoreceptors ('pixels') in the human retina is 63 million. Approximately 3 million of them transmit focused, color-coded information.
Background
In essence, each photoreceptor on the retina acts as a photosensitive sensor. We have rods and cones in our retinae. Rods confer gray scale vision, while cones are responsible for color vision.
The raw average tally of rods in the human retina is 60 million, and cones count a little over 3 million (Jonas et al, 1992). Hence, we could conclude we have 63 megapixels per eye available.
However, this does not mean that 63 million pixels are sent off to the brain. Instead, just as with a JPG image, it's instantly reduced in size even before the information leaves the retina.
Most importantly, rods are specialized for scotopic (night) vision and 10 to 30 rods connect to a single bipolar cell (Kolb, 2011). Hence, this feat only reduces the number of 'rod pixels' to about 3 million. Cones generally synapse onto a single bipolar. Hence, 6 megapixels leave the retina approximately.
The retinal image is generally focused onto the fovea, which is the central 18o of the total ~160o that is covered by a retina (Fig. 1). The remainder of the retina may receive a blurred image projection.

Fig. 1. Image focussing through accommodation on the retina. Source: Health Problem and Solutions
The fovea is densely packed with cones and contains nearly all of them (fig. 2).

Fig. 2. Distribution of rods and cones in human. Source: (Kolb, 2011)
Hence, the focused part of the image may be encoded by as little as 3 million cones. Since rods don't provide color information, it can be concluded that focused, color-coded information is conveyed by 3 million photoreceptors per retina.
Ultimately, however, it is important to note that the brain fills in missing gaps. For example, the optic disc, i.e. the point where the optic nerve leaves the eye, measures about 1.5 mm in diameter (Kolb, 2011). Given that the total diameter of the retina is about 30-40 mm this is quite a big blind spot. The brain simply fills in that gap by estimating what supposed to be there. In fact, many people with degenerative diseases of the retina don't even notice their deficits until they start bumping into objects that they did not notice. However, they do not see black holes, but instead their brain has been filling in the gaps with the information available in the remaining image, just like it does with the optic disc in normally-seeing people.
References
- Jonas et al, Graefes Arch Clin Exp Ophthalmol (1992); 230(6):505-10
- Kolb, Webvision, The Organization of the Retina and Visual System, Simple Anatomy of the Retina (2011)
- Kolb, Webvision, The Organization of the Retina and Visual System,
Circuitry for Rod Signals Through The Retina (2011)

Actually the human eye has variable resolution, with higher resolution around the fovea and lower as we move away from it. So I don't think the 576 MP is correct.
Our eyes are really horrible in many optical properties. The brain makes up for these errors and corrects everything, so in this sense your question is a poorly proposed one, as we should probably perhaps stop improving resolution of camera sensors and start improving the software that analyses the data they receive.

+1 for a reasonable answer, but can you back this up with citations?


text:
Why would glucocorticoids promote glycogenesis and not glycogenolysis?
I read in a textbook that glucocorticoids can stimulate the synthesis of glycogen. I do not understand this at all—shouldn’t glucocorticoids try to increase the blood level of glucose? Why would they be storing glucose as glycogen in the liver and muscles like insulin?

Interesting. What is the textbook? Which tissue or cell type does this refer to?

Glucocorticoids have a number of physiologic effects on glucose metabolism, inflammation/stress response, bone metabolism, etc. In general they are called glucocorticoids because they were originally found to be associated with increased blood glucose concentrations. Simply put, glucocorticoids antagonize the actions of insulin and create a state of insulin resistance, as well as increasing the expression of enzymes involved in glucose metabolism. They have a number of effects on all sorts of tissues and biological processes.
With regard to your question specifically, it makes sense that glucocorticoids stimulate glycogen synthesis, because it will allow the body to store more glucose as glycogen and increase the body's capacity for liver glucose production (i.e. glycogenolysis). Remember, at the same time glycogen synthesis is being increased, the glucocorticoids are inducing a peripheral insulin resistance that antagonizes insulin action in skeletal muscle and fat that also leads to increasing glucose concentrations in the blood. Moreover, free fatty acid are released from adipose tissue to be carried via the circulation to the liver so they can be oxidized to produce ATP for gluconeogenesis.
There is an excellent chapter that describes the effects of glucocorticoids on glucose metabolism in the major metabolically-active tissues (e.g. liver, white adipose tissue, skeletal muscle) by Kuo et al from Vol 872 of Advances in Experimental Medicine and Biology (pages 99-126). The book is not open access so I can't paste a picture of any of the figures, but they essentially show what I describe above. Here is another link to a very nice review article in the Journal of Endocrinology that has some great figures showing fuel redistribution in response to glucocorticoids as well.

