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How can homosexuality evolve despite natural selection?
I would imagine that the answer to this question would be population control, especially since even if one sibling is homosexual this does not necessarily mean that the other siblings will be too.

I suggest you change the question to "How can homosexuality evolve?"

I suggest a title change too. Evolution does not assume a purpose. I suggest "How can homosexuality be maintained genetically in a population?"

Why does it need an evolutionary explication? Not everything needs to be selected for. This is like asking why myopia (which in certain parts of the world can have a prevalence of >70%) evolved despite natural selection...

@nico because it seems like homosexuality would be heavily selected against but it appears to be highly prevalent anyway, seems to me the OP is interested in possible explanations as to why it seems natural selection has failed to get rid of it - i.e. how can a seemingly negative trait persist? does it have some kind of benefit which may slow/reverse the effects of selection?

@rg255 you're right.

@rg255: I reapeat my point on myopia. Furthermore you should consider that homosexuality does not in any way imply sterility.

@nico Correct, it does not imply sterility but, reproductive success does require the combination of both male and female gametes. If someone is homosexual that is far less likely to occur. The evolution of homosexuality, and the subject of myopia, is not a question of "why does X, a seemingly pointless trait, evolve?" but instead is more "why does X, a seemingly detrimental trait, evolve?" - I think it is a valid question because when we consider the effects of selection then homosexuality is paradoxical, hence several theories have been developed to try and explain it.

@rg255: I think the main problem is that whe should not ask "why X evolved", but rather "why X was not selected against" which is a very different thing.

@nico I think that is what this is- by asking why it hasn't been eradicated? They are effectively asking what possible benefits could save the trait

nothing evolves despite natural selection - its a contradiction to the definition and forces behind evolution.  Any trait that shows up which is not selected for does not last long.

@nico Ah, but it is extremely useful to seek an evolutionary explanation of myopia. The key is not to ask why it evolved, but instead to ask, as shigeta points out, why it has not been eradicated by natural selection despite being highly heritable. Searching for the answer leads one to the role of early environment (interacting with genetics), suggests possible interventions, and provides one of the classic examples of disease caused by mismatch between modern and evolutionary environments. One example

@corvus point is asking "why x evolved" implies the fact that evolution is somehow finalistic, which it is not.

@nico Huh? Asking why something evolved is not finalistic at all. E.g. "Why did penicillin resistance evolve in E. coli around 1945?" "Because people started using penicillin as an antibiotic in 1943, thereby selecting for penicillin resistance in human commensals."

@Corvus OK, my previous comment didn't come out quite all right. What I mean is that thinking that every single thing in existence evolved for a reason implies evolution is finalistic. Certain things are just not selected against, despite not giving a clear evolutionary advantage. Penicillin resistance is a good example of a trait that was positively selected, but that does not mean (as many put it) that "the bacteria evolved the resistance because there were antibiotics around" (finalistic view), but rather that "some bacteria which happened to have the AmpR gene were more fit and expanded"

@nico I totally agree that many traits are not adaptations. And I agree that final cause explanations are generally inappropriate forms of evolutionary explanation (though teleological language be an acceptable shorthand among researchers who are all clear on the subtleties). I think we're pretty much on the same page here.

@Corvus BTW: Your assumption about antibiotic resistance is wrong. It didn't evolve in 1945, it is a quite old mechanism. Almost as old as the "development" of antibiotics in funghi is.

@Chris I specified "in E. coli". Of course a wide range of resistance alleles have circulated in bacterial populations for tens of millions of years. But penicillin resistance was rare or nonexistent in E. coli when penicillin was introduced in the early 40s and became common within a few years. This change in allele frequencies in a specified population is the very definition of evolution.

@Corvus I wouldn't exclude that there are some E.coli in the wild which where resistant. It is a new phenomenon to a human environment, but the mechanisms are old. They simply acquired it from the environment.

@Chris of course. The resistance alleles were doubtless acquired by horizontal gene transfer, probably from soil microbes.

Several years back, results of a twin study (Zietsch, et al., 2008; popular press in The Economist) suggested that genes associated with homosexuality make heterosexuals who carry the same genes more reproductively successful. This would explain the observation that, for example, sisters of homosexual males have more offspring.

We show that psychologically masculine females and feminine men are
  (a) more likely to be nonheterosexual but (b), when heterosexual, have
  more opposite-sex sexual partners.

So if more sexual partners in heterosexuals is correlated with more offspring, then the genes associated with homosexuality may lead to more offspring in heterosexuals that carry them. So these "homosexuality" genes could easily be maintained in the population by conferring a reproductive advantage to siblings.
The authors conclude:

Taken together, these results suggest that genes predisposing to
  homosexuality may confer a mating advantage in heterosexuals, which
  could help explain the evolution and maintenance of homosexuality in
  the population.

do the authors discuss the possible effects of having a homosexual twin sibling? being raised with a homosexual twin might influence their sexual behaviours in a social and psychological context (i.e. the number of partners, rates of courtship, courtship style...). & how to separate these effects of nature vs nurture? I guess one could compare identical twins separated at birth but this is not perfect and would be highly limiting on sample size. Also non-related adopted siblings in which one is homosexual could test the nurture effect.

This study only suggests that genes effect promiscuity. That would explain the observation that sisters of homosexual males have more offspring, as well as why, when heterosexual, they have more sexual partners. Gay men are also known to be statistically more promiscuous. The study suggests that the tendency is genetic, but that the tendency is promiscuity, not homosexuality.

Obviously selection would appear to not favour being homosexual, in an evolutionary sense it represents somewhat of a decrease in fitness: Homosexuals fail to reproduce successfully due to the requirement of both male and female gametes and reproductive organs, therefore significantly fewer than the average heterosexual couple. Certainly I don't think it would have evolved as some kind of population control method - group selection theory is generally discarded in favour of a gene-centred theory (see Dawkins for popular science literature)
There is debate about whether someone can be biologically "preprogrammed" to be homosexual, this can occur genetically or epigenetically. Genetic models have used kin selection, overdominance, sexual antagonism in the past and are briefly discussed in the following article on epigenetics. Recent work has looked at possible models by which heritable homosexuality could arise by epigenetic markers and this was covered in a lot of mainstream media (1,2.. just google epigenetics homosexuality). This quote is from their abstract and explains one reason it is difficult to pin down heritable causes of homosexuality:

Pedigree and twin studies indicate that homosexuality has substantial
  heritability in both sexes, yet concordance between identical twins is
  low and molecular studies have failed to find associated DNA makers.
  This paradoxical pattern calls for an explanation.

By their readily testable model they have shown possible (& plausible) conditions under which the "epi-marks" which cause homosexuality could spread through populations.
Genetic studies of twins where one is homosexual have also revealed links between genes and a mating advantage. For example if in a pair of male identical twins one is homosexual, the other has a mating success greater than that of the average male. However, it could be that this link is found because of social reasons (perhaps someone who has grown up with a homosexual sibling may have a different mentality or lifestyle socially which could help them increase reproductive success).

Note: I have no problem with a person's sexual orientation & the rights/ethics of homosexuality is not the topic of this question & answer. This is purely an answer to the obvious evolutionary conundrum.

Comments are not for extended discussion; this conversation has been moved to chat.

This is not a subject I know well, but I can point to several recent textbooks on homosexuality in animals, all with an evolutionary perspective. I remember that Bagemihl's book got good reviews when it was published. In general, I think it is important to acknowledge that homosexuality is common in many animal species and not just humans:

Bagemihl. 2000. Biological Exuberance: Animal Homosexuality and Natural Diversity
Sommer & Vasey (eds). 2006. Homosexual Behaviour in Animals: An Evolutionary Perspective
Roughgarden. 2009. Evolution's Rainbow: Diversity, Gender, and Sexuality in Nature and People
Poiani. 2010. Animal Homosexuality: A Biosocial Perspective

For a good review, see Bailey & Zuk (2009) Same-sex sexual behavior and evolution. Trends in Ecology & Evolution, 24(8):439-446. (link to a pdf: http://www.thestranger.com/images/blogimages/2009/09/14/1252958575-evolution_of_homosexuality.pdf)

Do any of these books demonstrate that animals are born gay? Animals do all sorts of things sexually, but what evidence does anyone have that animals are born to behave that way (that they are not simply more promiscuous)?

@CarlSmith I don't know exactly what you mean with born gay, especially in relation to non-human animals. What we can observe is behaviour, and homosexual behaviour (which might be roughtly translated to sexual preference), not thoughts and intent. I don't know this literature well, but there might be studies of sexual preference across time for individuals of certain species, which might get closer to the issue of being born gay. Individuals that only engage in homosexual behavior would (sort of) imply that. However, in some species, sexual behavior varies a lot within the same individual

Thanks for the clarification. I don't understand how anyone could possibly determine which animals were born gay. Still, I'm a computer programmer that never studied biology, so it's probably just total ignorance on my part.

