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Why don't all organisms reproduce asexually?
According to a comment at Why are not all species hermaphrodites?, asexually reproducing species go extinct more easily. However, I don't think sexual reproduction is a true evolutionary stable strategy. Since humans reproduce sexually, somebody with resistance to malaria and no sickle cell anemia can produce a kid with sickle cell anemia. For any sexually reproducing species, if a mutant asexually reproducing individual that happened to have the right genome arose, her clones would outcompete the rest of the species because almost none of them would produce an offspring with a bad trait, because they have weaker genetic drift against advantageous traits and so have a larger amount of some of them, and because they would be so slow to evolve by genetic drift to be unadapted to all those future sudden changes in the environment that they're already adapted to. Wouldn't an asexually reproducing snail from a species that snakes eat with the mirror image form from most of its species have the advantage of being harder to be eaten without having trouble finding a mate. Maybe just like humans could evolve to have resistance to malaria without the risk sickle cell anemia if they reproduce asexually, maybe if a mutant asexually reproducing cheetah with the genome that would make its clones spread arose, its clones would evolve to be furless poikilotherms that can thrive the low night temperatures because that would enable them to chase their prey longer before they became too hot to continue the chase because they would start at a lower body temperature, and individuals with that trait would never produce an offspring with any costly trait that comes with it except for a tiny costly trait.
In addition to that, if a mutant female asexually reproducing individual arose in a sexually reproducing species with the right genome and the species currently was in an evolutionary stable strategy with monogamy with each couple just able to get food fast enough to rear two children, the mutant female would also get a mate and with his help still be able to get food fast enough to rear two children both of which have entirely her genome, and then her asexually reproduced clones would spread very quickly. Once the species reaches a new evolutionary stable strategy where each individual can only get food fast enough to rear one child because there are so many females taking the available food, they may still have a slight evolutionary advantage over other species that's not nearly as high as the evolutionary advantage of asexually reproducing individuals was over sexually reproducing individuals of the same species earlier.
Source: https://www.ncbi.nlm.nih.gov/pubmed/16217668

The overwhelming majority of species in the animal kingdom reproduce sexually, yet you don't think sexual reproduction is a true evolutionarily stable strategy?  Is it just a fad that will be abandoned within the next billion years?

The question at http://biology.stackexchange.com/questions/5148/why-are-not-all-species-hermaphrodites is a good question. I don't see why this one wouldn't also be. I think a lot of people who can answer that question can also answer this one.

Please link to the comment you are referring to in the other question. If it does not contain a citation supporting the claim that asexually-reproducing species go extinct more easily, please provide your own citation supporting it.

The evolution of sexual reproduction is a big and very common subject in evolutionary biology. As your question is not very specific, you should probably just start by reading the wikipedia article to get familiar with the main hypotheses.

Read about Muller's ratchet. If you think sexual reproduction is not an ESS but it exists in nature then perhaps your model is wrong and you need to revise it. Also look at this post

Just because a mutant with a certain trait would spread if it arose doesn't necessarily mean it's going to just happen to arise in the first place. When I say sexual reproduction is not a true evolutionary stable strategy, I mean that if a mutant asexually reproducing individual with the right trait arose, it would spread and resist going extinct after the next sudden change in environment. Most of the existing asexually reproducing species went extinct because they didn't have the trait that made them already prepared for those sudden changes in environment that happened later.


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Are all fish that can live in either salt water or fresh water bigger than some critical size that is larger than the smallest of fish?
I cannot understand this answer. I don't know much about biology or have a lot of trouble recalling stuff from a university biology book I bought for a course I never took because it was so long ago and it was confusing even then. I think I once learned that salmon can live in salt water or fresh water. According to https://fishcostarica.org/this-fish-lives-over-60-years/, tarpon can also live in fresh water or salt water. It seems to me that for tiny fish, they deed a different type of body with more solutes inside the cells in order to live in salt water and the tiny fish that can live in fresh water have a different type of body with fewer solutes inside the cells. And advantageous traits come with costly traits so a small fish that could do both would have more of a costly trait and therefore be outcompeted to extinction. There are plenty of fish in fresh water already eating the resources in the fresh water and plenty of fish eating the resources in salt water. And being able to move back and forth between them doesn't really enable a small fish to get more food. I think a big fish on the other hand would have a much slower rate of osmosis so it can easily pump water our as fast as it is getting absorbed into the cells or in as fast as it is getting absorbed out of the cells. Salmon also have some reason to go back and forth between fresh water and salt water.

Timothy, you should word the title better: bigger than the smallest of fish is about 8 millimeters:  what size is bigger than a critical size that is bgger than 8 millimeters, that doesn't seem very big?, i am confused already.

@aliential I guess I'm asking whether it's the case that there is some critical size bigger than the smallest of fish where it tends to be evolutionarily harder to live in both salt water and fresh water.

Theres small species known to be Euryhaline. The comment you just wrote is a lot easier to read wording than the original question text, you should edit the question with just those words.

"It seems to me that for tiny fish, they deed a different type of body with more solutes inside the cells in order to live in salt water and the tiny fish that can live in fresh water have a different type of body with fewer solutes inside the cells. And advantageous traits come with costly traits so a small fish that could do both would have more of a costly trait and therefore be outcompeted to extinction." Do you have any evidence for that claim? And what does body size have to do with anything? I'm struggling to understand what the purpose of this question is.

Also, please note that the answer you linked to was to a question about anadromous fish - those that migrate up streams to spawn. There's a big difference between that and euryhaline fish, which can survive in salt and fresh water. I would imagine that anadromous fish would tend to be bigger, given the strenuousness of their migrations, while euryhaline fish could be any size at all.

Mollies , there are a few kinds , many are 2 to 3 " , live in fresh or salt . They seem to prefer fresh but often live in sea coast areas where tides ,etc. may cause intermittent changes between fresh and salt ( and brackish of course) . I used black mollies to start a salt water tank, I had a couple in the salt for months because it was not easy to catch them in a large tank. I expect there are other small fish such as puffers.  The mollies adapt very quickly , just drop them in whichever water and they behave normally.

You just give a single example. That doesn't tell me whether they're a tendency that way.

There are also some really small fish. I guess I defined big to mean big enough to be able to live in salt water or fresh water. There are some really small fish. If an answer confirming that none of the fish that size can live in either salt water or fresh water will do.

I fixed my the titled of my question.

Wikipedia has a listing for brackish water aquarium fish ; most can be in fresh or salt water.

I didnt read beyond the paragraph about your study books situation, Euryhaline on wiki reveals tiny euryhaline fish... 4-5 cm Fundulus heteroclitus which presumably can withstand salt changes as juveniles, 2-3cm.
Probably there are species a lot smaller because individual cells perform the osmotic rebalance, and cells are much bigger thans water and salt, so a smaller fish can just develop more of apparatus for osmotic balancing.

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Can genes that activate transcription factors also called be called transcription factors?
If the sole known function of a gene is to activate a transcription factor, would that gene also be considered a transcription factor, or is there a word for such genes that are further upstream on the transcription activation cascade?

Yes.  For an example, see this list of targets of NF-kB (a transcription factor).  Many other transcription factors are included there.  As for a TF that does nothing except activate another, single TF?  I don't know that those exist - TFs tend to modulate multiple genes.

From the wikipedia article on TFs:

In molecular biology and genetics, a transcription factor (sometimes called a sequence-specific DNA-binding factor) is a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to messenger RNA.

The nature of the gene affected is irrelevant, a protein is a transcription factor if it binds to a gene's promoter and regulates that gene's transcription. Whether the regulated gene also codes for a TF does not enter into it.

You need to re-write your question, it is ambiguous and your use of terms is incorrect... Assumption: by "activation" you mean "activation of transcription resulting in the expression of the transcription factor"
1) Transcription factors are proteins
2) Genes are comprised of DNA elements
A transcription factor can be involved in initiating the EXPRESSION of a transcription factor, whereafter that second distinct transcription factor initiates the EXPRESSION of another gene that encodes another transcription factor.
Answer: No, genes do not "activate" transcription factors*
*Unless you are proposing the philosophical question of whether the DNA binding domain itself, which endows the transcription factor with a state of being active duty (i.e. fulfilling its purpose as a transcription factor), and thus that purpose is fulfilled only when the DNA binds the the TF, then a DNA binding domain can indeed "activate" the TF... but I'm pretty sure this isn't what you're asking.

I simply meant to ask whether there was another term for a transcription factor upstream on the activation pathway of another transcription factor. Does that make more sense?

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Crick’s Central Dogma — Counter Cases
I was recently reading about non-coding RNAs being a counter example to Central Dogma of Biology. Can someone add more cases which violate the Central Dogma? Thanks!
UPDATE - Reference of lncRNAs violating Central Dogma:

Although the central dogma remains a core tenet of cellular and
   molecular biology, the appreciation of lncRNAs as functional genomic
   elements that defy the central dogma may be essential for fully under-
   standing biology and disease. [Iyer et al. Nature, 2015]

No, neither of those are counterexamples to the central dogma, as stated by Francis Crick: the dogma only says that information does not flow from protein back to DNA and RNA. Crick was well aware of RNA viruses. See his paper http://www.nature.com/nature/focus/crick/pdf/crick227.pdf

@Roland Thanks for highlighting the virus thing. Please have a look at updated question (with reference of statement)

Well, I guess Iyer et al never looked up the original definition of the central dogma :)  I know many textbooks have simplified / corrupted the concept to mean "DNA --> RNA --> protein", but that's a strawman ... In a sense it's just arguing about definitions, but to be correct, lincRNAs do not violate Crick's statement of the dogma. I suggest you read Crick's 1970 paper to get some context.