There is increased insulin/glucagon ratio due to glucocorticoid (increased blood glucose level or insulin resistance) leading to stimulation of glycogen synthase and inhibition of glycogen phosphorylase causing glycogenesis.
2.There is large amount of glucose in liver due to gluconeogenesis. Since Vmax of glucokinase is much higher than that of hexokinase, they are converted to glucose 6-phosphate. Glucose 6-phosphate has allosteric stimulation effect on glycogen synthase so glycogenesis occurs.


text:
What is the difference between cell, membrane and animal based assay?
I am reading a review about MRP1, discussing it's ability to extrude different compounds from cell interior. When describing the different experiments conducted to observe the MRP1's reaction to different modulators, the writers refer to cell based, membrane based an animal based assays.
What is the difference between these three assays? What would be the purpose of choosing each of them for a specific test?
Thanks alot,
Yaron.

Can you perhaps link the review you are reading?

Sure,
http://www.annualreviews.org/doi/abs/10.1146/annurev-pharmtox-011613-135959


text:
Why are bacterial cultures necessary?
I notice that in a lot of bacteria testing procedures the sample has to be cultured. You place the sample in agar or another growth medium and wait for the bacteria to proliferate before examining them.
Why is this necessary? If the bacteria are present in the sample, can't you just examine the sample directly with a microscope to find them? Is it a needle in a haystack problem?
For example, a listeria bacteria is about 1 micrometer in size and has a positive gram stain. So, at 1000x magnification the organism would be 1mm in size in the objective which is highly visible. Even at 100x magnification you should still be able to see a tiny dot and be able to zoom in on the dot.

With only a microscope, you might be able to find the bacteria, but how do you know what kind of bacterium it is?
Taking Listeria, under a microscope, it looks like a small rod. Well, so do lots of other bacteria. If you only see that one bacterium, you can't take it and do any further tests with it, you can only see it.
So we do cultures, where bacteria multiply and form colonies. Whether they even grow under these conditions already tells you a lot - a lot of bacterial species won't grow colonies on The type of colony is another factor in determining what bacterium we are looking at - does it have fuzzy or clear edges, what color is it, is it "shiny"?
And then, with that culture, further tests can be done, like what chemicals the bacterium in this colony can break down, what they produce, whether they can be stained with certain dyes, etc. Many times this is needed because bacteria look very much alike (round or rods).
For Listeria specifically, there are special plates used as a growth medium that has certain chemicals added that makes their colonies appear red-violet. Other bacterial species won't show this color even if they do grow on the plates.


text:
Can we create custom gene/protein?
Does it possible to create any custom gene or protein we want with current technology?
I have a protein sequence or a gene sequence about 4000 bp write down on my computer, is there anyway to "print" it to real gene molecule or protein molecule (for example use chemistry and enzyme and automatic machine..) ? What is the challenge ?

Yes, this is possible. The challenges depend on many factors that are specific to the gene/protein. I don't think this can be answered in a generic way.

Yes, there are well established methods for synthesizing DNA with any sequence you want. Several commercial companies will accept DNA sequence (a text file) and generate the DNA for you. Genscript for example is well known.
Synthesizing the protein can be bit more tricky, depending on what it looks like and what you want it for --- proteins are way more heterogenous than DNA. There are commercially available cell-free protein synthesis systems that might be useful if you are merely interested in a peptide. Most people express the protein of interest in cultured cells though. In either case there is some biochemistry work to purify the produced protein. Genscript provides protein synthesis services as well. (No, I'm not paid by them, just don't have the energy to google other companies :)
In most cases, this works fine, and with a bit of tweaking you can produce quite large amounts. But for some proteins that depend on posttranslational modification for their function, expression can be difficult: see Can any enzyme be produced?


text:
What does the "*" in haplogroup I2A1* mean?
I have been told that the "asterisk" in the Haplogroup 12A1* means it doesn't move down stream? What exactly does that mean in layman's terms?