There is an interesting theory coming from a slightly different, yet related, field. It was developed by Paul Vasey and Doug VanderLaan of the University of Lethbridge, they are both evolutionary psychologists:

An Adaptive Cognitive Dissociation Between Willingness to Help Kin and Nonkin in Samoan Fa’afafine (or direct link)

They called their theory the "helper in the nest" hypothesis. It basically states that gay people compensate for their lack of children (this has been been covered thoroughly in the other answers) by offering an indirect benefit through enhancing the survival prospects of close relatives. And they do so by being “helpers in the nest”, by acting altruistically toward nieces and nephews.
Their study was conducted in Samoa, and they chose the country because males who prefer men as sexual partners are widely recognized and accepted there as a distinct gender category (called fa’afafine - neither man nor woman), which makes for a clearly defined sample for study. It's worth mentioning though that the authors see Samoan culture as very different from most Western cultures. Yet, they affirm Samoa’s communitarian culture may be more—not less—representative of the environment in which male same-sex sexuality evolved eons ago.

Looks like only the Abrahamic religions are against homosexuality. In no other mythology I've found anything against homosexuals.

Apparently, Buddhism is homophobic and transphobic (and discriminates against people with disabilities too): https://en.wikipedia.org/wiki/Buddhism_and_sexual_orientation

There are a lot of theories about how homosexual behavior might be maintained in a population or provide some evolutionary advantage. One thing to remember though is that there is a big difference between homosexual behavior and obligate homosexuality. One could quite easily confer benefits, like any other intra-sex social interaction. The other carries a huge fitness cost. However it's not clear that obligate homosexuality has been common in humans. It is in our current culture, but historically, it's possible that most people (particularly women) would have had children because of cultural pressure to do so, regardless of sexual orientation. Without knowing more about cultural influences on reproductive rates, we can't say if there even is a mystery to be solved here.

Humans have a wide variety of triggers for sexual arousal. I think that having a variety of triggers can beat having too few - ie it can result in more consistent reproductive success, especially within humans who do not have strong and obvious fertile periods and will have relatively few offspring. Where a strong sex urge exists and fertile mates are not available having other outlets - masturbation and homosexuality - may reduce the occurrences of harassment and rape and prevent strong sex drives being injurious or socially destructive.
Being homosexual does not prevent the ability to have hetero sex and many people who are homosexual by preference still persist in hetero relationships and have children. It isn't the preference but the inability to have hetero sex with fertile partners that would select against homosexual behaviours.

Are you saying that gay people have as many children as normal people, on average? If you're correct, then there is no evolutionary disadvantage to being gay.

I don't know how much so, but would expect less offspring, but my point is being "gay" does not, by itself, prevent most gay people having children, or even the desire to have them. I don't see any evolutionary advantage/disadvantage as independent of the social group and it's cultural imperatives. If it results in reduced conflicts over mates and supports positive contributions by those who don't have children then it raises the group's reproductive success. Any such individuals will share most of their DNA with the offspring of others - to no overall evolutionary disadvantage.

I think I understand your argument. You're saying that having some people adopt gay and lesbian lifestyles (that are often not lifelong), actually causes their tribe to be more successful overall?? So, even though gay people probably have less children themselves, they care so much more for other people's children that it more than makes up for their lower mean fertility (just like Dawkins' selfish gene)??

@CarlSmith - yes that is what I am saying - although I think caring for other's children directly, more than average, isn't necessary; just contributing to the group as normal, with less conflict over mates raises everyone's chances for survival. Yes, like Dawkin's Selfish Gene.

Ah. I see. That makes sense. I was looking for something more specific and tangible that could counter the obvious disadvantage, but reality doesn't owe me that. On reflection, what you're suggesting does seem perfectly plausible. Thanks for taking the time to clarify your argument for me, and also for not judging me for wanting an explanation. I honestly couldn't conceive of homosexuality evolving. I kept an open mind, just because I don't know much about the subject, but it seemed scientifically impossible to me. Thanks for changing my mind, mate.

A recent study using a massive pool of genetic data suggests that indeed genetic factors associated with homosexuality also confer a mating advantage to heterosexual individuals in the sense of being "more attractive".  Some quotes from the article:

According to an abstract the team submitted to the American Society for Human Genetics, whose annual meeting is under way this week in San Diego, the DNA signals linked to gay sexual experiences also appeared more often in straight men who had a larger number of sex partners. The team also notes that straight men with the gay-linked variants were, on average, judged more “physically attractive” than others (the researchers decline to say who did the judging). This, the scientists conclude, could mean that these variants also “confer a mating advantage to heterosexual carriers.”
Such trade-offs are a fact of evolution. For instance, gene variants that can cause sickle-cell anemia also lend protection against malaria. The resulting balance means the sickle-cell gene doesn’t die out. The researchers say their new findings about non-heterosexual behavior, though not conclusive, are consistent with such a Darwinian balancing act.

PS: I know this is in line with the most upvoted answer, but the nature of this study, I think, singles out the need for a new and more recent answer.


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What is background binding?
I'm reading a journal article about mitochondrial protein import and it mentions that one of the mutant proteins tested showed background binding with another protein. What the heck is background binding?

Was an IP involved by any chance? http://en.wikipedia.org/wiki/Immunoprecipitation#Background

"Background binding" usually refers to aspecific binding between two proteins. The details depend on the test that was used.

can you post a link to the article?

Background binding in this case would be the extent to which two proteins associate together by chance.
A hypothetical example: you may have a mitochondrial protein import complex.  Usually cases there is a specific peptide sequence the import complex binds to , but proteins without an import peptide sequence will occasionally be bound to the import complex.  This is called the background binding for the protein complex.  The experimentalists might have measured this by cutting the import peptide sequence off a mitochondrial protein for instance.
Any candidate would have to bind to the complex more than the background case to be considered a target for mitochondrial import.

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A program for cell motility assessment with a batch process function?
Cell motility assessment is a branch of experimental biology or medical science. One example could be an assessment of treatment effects on sperm motility of an animal. The standard procedure involves taking film clips of sperm (or any other moving objects) through a microscope and measuring average linear velocity of particles on these film clips. The program used for measuring these linear velocities is important, and there are not too many choices to my knowledge. However, my knowledge might be limited.
I have previously used CellTrak for measuring sperm swimming speeds. The program works well, but lacks a batch processing function. As the assessment bases on a considerable number of replicates, I end up with 1000-2000 film clips to be analyzed and clicking my way through CellTrak is a tedious and irritating process. Also CellTrak licence costs a lot of money for such a poorly written program.
Therefore, my question is: Is someone aware of a similar program to CellTrak, which includes batch processing option, or even better, which works through command line and can be looped? Are there open source options or extensions to widely used open source programs (ImageJ, Bioconductor, etc.)? Please give a short tutorial/personal experience to the usage of the suggested program (if any).

I wonder if you could adapt Digital Particle Image Velocimetry for your purposes. http://www.holomap.com/dpiv.htm

I don't know of a specific program but the MATLAB file exchange is likely to have scripts for that purpose. It may also help to migrate this to StackOverflow

ImageJ has several tracking plugins, a good one being TrackMate. Most of it's functions can be scripted in various languages and the Fiji distribution can also run in headless mode. It's open source and won't cost you any mony for a much lager feture set.
I personally have used ImageJ in headless mode scripted with its own macro language because it is relatively easy to learn.
TrackMate also should output average speeds for the tracks, if I remember correctly. Otherwise you would have to write a script to measure those from the tracking data. You can use the IJ macro language, Python, Java or one of the other supported languages.
In combination with a bash script wrapper for its headless mode I even use it in Makefiles to convert my tiff stacks to avi and put scale bars and time stamps on everything.
Hope this helps.

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What causes adenosine build up in the brain when awake?
Adenosine is an important hormone in sleep regulation.  It is postulated that when a person is awake, there is a build up of adenosine in the brain, which inhibits the neurons in the brain, and produces tiredness.  (See answer for more information:  What causes humans to be sleepy?)
However, I am wondering what specifically causes this adenosine build up.  I understand ATP (adenosine tri-phosphate) is broken down to ADP in the brain to produce energy.  I thought this ADP would then be used to re-generate ATP again etc, so I'm not sure how adenosine is built up in the brain over a day.
Basically I am unsure how Adenosine itself, as opposed to ATP or ADP, is produced during the waking state?
My theory is that during the high demand waking state there is insufficient energy to convert ADP back to ATP, and the excess ADP is broken down to adenosine somehow.
I would appreciate an explanation of how this build up occurs, and also an explanation of how this in turn how it induces sleepiness would be a plus.

You may find this interesting, although it is not directly related to your question: http://www.scq.ubc.ca/eyes-wide-open-dispelling-myths-and-uncovering-truths-behind-caffeine-consumption/. Also, I retagged your question - you might find these tags useful.

Adenosine causes humans to become sleepy. But how ?

During day time we consume food which is broken down into glucose. This glucose is broken down by "Glycolysis" in cell's cytoplasm during which ATP is produced. This produced ATP is is then used by body as an energy supplier. ATP breaks down into ADP and then AMP with the release of energy which our body consumes for doing work.

(Fig 1- Structure of Adenosine to ATP)
Adenosine is produced continuously and starts to accumulate around and in Adenosine receptors such as A1, A2a, A2b and A3 (as shown in fig below).Adenosine inhibit signal propagation and energy production in at least A1. (Not all the receptors induce sleep when they receive Adenosine.) "A1 receptor" receives adenosine and induces sleep. A1 receptors are implicated in sleep promotion by inhibiting wake-promoting cholinergic neurons in the basal forebrain.