Do not take it too seriously. Biologists - as most scientists - tend to find definitions for themselves and those are not always compatible with other definitions. And this also makes sense in the scientific progress, as otherwise you would have a hard time adapting theories and, as a consequence, definitions. Crick's definition is as far as I know not the common textbook definition most biologists might have in mind and therefore this is just an ongoing scientific debate, rather than an oathbreaker. ;) Make sure to use the definition you want to promote in publications. ;)

I have changed your title of "Central Dogma of Biology" to "Crick's Central Dogma". Crick proposed this in an article on protein synthesis, which you can read here. Crick had a training in physics and I would be surprised if he described himself as a biologist at that time. His Central Dogma died (or had to be modified) with the discovery of the reverse transcriptases of retroviruses, over 40 years ago.

@David "Central Dogma died by reverse transcriptase of retroviruses" Wasn't Crick already well aware of viruses (as mentioned in his paper and thanks to Roland for highlighting it)? I think majority of us overlook this part in his paper

Talha. I've changed my view on that as I mention in my updated answer. I think there was a general misinterpretation of Crick's Central Dogma when Temin and Baltimore discovered reverse transcriptase, which evoked the reaction I expressed. (I was there at the time. Presumably there is a Nature News and Views article about it.)

Crick’s Central Dogma was actually:

The Central Dogma
This states that once ‘information’ has passed into protein it cannot get out again. In more detail, the transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein may be possible, but transfer from protein to protein, or from protein to nucleic acid is impossible. Information means here the precise determination of sequence, either of basesin the nucleic acid or of amino acid residues in the protein.

So, although in my comment I stated that the discovery of reverse transcriptase was the first violation of this — as was generally regarded — this turns out not to be the case.
I remember that the case of reverse transcriptase was felt to be different from the existence of RNA viruses because it involved the flow of information from RNA to genomic DNA, which were generally represented by a unidirectional arrow in the opposite direction in diagrams of the dogma. The following is a typical illustration of that, taken from some University lecture notes that I found on-line and which are described as:

These diagrams ..., created originally by Crick, summarize the basic processes of information transfer within cells.

But the NCBI collection of facimilies of Crick’s documents include a 1956 diagram that is quite different and much more sophisticated:

And, so the central dogma has not been violated (certainly not by lncRNAs), unless you consider that it has by prions, where information of sorts is transfered from protein to protein.
Morals

It’s amazing what you can find on the internet.

Never believe what you find on the internet.

Footnote
I’ve seen the DNA → Protein arrow repeated as if it were fact in diagrams, although Crick only said ‘may’. I know of no example of this.
Cross Reference
I have just (June 2024) posted an answer to a different question about the Central Dogma on SE History of Science and Mathematics. It attempts to provide a historical context, but may be of more general interest.

This is really enlightening, both biologically and philosophically (in terms of history of science). +1

Loved the moral part, but David its Nature – not an XYZ sitting on internet and writing blogs. I have wrote the author email in this regard. Awaiting his [never coming] reply

@TalhaIrfan — You're right to feel aggrieved, but a little explanation of how things work may help. When a paper submitted to Nature is sent out for review it will be because the authors claim to have made some substantial scientific progress. This will be expressed in the Title and the Summary of the paper, and the referees will be most concerned with whether the work is really important and whether it is correct. That is their main job. Hyperbole that only appears in the final paragraph of the discussion will often be ignored with a shrug of the shoulders.

The "Central Dogma" is an obsolete concept.  It has no biological significance today. It's been outdated for decades since the discovery of reverse transcriptase, but it was never intended to be taken particularly seriously anyway; Crick deliberately gave it its portentous name as a provocative approach, to drive people to think more about the topic and look for the counterexamples he presumed were there.
Unfortunately, it seems that in some places -- notably India -- shoddy, ignorant teachers don't understand anything about modern biology and still believe that the Central Dogma has more than historical interest.  It does not; it should not be taught in biology course, let alone treated as a testable concept, and any mention of it should be limited to History of Science courses.
Because it is an outdated concept that no longer matches modern biology, and because these ignorant teachers still try to squeeze it into their courses and tests, many students (again, especially from India) are very confused, thinking that their understanding is wrong because it contradicts the Central Dogma.
If you need to parrot something for an exam, I sympathize with you, but don't make the mistake of thinking that the Central Dogma is a real, relevant, modern biological concept.

I agree that there is no particular reason to mention the Central Dogma in teaching (and I never have myself), but it turns out that you are wrong about it being wrong in the way you say. I'm not criticising you, because I've only just discovered what Crick actually said and drew, as shown in my updated answer.

Kind of makes the situation in India worse.  Not only are these pedagogues insisting on teaching an outdated, irrelevant, biologically meaningless concept, they're not even teaching it correctly in the first place.

— I don’t know about Indian universities but a comment by Anurag Chaurasia you may have seen in Nature recently would seem to express similar sentiments. I have been fortunate enought to have come in contact with students from India who have been most capable of critical thinking.

That's my point.  The people (often from India) who come to StackExchange with questions about the Central Dogma are obviously capable of critical thinking, because they are baffled by the useless, stupid garbage they're being taught.  They usually don't understand that they're being taught garbage, but they do understand that it doesn't make sense, and they blame themselves for missing something.  It's incredibly frustrating to see baffled question after question about the same thing, actively harming the understanding of clearly smart, clear-thinking people.

The central dog is an old 1950s concept that is obsolete and should be removed from the text box of the 2010s. It states that the flow of information from DNA->RNA->protein is unidirectional
Examples that goes against this idea are
Reverse transcriptase which transcribes RNA -> DNA. Reverse transcriptase was originally found in RNA viruses. But has since been found in transposons which can be though of viruses that permanently resides in the host cell.
Telomerase... uses to elongate the ends of chromosomes from becoming shorter (something that occurs on the lagging strand of DNA during DNA synthesis) the shRNA used by this enzyme only encodes a few base pairs (6-8bp depending on kingdom)... but it is an example of RNA->DNA
RNA dependent RNA polymerase RNA-> RNA (No DNA is required to make more RNA). has been found in yeast.. with the role of maintaining the centromere... and likely will be found in humans too, since centromeric structure is believed to  be conserved in the broad sense.
Prions. Where a prion serves as the template to cause a normal protein prion protein (PrPc) to undergo a change in folding and become the infectious prion (PrPsc). An example information in propagating between protein molecules. Protein-> protein
Then there is epigenetics... where proteins can leave methylation marks on genes (DNA)... changing the expression of the gene in an inheritable way. So information from proteins can flow upwards. While not DNA bases are changed, the DNA is modified. Protein -> DNA
There is also histone modification.. which can be inheritable depending on gene. But it is regulation of DNA by controlling how available that DNA is to being read by transcription machinery.
Then there is siRNA... which can and does modify gene activity. A weaker example of how information can flow from RNA -> DNA.
Next are proteins called cytidine deaminases. These proteins naturally convert cytidine to uracil. APOBEC modifies RNA.. creating a premature stop and thus a shorter APO-B protein with lower activity.. regulating lipid metabolism. So mRNA editing by APOBEC proteins changing the information in RNA aka Protein -> RNA. Next is AID, another cytidine deaminase but one that targets DNA. It used by the immune system to cause hypermutation and thus variation in the antibodies. A poor example of protein inducing genetic changes. Not controlled unlike the DNA methylation example.
Lastly there are ribozymes. RNA that have catalytic activity. So no need for the protein to catalyses a reaction.. RNA can do it on its own.

Jay - can you add some references to the terms you use in your answer? It would help other users follow along with what you are saying and definitely strengthen it.

These are all interesting examples of regulatory interactions, but it is not at all clear that any of them contradict Crick's actual statements.

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Why does vaccine development take so long?
The main principle behind a vaccine is to take a deactivated virus, "show" it to the immune system so it can "learn" how it looks like, so if and when the real virus does attack us, our immune system is already prepared for it. Vaccines have been developed using this idea even in the 1880's.
If that's the case, why does it take so much time and effort to develop a vaccine, for example, against covid-19? (and why are there several variants with different measures of reliability?) Is it only about balancing how strongly we damage the original pathogen, too much damage and our body might not learn the correct identifiers, and to little damage and it might still be active enough to cause the disease?

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I'm confused. In what way do you find the development of a COVID-19 vaccine slow?  From what I've read, it's by far the fastest developed vaccine in history — it's been less than a year.  Isn't that incredibly fast?  Doesn't it usually take 10-20 years?

@gerrit That would raise the question as to why it usually takes ten to twenty years. A year seems slow to me too, because to me as a layman it seems such a simple thing to 1. find a medium that the live virus multiplies in, and 2. find a way  to soak that live virus in a chemical that binds to its genetic material so that it cannot get reproduced by the cellular machinery. Especially since these two steps have already been done with many other viruses, and covid is just SARS, so a known threat for at least ten years or however long it's been since the (first) SARS outbreak.