From the 23andMe website:

Sometimes there are a few lineages that don't fit into any subgroup of a haplogroup. Since there isn't a mutation that links these lineages, they don't get their own subgroup. Instead, these lineages are given the main haplogroup label plus a star (*) to indicate that they are part of the main haplogroup but don't fit into any of the known subgroups

So there are defined subgroups for I2A1 (I2A1A and I2A1B) for which more information is available, but you dont fit into any of them.
What "doesn't move down stream" means, I have no idea.


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Why does oxidative phosphorylation require complexes 2 and 3?
I am learning about oxidative phosphorylation in cellular respiration now and do not understand the roles of complexes 2 and 3 in the process. Specifically, my textbook says that 2 and 3 pump H+ out into the inter-membrane space, just like complex 1 does.
Complex 1 pumps out the H+ from NADH, and I suppose that 2 would be needed to pump out the H+ from FADH2, but then why do we need complex 3? All the H+ has been pumped out already--there's none left!
Also, if this understanding were correct, there would be no purpose for the chain that started with NADH to go through complex 2 at all (because it already went through 1, as opposed to the chain starting with FADH2).
Thanks in advance for any clarification you can give.

Complex II does not pump H+. What textbook are you using?

"Chemistry: The Central Science, 13th edition".

The numbering of the complexes in the respiratory chain is confusing, as it creates the impression that the chain is structured like
Complex I $\rightarrow$ Complex II $\rightarrow$ Complex III $\rightarrow$ Complex IV
... but this is wrong. There are in fact several ways of feeding electrons into the respiratory chain. They all begin with one enzyme E that oxidizes an electron carrier in the mitochondrial matrix, such as NADH, FADH2, or ETF (electron transfer flavoprotein) and transfers electrons to coenzyme Q, which is then processed by Complex III, after which electrons are handed on to Complex IV. Both complex III and IV pump protons. But there are several options for the first enzyme E:

Complex I (NADH dehydrogenase). This handles all electrons from NADH (from many sources in oxidative metabolism) and is typically the major source of electrons in the chain. It is the only enzyme E that also pumps protons itself.
Complex II (succinate dehydrogenase) accepts electrons from succinate (a step in the TCA cycle).
ETF dehydrogenase accepts electrons from reduced ETF, notably from fatty acid oxidation.
Glycerol-3-phosphate dehydrogenase accepts electrons from cytosolic NADH (from glycolysis) via the glycorol-3-phosphate shuttle.

There are more alternatives, but I think these are the most important ones. So you are absolutely correct that when NADH is the substrate, Complex II is not involved. There is in fact not one respiratory chain, but several possible chains with different starting points E,
E $\rightarrow$ Complex III $\rightarrow$ Complex IV
You might think of this as a "fan in" structure where the various enzymes E all converge on Complex III. (I don't have the energy to draw this :)
As for the proton pumping at Complex III, it is not the case that the H$^+$ pumped are exactly those derived from NADH --- the system is more complicated than that. The respiratory chain(s) convert chemical energy from the redox reactions into potential energy (a proton gradient), but most of the H$^+$ pumped are obtained from the mitochondrial matrix. The exact number of protons varies depending on the substrate: for example, the 2 electrons donated by NADH at Complex I is sufficient to pump up to 10 protons. Actually, the stoichiometry is not fully understood, and there isn't really an exact integer number of H+ pumped, because this pumping is an imperfect physical process --- there is leakage, protins slipping back into the matrix etc.

Complex 1 pumps protons, but Complex 2 does not. Both, however, take electrons from the electron carriers (NADH, and FADH2) and transport them inside the membrane to Complex 3. At Complex 3, the electrons are transferred via the Q-cycle to Cytochrome C which resides on the exterior of the membrane. In the process of transferring the electrons to Cytochrome C, Complex 3 also pumps protons. Cytochrome C moves from Complex 3 to Complex 4, where Oxygen functions as the final electron acceptor, while more protons are pumped.
Also a little clarification, Complex 1 and Complex 2 both donate the electrons to coenzyme Q 10/ubiquinone which is solubilized in the membrane. Complex 1 does not donate its electrons to Complex 2. Coenzyme Q/ubiquinone is what enters Complex 3.
Edit:
Complex 2 only accepts electrons from succinate oxidation to fumarate. ETF, and Glycerol-3-Phosphate dehydrogenase function much like Complex 2 in that they donate electrons to coenzyme Q without pumping protons. However, unlike Complex 2, these two enzymes are not trans-membrane proteins. ETF is associated on the matrix side of the inner mitochondrial membrane, and Glycerol-3-phosphate is associated cytosolic side of the inner mitochondrial membrane.