Continuous inhibition of A1 receptor by Adenosine slowly induces sleep by relaxing the brain and muscles but without substantially weakening their abilities!
How is Adenosine metabolized ?
During sleep the accumulated Adenosine is metabolized by Adenosine deaminase enzyme which catalyzes the irreversible deamination of 2'-deoxyadenosine and adenosine to deoxyinosine and inosine. With the reduction in the Adenosine content the body is excited from sleep slowly.
So in short summarize:

The accumulation of adenosine during waking periods is thus associated
  with the depletion of the ATP reserves stored as glycogen in the
  brain. The increased adenosine levels trigger non-REM sleep, during
  which the brain is less active, thus placing it in a recovery phase
  that is absolutely essential—among other things, to let it rebuild its
  stores of glycogen.
Because adenosine is continuously metabolized by the enzyme adenosine
  desaminase, the decline in adenosine production during sleep quickly
  causes a general decline in adenosine concentrations in the brain,
  eventually producing conditions more favourable to awakening.

(Refer this page: MOLECULES THAT BUILD UP AND MAKE YOU SLEEP)

Glycolysis requires ADP to make ATP. So if all the ADP and AMP is becoming adenosine and getting hydrolyzed by ADA, where does new ADP come from?


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Expanding the SETI initiative to seek intelligent data within DNA sequences?
I've recently read a couple articles dealing with long term data storage, and DNA was suggested as one of the prime candidates for long term storage of digital data additionally, there is this article which deals with decoding of long storage data. These popular articles, though simple do mention important concepts- how packets are stored in DNA use addressing schemes, redundancy of storage, writing for a recipient who may be using a different language, etc.
This made me think - we have the SETI initiative which is looking for signs of (intelligent) life in the universe. That organization was created long time ago, and uses technologies of those days - radio waves. The modern science knows that we can store a lot of data in DNA, and that most organism DNA contains only a small fraction of protein coding sequences and a large amount of non-coding material. If I understand correctly, some of the non coding material is repetitive and highly preserved. Has anyone considered expanding the search for intelligent life to include examination of DNA for messages that might've been left by other intelligent species actually visiting earth?

You suggest an interesting idea, but what's the question?

Unfortunately most of the highly conserved non coding material that you mention comes from viruses which are not really prime candidates for intelligence.

The question is about bioinformatics - is anyone looking for "long storage" data within DNA sequences.

+1: I had the idea about DNA as database too, but it didn't occur to me to marry that thought with distributed computing initiatives! Well done!

DNA as a storage medium is usually not incorporated into organisms, as I understand it. Looking at e.g. this article, they do not appear to be talking about DNA stored in an organism, but rather synthesizing naked DNA that would then probably be stored as a desalted solid under non-reactive ambient conditions (the most stable case). Organisms have an annoying habit to mutate, and there would be no selective pressure to maintain such a message (without a lot of extra complicating bioengineering).

There are now (2022) efforts in this direction, e.g.: https://www.cnbc.com/2020/02/28/how-nasa-is-using-synthetic-dna-in-its-search-for-alien-life.html ; These approaches however would be more inclusive as searching for molecules that resemble DNA (also in terms of storage) but might are formed through slightly different chemistry. Further the first step seems to be finding molecules (rather than already investigating their sequences).

@uhoh Interesting - would it be more likely to get an answer at the Bioniformatics SE, rather than here?

@bob1 That certainly could be, thanks for the reminder! This question is too old to migrate so one would have to post a new question. I don't think I'll do that but anyone else is welcome to.

@MaximilianPress "...is usually not incorporated into organisms..." *by humans. This question is about "Expanding the SETI initiative..." by searching for sequences put into earthbound genomes long ago by extraterrestrials if I understand it correctly.

@tsttst that would be worth expanding into an at least partial answer.

@uhoh All of the research referenced by OP seems to be predicated on storage of DNA outside of organisms. I don't think long-term information storage as exogenous DNA inside of organisms makes sense; we have a hard enough time with short-term DNA storage as e.g. plasmids or BACs. Willing to be proved wrong about this, just seems implausible.

@MaximilianPress yes I understand. We do have the concept of conserved sequences but resistance to mutation may require they are either necessary for life or quite durable due to some error correction or redundancy which may not be a fully explored bioinformatics concept yet. Wild speculation to illustrate a point; perhaps the huge genome of some plants contains so many copies of the same message encoded in so many different ways that it can be reconstructed even after substantial mutations?

@uhoh We're getting a little off-topic, but sure. Mutation resistance is a feature of some organisms, look at D. radiodurans. There are many error correction processes that are normal in cell biology, they just aren't perfect. Conserved sequences are usually conserved for a functional reason as you say, we usually can understand why. In terms of very large genomes like redwood, they are mostly the outcome of polyploidy or arms races between selfish elements. shrug

Let's extend your idea a bit... Ok, there are conserved sequences that we may not know what their function is. Let's assume that they are indeed not functional and are some kind of message left by an ancient form of intelligence.
How would you go about detecting that? It is already given that they are highly non-random, but this is not surprising and many "non-message" sequences have this property. Also consider that these sequences are quite short, meaning that they will have low information content. This means that if you check enough conversion codes and use imagination, you would probably be able to find several "messages" which are "hidden" there (e.g. "bible codes" etc). In other words, as I am a scientist that deals with probability and pattern recognition frequently, you will have a very hard time trying to convince me that you found a real hidden message... Formally, you don't have a satisfying background model.
The main difference from SETI is that there they know that their background is essentially random noise, so it is much easier to detect "intelligent" messages.

Very good point. What originally inspired the question was that the "data in DNA" encoding linked in the question uses very short 96 bit "packets", preceded by a 19 bit addressing sequence. While the payload can vary, the presence of the address within each packet gives hope of detection. As far as I understand, this is how genes are detected - by their promoter/terminator sites.

DNA in living creatures is just not a very good storage method. Critters can go extinct or mutate your 'message'. Theoretically you could plant a sequence of non-coding DNA in a large number of completely unrelated organisms, and that consensus sequence would last a little while. It would decay pretty quickly without selective pressure, though. In fact, you could look for these right now. Go BLAST species that are unrelated looking for highly-conserved noncoding sequences. Worst case scenario you discover a new method of gene regulation or something.

Since the initial posting of the question, the SETI institute has indeed thought about the possibility publicly.
A related question however is if aliens would also use DNA, or another chemical compound with similar properties for storing and passing information. The search for latter types of molecules is also ongoing, even with funding of a space agency (article).

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What is the best way to express two proteins in a mammalian cell?
I have two proteins and I will be preparing a vector with both genes for stable transfection. Each protein will have their own promoter and I will use piggyBac vector to insert a single cassette with both genes in it into the chromosomes. My questions are:

If I use the same promoter (CMV, SV40 or an inducible one) for both genes how would this affect the expression levels? I read in some papers that one of the genes might get expressed lower than the other. If you have first-hand experience I will be grateful if you share it.
If I use the same promoter for both, but put them far away (i.e. ends of the cassette) would the expression levels get affected again? It sounds simple enough but I think people would have published something if they had a good result with that.
If I use different promoters for each gene (e.g. CMV for one and Tet-inducible for the other) how would it work? I couldn't find a paper which used this and I would like to continue with this approach; therefore, if you have any experience I will be really grateful for any help.

I don't want to use IRES or 2A-peptide. I would like to be able to control this experiment in transcription stage.

I was going through my questions and realized this is still unanswered. Well, I have the answer now.
I designed the construct with two separate promoters (CMV for one and Tet-inducible for the other) and got really good results. I haven't had any difficulties in expressing the proteins. I was able to control the Tet-inducible one very nicely and got steady levels of the other protein with CMV.
Long story short: you can safely put two genes under two separate promoters, prepare stable cell lines with them and get good expression levels.

You can use a bidirectional promoter. The problem that you mentioned about proteins not expressed in same level happens because of competition for polymerase. But there are well optimized parts and also commercially available vectors that work fine.
You can clone genes in a serial order. It won't be a problem. Just leave a 100bp linker after the polyA signal of previous gene. If your cassette becomes too huge, then insertion becomes slightly difficult. That's why people use IRES or TA-peptides, etc.
Retroviral based insertions work quite decently, but you can't control copy number variation between different cells.
You can use two different promoters. The dynamics will depend on the promoter strength and concentration of inducer.

Thanks for your reply. I looked into the bidirectional promoters too but decided to try two different promoters. I really didn't want to go with IRES or 2A because I am too afraid to interfere with the interaction, better not risk it :). I will start the experiment shortly and share my experience in here when I get some results.


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What is immunopanning (vs. immunoprecipitation and FACS)?
I had never heard the term before today. From what I can tell, it's using antibodies to purify a cell population of interest. I would appreciate more details, especially in how it differs from "immunoprecipitation" of cells via cell surface markers, and FACS.