@MatthewChristopherBartsh : I'd answer your raised question with this: https://xkcd.com/1217/

Roni Saiba's answer does a good job of explaining what goes into current vaccine development and why it takes so much effort, but I want to directly address the question of why we can't just grow some virus, kill it with UV and have a protective vaccine.
The answer is that not all immune responses to viral antigens are helpful in fighting infections of that virus. In some cases it can be harmful; antibodies to dengue virus of one serotype will attach to viral particles of another serotype but aren't able to inactivate them. The attachment of antibodies to active viruses makes their absorption by cells more efficient, and infections where this antibody-dependent enhancement occurs are more severe than first-time dengue infections.
Some viruses have evolved mechanisms to capitalize on this. The reason we need to get a new flu shot every year is that influenza viruses present a "knob" at the end of their glycoprotein that can change its structure and still retain function. This part is much more 'visible' to the immune system than parts of the virus that can't tolerate changes, so the immune response to this variable part outcompetes and prevents an immune response that would provide long-lasting protection. Conserved stalk-targeting vaccines are being intensely investigated for this reason. SARS-CoV-2 may have a immune-faking mechanism as well: the "spike" glycoproteins responsible for binding the ACE2 receptor and entering the cell convert to their post-binding form prematurely part of the time. Antibodies that bind the "post-fusion" form of the protein don't inactivate the virus, and this form sticks out more so may serve to compete for immune attention with the pre-fusion form that would provide protection if bound by antibodies.
In this last example, we can see that a vaccine made of killed SARS-CoV-2 virus particles would be useless if all of the spike proteins had converted to the post-fusion state. The mRNA vaccines therefore don't encode the natural spike protein, but a mutated version which can't convert to the post fusion state as easily:

S-2P is stabilized in its prefusion conformation by two consecutive proline substitutions at amino acid positions 986 and 987

In conclusion, viruses and the immune system are very complicated. Simple vaccines work for some viruses, and don't work for others. When they don't work, the reason is always different, but hopefully I've communicated some general understanding of the background issues.
EDITS:
This doesn't relate to the rest of my answer but I want to respond to Ilmari Karonen's and there is not enough room in a comment.
Looking at the timeline for SARS-CoV-2 vaccine development gives a very misleading impression of how long it takes generally. This is because ~90% of the development work was already done before COVID-19 was ever identified, in the 18 years since the SARS-CoV-1 outbreak started in 2002. Vaccines against SARS were developed and tested up to phase I trials, but couldn't proceed further since the virus was eliminated. I discussed this in a previous answer to a similar question, but to expand/reformat, here's some of what we knew and had available on March 17th 2020, when the "covid vaccine timeline" begins:

Identified the receptor as ACE2, and knew that antibodies targeting the receptor binding domain (RBD) of the spike protein neutralize the virus. Protocols to test that these were also true of SARS-CoV-2 were already developed and validated. Without this there would have been a lot more trial-and-error experimentation and false starts with vaccine candidates that looked promising but didn't pan out in testing.
Animal models. There is no naturally-occurring model organism for COVID-19. This is a subtle point because other animals can be infected with the virus, and some develop morbidities because of it. However, these are different enough from what we see in humans that something that protects against the reactions we see in the animal can't be assumed to protect against the reactions that cause problems in humans. For SARS, researchers developed transgenic mice that used the human version of ACE2, and showed that the disease they got from SARS were analogous to the disease humans got. This took several years, and the colony was still available when the virus causing the outbreak in Wuhan was identified as SARS-like and researchers started looking for animal models. As an aside, in an interview on This Week in Virology that I can't find right now, one of the maintainers of that colony said they were months or weeks away from shutting it down and euthanizing all the transgenic mice when the pandemic began, so if funding had been just a bit tighter we probably would not be having this particular conversation now.
How to stabilize the pre-fusion form of coronavirus spike proteins had been determined from work on SARS and MERS vaccines.

In addition to these, a large amount of miscellaneous knowledge about coronavirus functions and the immune reactions to them had been accumulated, and this sped up development, and increased confidence in results, which allows vaccine candidate production and testing to proceed more aggressively.
Historically, vaccine development has taken years or decades of research after the need has been identified. Testing is still longer in many cases, but the current case is very unusual.

So, to sum it up, is it that some viruses are simple enough that the strategy of "breeding them in a petri dish, heating them up and we have a vaccine" strategy works (this is why there are some 130+ year old vaccine manufacturing methods which still work), but other viruses are more complicated to defend against, so more special solutions have to be developed?

It's not really a matter of simplicity or complexity. Smallpox is one of the most complex viruses to infect humans (186,000 base pair genome vs. 13,000 for flu) but it's defeated by innoculation with an attenuated strain. Yellow fever is closely related to dengue, but a very effective YFV vaccine was developed in 1938, while DENV still can't be vaccinated against with 2020 technology. It's kind of random. Our immune systems have a lot of tricks, and different viruses have different strategies to defeat them, and they are better and worse at evading different parts of the immune system.

Very interesting, well-written, and informative, and I would love to upvote it, but I can't: IMHO it doesn't answer the question. It hints at an answer, but it is mainly only implying that it's too hard for us to understand, and we should just trust and respect and thank the researchers that came up with a vaccine, and stop asking why it took so long. To really the answer the question, you would need to explain/prove how/that the effective inactivated vaccines such as from Sinopharm and Sinovac required so much time to be developed and used (and even now many people have not been vaccinated).

You completely ignore Sinopharm when you talk of "killing it with UV", apart from the fact that talk of killing a virus is not appropriate since it isn't alive as such. You can only alter it so that it can no longer get itself reproduced. "Neutered" would make as much sense as "killed". You don't explain how all this complexity that you teach in a very readable way (thanks for a great read) prevents a trial and error approach from succeeding. Specifics were lacking. The specifics of the development of Sinovac should have been covered and how it related to the post fusion form and so on, IMHO.

You keep saying "sometime this" or "sometimes that", when to explain how vaccine development always has taken a long time (including the covid vaccines, IMHO) you need to be saying something like "always...". "SARS-CoV-2 may have a immune-faking mechanism as well", you say. Isn't this known? Again, something that only may be the case does not explain why the first covid vaccine took (rather than "may have taken") so long to be developed. To change the subject: "couldn't proceed further since the virus was eliminated" ignores the beliefs about what is ethical that prevented CHIM being used.

CoronaVac is indeed a blind spot of this answer, but I haven't since found enough useful info to justify updating it again. I didn't give a concise, definitive answer to the question because I don't believe one exists. The topic is indeed very complicated. Readers don't need to blindly accept the conclusions of experts, but if they want to understand 'why' questions about vaccine development, it will require substantial time investment; much more than a SE question or a review article in a journal can provide. My goal was to provide a broad view that could serve as a starting point.

Please "@" me when you reply to me. I really feel fobbed off by the answer, and by your most recent comment although, of  course, feelings don't trump reality. You don't mention in your answer anything about CHIM being rarely allowed for supposed ethical reasons. Surely if CHIM (human challenge) was freely used (within reasonable ethical constraints such as informed consent) vaccines would be developed faster, and therefore a reason they are not developed faster is that CHIM only rarely is allowed to be used? Correct me if I'm wrong: clinical trials are a time-consuming part of development.

@MatthewChristopherBartsh I am sorry I made you feel fobbed off. I think you would be better served asking about these points in a separate question. I did not address CHIM because I am not familiar with the acronym and did not find anything that seemed relevant when I looked it up. I've since skimmed some reviews and it seems to be used on well-characterized diseases that have resisted past vaccination campaigns. I don't think it could speed up vaccine development for a new disease.

There's no need to apologize. If it was sincere (I really can't tell), accepted. Maybe I misjudged you. I wasn't saying you were fobbing me off, just that that's how it looked to me. My complaint was equally towards you and everyone who voted your answer up to the top. It calls to mind (for me) that Biblical scene where God says to Job, “Have you visited the storehouses of the snow or seen the storehouses of hail?"
Could you give me some links to what you found when you looked it up (that did not seem relevant) and also to some of those reviews you refer to? ("some" means at least one :))

@MatthewChristopherBartsh here is the chim report I looked at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627502/

"Potential benefits
Accelerating or streamlining vaccines/treatment relevant to
the national health burden." That's a quote from the well-written paper that you linked to.  "They provide an efficient framework for selecting vaccine and drug candidates for further development and can be carried out on a much smaller number of volunteers, and much more rapidly than Phase IIb-III studies. Protection against specific microbial strains can be evaluated in a controlled setting, and biomarkers to resistance and protection against infection can be efficiently assessed." How is that not relevant?

While the existing answers are great and cover a lot of the difficulties in vaccine development, I feel that they fail to address (or at least sufficiently emphasize) the fundamental misconception at the core of the question:

If that's the case, why does it take so much time and effort to develop a vaccine, for example, against covid-19?

The answer to that question is simple: developing a vaccine does not take much time.  What takes a lot of time is testing the vaccine and making sure that it does not have any unforeseen side effects.
For example, let's take a look at the Pfizer/BioNTech COVID-19 vaccine, since it's been in the news lately.  To save time and research effort, I googled for "pfizer covid vaccine timeline" and found this article from Financial Review, whose timeline I will further summarise below:

March 17, 2020: Plans to develop the vaccine are announced.
April 29, 2020 (six weeks later): First tests on human volunteers begin.  At this point the vaccine development is essentially done, and the vaccine has presumably also already passed initial tests using in vitro cell cultures and animal test subjects to ensure that it at least seems to be doing something and doesn't have any obviously bad side effects.  (The first human trials are done with four different variants of the vaccine, because the developers obviously want to minimize the risk of having to start over from scratch in case one specific variant turns out to be ineffective or dangerous.)
July 1, 2020 (two months later): Preliminary results from the first human tests are announced.  One particularly promising candidate vaccine out of the four initial variants is chosen for further testing.
December 2, 2020 (five months later): The UK is the first country to approve the vaccine for use through a "rolling review" system, which allows a novel vaccine to be temporarily approved for emergency use in an epidemic even while it still undergoes further testing.  Requests for similar emergency use authorizations are currently under review in other countries, including the US and Canada.

So, basically, even under this extremely accelerated emergency testing and approval regime (which squeezed into months what would normally take years), the actual development of the vaccine took less than 20% of the total time from initial planning to approval.  All the rest is just testing, testing and more testing.
Now, the other answers have already covered pretty well the reasons why all this testing is needed, but let me anyway give a quick summary for completeness:

Vaccines intended for humans need to be tested in humans, because that's the only way to be sure that they work and are safe to use for humans.  Cell cultures and animal models can never give a fully accurate picture of how the vaccine will interact with the complete immune system in a real human body.