I think this is inaccurate on Complex II, it is not a generic acceptor of reduced FAD. As I understand it, complex II contains a bound FAD cofactor, but this functions like prosthetic group and is exclusively devoted to oxidizing succinate; it cannot accept reduced FAD from other sources. FAD from fatty oxidation, for example, goes via ETF dehydrogenase.


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Can the spinal cord contain an "epileptic focus"?
I was wondering, is there a possibility of an something similar to an epileptic focus to exist within the spinal cord?
Note I am using the terminology "epileptic" loosely here, principally for the lack of a better name for it. When I say epileptic focus I mean an excitable area capable of sustaining a pathological rhythmic electrical activity which may or may not extend to other areas of the central nervous system.
I believe it is due to the connection types that occur within the spinal chord (closed loops that exist there are resistant to this) and as such this might be true for other CNS areas (epileptogenic susceptible tissue might be specific of cortex areas). But I did some research on the topic and couldn't find any data on this.
If it isn't possible to have this problem on the spinal chord then, why is that?

What I did find is that some types of damage (http://www.ncbi.nlm.nih.gov/pubmed/1775364) may trigger something like an epileptic focus - couldn't find if it is becomes a permanent inductor of seizures, probably not.

Another possibility is that electrical activity within the spinal chord is hard to measure (http://jn.physiology.org/content/73/1/399.short mentions briefly this difficulty)

Short answer
Epilepsy is a disorder confined to the brain.
Background
Terminology is crucial in this question. The International League Against Epilepsy (ILAE) defines epilepsy as a disorder of the brain characterized by an enduring predisposition to generate epileptic seizures and by the neurobiologic, cognitive, psychological, and social consequences of this condition. ILAE defines an epileptic seizure as a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain (Fisher et al., 2005).
Hence, by definition, epilepsy is a disorder of the brain. Note that the ILAE is an authorative organ and their definition overrides whatever your medical textbook on internal medicine says.
An epileptic focus is a commonly used term, but as far as I know not well-defined. It's often used in relation to EEG and other methods such as MRI and PET that attempt to define the hot spot of seizure activity. More strictly defined terms in this regard are eloquent cortex and epileptogenic zone. The eloquent cortex refers to any cortical area in which injury produces symptomatic cognitive or motor deficit. The epileptogenic zone refers to the region of cerebral cortex that is both necessary and sufficient to generate epileptic seizures. Its entire removal can be used as a treatment for intractable epilepsy (Richardson, 2003).
With regard to your question, I expect you are referring to the epileptogenic zone. By definition, this refers to a region in the brain.
References
- Fisher et al, Epilepsia (2005); 46(4): 470-2
- Richardson, Brit Med Bull (2003); 65: 179–92
Note
I expect this answer may not be entirely satisfactory. If you are looking to the  physiological basis of the occurrence of seizures and why they occur in the brain and not in the spinal cord, it may be wise to formulate a more specific separate question. Preferably do not grossly edit this question given it received three answers. vervet's answer on focal epilepsy clearly shows the confusing terminology in epilepsy world. Focal epilepsy is not the same as an epileptic focus. However, epileptic focus is a term often used for focal epilepsy. Long story short, specific answers need specific questions, preferably with the definitions embedded to prevent deleted answers and under-appreciated answers like vervet's.

Thanks for the well-round well composed answer, but you are right, I this is not the answer for which I was looking.

I've made (hopefully) suitable edits to made clearer what I meant.

Why the downvote?

Because you knew you were not answering my question but answered it anyway.

Also, because you defined epilepsy as a brain disease (ok, according to some reliable sources) but my question is intrinsically related to why is this a brain disease and not a CNS disease. Some older sources would treat is as more generally as a CNS disease, such as http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1675106/ and this is what I want to clarify.

I would remove the downvote, since you seem to have done it in good nature, but stackexchange does not let me.