Immunopanning is essentially an immunoprecipitation (IP) of cells using an antibody immobilized to a solid surface, like a cell culture plate. Conventionally, an IP is performed using small agarose or magnetic beads (~50 to 150μm in size) conjugated to an antibody or Protein A/G, and can pull down individual proteins, protein complexes, and/or nucleic acid complexes.
Cells are much larger than protein complexes, obviously, and for the most part much smaller than beads, but they can be damaged during a traditional IP, so immunopanning utilizes a single solid surface coated with the specific antibody or cell-surface protein ligand of choice. In this article (free PDF here), retrograde axonal transport was used to selectively label specific populations of neuronal cells with the extracellular portion of cholera toxin β (CTB) adsorbed to fluorescent beads, then the cells were purified using an immobilized anti-CTB antibody.
Fluorescence-Activated Cell Sorting or FACS is another way to purify cell populations. Cells are labeled with a fluorescent marker (either conjugated to an antibody specific to an extra-cellular epitope, via absorption as in the example above, or by expression of a fluorescent transgene like GFP), then scanned in a flow cytometer. Cells which match certain parameters or "gates" in the machine's software are then diverted into a separate collection chamber, allowing for the generation of a quite pure cell population.
However, as the authors point out in their paper above, FACS requires an expensive piece of equipment (can be over US$100,000), can be harsh on the cells, and is dependent on the availability of an antibody to a cell surface marker specific to the desired population of cells. Immunopanning is much less expensive, is more gentle on the cells, and in the authors' case was really the only choice for purifying their cell population of interest, as no specific biomarkers were available. It certainly won't replace FACS in the long run, but is another tool for investigators to use when studying specific cell types.

So immunopanning is "gentler" than immunoprecipitation because a flat surface is used rather than beads (and thus, there is no centrifugation step to isolate the beads)?

@dd3 - right. Also, you don't have the beads physically interacting with each other in the tube, potentially crushing or tearing cells. A cell could easily be tightly bound to two beads, one on either side, and possibly ripped apart when they separate. It's also much easier to remove cells bound to a plate than it is to separate the cells from the beads after the wash steps.

Thanks.  I've never done any of these before (just read about them being used in papers), so all of your links were very helpful.

@dd3 - no problem at all, I'm here to help. Thanks for checking it answered!


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Is there a Pharmacology Textbook that Satisfies the Conditions listed in the Body of this Question?
The conditions are:

As extensive and explanatory as Goodman and Gilman's The Pharmacological Basis of Therapeutics, Twelfth Edition
With additional extensive and thoroughly explanatory information on drugs (e.g. flupirtine, piracetam, nefopam, etc.) that are used elsewhere in the developed/semi-developed (like Russia or China) world (e.g. European countries) but not in the US.
Additional information about the medically recognised (in some of the world at least) herbs cannabis sativa and hypericum perforatum (St. John's wort; recognised in Germany).

If there is no such book then the European (or a European, like for instance the British equivalent. So long as said equivalent comes in English) equivalent of Goodman and Gilman's will be accepted.

We're encouraged to use Rang & Dale's pharmacology but I don't know if it will go into enough detail for you.  You might also want to try and get your hands on a BNF for the clinical side of pharmacology if you're interested in UK practices.

@BrentonHorne: If you found the book you are searching for do tell us.

@RoryM : If you convert your comment into an answer this question may be saved from deletion.

A title called Essentials of Medical Pharmacology fulfills these criteria and is quite popular in India.
Reference to the current edition:
Tripathi KD. Essentials of medical pharmacology. 8th ed. New Delhi: Jaypee. 2019; 1064 p.


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What does "Psychomodulatory" mean in the context of potentially psychoactive drugs?
What does "Psychomodulatory" mean in the context of potentially psychoactive drugs? That is, in this journal article http://www.sciencedirect.com/science/article/pii/S0028390812001931 in the discussion (you will need special privileges to access the article via an institute or personal subscription or by paying for access) in the last sentence of the first paragraph it says

However, euphol even when given in very high doses, (up to 100 mg/kg)
  it did not show any evidence of psychomodulatory effects in the CNS

To me, "psychomodulatory" would mean "eliciting a significant change (up or down) relative to baseline or compared to a control, placebo, or carrier," here specifically in CNS function.
This statement appears to refer to the results presented in section 3.8, Effect of euphol in the cannabinoid tetrad tests. Across a range of doses (3-100 mg/kg) and across four different assessments of CNS function: locomotor activity (rotarod), catalepsy (time to move off of a suspended ring), analgesia (tail flick in response to thermal stress), and body temperature (self explanatory). The results of these four are summarized in the figure below.

Basically the effects are not significantly different from each other between dosages or times. The lines sit more or less atop one another. Compare to this figure, where the differences are significant:


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Effect of zero selection (pressure) on the population health
Evolution naturally produces better features: stronger muscles, teeth and minds. Killing the weakest, evolution wipes defective genes out of populations.
The mutations are necessary for advance. However, they are random and, thus, mostly negative. Right? How does the nature eliminate them from the population?
I see that one mechanism is polygamy: male have higher mutation rates. They tend to reproduce as much as possible. Female have lower mutation rates, they couple with only with best men and contribute much more to their offsprings. So, men generate as much random solutions as possible, whereas the role of female is to conserve the best of them. This means that the most of the male (bad mutations) die unreproduced. This eliminates the bad mutations and favours the progress of good qualities. The higher animals started to form harems and tournaments over their ownership. This further fosters the elimination of weak men and profileration of strong genes. However, human monogamy has disabled this selection mechanism. Best men are dedicated to only one woman. Other women cannot mix their genes with other good genes from previous generations. They are forced to look at the low quality men, who carry degenerate mutations. Might be it is monogamy that makes us human but it implies that all genes reproduce.
Yet 100 years ago it was not a big deal since we still had another filter: our grandfathers were born in families that had normally 10 children (I am speaking about Russia) and only 2-3 survived until reproduction (the population increased really slowly). I bet that those who survived had really good health: thanks to the bad health and immense selection pressure, the negative mutants are eliminated immediately and population maintains a perfect genome (aka biologic health). Killing more weakest in the current generation improves the health of next generations.
However everything has changed during the 20th century. The advances in economy and medicine have almost eliminated the selection. The selection pressure has relaxed to essentially zero so that everybody survives and leaves the same amount of offspring (and some scientists are even concerned that degradatory individuals leave more offsprings than the prosperous ones). We have even eliminated the infant mortality. We use baby incubators so that the people with the weakest health could survive and reproduce as normal and we are proud of it. It may sound strange but the mutation rate has not changed at all. Does it mean that the human genome is in danger?
I see the situation like you have inherited a perfect mechanism and decided not recovering it from the inevitably adverse action of entropy, that degrades it constantly. There is a constant chance, d, that every good gene is affected by a mutation. It is a fraction of healthy genes that will fail passing to the next generation. This will leave only (1-d) genes healthy in the next generation. The fraction of healthy genes will melt like 1, (1-d), (1-d)², (1-d)³, an so on, with every generation.

You see the fraction that stays healthy over generations. It decays exponentially. Any utility turns into entropy (aka garbage) exponentially, if not protected. Is this model correct? How quickly does this dissipation go? What is d? Let's assume absolute survival and equality in the reproduction rate among all groups people. How many generations is needed to lose 50% of good qualities?

I need to point out one thing, natural selection does not bring species to perfection.  The best mutant may not be selected for many reasons.
When you have no selection pressure then you have neutral evolution concurring and what takes over instead of natural selection is genetic drift.  Genetic drift is just sample error.  Say you have 1,000 individuals in a population and all of those individuals reproduce, in the next generation all the genotypes would be in the next population.  Now imagine if you only had 10 individuals in the population and only 5 of those individuals were randomly selected to produce 10 individuals in the next generation (the parents die every year).  There is no selection pressure but just by chance some individuals reproduce and some don't.  If you do this over and over again what you will see is that some genes become fixed in the population, meaning that there is no other genotype in the population.
This fixation at small population sizes can occur with either beneficial or deleterious mutations.  Obviously if a mutation is very deleterious the individual will die but slightly deleterious mutations can become fixed in the population as well.
There is an entire field of biology devoted to this study.  It is called population genetics.  The probability for fixation for an allele is its proportion in the population.  This proportion can be calculated by 1/2N, where N is the population size.

Even if a species lives in abundance, there is still an evolutionary arms race: who reproduces the fastest? Even slight advantages in reproduction rate multiply over the generations.
There are, however, cases where selection pressures on specific traits have vanished. For example, for fish living in caves, there is not selection pressure to be able to see, and they lost  their eyes. A more complete discussion can be found in this paper: "Relaxed selection in the wild" -- see also this summary with a funny cover image of a species living in abundance.


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How might IVF (and related technologies) alter epigenetic marks?
I was reading up on KCNQ1, which encodes a voltage-gated potassium channel, and I discovered that it happens to be only maternally expressed. This is regulated by KCNQ1OT1, a non-coding RNA, which is also epigenetically regulated (expressed only paternally). Mutations in KCNQ1OT1 are associated with Beckwith-Wiedemann Syndrome (BWS).
Further reading led to the discovery that there are ART-related (assisted reproductive technology) cases of BWS due to loss of methylation at KCNQ1.
However, this article found epigenetic stability of KCNQ1OT1 methylation in cultured human embryonic stem cells, which leads me to think that KCNQ1 might also have been properly methylated.
So what exactly are assisted reproductive technologies doing that can disrupt inheritance of epigenetic marks (that culturing hESCs doesn't do)? (Is this understood for any gene?)

I recently asked a professor who works on stem cells about this, and he says it's probably an isolated case, and maybe even an experimental artifact.  I'd be interested to hear if anyone else thinks of an alternative explanation.