Because all human bodies are different, any new vaccine (or other medical treatment) needs to be tested with as many different people as possible, with as many different ages, ethnic backgrounds, pre-existing conditions, etc. as possible, to make sure that there are no harmful side effects that only show up in a small subset of the population.

Also, when testing a vaccine, one of the most important things that need to be confirmed is that it actually prevents the disease.  But since it would be grossly unethical to deliberately expose test subjects to a dangerous infection, the only way to test that is to vaccinate a lot of volunteer test subjects and wait for some of them to get naturally exposed to the disease (and then compare the vaccinated test subjects with an unvaccinated control group).  This waiting takes time, and since (for most diseases) most of the test subjects will never get exposed and infected anyway, it means that a lot more subjects are needed.

Because human testing in inherently risky (but necessary), nobody wants to take the unnecessary risk of administering a completely untested vaccine to a large number of people.  But a large number of people still need to be tested to confirm that the vaccine is safe for everyone.  Because of this, testing is invariably carried out in multiple phases: first with just a small number of volunteers, then (if no severe issues show up in the initial tests) with a slightly larger group, and then with an even larger group, and so on.  But since each new phase can only be started after sufficient data has been collected from the previous phase, this multiplies the already long duration of the testing by several times.

FWIW, most of the same issues apply to all new medical treatments, not just to vaccines.  New drug development and testing is also notoriously slow and expensive for pretty much the same reasons — and even then there are plenty of cases where major side effects were only discovered when the drug was already on the market.
One issue that does specifically affect vaccines is that they're preventative treatments that must be administered to a large fraction of the healthy population, not just to already infected people.  (Even only vaccinating specific groups at high risk isn't generally sufficient to provide herd immunity.)  This means that their safety needs to be tested to a significantly higher standard (since many more people will be receiving the vaccine) and that, as noted above, determining their efficacy requires a must larger pool of test subjects (since not all subjects will be exposed to the disease).
Anyway, the upshot of all this is that if it weren't for all this testing and re-testing, we could've had a COVID-19 vaccine in April, or maybe earlier.  (Moderna started their vaccine development already in January, and their first human trials in March.)  But even in the face of a global pandemic, the testing is still necessary to make sure that the vaccines that eventually do get approved and widely used will in fact do what they're supposed to do, and that any side effects they may have don't turn out to be worse than the infections they prevent.

BTW, this need for extensive human testing to confirm the safety and effectiveness of a vaccine even after it has been developed is not just the reason why even one company will often develop multiple initial vaccine candidates in parallel, but also one of the main reasons (besides simply capitalism) why there are so many different competing vaccines being developed by different companies.  Basically, even the companies that were late to start their vaccine development and testing could, for a long time, still hope to be the first ones to market if testing happened to turn up serious issues with their competitors' vaccines.
Of course, other reasons exist too: the second, third, fourth etc. companies to get their vaccine approved can also expect to win a decent share of the market, especially if their vaccine happens to be cheaper, more effective and/or easier to store and transport than the alternatives.  Also, many countries may prefer to use a locally developed and produced vaccine if one is available in order to limit their dependence on foreign suppliers.

That's a really great summary, and good points! Indeed, I can imagine that if it wasn't a vaccine, but a treatment to administer to the already ill, then in case of a very deadly illness people would be more eager to undergo the treatment no matter how risky it is, if the alternative would be a high chance of dying of the disease they already have.

Some trials do involve deliberate exposure, if the outcome of treatment after early detection is good. My mom did a trial for a malaria vaccine where they literally had malaria-carrying mosquitoes bite her (the mosquitoes were in a cup covered with cloth, the cloth side was held against the skin until a certain number of bites were observed). The participants had 2x daily observation and blood draw for (I think) a week or so and obviously the treatment was immediately to hand in case anyone actually developed malaria.

I'm against calling it "Pfizer's vaccine" when the people who actually developed it work at BioNtech.

@smcs Fair enough, changed.

While the list of withdrawn drugs is great, I believe we should distinguish between cases when a drug was the safest available at the time of introduction, and was withdrawn later as a safer alternative appeared, and cases when a drug genuinely turned out to be worse than its indication.

There's also the fact that the only way to be absolutely sure what the long term effects are is to wait long term. Right now, we can be pretty sure that there aren't problems that show up on a six month delay. And that is strong evidence that none show up on a one year delay, but we can't be absolutely sure. And we can be pretty sure that the vaccine gives immunity for several months, but we can't be completely sure that it gives immunity for a year.

While it is true that deactivated (e.g. heat killed viruses) are used in some cases, the Pfizer, Moderna vaccines are in fact mRNA vaccines. The figure below from the Oxford website details the processes involved in vaccine their DNA based vaccine development. This Moderna page has a video detailing their approach as well. Pfizer also has a nice video explaining the process of mRNA vaccine development.
As you can see, it is not an easy process. A prerequisite of both their solutions is the knowledge of the SARS-CoV-2 genome sequence (in this case the genome is a single stranded RNA). This requires some time to get done and once the data is available, one has to wait for others to verify it to some extent. Interestingly, the Moderna video says that they had a human ready vaccine in 42 days.
The differences in efficiency can stem from multiple factors:

What vector is used to deliver the vaccine
How the mRNA is tweaked to produce Spike glycoprotein
Physiology of the individuals receiving the vaccine

and many other factors which are beyond the scope of a single answer and can be proprietary knowledge of the manufacturers.
Another significant addition to the 'time' factor is the clinical trials. Pfizer and Moderna require two doses spaced over 3-4 weeks for their phase-I trials. Since these vaccines are being rapidly developed, and you are amidst a global pandemic, you get only 1 chance at a clinical trial (and subsequent profits) and you have to make it count. Various national regulatory authorities also need to keep the health of their citizens in mind. Thus there is immense pressure to get these trials done right and the global consensus in this case seems to be taking a slightly long duration of clinical testing.
Regarding the last question, no, none of the Oxford, Pfizer or Moderna vaccines care about damage done to the original pathogen because there is no pathogen being delivered.

@Chris I cite from Mulligan et al., "who were randomized to receive 2 doses—separated by 21 days—of 10 μg, 30 μg or 100 μg of BNT162b1." I wanted to convey this as two doses in my answer.

"the promising Covid-19 vaccines are in fact mRNA vaccines. The figure below from the Oxford website details the processes involved in vaccine development" Isn't the Oxford/AstraZeneca vaccine in particular not an mRNA vaccine but inactivated virus?

@AndreKR what I understood from the Oxford website is the delivery vector is a weakened adenovirus i.e. has the disease causing genes removed from its genome. These viral particles are then packed with spike glycoprotein sequence in the hopes that human cells will express these on cell surface leading to immune response. On the other hand Pfizer and Moderna use lipid nanoparticles for their delivery.

Not sure this answers the actual question that was asked. The premise of the question is essentially: "Injecting a deactivated virus ought to be quick and easy. Why then hasn't a COVID-19 vaccine been developed quickly and easily?". You've stated that most vaccines in development have been mRNA vaccines. But that doesn't address why there hasn't been a quick and easy vaccine based on the first approach. I believe this is what the OP wants to know.

@JBentley I had not thought of the question that way. In principle mRNA vaccine development is faster than validating the protocol for deactivating a virus (i.e. delete replication related proteins from the genome) in a reproducible manner. Then is the issue of mass producing these viral particles and remember their replication related genes have been removed, so you need to to some clever transgenics. On the other hand, as soon as you know the genome sequence for a viral surface protein, mRNA vaccines can be developed and their delivery is less complicated.

Should also be noted that the mRNA route is considerably faster (if it works) than the deactivated virus one.  I imagine there are (or were) groups following that method as well.

For an mRNA vaccine, it's necessary to know which viral protein will confer immunity, which isn't trivial. For SARS-2 this was accelerated by 20 years of SARS-1 research but in the general case would probably take more time than validating inactivation protocols.

@user253751 I will change my answer to reflect Pfizer and Moderna are using mRNA vaccines and not Oxford as i understand. User timeskull is more knowledgeable on the subject and they will likely have the right answer.

"the global consensus in this case seems to be taking a slightly long duration of clinical testing." NO, you simply don't understand! The amount of time that's been taken for efficacy trials is INCREDIBLY short - it usually takes YEARS to develop a new vaccine!

@MattDMo The AstraZeneca (“Oxford”) vaccine AZD1222 is definitely not an mRNA vaccine (see e.g. https://www.nature.com/articles/d41586-020-03441-8).

@MattDMo The oxford vaccine is not an mRNA vaccine. I did not get any notification that you had forced edits on my answer. I thought that the owner of a post needs to accept edits. PLEASE do not force edit answers.

@RoniSaiba The entire Stack Exchange system is based around collaborative community edits. Please see this help center article to learn more about it. I apologize that edited in some incorrect information to your answer, but I did fix several other issues as well. I've been an active member of this community for 8 1/2 years, since it was in beta, and have done a lot of work to accrue enough reputation to have the privileges that I do, including not needing to have edits approved. I'll continue making edits when I feel they need to be made.

@AndreKR In this context, "inactivated virus" means the virus being vaccinated against (the covid virus) is inactivated. The Astra-Zeneca vaccine is a hollowed out (so to speak - its genes are "dead") adenovirus (in a sense, "inactivated", but that doesn't count here), stuffed with a bit of artificial DNA that codes for the covid "spike" (a misnomer, since it's now known to be a soft, flexible, club shaped projection) protein (or part of it). It is also not an an mRNA vaccine, because it uses artificial DNA to achieve the same result: making the cell machinery produce "spike proteins".


text:
Where do plants obtain the metal ions needed for biological processes?
Enzymes employ metal ions (e.g. Mg, Cr, Mn, Fe, Co, Ni, Cu, Zn) for catalysing certain reactions.
Let's consider planting a seed. Where will it obtain these metal ions from? Just from water?