Epilepsy is a brain disorder caused by abnormal electrical activity in the brain, which is what often produces seizures. Focal epilepsy just involves part of the brain, while generalized epilepsy cannot be localized to a specific part.
A focal epilepsy could therefore not be caused by a spinal cord lesion.
Some conditions also affecting the spinal cord may predispose patients to epilepsy. For example, multiple sclerosis patients are known to have higher rates of epilepsy. However, the epileptic focus is still in the brain.

You didn't answer what I asked and you didn't put in any pertinent references. Also I was not asking about spinal lesions, nor multiple sclerosis. Epilepsy is usually described as CNS disease and the spinal cord is a part of the CNS

Also I was not talking about lesions or diseases of the spinal cord, since I know that if you put something there you can cause a seizure http://www.ncbi.nlm.nih.gov/pubmed/21992196, what I meant was a spontaneous focus or a spontaneous activity without generalization.

@user27221 What I am saying is epileptic seizures always originate in the brain. Spinal cord seizures are much less common. If your question is about seizures in general you should remove the word epileptic.

As defined by Harrison's Textbook of medicine: "Epilepsy describes a condition in which a person has recurrent seizures due to a chronic, underlying process.", whereas "A seizure (from the Latin sacire, “to take possession of”) is a paroxysmal event due to abnormal, excessive, hypersynchronous discharges from an aggregate of central nervous system (CNS) neurons." The names are not related to any spacial aspect whatsoever.

+1 for the distinction between focal and generalized epilepsy.


text:
What is the human species divergence time
How far back along the evolutionary tree do we have to go to find divergence to a completely different species to Hom. sapiens? I don't count Neanderthals because it seems that part of our genome contains fragments of Neanderthal DNA, and therefore, according to the species definition, Humans and Neanderthals could not have been an entirely different species. What about Denisovans? Is enough known about their DNA to consider them a completely different species? In fact, is it even possible to distinguish 'a species' from the DNA alone?

http://www.ncbi.nlm.nih.gov/pubmed/?term=%22Hominidae%2Fclassification%22%5BMAJR%5D This MeSH search should provide you with plenty of answer.

Our DNA contains fragments from many many many species, as a species doesn't get an entirely new DNA sequence when they split from another. While Homo sapiens and Homo neanderthalensis were able to interbreed, they are definitely considered separate species by the majority of biologists.

@MattDMo A majority is definitely a stretch, many consider them another sub-species.

Do you also consider tiger and lions as different species? (Limited) Gene flow between the two groups has occurred. (Due to female hybrids being fertile.)
There is evidence that gene flow between humans and neanderthals was also restricted. Neanderthal genes regulating fertility, speech, neural activity are absent in human (No Neanderthal Y chromosome has ever been found in human population either), although neanderthal genes for immunity, hair and skin and coagulation have been retained. This selective-ness is pretty much a sign that hybrid fertility was reduced and that there was selection pressure to remove Neanderthal genes that govern fertility from the human population. And this is the hall mark of different species.
If you still discount neanderthal as a separate species due to limited gene flow between the two groups. Then Denisovans are also not another species because there has been limited gene flow from Denisovans into humans (Melanesians and Aboriginal Australians)

In fact, is it even possible to distinguish 'a species' from the DNA
  alone?

It is possible if you have a pure nonhybrid sample of all three species. Which was obtained from human (africans do not have neanderthal DNA), neanderthal (from various samples),  Denisovans (from a single finger bone of a female from the Denisova Cave in the Altai Mountains in Siberia)
I guess the next homo species we are aware of and have no evidence of gene flow is homo erectus (mainly because we don't have DNA from Homo Erectus)... however there is some indication that Denisovans did interbreed with an older and still unknown population of homo...
And if true you start getting into a ring species problem.... both ends of the ring are infertile and by definition are different species... yet if all member populations of the ring are still alive... gene flow between the two species is possible. So are they different species or are they not.

The erectus line that gives rise to antecessor is your best bet, at about 1.2 MYA. http://www.nature.com/nature/journal/v485/n7396/full/485033a.html
part of the problem is you are hitting the limit of where the term species is useful, once you get really close to the speciation event the term breaks down becasue everything is a ring species once time is included. Erectus includes both our ancestors and populations wholly isolated from us. Its like trying to draw a line between yellow and orange on a spectrum.