I was at a talk last year where some geneticists were starting to look at the effect of IVF techniques on genetic issues.  Because of the work being done and the inclinations of the clients involved, this has not been studied very much.  One presumes that since zygotes are still used, there will not be much epigenetic effects due to methylation patterns - its the same cell stocks being used in vitro and in vivo.
There may be an effect on genetics because the natural selection process.  Spermatogenesis and oogenesis is a highly selective process; only a small fraction of the ova generated by the ovaries ever mature and a large percentage of sperm generated are not motile or have other irregularities.  During fertilization, sperm competition obviously throws out all but one in 250 million.  It also appears that there are processes in the fallopian tubes that can store the sperm for several (up to 5) days before fertilization.
So while its not strongly established one can see how various IVF processes vary from in vivo fertilization.  This could have an impact on epigenetic factors, although different sperm vary genetically due to Meiosis and this would be a big source of genetic variation in the outcome.


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What's the difference between life expectancy of cigarette smoker and general population?
Some say that smoking cigarettes will shorten lifespan. By how many years is the lifespan of a typical smoker shortened? What are the common cause(s) of death among smokers? Are there any known statistics for cigarette smoking and life expectancy?

The difference in life expectancy between smokers and non-smokers appears to be at least 10 years on average, in a survey of American adults between 1997 and 2004.
The same paper lists causes of death (higher among smokers than non-smokers, as measured by hazard ratio), although this is not exhaustive: lung cancer, other cancers, ischemic heart disease, stroke, other vascular disease, and respiratory disease have an adjusted hazard ratio of 1.7 or more, with 94% of lung cancer deaths attributable to smoking among female smokers, and 93% to smoking among male smokers.
If you have access, you will probably find Table 2 (hazard ratios) of interest.
Figure 2 shows the survival probability:

I have added Figure 2 to the answer (it is free to view and it is clearly fair use anyways)

@nico: may I ask how you extracted it? I couldn't find a link.

There is a link to the PDF on the right, copied, saved it on my HD then uploaded it here (or you can just grab a screenshot).

What is interesting is the multiplicative effect of industrial disease with smoking,  in lectures (regrettably unreferenced slides) we are advised that in the case of asbestosis risk ratio for lung cancer (not mesothelioma)  is 7 in a non-smoker but a staggering 93 in smokers with asbestosis.

Bravo. I am speechless. Do we have the same data for ganja?

@JimThio: I think that data is a little harder to come by, given the different legal status in different states (I am not aware of research outside the US).  You might find this interesting though: http://www.nap.edu/catalog.php?record_id=6376

@JimThio while marijuana actually has some protective effects (as demonstrated in mice, don't have the reference at hand), the basic problem in smoking is the act of smoking itself not what it is that you are inhaling. Whether you smoke weed or tobacco, you are still inhaling carbon monoxide and screwing up your haemoglobin and you are still ingesting free radicals and screwing up your DNA. Sorry (and I truly am, I am a heavy smoker of various substances).

@terdon: seriously doubt you would ever "ingest" (although inhale would be the correct word) free radicals from smoking. They are too short lived and reactive to be actually directly inhaled.

@nico, The gas phase of cigarette smoke contains small oxygen- and carbon-centered radicals that are much more reactive than are the tar-phase radicals. and that's just the first random reference I found. Also, although I live in France, English is my native language :). Ingest is quite correct in that context. The Oxford Dictionary Online even uses this phrase as an example of the word's usage: "they ingest oxygen from the air"

@terdon: I mantain that you inhale smoke, you do not ingest it. Ingest is mostly used for food (Oxford English Dictionary, offline edition :P). English aside, I do not doubt that smoke contains radicals, what I am saying is that they are most likely not those that directly affect DNA. They will rather generate cascade reactions creating new radicals, oxidising proteins and so on, especially in such a oxygen-rich milieu as the lungs.

@nico I only used ingest to avoid a third repetition of inhale so I won't push the point :). As for whether they directly affect DNA or start a cascade, I honestly have no idea. The abstract of the paper I linked to seems to claim that both are true: "Cigarette smoke contains two very different populations of free radicals, one in the tar and one in the gas phase. [...] In addition, we have shown that the principal radical in tar reacts with DNA in vitro, possibly by covalent binding". Anyway, my main point was just that whatever you smoke, the act of smoking is harmful.

@terdon: agree. I was just nitpicking


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How are geneticists able to isolate gene functions?
As an example, this Scientific American article describes a known area in the dog genome that metabolizes carbohydrates.
How is it that researchers are able to determine specific functions such as this?

Lots of ways. Gene knockout, gain of function, biochemical assays, etc...

@LanceLafontaine if you have a more detailed answer, please submit it as an answer rather than a comment.

@LanceLafontaine suggested a few ways above, but I would recommend reading this section
in Alberts' Molecular Biology of the Cell, which gives a more descriptive overview of some approaches, but even that is not exhaustive.
An extremely simplistic and also not exhaustive summary:

observe mutants, see what processes are disrupted, and map these back to particular mutations
mutate a gene and see what processes are disrupted
biochemical studies to see, for example, which proteins (which are gene products) interact in vivo and things like where they're localized, which may hint at function.
analyze structure of proteins, see how similar they are to other proteins with known function, and infer that the protein of interest probably has a similar function

EDIT: The link to Alberts is to the 2002 edition (which is free online; the latest edition of the textbook costs around $200), so things have come a long way since then, but the underlying approaches are still in use.


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If life is discovered on another planet, will it likely be classified using the current domain/kingdom/phylum system?
This may be a stupid question showing my lack of understanding of taxonomy, but I was wondering if the current classification system we use contains broad enough categories to include new life forms, if they are discovered on other planets?  Would this depend on whether or not the new organisms could be shown to be evolutionarily related (eg have DNA), or are the highest levels of organization independent of relatedness and more dependent on physical similarity?

This is actually kinda interesting, because I asked a similar question on worldbuilding (the answer was about the same).

Background
There are basically three highest taxonomic levels: bacteria, archaea and eukaryotes. Many sources distinguish only prokaryotes and eukaryotes, subdividing prokaryotes into bacteria and archaea. Other sources posit archaea as a third domain on the highest level. That's a long debate though and fortunately not the topic here.
By appearance, the dual-domain system makes more sense because archaea and bacteria look very much alike under a microscope, and can both be clearly distinguished from eukaryotes (which have membrane bound nuclei). At the same time, comparing genetic structure and the protein machinery that interacts with DNA, eukaryotes and archaea are very similar and bacteria are clearly different from both of them. This demonstrates how appearance and molecular organisation have been typical criteria for distinction between branches of the evolutionary tree.
There are, however, many features that even those three most basic branches of life share, and they are in no way simple or few in number. For example, all extant life uses DNA to store genetic information and proteins for almost all processes governing the various reactions going on at any time in a cell. However, RNA for example is able to perform both the information storing function of DNA as well as the catalytic functions of protein. This just shows how the principles behind life are not unique to the molecules in use now, and extraterrestrial "life" may work by the same principles on an entirely different molecular basis.
Extraterrestrial life
If you want to know whether life found on another planet could be fit into our current classification system, the answer would be: No, most likely it will not be classified using the current domain/kingdom/phylum system. This is because our system describes evolutionary descendency, so unless this newly found life shares some common ancestor with an organism on earth, it would have to be classified in an entirely new system. (Of course this is subjective as you may find it more likely that it does share a common ancestor [Panspermia], while I personally find it more likely that life would have evolved entirely separated on this other planet seeing as we haven't heard of any life within reasonable distance.)
However, it is possible that this new life will follow the same evolutionary rules such as natural selection, and similar evolutionary pressures may drive to evolve similar properties. It may then be possible to draw parallels to characteristics of the current classification system, especially based on molecular function, and possibly appearance (micro- and macroscopically).

I disagree. Our current classification system is based on classifying evolutionary history from a single common ancestor, not function. Function is used to assess evolutionary relationships.  Excluding panspermia, any extraterrestrial life would represent a completely unique evolutionary history and could not be classified.

Valid point, does that sound better? I have to say that this made me realise the question could stir discussion more than encouraging an objective answer, so may be a candidate for closing.

Yeah I think that captures it.  I am not sure this question is more contcontroversial than phylogeny in general :)


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Onset of Autophagy
Fasting and Intermittent Fasting (IF) have been proven to start autophagy (cellular self-digestion). How long does the average man and woman have to wait for autophagy to begin? Does diet prior to fasting effect the onset of autophagy? And lastly, does longer fasting produce more efficient autophagy than IF?

Would you happen to have a reference for your first statement?

http://www.ncbi.nlm.nih.gov/pubmed/21471734; http://www.ncbi.nlm.nih.gov/pubmed/20534972; http://www.ncbi.nlm.nih.gov/pubmed/19200897;

Thanks for the links.  This appears to be a related question that might help: http://skeptics.stackexchange.com/questions/1696/does-intermittent-fasting-improve-immune-function-through-autophagy

Does not quite answer my questions. I am more interested in how long after a fast starts does the mechanism of cellular self-digestion begin.

Yes, but the references might point you in the right direction.  The main issue I see is that a lot of work has been done in non-human animals -- you (or someone else who is familiar with this area, which is not me) might have better luck looking up the signaling pathways involved involved and seeing when and how they turn on in response to fasting.  Another keyword to consider is "starvation".