Yes. From the soil.

@WYSIWYG then how hydroponics work? (Growth solution seems to only have N, P, K)

Even analytical ultra pure NaCl has so much Ca2+ in it that it would disrupt intracellular processes. Even if it says only N, P and K, there are still sufficient trace metal impurities.

@Ashafix ...which come from the water content..?

Water and nutrients like fertilizer.

Many ions are absorbed by the plants via the action of bacterias. Fe or B for example require chelating action from microbes. P and S need to be oxidised to enter the plant as well.
Source: Le sol, la Terre et les Champs - http://www.sangdelaterre.fr/index_135_151.html


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Why is AUG the initiation codon?
Is there any reason why AUG is the initiation codon?
Can’t translation start with different codons?

I have removed the following line from the original "Why is there a need for an initiation codon ?" and posted as a separate question. This has not been answered here, so there seems no harm done to any answers, and by doing this one is giving a chance for that part to be considered on its own merits. It is also in keepting with SE policy on not posting multiple questions in one, although I understand the original poster feeling that they are part and parcel of the same thing.

I have now posted the separate question here: https://biology.stackexchange.com/questions/82444/why-did-translation-develop-a-specific-codon-for-initiation.

A good question (if a little mixed up on transcription vs. translation!)
AUG is not always the start codon, but whatever the codon is it will always code for Methionine (or fMet, but still a variation on Met), even if the codon codes for a different amino acid otherwise. A  separate transfer RNA (tRNAi, the initiator tRNA) is used for the arrangement of this first step, guided by eIF2 [in eukarya].
In this respect it's less a question of "why AUG" than "why this specific initiator tRNA", the answer being that it's got certain sequence elements and modifications that distinguish it from the elongating tRNAs which bind elongation factors and hence are targeted to the ribosomal A and B sites instead of the ribosomal P site (with function being dependent on form, basically it's shaped to set up transcription rather than to elongate an existing nascent chain polypeptide).

"Identity elements appear to finely tune the structure of the initiator tRNA, and growing evidence suggests that the body of the tRNA is involved in transmitting the signal that the start codon has been found to the rest of the pre-initiation complex." — Kolitz and Lorsch, 2010

The other start codons are just from natural chemical variation (or evolution, whichever way you want to look at it) giving rise to different codon-recognising protein shapes.
The machinery for starting translation works, and as such is "conserved" - evolution has kept it, and that's why it is always the same codon (more or less). Archaea have a very similar shaped tRNAi acceptor stem, and is an equally good ligand, which shows how ancient the system is and gives an idea of how fundamentally difficult it must be for an organism to change a system like this through mutation (3.5 billion years of evolution can't be wrong! etc. haha).
Not to just gloss over the part where I said that non-AUG codons get used too (in yeast and mammalian cells), the following is from a study in which it was found changing 1 (and only 1) of the AUG bases still permitted translation initiation:

"Naturally occurring misrecognition indicates that discriminating two base-paired near-cognate codons from the perfect three-base-paired AUG
  codon is subject to mistakes. Mutations in translation
  initiation factors, such as eIF1 and eIF2b, further increase the levels of these mistakes.
Two base-pairing interactions between non-AUG codons and the anticodon of
  the Met-tRNAi are sufﬁcient to trigger translation initiation, suggesting that wild-type eIF1 plays a role in
  monitoring proper base-pairing interactions when scanning for the AUG start site. It would be predicted that
  the Met-tRNAi, not a cognate tRNA matching an individual non-AUG codon, is used in translation initiation at these non-AUG start codons.
The translation initiation complex will bind only the Met-tRNAi as
  opposed to other tRNAs because Met-tRNAi has unique
  sequence and structural features that allow it to be
  loaded onto eIF2 of the ternary complex and enable it
  to ﬁt into the P site of the ribosome" — Maduzia et al, 2010

Basically the consensus is that it's not really possible to say why the methionine codon, "it's just a structural thing", which is a bit of a circular argument really.

perhaps usage of methionine might have a metabolic reason. Methionine is an essential amino acid and is important for methyltransferases (SAM). So it might be vaguely possible that using Met for initiation is a metabolic checkpoint.

@WYSIWYG: it looks like it all has to do with translation initiation efficiency.

From recent empirical research (Wang et al., 2018) on eukaryotes, basically the non-AUG start codons have context-dependent [translation initiation] efficiency, while AUG is a "sure thing", i.e. the nucleotides surrounding it have little impact on its efficiency.

There are some theoretical biochem explanations for this, which I'll just quote as-is:

We demonstrated that non-AUG codons are more dependent on their surrounding nucleotide sequence context than AUG codons. Base pairing between an AUG start codon and anticodon of the initiator tRNA along with interactions between the scanning ribosome and the nucleotides surrounding the start codon (e.g., the interaction between Arg55 of eukaryotic initiation factor 2a and the -3 position [...]) cause the preinitiation complex to shift from an open conformation to a closed conformation so that translation initiation can occur. Most preinitiation complexes undergo translation initiation when they encounter an AUG start codon whether it is an efficient or inefficient context because the strong interaction between the codon and anticodon provide enough energy to drive the conformational shift. However, mismatches between a non-AUG start codon and the anticodon reduce the binding energy from the codon and anticodon. Therefore, the contributions from interactions between the preinitiation complex and the ‘context nucleotides’ likely become more significant and necessary. We also showed that sequence context, specifically the +4 position, affects the efficiency of each non-AUG start codon differently. The observed differential effect of the +4 position demonstrates that sequence properties can have codon-specific effects on TIS efficiency. It is possible that there are other properties with codon-specific effects. Furthermore, differences in these properties between reporters may explain why some previous studies have identified GUG or ACG as the most efficient non-AUG start codon [...] while others are in agreement with our findings [...].

Also pointed out in the paper, in some corner cases (specific sequences) a sequence containing a non-AUG codon can be "as efficient as" another sequence that contains an AUG. (From the box plot it looks to me like some non-AUG sequences have better efficiency than some AUG sequences, but the paper phrases it as "as good as".)

Anyway, this inversion of efficiency only happen in on some specific sequences. On average over all sequences, AUG has the best efficiency.

If we go [farther back in evolutionary time] to prokaryotes, a similar study of all potential starting codons has been done on E.coli in 2017. The picture is a little bit different in the sense that while AUG is still ahead in terms of efficiency, but together with GUG and UUG does form a cluster of its own, well ahead of the rest.

The standard explanation for this that I found in a review is that AUG, GUG and UUG are all decoded by fMet-tRNAfMet. (Also given in an answer here, based on an older review.) Actually the older review does offer tiny bit more insight:

AUG is the most common initiator codon because it forms the most stable interaction with the CAU anticodon in fMet-tRNA

Of course, one could equivalently ask how comes this enzyme co-evolved with the start codons (that it decodes). But I haven't found an answer to that. I'm probably going to ask that as a separate question.

You fail to mention that this analysis only applies to eukaryotes, where the selection of the initiation codon is very different from that in prokaryotes, which utilize Shine and Dalgarno sequences that interact with rRNA. It is therefore difficult to see how this can be a basic answer to the question.

@David: it did occur to me that before AUG was strongly selected in eukaryotes it was probably somewhat more weakly selected in prokaryotes. But I couldn't find a study along the lines of this one for prokaryotes. Perhaps there are well-known theoretical considerations that answer that part... which I'm sure you'd like to share as an answer.

@David: silly me, there actually is a (2017) paper like that https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397182/

@David: aren't both papers the accepted answer quotes about eukaryotes?

I have now provided the sort of answer that I think addresses the question, although the ideas in it are not mine — I'm recounting someone else's idea. I think your remark about AUG and the met-tRNA anticodon begs the question. We know that as AUG in the genetic code is methionine. But why was methionine chosen in evolution as the initiating amino acid? I don't think the paper you discusses address this. They are concerned with contemporary evolved initiating tRNA and its interaction with mRNA.

First of all, it is the coding sequence, the open reading frame (ORF), and not the gene that starts with an AUG. Also, there are actually quite a few ORFs that start with different initiation codons, they are just the exceptions rather than the norm.
As for the need, you can think of START and STOP codons as punctuation. The AUG is read like the first (capital) letter of a sentence (if you will allow me to stretch the definition of punctuation a little). Read up on the process of translation, the ribosome  will attach to the mRNA molecule which includes UTRs, it uses the AUG codon as an indication that it should now start translating.
UTRs are the untranslated regions and often contain regulatory sequences that can control translation. However, these should not be in the final protein product so the cellular machinery needs a way of knowing where the UTR ends and the coding sequence begins.

I could not understand the first line.Please help.

@biogirl I think lmmx explained it perfectly but a gene consists of much more than the protein coding transcript. Genes typically include promoters, enhancers, various splicing signals, introns etc. AUG (usually) marks the start of translation, the sequence that codes for proteins it does not mark the start of the gene.

The transcript certainly does not start with AUG. It is the *reading-frame" or the protein-coding region of the mRNA that starts with AUG.

@David oh good grief! I can't believe I wrote that. And I edited this answer yesterday and still managed not to notice! This is my field, for crying out loud! Thanks for the heads up; fixed now.

Forgiven. I’m writing a paper on protein structure at the moment and just before sending it to a colleague discovered a couple of places where I had written “base pair” instead of “hydrogen bond”.