That's something that's measured by generations.
If the neanderthals bred with humans after divergence times in a range of 631–789 KY, that's roughly 30,000 generations distance, at which stage their genetics converged again.
The notion of a species is so flexible, that Neanderthals and Sapiens are considered different species, and also Sapiens is a hybrid of both.
Horses and zebras can still nearly interbreed after 900,000 generations divergeance and 4.5 million years.
What counts is the number of chromosomes. If they have the same number of chromosomes, the species can mix genetically. If they have odd numbers, the species wouldn't have a chance to converge again.
Mammals mutate more diversely than other tetrapods and birds, i.e. bats and whales are more different than any two species of bird. Mammals have less protein diversity and gene diversity than species that can hybridize after longer speciations(some birds can be viable after 20mn years), and they have more gene control variations which regulate complex metabolism traits which have to be compatible in both parents.
https://en.wikipedia.org/w/index.php?title=Hybrid_inviability&action=edit&section=1


text:
What is the normal blood water content
What is the normal water volume per 1 L of blood, and how much deviation from that norm causes dehydration or hyponatremia?

The human blood contains about 45% of erythrocytes and 54.3% of plasma by volume. The plasma contains about 92% water, while the erythrocytes, about 64% by weight.
The blood is slightly less than 80% water.
Dehydration occurs when water intake is insufficient to replace free water lost due to normal physiologic processes (like sweating, urination etc). Hyponatremia is low sodium concentration in the blood. Usually, the Sodium and water concentrations in blood are regulated independently. Hyponatremia can be caused by intake of to much water, which reduces the sodium concentration.
References: The sodium, potassium, and water contents of red blood cells of healthy human adults by L J Beilin, G J Knight, A D Munro-Faure, and J Anderson, J Clin Invest. 1966 Nov; 45(11): 1817–1825.


text:
Does a DNA sequence has its own derivation tree or pattern?
I am new to bioinformatics and natural language processing. In linguistics, they have Treebank - derivation/parse tree for each sentence. For example, a sentence "Sara sleeps" can be visualized by a tree: Sentence -> Subject Verb, Subject -> Sara, Verb -> sleeps.
I've heard about Genbank, a database for nucleotide sequences. Does a DNA has its own derivation tree, or is any pattern in a DNA sequence already known with current technology? I only heard about repeats.

Hello kate, I don't understand your question. The "derivation tree" you are describing is a structure which is specific to linguistics. How could a DNA have such a thing? It does not represent human language.

Thank you for the comment. I think DNA has its own "language" which is probably unknown yet. My question is,(1) is the "language" of DNA already known? (2) is there any hint already known for understanding the "language" of DNA? Hint might be anything, such as patterns.. because I don't really understand much about bioinformatics.

DNA does not have its own language, it's a simple storage medium. It encodes information, but not in any way similar to a human language. Maybe this encoding fulfils the definition of a formal language, but if you have never gone into that branch of maths, any comparison will be more confusing than enlightening.

So better to think it as a storage medium.. Thank you very much!

The Gene Ontology Consortium might be of interest to you.

Thank you for the valuable information. So to understand the "language" of DNA, or at least to understand how DNA sequences are derived, simply parsing the nucleotides/DNA sequences is not enough because they are mere storage? To cover protein etc is too big for me for now, but it is interesting.

@kate I still don't understand your question. What are DNA sequences supposed to be derived from?

By "derive" I mean as in "derivation" or "derivation tree" in formal languages field.

I think protein (not DNA) domains might be something close to what you are looking for https://www.ebi.ac.uk/training/online/course/introduction-protein-classification-ebi/protein-classification/what-are-protein-domains

Thank you very much for your all warm and informative comments. I thought that studying DNA sequences only is enough but it seems that's not the case; it's much more complex than the languages that human made by themselves. Hope I can catch up on proteins and gene ontology, at least grasp the basic understanding. Thank you very much for your help.

From your example I guess that by "deriving" you mean something like decomposing into elements with diverse functions. Maybe we could apply this concept to DNA sequences: Some parts code proteins, which are decomposed into triplets, each of which codes an amino-acid. Other parts have regulatory functions: They can be motifs not coding a protein, but instead allowing a protein or something else to bind and modify the expression of nearby protein-coding parts. Other parts may contribute to the physical structure of the chromosome, or may have no function at all.

Yes, this is what I mean. Thank you very much for your answer! Do all these - e.g. where is the part in a DNA sequence that involve in  function x - already known?