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DNA gel extraction: chemical contaminants
I am performing a gel extraction to purify DNA after a double digest with EcoRI and BamHI.  After the gel extraction I need to complete a ligation step before bacterial transformation.  The problem I am having is that the DNA after the gel extraction have some kind of chemical contaminant that won't allow me to quantify the DNA using the Nanodrop spectrophotometer.  I am getting very low 260/230 ratios.
Has anyone had some issues with this?
I am using the Qiagen Qiaquick Gel Extraction Kit.

It could very well be that your digestion isn't proceeding very efficiently and you're just getting low yields. Do you have high A260 and A230 readings both?

Agree, you should check the reading before digestion and see what amount of DNA you're working with.

Have you tried using alternative DNA measurement methods like a Qubit?

That always happens to me but my yields and DNA are always fine. Running it on a gel to check the amount works just as well even if it takes a little longer

I am going to follow the advise I found ( http://seqanswers.com/forums/showthread.php?t=15165 ) and get back if it works.

Here are some possible reasons:

Your yield is very low, which you can infer from a low 260 absorbance. Either make sure your restriction digest is efficient or add more substrate to the digest reaction.
Carbohydrate contamination, which will cause high 230 absorbance. Wash the column one more time with buffer QG (the step is described in the Qiagen gel extraction manual; if you're already doing a wash with buffer QG, do an extra one).
You didn't dry the column enough and some ethanol from the wash remains in the sample. This can also cause high 230 absorbance and your sample with smell of ethanol. Place your column in an empty collection tube and spin it down for a long time (15-20 min). Don't worry, the DNA can withstand it.

I tried your suggestions but still no luck.  I checked the concentrations of the plasmids before digestion and I had about 1000 ng/ul.  I did the additional QG wash step.  I also spun the residual ethanol out for 20 minutes.  I even did an non DNA gel extraction and ran a spec using a Nanodrop with a water blank and its not clean.  I have done many of these before but I am in a new lab now and I don't get quality extracts like usual.  I will give a new kit a try and see what happens.


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Least painful way to die
There is a lot of talk about inhumane treatment of animals and how we don't kill them in the proper way. I wonder how much research is done on this subject. What is the overall least painful way for an animal to die?
I also wonder if this would be the same for a human. It is often said that its least painful to die in ones sleep and i wonder if this is true. I wonder what is the most humane way to execute a capital punishment (if that is at all possible)

Should we be worried?

hah, yea it does sound pretty grim. I think the actual answer is not something that is easily available to most people. I just wonder how much we actually know about it because people keep screaming for more ethical treatment and i just dont know if we even know what that would be. And if seemingly more ethical treatment (like sedating animals before) are actually more ethical. Chemical ways might seem easier on the eyes but they actually better.

Part of the problem is: how do you know when an animal is suffering or in pain? Maybe looking into pain management research that uses animal models would be informative.

The American Veterinary Medical Association (AVMA) has thought about humane methods of euthanasia quite a bit and has an extensive (102 p. PDF) set of guidelines for the euthanasia of animals. The guidelines are not the same for all animals. Some examples:
Companion animals (e.g., dogs and cats): injected barbiturates are recommended
Laboratory animals (e.g., mice and rats): injected barbiturates are acceptable as are inhaled agents (isoflurane, carbon dioxide).
As for humans, you might look into the physician assisted suicide literature. I think that these generally use a sequence of drugs. As far as natural deaths, kidney failure is supposed to not be very painful.

Good answer but... there is a big point to be made on lab animals. Certain drugs may or may not be appropriate if the animals are to be used for experiments, as the drug may inficiate the results (e.g. I would avoid barbiturates if the animal's brain is being used for doing electrophysiology afterwards)


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205 nm UV-Vis readings
Typically we determine the concentration of proteins using a 280 nm reading. However, it is reasonable to use 205 nm. I was curious about the effectiveness of this method.

What evidence do you have for the reasonableness of reading at 205?

@MattDMo: I guess it is because usually nucleic acids are measured at 260. However, I am not sure 205 would remove DNA background noise... These are very approximative quantifications anyways, and only give a general idea of protein concentration.

@MattDMo, I didn't want to lead the question but I was looking over this paper. There is a scientific basis for the quetion. http://onlinelibrary.wiley.com/doi/10.1002/pro.2253/abstract

This may be what you are looking for. The conversion formula is:
$$
\text{Protein concentration (mg/ml)} = \frac{ (\text{Absorbance at 205 nm})} {31}
$$
The first, Scopes, does indicate that nucleic acid contaminants will confounding 205 nm absorbance readings. It seems as though this spetrophotometic calculation is feasible for relatively pure protein species.

DNA absorbance seems to be as high at 205 as at 260. http://faculty.evansville.edu/be6/b4454/DNAspectrum.gif?dur=2225

You would appear to be correct. What is not shown is relative absorbance of protein and nucleic acid at 205 nm. NB: I have not followed up with the two references linked from that page I posted.

I wanted to emphasize that A280nm is more sensitive, as tryptophan's absorbance is highest. So you can detect the smallest concentrations with A280nm. For proteins with little-to-no aromatics, or for proteins with atypical compositions (and unknown absorption coefficients), the absorbance per-unit-peptide bond is more general. (That's what A205nm is probing.) But as others have said, contaminating nucleic acids will also absorb at that wavelength.


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How might gene clusters like the lac operon evolve?
The obvious answer for a gene cluster is gene duplication and mutation of one or both genes. But the genes in the lac operon seem not be so functionally/structurally similar (as compared to the Hox gene cluster, for example), so I was curious as to how they ended up physically associated in the first place.

Operons, often but not always, contain clusters of genes (under the control of an operator region) which are involved in the same metabolic pathway. There have been several theories for how these groups of genes have arisen but the current feeling seems to be based around the regulation of the genes in question 1. To facilitate co-ordinated gene regulation there may have been strong selection for physical clustering of genes involved in a particular process. By being physically clustered this also means that all the genes within a given operon are probably subject to the same chromatin remodelling and will then be more easily switched on and off under the appropriate conditions i.e. all turned on when they are needed and switched off when they are not.
Operons with similarly arranged genes have been found in different micro-organisms, leading to the thought that the operon was an ancient and evolutionarily conserved arrangement [2]. The figure below from Fani et al. 2005 presents two possible ways of generating the current state of genome organisation for present day proteobacteria.

If the operon is an ancient arrangement we would predict high gene conservation within operons; but genome analysis of different micro-organisms shows this not to be the case (i.e. gene conservation is low and operons are pretty unstable). Accordingly, another author suggests that due to the lack of conservation, operon structure is pretty plastic and can change readily during evolution [3]. Indeed, Fari et al conclude in their paper that the histidine biosynthesis operon has been a construction or re-construction event from scattered genes and not from the descent of an ancient arrangement:

Our model suggests that the his gene organization in the extant proteobacteria arose from a gene scattering in the genome of the proteobacterial ancestor. The model also predicts that all or most of the his genes (except for hisD) were monofunctional and that they underwent a progressive clustering and compacting which occurred together with gene overlapping and fusion events

They found, as you suggested, evidence for several gene modifications which included elongation, duplication and gene fusions. As for what caused the progressive clustering, see reference 1 again.
Obviously different operons are probably going to have formed in different ways in different organisms and I don't think we can rule out the 'ancient arrangement' argument completely. It's a pretty broad and confusing topic and there's a lot of literature, I hope the examples I picked and have listed are useful!
1 Osbourn, A. and Field, B. Operons. Cell. Mol. Life Sci. (2009) 66:3755–3775
[2] Fani et al. The Origin and Evolution of Operons: The Piecewise Building of theProteobacterial Histidine Operon. J Mol Evol (2005) 60:378–390
[3] Itoh et al. Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol Biol Evol (1999) 16(3):332–346


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What is the brightest color a light source that only emits blue frequency light can achieve?
Let's say there is a luminous light bulb that only emits blue light, and you (or a camera if you prefer) look at it from a close distance. Will the maximum brightness perceived not have any "white" to it? Because there is no white light if it's all blue. Probably the brightest it could be would be solid blue? Therefore, blue photons could produce a range of color of black to solid blue depending on the luminous or amount of photons hitting your eye per second? If that's the case then what happens if you raised the intensity of the bulb to an extreme? Is there a cut off point where even if you add more intensity to the bulb, you still see the same solid blue color?

You should probably narrow your question down to a blue laser emitting a specific frequency of light.  There is no such thing as white photons.  "white light" is perceived when there is a roughly equal mix of frequencies.

@BrandonEnright I am aware of that, I didn't say white photons.

I think the perception tag might be appropriate here, since the photons will always stay within a narrow spectral region and the "darkness" or "whiteness" of the light is merely determined by the lowest sensitivity and the saturation level of the receptors in our eyes, which depend on the number of photons (which determines the intensity of the light).

@Nathan hm, good point. (Flag it!) It's sort of borderline, because there is a fair amount of physics involved in understanding how our retinal cells respond to different wavelengths of light, but the fact that this is really about color perception does suggest it as being off topic.