Interpretation of the Question
There are two questions here. The one about alternative start codons is factual and has been well answered by Louis Maddox. The other is an evolutionary question which I would recast as

“Why was methionine selected as the initiating amino acid?”

Like Louis Maddox I would have said that this was almost impossible to answer. However, it turns out that there is at least one hypothesis — perhaps related to the comments on Maddox’s answer — so I feel it useful to present and discuss it.
The Regulatory Hypothesis for methionine as initiator
This hypothesis was presented by Bhattacharyyaa and Varshney in a paper in RNA Biology (2016).  (A personal or institutional subscription may be required for access to the full version.) Their argument can be summarized as:

Methionine does not perform a role in proteins that other aliphatic
amino acid side-chains could not, and is one of the rarest of amino
acids in proteins.
The synthesis of methionine has the highest metabolic cost among
amino acids
The synthesis of methionine (and N-formyl methionine) depends on
one-carbon metabolism.
Hence its adoption as an initiator of translation could have been
to ensure that protein synthesis only occurred when there was
sufficient energy in the cell for one-carbon metabolism, and, by
implication, for protein synthesis itself.
In addition, the requirement for S-adenosyl methionine for the
methylation of rRNA and certain tRNAs would represent a specific
coupling to other components of protein synthesis.

[Methionine synthesis — from Berg et al., Section 24.2.7]
Comments
A difficulty I personally have with this hypothesis is that I would expect a mechanism to evolve first, with regulation only appearing later. One possible way round this would be if methionine had displaced a similarly hydrophobic amino acid such as norleucine from the early genetic code, as suggested by Alvarez-Carreño
et al..  Before this, one would assume that initiation did not take place at a specific codon, as discussed in relation to another SE Biology question.

[Formylation of Methionine — from Berg et al., Figure 29.21]


text:
What does chrUn mean in the output from a Bowtie run on human sequences?
After having performed an alignment using bowtie2 and GRCh38 as a reference sequence, I got inusual matches on chrUn.
Here a small part of the SAM file:
@SQ     SN:chr22   LN:50818468
@SQ     SN:chrX    LN:156040895
@SQ     SN:chrY    LN:57227415
@SQ     SN:chrM    LN:16569
@SQ     SN:chrUn_KI270424v1     LN:2140

All the other chr values are clear to me (M indicates the Mitochondrial DNA, while 22, Y and X are just the usual chromosomes number/name) but I couldn't figure out what chrUn stands for and what about that code after the _?

Usually "Unknown". Sequences that have not been assigned to one of the chromosomes. I think this is from the Human genome, which has multiple sequences not assigned to a chromosome, so they have identifiers (the KI...)

@skymningen Thank you. If you add a reference and post it as an answer I will accept it.

There is no reference for this, other than experience, sorry.

It is for unassigned sequences. See this reference from the UCSC Genome Browser FAQ: https://genome.ucsc.edu/FAQ/FAQdownloads.html#download11

I presume chrUn_KI270424v1 refers to a scaffold or sequence that has not yet been assigned to a chromosome. The designation after the Un (unknown or unassigned?) may refer to a particular single sequence or a scaffold. You will be able to determin this by examining the reference sequence and its documentation.
(My assumption is based on the sort of thing one finds in the various versions of Drosophila reference genomes, with which I am familiar. So I can’t help you with the specifics of the human genome.)


text:
HSL Lightness vs Eye sensitivity
In a monochromatic spectrum, is the human eye equally able to distinguish between lighter colors just as it is in distinguishing between darker colors? I mean is there really a linear relationship between the Lightness property in the HSL color model and the perceived brightness?

Related question

I'm not sure this is really the best possible SE site for this question; my answer below, at least, has very little biology in it. There's no "Colorimetry Stack Exchange", but I'd think this would be on topic e.g. at [graphicdesign.SE]. Alas, they don't have MathJax... maybe [physics.SE] would be a better fit? Or [cogsci.SE]?

No, the L axis in the HSL color space does not really correspond to lightness as perceived by the human eye, except in the very crudest sense that, for given values of the H and S components, increasing L produces an increase in the perceived lightness.
The L component of the standard HSL color space is simply calculated as the average of the lowest and the highest RGB component of the color (in whichever RGB color space in being used): $$L = \frac{\min(R, G, B) + \max(R,G,B)}2$$
This definition alone should make it obvious that the L value cannot correspond to perceived lightness, since it completely ignores the middle one of the three RGB channels.  Thus, the color (R=0, G=0, B=1), i.e. pure $\color{#0000ff}{\rm blue}$, has exactly the same L value (0.5) as the color (R=0, G=1, B=1), i.e. $\color{#00ffff}{\rm cyan}$, yet it's obvious at a glance that the latter color is visually much brighter.
Indeed, the HSL color space doesn't even try to match the perceptual lightness of the colors; rather, the definition of the L channel is chosen because it has the convenient feature that it maps black to L=0, white to L=1, and all the six maximally saturated pure RGB colors (red, yellow, green, cyan, blue and magenta), despite their wide perceptual lightness differences, to L=0.5.

A much better approximation to the perceived lightness of a color is the luma Y', which is defined as a weighted average of the RGB channels.  The precise weights depend on the definition and the RGB color space used, but a common choice (from ITU-R Rec. 709) is: $$Y' = 0.2126\, R + 0.7152\, G + 0.0722\, B$$
The weighs are chosen to account for the different perceived lightness of the different RGB primary colors.  A striking feature is the that the green component alone accounts for over 70% of the luma, nearly ten times as much as the blue component.  Yet a visual comparison of $\color{#0000ff}{\rm 100\%\ blue}$ with $\color{#00ff00}{\rm 100\%\ green}$ does clearly confirm that this choice of weights is justified: the pure green appears much brighter than the blue, and almost as bright as the cyan (which is their sum) above.

However, the definition of the luma still ignores the non-linearity of both the standard RGB color spaces (such as sRGB) and the human eye.  While these two effects partly cancel out each other, allowing luma to be used as a reasonable approximation of perceptual lightness, for truly accurate results they need to be accounted for.  This involves several steps:

Convert the RGB color into a linear color space.  For sRGB, the following formula may be used: $R_L = f(R), G_L = f(G), B_L = f(B)$, where: $$f(C) = \begin{cases}C / 12.92 & \text{if } 0 \le C \le 0.04045 \\ ((C + 0.055) / 1.055)^{2.4} & \text{if }  0.04045 < C \le 1 \end{cases}$$ (Here, $R$, $G$ and $B$ are the sRGB component values, and $R_L$, $G_L$ and $B_L$ the linear ones, both scaled to the range from 0.0 to 1.0.)  Alternatively, a very close approximation to the formula above is given by simple gamma-expansion with $\gamma = 2.2$: $f(C) = C^{2.2}$.
Calculate the relative luminance as a weighted average of the linear RGB component values: $$Y = 0.2126\, R_L + 0.7152\, G_L + 0.0722\, B_L$$ (The weights are exactly the same as for the luma formula above, because that's where they come from; the luma calculation just blindly applies them to the gamma-compressed RGB values.)
Convert the relative luminance value into an approximation of the percieved lightness, using something like the CIELAB formula: $\ell^* = 1.16\, g(Y) - 0.16$, where: $$g(Y) = \begin{cases} \tfrac13 \left(\tfrac{29}{6}\right)^2 Y + \tfrac{4}{29} & \text{if } 0 \le Y \le \left(\tfrac{6}{29}\right)^3\\ Y^{1/3} & \text{otherwise} \end{cases}$$ (Note: In the CIELAB standard, the $L^*$ value ranges from 0 to 100, but for the sake of consistency, in the formula above I chose to define $\ell^* = L^* / 100$, so that its range is also from 0 to 1.)


text:
Does one neurotransmitter travel all the way through the nervous system?
Nerve impulses of course go really fast, but the neurotransmitters have to travel through millions of nerves, so how can it go that fast?
Is it a sort of relay with lots of neurotransmitters taking over at each nerve cell, or do the neurotransmitters go all the way from A to B?

What sparked your question? Were you reading something? Watching a movie? If so, what? A little background might help me answer it in a way that fills the gap you want to fill. The reason I ask is that your question seems to hint at a subtle misunderstanding about what a neurotransmitter is. Have you read this?

It's beginners level Psychology. I guess they're more like chemicals that aid passing of electrical signals?

You've got a few things mixed up here:
A signal may travel down a pathway, passing through several neurons (e.g. around 4-8). However, this signal is not always in the same form: From one end of a neuron to the other, it is merely an electric potential which travels down the neuron's cell membrane (from the dendrite to the axon hillock, where the cell decides whether to carry the signal on; if yes, a new potential is sparked to travel down the axon).
When the potential reaches the end of a neuron, i.e. an axon terminal, it causes exocytosis of neurotransmitter. The signal has become chemical now. This diffuses through the synaptic cleft to the next neuron, where it acts on ion channels in the membrane to cause a new electric potential.
So the actual distance a neurotransmitter travels is only the distance between the two membranes at the synapse, i.e. the synaptic cleft. This is only about 20-40 nm wide, so it's fairly rapid :)

Huh, thanks! You mention it only being 4-8 neurons. I can't imagine there being so few between, say, the fingers and the spine? How long are these things?

@DarkLightA some are pretty long. In a human body, they can be more than a meter in length.

Wow! I read there are several billion of them? Is this because every nerve ending has its own connection to the spinal chord?

@DarkLightA Yes, that's probably around the number of neurons you have in total in your body. The actual pathway that a single signal will follow doesn't usually comprise that many cells though. Example: pain (e.g. papercut) -> cell 1: sensory neuron from periphery (e.g. finger) towards spinal chord -> cell 2: afferent neuron from spinal chord towards the thalamus in the brain -> cell 3: thalamic neuron into various brain regions (exact number of cells here varies as far as I know) -> result: you feel pain. Could be I forgot the odd neuron here or there in this pathway but that's the gist.