There are regulatory motif databases, and prediction algorithms for functions in a sequence, but all this is not fully known. Indeed, things are rarely fully regular in biology, so every bioinformatics predictions ideally should be completed with experimental confirmation. Also, the same sequence can sometimes be parsed in various way: a single DNA sequence may encode several proteins, depending on which portions are actually translated into amino-acids.
Some keywords you may be interested in: start codon, stop codon, open reading frame, 3'UTR, 5'UTR, binding box.


text:
Metabolic control theory: proof of the summation theorem?
I'm looking for a rigorous proof of the summation theorem of metabolic control theory. The only sources I find are the original papers by Kacser and Burns 1973 and Heinrich and Rapoport 1974, both of which are unclear to me.
The summation theorem is the following. Consider a linear metabolic pathway
$X_0 \xrightarrow{E_1} X_1 \xrightarrow{E_2} X_2  \cdots \xrightarrow{E_n} X_n$
Let $J$ be the steady-state flux through the pathway, and let $e_i$ be the concentrations of the enzyme $E_i$. The flux control coefficients $C_i$ is defined as the partial derivatives
$C_i = {\partial (\ln J)} / {\partial (\ln e_i)}$
The summation theorem states that for any such system, it holds that $\sum_{i=1}^n C_i = 1$. Intuitively this means that if the concentration of some enzyme has a large impact on flux, then the other must have a relatively smaller impact. It seems reasonable, but is far from obvious I think. So a proof is needed.
The proof (sketch) given by Kacser and Burns seem to rest on the assumption that $\partial (\ln J) = \sum_{i=1}^n \partial (\ln e_i)$, and given this, the proof is trivial; but this assumption is never explained further. Heinrich and Rapaport states the summation theorem in passing (p.94, "it is worth mentioning that the following relation holds"), but I don't see a proof. (But their paper is rather dense so I may have missed it.)
Anyone know of a proof of the general case?


text:
If dolphins can see sound, can they say images?
Dolphins determine their surroundings by listening to echoes. Can they mimic those echoes and communicate it to other dolphins, transmitting an "image"? Does the same go for all echolocators?

Until a day comes when you can tell one dolphin what image to "transmit", and then ask another what image it "saw", it's pretty hard to imagine an experiment that would let you test that idea.

Humans can get some spatial information from the sounds that they hear.  Close your eyes, and listen to some good stereo mixes of music through headphones, and you will get a sense of a "space" around you with different instruments at different locations within that space.  Now try listening to the same mix in mono (or, with just one ear bud in place.)  All the spatial information is gone!  Whatever sounds one dolphin is able to make, it's still just one dolphin---just like one earbud...

Cheers, that makes sense.

Humans and dolphins can selectively encode which elements of an image they wish to transmit using serialized code.
The transmittance of images in single bursts to multiple recipients doesn't exist except in cameras and projectors, in single beams. It's highly unlikely even that humans use any long distance echogram projection technology.
Echogram transmittance would require 2d graph imaging organs through which to redraw and send the echogram in the direction of the receiver, same as the film/pixels and lense in a projector.
Sound is a lo-fi acquisition method. So bouncing an echogram to and from a source makes it even more lo-fi.
They would have to direct the echogram to a specific respondant using a kind of rotation, and to aim it just right.
The lense that the dolphins use to focus the sound is called a melon, and it's made of wax and fat. I think it's highly unlikely that they have a kind of image grapher and lense system to speak echograms. Nice idea!

I edited the response so that it makes more sense.

I have just asked a similar question in scifi.stackexchange and the reason is, I believe your idea can be found in a book written perhaps 60 years ago. I asked who the author was and/or the name of the book.
I am pretty sure this has been substantiated by researchers -- not recalling how the experiment was set up but I think it essentially involved simulating the dolphin echolocation process and then comparing sounds the dolphin emitted when shown the object or perhaps the researchers produced the sounds for a dolphin and asked the dolphin the choose from among objects.
So while a human might draw an object to explain to another human what they wanted, etc., a dolphin could do the same thing with sound. Perhaps their nouns all resemble the signals that come back during echolocation but I would also bet they abbreviate them since their probably is a lot of excess information in the signal from an actual object.
They would have the natural idea of "instance" and "class" (I speculate). And if cetacean language does consist of abbreviated signals from objects, I do not wonder why they have such large brains.
Here is a link that seems to indicate the answer to your question is "yes":
https://www.cymascope.com/cetacean.html

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