'"white light" is perceived when there is a roughly equal mix of frequencies.' Not even that. White light is perceived when there is a roughly equal excitation of the three distinct types of color sensitive photocells in the eye, and they each have a broad sensitivity. Which is essentially the same information you need to answer all of these "How do humans see XXX?" questions. We've accepted them in the past because (1) there is some physics in them and (2) there was nowhere else for them to go, but at this time I would favor moving them out.

Generally, looking at the ray of a fairly powerful laser (3-4W) you still see it of whatever color it is (blue, red etc, but not white). NOTE: be careful if you try this, it may be very dangerous! Never look directly into the laser beam.

The color that human vision perceives for a specific frequency of light (prior to saturation of any cones) is derived from the relative responses of different cones.  For example, at about 480nm, the response of S and M cones are roughly equal.  However, the human eye is not able to distinguish pure colors (single wavelengths) from combinations of wavelengths which produce the same response in each of the three cone types.
It is possible that a blue light source could appear white to the human eye, because the cones which inform our perception of color are not strictly monochromatic.  Rather, they have a range of sensitivity across the spectrum, and all cones are at least somewhat sensitive to blue light.  (See this diagram.)
If the blue light is so intense that it saturates all cones, S (blue), M (green), and L (red), then it will be perceived as white light.  However, in order to saturate the low-sensitivity M and L cones, the intensity of the light would be blindingly high.  Prior to this point, but after saturating the S cones, the apparent color of the light would shift toward green before eventually appearing white.  For intensities that are not saturating to any cones, the hue of the color blue will remain constant, while it's value (or lightness) may change.


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Which Enzymes Catalyse the Deacetylation of Drugs in the Human Body?
If you would like more specifics seeing how I realise that this question is very broad and may be difficult to answer in general then hopefully the following will help you out:

I am particularly interested in acetyl groups bound by carbon single bonds
Drug metabolism in the liver particularly interests me
The drug paracetamol's (acetaminophen) deacetylation to p-aminophenol is of particular interest to me.

Acetyl esters can be deacetylated by carboxylesterases.
In case of an acyl/aryl group attached to acetate group (e.g., benzoate), I guess it will first undergo ring opening and then beta oxidation (as in case of tyrosine).
Paracetamol -> p-aminophenol is a deamidation (I am not sure, but enzymes like ornithine decarboxylase can do that job... just a guess).


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Is it technically possible to make someone see something when their eyes are closed?
I'm writing a little article and need any information about how human vision works and latest
technologies and discoveries around. Actually its not a professional article. Its for a group of my friends.
In fact I'm looking for any possible way to make someone ACTUALLY see when their eyes are closed. I don't know maybe convince some of brain cells that a real pulse is coming from eyes, but in reality its coming from a computer; or something like that.
I call it a virtual vision, myself.
Do you guys know if there's any professional article, discoveries or technologies available about this topic?
I'm very very interested in this topic by the way.

One side note: even with eyes "closed", light penetrates your eye lids, and you can see things. Of course they are very very blurry.

Two weeks ago, I watched this video. http://www.youtube.com/watch?v=qLziFMF4DHA&list=UUTVCr29RCZJI0CIG2SJgPgA&index=9
In here, how this guy sense the things around him is not clear (it says he uses echo location to navigate, but is it really true?). However it is an interesting documentary. I hope this will help you as a different example.

Yes, this is most certainly possible and already being done. As long as the visual cortex of the brain (in the occipital lobe, i.e. at the back of your head) is functional, the correct stimulation will produce visual perception.
In cases of blindness caused by malfunction of the retina, meaning that the rest of the visual pathway is functional, this is the most promising approach to restoring vision. See Visual prosthesis and the TED talk on it.
"Virtual vision" as in projecting a whole field of vision (reflecting the real surroundings) is the big ideal target that this technology is aiming for. Of course as soon as they manage to make a working prosthesis for blind people, someone will probably try to make it non-invasive and easily usable for commercial exploitation.

Astronauts discovered that the answer is yes: After a number of astronauts reported seeing "light flashes" even with their eyes closed while in space, subsequent experiments on earth determined that Cosmic rays can trigger all sorts of unusual visual stimuli through closed eyes and in otherwise complete darkness.

One of the things that you could also consider are the experiments done with LSD: if I recall correctly, LSD (or drugs coming from certain mushrooms) cross your neural circuits. You end up "smelling what you see", and "seeing what you smell", etc. In this sense, you would be able to see with your eyes closed, although this is a very particular (yet, interesting) case

I am not an expert on this subject, but essentially what you would need is to have a machine interface directly with neurons.
Neuro-mechanical interface is something which interests many scientists but unfortunately we are only at extremely early stages - even getting accurate readings from a single neuron in vivo is a very challenging task. To achieve virtual vision you would need both technology to accurately interface with many many neurons and to fully understand how the neurons encode visual information. I think these are huge challenges so it will probably take a while to get there.
Until then I guess we will have to stick with VR glasses...


text:
Why Do Nerve Signals Get Crossed?
First off, I don't know if this is a normal healthy thing to occur. There have been many times where I have an itch on say my arm and I scratch it, only to feel the scratching elsewhere on my body. I assume somewhere along the transit of the touch signals to my brain the signal gets mixed up and is processed incorrectly.
So my questions are:

Why does this mixup happen? (chemical imbalance, damaged nerves, etc..)
How does my brain correspond the touch to somewhere else? (what is the process behind it)

You might be interested in this. And this.

@terdon: Thanks for the links, but interesting as they are they don't answer why the touch signals get crossed =o(. Irregardless if it is an itch or another form of touch, the brain should not be interpreting a touch on one part of the body as coming from another part. My question is why this mixup occurs and how the brain is incorrectly processing it.

I know, that's why I posted a comment and not an answer. Just thought you might be interested.

Could you clarify exactly how the sensation is wrong for you? You are supposed to have an itch for whatever reason, and when you scratch it it's supposed to go away and you get the touch sensation of your fingers instead. All in the same place of course. Are you saying that the actual touch sensation of your fingers on your skin is mislocated? If so, is there a regularity to where it is mislocated (e.g. symmetrical to body axis)? And does this only occur on skin that was itching before, or any part at any time?

@Armatus well the last time it happened I got an itch on the back of my arm and scratched it only to feel the scratching on my lower back. I don't recall which body axis they were at, I'll have to note that next time it happens, but it's rare. No, it does not occur on skin that was itching before.

What I meant was things like, if it was mislocated on the same spot but opposite side of the body for example; but it seems to be random. The other question was what exactly causes it to happen - does it only occur when you are scratching yourself after you were itching or also in other situations?

@Armatus I've only observed it happening when there is a random itch, but no prior itching, but not all itches have it happen. That's why it is so rare, I've only experienced it around two dozen times in the past ~15yrs. I'm 23, I'm assuming it may have happened when I was younger, but I never thought much of it since was just a kid.

How clear is that sensation? Does it correspond to your finger movement, i.e. are you certain that it is a misprojection of the sensation (onto the wrong part of your body)? With such a rare occurrence it could just be a random error.

@Armatus yes, it does correspond. If I stop scratching the itch, the touch sensation on other area of body stops, and if I start again it starts. I can't reproduce it later on, maybe because I can't find the exact spot the itch was, which is where the error is being triggered. If it is a random error, how and why would such a thing occur?

My mother explained this to me when I asked because I also get the same thing. I believe it is hereditary because she also gets this. She called it twisted nerves but it is not common at all. Scratch your side, feel it on your leg, go to your leg you feel it on your arm, scratch your arm and then you feel it on your back. No, it doesn't happen all the time and is a weird feeling when it does. It doesn't have a magic button where it always happens in the same place for the same reason because it isn't caused from an injury. My mother participated in a medical questionnaire when she was in her t

I get a similar weird nerve sensation happen to me. I can run my fingers down or up the outside of my leg and i feel the sensation on the inner side of my leg? Its weird and i have had it happen in different places on my legs. I would like to know WHY this confusion of sensation happens? I do suffer from multiple level high grade thoracic (T5 to T10) cord compression from herniations onto a tethered thoracic spinal cord (stuck to the bone) peripheral neruopaphy and autonomic nervous system dysfunction, (ideopathic Hypersomnia, Gastroparesis, swallowing difficulty, heart palpatations and low BP

Well nerve crossing or misinterpretation of nerve signal by the brain does not happen all the time. In case it happens frequently then I guess it would be Multiple Sclerosis or might be Fibromyalgia syndrome. In multiple sclerosis, the Myelin sheath surrounding neuron when gets damaged causes certain problem with nerve signal transmission to the brain. But that is not the main cause. The main cause can be found in Neuropathy:

When nerve cells are damaged, perhaps by a temporary restriction in their access to oxygen, they too atrophy or shrink a little, thus the synaptic junctions widens.  Just like with a spark plug in your car or lawn mower, if this gap gets too wide, the spark cannot make the jump. A normal sized nerve signal cannot jump this enlarged gap either, so the signal either does not get through or it gets misdirected to another part of the body and is misinterpreted as pain.

So I can say that the nerve cells in the place where you feel real pain fails to transmit the signal to brain via its neighboring nerve cell instead that signal passes through some other node randomly (or it might take the same path every time you touch the pain area) and signal the brain which gets misinterpreted and make you feel that you have pain in the misinterpreted region.