The bit inside the brain could be quite a lot I think, hundreds or thousands even. Plus, a single stimulus doesn't activate just a single sensory neuron, and there are also cross-interactions of adjacent pathways.


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Have novel interactions or pathways been predicted by GRN or PPI data and later confirmed by experiment?
I've been learning about the gene regulatory network (GRN) and protein-protein interaction network (PPI) recently.
I've found a huge amount of extremely interesting papers about how biological network data is accumulated and how it can be studied.
However, what I haven't found is any examples where the network data was used to make a novel prediction which was later experimentally shown to actually exist.  What are some of the cases where this has happened?

There is very interesting work in this regard done by Ed Marcotte. An overview of the "machine" and its conservation across species is here. The point here is the machine or network is conserved, but used in different ways in different organisms. Hence, the phenotypes of mutants might be different, but they'd be consistent across many variants in the components of the machine.
One paper of his describes a tool, which uses well developed guilt-by-association principles upon a human gene network to identify associations of gene sets. This is available at www.functionalnet.org/RIDDLE.
Look at their approach to prioritizing candidate disease genes by network-based boosting of genome-wide association data.
Some specific examples of the conserved "machine" are given in this elegant PNAS paper. It is nice how they tested the genes in Xenopus embryos.

Eric Davidson should be your first port of call for GRN related work!
He published a great paper not so long ago demonstrating exactly what you're talking about. By including spatio-temporal dynamics of gene expression (e.g. differential equations modelling the time scale of gene expression) they constructed a boolean logic based predictive model for gene expression in early sea urchin development. Their results were not only accurate, but actually made predictions about genes that they hadn't experimentally tested...
Check it out:
http://www.caltech.edu/content/modeling-genes-development
and paper:
http://www.pnas.org/content/early/2012/08/22/1207852109.abstract


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Cereal Alpha and Beta Amylase temperature range and reaction rate
This question is motivated by a practical application in bread making.
While it is well known which are the optimal (highest reaction rate) temperatures for both alpha and beta amylase, I am not able to find any precise information concerning reaction rate as a function of temperature.

How does alpha and beta amylase activity change when temperature decreases?
At which temperatures does their activity stop?


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Long term liquid food diet by blending/grinding all quality foods one would normaly eat, not any weight loss or prepared drinks
I want to know what are the effects of not using your teeth to grind foods but preparing it before eating with blending and grinding them into a liquid.
Here I am not talking about any weight loss or fitness industry prepared drinks. I mean the ordinary raw and cooked foods like meat, vegetables, cereals, and fruits that one would normally eat in classic meals.
Would this decrease of work done by teeth and digestion system have positive or negative health effects?

I would definitely have a negative effect on mood. Why would you deprive yourself from the pleasure of eating a proper meal?

Don't get me wrong I love eating proper meals, however I don't see pleasure in eating to be my essential need. I could only regard it as an addiction if I needed it to improve my mood. I am only concerned about health effects when helping my body to process food.

It would probably only be a positive thing -- ultimately, you're increasing surface area of the food particles, which is what our digestive systems try to do anyway in order to absorb the most nutrients.

@Alexandria: any proof of that? Eating is not merely digesting food for sustainement, it is a much more complex event. What would happen to the secretion of food-related hormones for instance? Would satiety be obtained at the same point? Would you tend to eat less because of the lack of "aesthetic" appeal of liquid food? What would be the effect on the dopaminergic reward systems in the brain? What would be the effect on intestinal microbiota?

there is a pop nutritional concept of micronutrients, that yes the nutrients would be absorbed into your system more efficiently.  Its a reasonable argument to me.  Still if you are grinding up cheetos and lucky charms you're going to get faster sugar absorption into your system and it should increase the chance of diabetes.  if its broccoli kale and carrots it might help.  if its fewer calories with no meat, even better I think.

This New Yorker piece on "Soylent" is not peer-reviewed research, but goes into a lot of good, well written detail on the topic, including quotes from nutrition scientists, and anecdotes from users. It might make a good starting point. +1 for a good exploration of the cultural, as well as nutritional issues. http://www.newyorker.com/magazine/2014/05/12/the-end-of-food?currentPage=all

I was in a car accident age 19. Jaw was wired shut, food access was limited to one broken front tooth. It was liquid diet or nothing.
 So, I drank a lot of foods in liquid form, ( soups, etc. ) and a lot of Gerber's baby foods, and just about anything that could be pulverized in a blender.
 I gained weight like crazy. About 15 pounds in 2 months.
 The body takes advantage of having the harder work of digestion done for it. One of the advantages of cooking food is it's easier to digest. It is believed by some that such benefits to our life are the reason humans became the dominant force on this planet.

Well, the only logical explanation for your weight gain is too many calories. The weight gain is not relevant to me because I would control the amount of calories as I do with normal food.


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Indestructible Super Shrimp
How are shrimp and other animals able to not be crushed by the 1000x greater pressure at the bottom on the Mariana trench?
Wiki says the trench is home to "large living creatures such as a sole or flounder about 30 cm (1 ft) long, and shrimp"
I understand natural selection, but what features has evolution "selected" that enable soft flesh and bones to not be instantly crushed like our own skulls would be at that depth?

Should I ever have a band, I'll name it "Indestructible Super Shrimp".

Aquatic animals brethe the water around them and this equalizes their body pressure with that of the surrounding environment.
This is how you can still find say a piece of pottery or a watch from a shipwreck... They are filled with water and don't experience the pressure.
Such pressures do affect humans because we breathe air and so we can't adapt to pressures underwater and we need a shell that allows the ship environment to be tolerable for humans beyond a couple of hundred feet or so.
I think the change of pressure would also affect fish or other animals If they dropped in depth too quickly.


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Is there any source for raw data of SNP genotype frequency?
On sites like SNPedia, some pages contain the frequency of the SNP in question in different populations, based on published research. I'm trying to write a script that takes 23andme data and compares it with SNP frequency to find rare SNPs that the user possesses. I'm thinking that the only way to do this might be to scrape it from a SNP database. Is there anywhere you know of that makes this information available in a more accessible format, ideally preformatted for parsing?

I found what would be a good source, but the links are dead: http://snp.cshl.org/downloads/index.html.en

Here's another, but it's about as clear as mud: http://useast.ensembl.org/info/docs/api/variation/variation_tutorial.html#alleles

There was also the Frequency Finder, but the NIH mirror and so is the UChicago mirror (which Google suggests was hacked): http://bioinformatics.oxfordjournals.org/content/20/3/439.full.pdf

I encountered the same problem about a year ago.  After digging through several databases, the only answer I could come up with was the 1000 genomes project. That's when I let the dream die, but would certainly be interested if you decided to tackle it.

You might be able to get some raw data on SNP frequency by batch querying the dbSNP database.  I have not used it myself, though.

This is one of the reasons the 1000 genomes project was created.

Have you looked at ALFRED (The ALlele FREquency Database)?  The data is from 2011, but seems extensive and has downloadable zip files at http://alfred.med.yale.edu/alfred/alfredDataDownload.asp


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Does eating hard food really cause wisdom teeth to erupt properly?
According to the article Bad molars? The origins of wisdom teeth, in our evolutionary history, people were eating harder food like nuts and had unimpacted wisdom teeth. Later, that article appears to have jumped to the conclusion that if you eat hard food, that can actually cause your wisdom teeth to erupt properly. I don't see any reason for that conclusion. Maybe they made that mistake because it's a reasonable mistake to make but it's actually not true. I think that in our evolutionary history, people reproduced at the age of about 14. Although at the age of 28, I started getting an infection from an impacted wisdom tooth and had to have it removed, that was probably already nearly grandparent age according to our evolutionary history and that explains why the natural selection against that type of problem at that age was weak. Maybe after we started eating soft food, we had an evolutionary advantage in having a smaller jaw but the evoluionary cost in having a smaller jaw was smaller because we could just evolve to slow down the growth of the wisdom teeth to delay the potential problems it causes to grandparent age. Just because a change in diet affected the way we evolved doesn't mean a person's actions affects the way their own body grows at the individual level. I do realize that it some cases, ones own actions affects the way their body grows.
You may be thinking "Why didn't you ask the question 'Why did we evolve to have impacted wisdom teeth when it sometimes causes a severe infection?' before asking this one? You could have used its answer to help you ask this one better." I could do that but then I would just end up explaining that I Google searched "why did we evolve to have crowded wisdom teeth if it can lead to infection" and then got the article Bad molars? The origins of wisdom teeth as the first search result. That's the very article I linked earlier in this question that I explained why I suspect is inaccurate. I don't think it would have been better to ask that question first and then explain how the first search result didn't answer my question when that search result is in fact inaccurate. If the question I have can be answered, some way of asking a sequence of questions and picking which Stack Exchange website to ask each of them on that will get me an answer to the question I have has to be accepted.

Now I see that they just said chewing hard food can't hurt and science does not yet know if it will actually work. I guess it's fine that I asked this question because I didn't realize at the time I asked it that the article said that and then looked back and saw that it said that but if I had read it carefully in the first place, there would have been no need to ask this question at all. I guess now that I've asked it, it's better to leave it the way it is instead of correcting it to explain what the article really says because if I fix it up in that way, people will just think I'm a jokester

who asks totally useless questions.

This is a good question, questioning your assumptions is a major part of establishing the validity of a hypothesis.

Yes
The relative size and robustness of the jaw does appear to be strongly affected by diet, significantly more so than other parts of the skull. This is not that surprising many developmental pathways interact with physical activity. Bones in particular often rely on a certain amount of stress to develop properly. It is not all that different from low scale bone atrophy.
Size of the jaw of course effects how much space there is for wisdom teeth. As for the evolutionary effect, consider we have only had access to soft processed food on any scale in the last few generation, that is not much time evolutionarily.
Source


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Genetic linkage greater than 50 centimorgans
Classically, the linkage between two loci can be measured in centimorgans (cM), which represents the percent chance that these two loci will recombine an odd number of times (generating a recombinant genotype).
Due to independent assortment, markers on different chromosomes are expected to recombine 50% of the time. As I understand, if one conducts a classic experiment and counts various progeny, then deduces the apparent linkage, values of 50 cM or more are interpreted as "impossible to determine whether on separate chromosomes or just recombines very often". See (source), with grammar corrected:

The final point that we need to make regards the maximum distance that we can measure. Because of the way in which the calculations are performed, we can never have more (than) 50% recombinant gametes. Therefore the (maximum) distance that two genes can be apart and still measure that distance is just less (than) 50 cM. If two genes are greater than 50 cM apart, then we can not determine if they reside on the same chromosome or are on different chromosomes.

Wikipedia gives an analytical solution and also remarks that (d is physical distance):

The probability of recombination is approximately d/100 for small values of d and approaches 50% as d goes to infinity.

However, what happens if the linkage is greater than 50 cM? It seems like classical experiments aside, such a situation is possible in reality.
For instance, yeast chromosome IV is 1530 kb long, and averages 0.31 cM/kbp. Let's take two genes on Chr.IV:

DNF2 is at about +631 kb.
TOM1 is at about +1370 kb.

The physical distance between these is about 734 kb. According to the cM/kbp value, the centimorgan distance is $734\text{ kb} \cdot 0.31\text{ cM}/\text{kb} = 228 \text{ cM}$ . How to interpret this 228?
If I mate a haploid yeast which is DNF2 TOM1 with another which is dnf2 tom1 (lowercase indicating minor allele rather than deletion), then sporulate them, what is the chance of getting spores with DNF2 tom1 or dnf2 TOM1 genotypes?
I realize that the cM/kbp value is only a simplification and that in practice linkage is a more complex phenomenon. Nevertheless, it seems plausible that several crossover events can happen on Chr.IV since it is so big. This includes the possibility of 1, 3, 5 and more crossovers which would create a hybrid (assuming they all happen between these two loci), as well as the possibility of 2, 4, etc crossovers which would create a non-hybrid spore (at least as far as our chosen markers are concerned).

Understanding the statistics we use when talking about recombination rate is an important question that is unfortunately too often dismissed in an intro course to evolutionary biology or population genetics and that is misunderstood by many. I have a partial understanding of it but hopefully, I'll manage to write a decent answer.
#Short answer
A recombination rate and a genetic distance (in centiMorgan) are two different things. While the recombination rate is bounded between 0 and 0.5, the genetic distance is bounded between 0 and infinity. There is a one-to-one function from the genetic distance to the recombination rate. For small recombination rate, the recombination rate and the genetic distance take very similar values but for greater values, the recombination rate is much lower than the genetic distance.
#Long answer
There is a tiny bit of math below. These equations are mainly for curiosity as one can understand the answer without understanding the maths behind it.
Definitions of $r$ and $M$
You are getting confused between two different statistics

The rate of recombination $r$ between two loci
$r$ is the probability for two loci to remain in the same gamete after recombination occurred. This probability cannot be greater than 0.5 ($0 \le r \le 0.5$).
The distance in Morgans $M$ (or more commonly in centiMorgans) between two loci. $M$ is the expected number of cross-over that occurs between the two loci.

Morgans and centiMorgans
You will note that I talk in Morgans rather than centiMorgans, which is not typical in the literature, but it helps at conveying the intuition of what it means. If $150$ centiMorgans $=$ $1.5$ Morgans. For two loci distant by 1.5 Morgans, the expected number of cross-over between the two loci is 1.5 (by definition). Below are some more explanations on these two definitions with some drawing :)
Case study with loci A and B
While $M$ and $r$ are closely related, they are not exactly the same thing. Consider the following sequence with the loci A and B
---[A]------------------[B]---

Let's assumed the two loci are very far apart and $M=2$. The probability of having exactly $k$ crossovers is therefore given by a Poisson distribution with rate $M=2$
$$P(k) = \frac{e^{-M}M^k}{k!}$$
Let's say for a given case that $k=1$ (a single cross-over occurred). This cross over is represented by a "/" below
---[A]-------------/----[B]---

Here clearly the two sequences at loci A and B will be separated. Let's say now that $k=2$ (two cross-over occurred).
---[A]---/-----/--------[B]---

Here, even if crossovers have occurred, the two sequences at loci A and B will remain together. Only the sequence in between the two cross-overs will come from the homologous chromosome.
Relationship between $r$ and $M$ - in words
You might see it coming from the previous section. The probability $r$ of these two loci A and B to be separated via recombination is the probability of an odd number of recombination events to occur between them (knowing that $M$ is the expected number of cross-overs).
Relationship between $r$ and $M$ - in equation
Let's calculate first the probability $p_{even}$ that an even number of cross-overs occur. This probability is just
$$p_{even} = \sum_{k = 0}^{\infty}{e^{-M}M^{2k} \over (2k)!}$$
, where I just added the constant $2$ before $k$ at both the numerator and denominator. With some algebra and trig, one can show that
$$p_{even} = \sum_{k = 0}^{\infty}{e^{-M}M^{2k} \over (2k)!} =
e^{-M}\sum_{k = 0}^{\infty}{M^{2k} \over (2k)!} = $$
$$e^{-M} \: cosh(M) = e^{-M}\left ( \frac{e^{M} + e^{-M}}{2}\right ) =
{1 + e^{-2M}\over 2} $$

As, $r = p_{odd} = 1 - p_{even}$,
$$r = 1 - {1 + e^{-2M}\over 2} = {1 - e^{-2M}\over 2}$$
Here we go! We have our relationship between $r$ and $M$! Let's graph it
#Relationship between $r$ and $M$ - on a graph
I just graphed the above equation in Mathematica (Plot[y = (1 - Exp[-2 M ])/2, {M, 0, 5}])

Here is the same graph but zoomed on lower values of $r$ and $M$ (Plot[y = (1 - Exp[-2 M ])/2, {M, 0, 0.1}])

We clearly see from the graph that for low values of $M$, as $M$ increases $r$ increase quasi linearly ($M≈r$). For greater values of $M$, $r$ still increases but slower and slower until reaching an asymptote / plateau at $\frac{1}{2}$. $r$ is indeed bounded between 0 (when $M=0$) and $\frac{1}{2}$ (when $M=\infty$).
Note, the fact that the sum of probabilities of every even $k$ in a Poisson distribution is always lower or equal to 0.5 is an interesting math fact in itself!

From a deleted comment by @emre : You should start with
$p_{even}=\sum_{k=0}^{\infty}\frac{2}{2}\frac{d^{k}e^{-d}}{(k)!}$. Because, simply, $\sum_{k=0}^{\infty}\frac{d^{2k}e^{-d}}{(2k)!}\not=\sum_{k=0}^{\infty}\frac{d^{2k}e^{-d}}{2(k)!}$

Just to be clear, markers on different linkage groups (chromosomes) do not recombine 50% of the time. It is just that unlinked mutations co-segregate 50% of the time.
This is a direct quote from Strickberger's textbook "Genetics" 3rd ed. 1985 p 397:

>
  After many tests involving numerous sex-linked genes, the entire X chromosome of D. melanogaster was mapped and found to have a length of 68 map units. This, however, does not mean that there is a recombination frequency of 68 percent in a linkage experiment between yellow and bobbed which are at the extreme ends of the X chromosome.  As explained previously, no more than 50 percent recombination is expected between any two loci, since only two of four chromatids in a meiotic tetrad are involved in any particular crossover point.  In fact, the actual recombination value observed between yellow and bobbed may be even less than 50 percent in a linkage experiment for the simple reason that not every X chromosome bivalent may have a crossover in that particular interval.
  <<

1 percent recombination = 1 map unit

Now that we know what this 68 does NOT mean. Can you explain what it means and how to interpret it?

If you are trying to use meiotic recombination between visible markers to construct a genetic map of a chromosome then you will need multiple linked genetic markers. Once you order the markers with respect to each other then you do additional mapping crosses to get accurate recombination rates (cM) between the pairs of adjacent linked markers. Then you sum those distances up to get the total length of the linkage group in map units.

So if you have know that two genes are tightly linked to the two telomeres: TEL-A----Z-TEL, and you have a couple more well-placed genes between them: TEL-A-----D----------H---------Z-TEL.  If A is 18 cM from D, and D is 20 cM from H, and H is 30 cM from Z then the total distance from A to Z is 18 + 20 + 30 = 68 map units. If however you  mapped the distance between A and Z using just those two markers you would calculate that they co-segregate 50 percent of the time, and may be unlinked. So if you know they are linked but you get 50 cM then you know you need more markers for your map.

Yes, that's exactly what I would be suggesting to include in the answer :)

You're killing me! (by which I mean LOL). Sorry, I wasn't trying to be deliberately dense or obtuse. I was confused because I know you have a rep of like 10X mine, and that you are an expert on evolution (among many other things), but for some reason my frame of mind when I wrote those comments was "he genuinely doesn't know, so I will try to explain it explicitly" and I didn't clue in at all to the StackExchange mantra subtext of improving my existing answer. I am almost totally off of Bio, I just found it too frustrating. So once my initial enthusiasm wore off, I drifted away.