This is part of a neuro issue...like seeing numbers in color, or touching something but feeling it in another part of your body. The sensations are processed in the brains communication area and ifeas/sensations get mixed or crossed. 4% of the population has these experiences. You aren't odd; you're exceptional.

Welcome to SE Biology. Because this is a straight Q & A site rather than a chat site, our expectations of answers are perhaps different from other sites. You can read the help on writing good answers here. In particular, we expect you to provide evidence of some sort in support of opinions or information you provide. This is best done by a reference to a scientific paper or a reputable source on the internet, such as Wikipedia or one of the text books on NCBI bookshelf. I suggest you might consider editing your answer with this in mind.


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How Common are Paraneoplastic Syndromes in Cancer Patients?
I recall reading around one in four cancer patients will suffer a paraneoplastic syndrome during the course of their illness but I can't find where I read this and I can't find any reliable sources to back this up.

The incidence of paraneoplastic syndromes appears to be variable and dependent on the kind of cancer. Estimates by Baijens and Manni (2006; Eur Arch Otorhinolaryngol 263: 32–36) are 1% to 7.4% of all cancer patients, however they are citing Gulya (1993; Laryngoscope 103: 754–761) and Zuffa et al. (1984; Neoplasma 31: 231–236) for the data.
Pelosof and Gerber (2010; Mayo Clin Proc 85: 838–854) make the particularly salient observation that

As patients with cancer live longer, and as diagnostic methods
  improve, this prevalence will likely increase.


text:
In which month should I map maritime vegetation?
I'm studying habitat use by Brent Goose in the UK, a species that feeds on maritime vegetation. It's main food types are Zostera sp., Ruppia sp., Ulva / Enteromorpha sp. and Puccinellia sp. I plan to map these vegetation types on an inter-tidal mudflat in North-east England during the summer.
I want to choose a month to map these vegetation types that will allow the most accurate mapping of their distribution of vegetation across the mudflat. I think there are two considerations 1. the month they easiest to identify 2. the month they are most visible.
Which month should I choose?

@kmm. Thanks for edit. What do asterisk around Enteromorpha mean?

That's just the markup for italics. For some reason the parser didn't like /*. I added spaces around / to make both genera italics.

One way to approach this problem would be to look at herbarium collections of the taxa that you're interested in. Usually, a flowering or fruiting specimen is easiest to identify; but no matter what character is best for your taxon, if you look at the herbarium collections and see that
-most of the collections identified to species, or
-the especially good-looking collections, or
-flowering/fruiting collections,
were made in a certain month or season, that could help you to narrow down your time window.
As a bonus, in reviewing herbarium collections, you'll have given yourself a step towards being able to identify the species.
Some herbaria have some collections online; here, for instance, are records and images for online Puccinellia collections at a number of UK herbaria.


text:
What is the gas inside a Capsicum pepper, and how does it get there?
Every time I make fajitas, I cut into bell and chili peppers and notice how hollow they are.  I always think to myself: what is the gas inside this pepper, and how does it get there?
Perhaps Capsicum peppers are porous.  I did a little kitchen experiment to try to find out.  (I'm afraid I don't know much about biology, so this "experiment" is likely to be flawed in at least one basic way, but I figured I should at least try to figure it out myself before asking.)  Here's what I did:
I filled a small container with water and submerged an uncut Anaheim pepper.  It was quite buoyant!  I put the lid on the container so it would stay submerged.  It didn't seem to become any less buoyant, and its interior didn't seem to fill up with water.  No bubbles emerged from the pepper, as least as far as I could tell.
So air doesn't seem to easily pass in or out of the pepper.  And of course they don't grow around air, so how does the gas get in?
Here are my guesses:

The fruit is porous to air, but the holes are small enough that, in my experiment, they were sealed by the surface tension of the water.
The fruit isn't porous to air when fully grown, but it is porous to air while it's still developing.
The fruit does some amount of photosynthesis, and the air is waste oxygen.

Nice one for the experiment :). Bear in mind that there are many many processes happening in living thing that can produce gasses. Breathing, photosynthesis, fermentation etc etc.

Yeah! This very issue puzzled me a year ago, and I asked several people, but received no reliable explaination. I also guessed, that air could it not be, as the fruit is growing from inside out of... well... "nothing", so the air must get into it, as the fruit doesn't grow it around, as the author here has written too.
Then, I thought, maybe some part of oxygen, the product of photosynthesis ongoing in the plant's leaves, in some natural way, gets into the fruit's inside, thus filling up the empty space, or... a kind of "blowing it up" (hmmm, well, well...).

To answer your question of what the gas is, how about the glowing splint test for oxygen! I guess it might work with a recently snuffed out match too. Cut a plug in the the pepper but leave it in place until you have the glowing match ready, then quickly open the plug and hold the match into the opening. It should relight if it is oxygen and you may hear a popping noise.
As for whether the surface tension is preventing the flow of air, you could try adding some detergent (washing up liquid or soap) to the water to break the tension and see what happens.
However, I have found an article suggesting the environment is, compared to the standard atmospheric concentration anyway, low in O2 and high in CO2 in two different pepper cultivars.1

Samples withdrawn from the fruit locule over time show that CO2 ranges between 0.5% and 3% (5000–30,000μmol·mol–1) (Fig. 2, top) while O2 ranges between 18% and 20% (Fig. 2, center), compared to the composition of standard atmosphere (400μmol·mol–1CO2; 21% O2)

1 Blasiak, J., Kuang, A., Farhangi, C.S., and Musgrave, M.E. Roles of Intra-fruit Oxygen and Carbon Dioxide in Controlling Pepper (Capsicum annuum L.) Seed Development and Storage Reserve Deposition. J. AMER. SOC. HORT. SCI. (2006) 131(1):164–173.

If we ever get a community ad on another site, I suggest "Biology: World changing research one pepper at a time".  Good suggestions, I'm tempted to try them!

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


text:
Why does the hydrolysis of ATP increasing entropy increase the Phosphoryl-‐transfer Potential?
I am currently taking a biology class. I do not understand this concept. I understand that the electrostatic repulsion of the negative charges, resonance stabilization and hydration stabilization all contribute. However, I do not understand why an increase in entropy would help. Wouldn't it be more favorable to have less entropy in a system?

The phosphoryl transfer potential is one way to think about the free energy available to do useful work when ATP is hydrolysed.
As you can see from the free energy equation below, a positive change in entropy will help to decrease (i.e. make more negative) the free energy change.
This is why an endothermic reaction can still occur spontaneously if the entropy change is big enough to create an entropy term that outweighs the enthalpy term in the Gibbs free energy equation.

ΔG=ΔH - TΔS
where:
T= temperature
G = Gibbs free energy
H = enthalpy
S = entropy


text:
EGFR, sialylation, and cancer progression
EGFR (epidermal growth factor receptor) has been intensively studied in cancer and treatments have been developed to inhibit EGFR signaling.  Sialylation of EGFR is known to block dimerization  and down regulate signaling.  I just read this paper:
Liu et al. 2011. Sialylation and fucosylation of epidermal growth factor receptor suppress its dimerization and activation in lung cancer cells. PNAS 108: 11332–11337. (basically just read conclusion if you don't have time).
What I don't understand is that the authors seem to say that increasing sialylation might be a good thing to prevent cancer progression since it inhibits EGFR dimerization.  However, wouldn't this go against almost 50 or 60 years of research that suggest that increased levels of sialic acid are one of the well known hallmarks of cancer that aid in its progression and metastasis?  What could explain this apparent discrepancy?

Wikipedia claims (without reference) that

Metastatic cancer cells often express a high density of sialic
  acid-rich glycoproteins. This overexpression of sialic acid on
  surfaces creates a negative charge on cell membranes. This creates
  repulsion between cells (cell opposition)[5] and helps these
  late-stage cancer cells enter the blood stream.

so I assume this is a summary of the "50 or 60 years of cancer research" that you mentioned. I don't doubt you, I've just never read up on this particular aspect of cancer. Be that as it may, there is a difference between a cell's expressing high levels of sialoglycoproteins overall, and inducing high sialylation of one protein in particular, in this case EGFR.
As you may be aware, EGFR dimerization induced by multiple methods, including EGF binding, overexpression, mutation, chemical or antibody crosslinking, etc. activates tyrosine kinase domains in its intracellular region to auto-phosphorylate specific Tyr residues in its tail, which then recruit adapter and scaffolding proteins which support downstream signal transduction.
The paper you read shows how increasing sialylation of EGFR reduces its trans-affinity for itself and inhibits dimerization, and hence the downstream signaling cascade. This is a good thing in certain types of cancer which are driven by aberrant EGFR signaling, whether through overexpression of EGF and/or EGFR, mutations in the kinase domains, mutations in the dimerization domains, or otherwise.
This paper is also a great example of an apparent bad thing turning out to be good, when properly targeted and controlled. Excess sialylation of a cell may be bad, but specific over-sialylation of EGFR could turn out to be very useful, if we can learn how to modulate and target it. Another common example of this phenomenon is radiation therapy. Normally, high levels of radiation are bad for your body, and can actually cause cancer, among a range of other illnesses. But, there are many different ways of specifically targeting radiation to a tumor to kill it while sparing (to varying degrees) the surrounding tissue and the rest of the body.

Thanks for the response Matt. I guess I just don't see how it is possible to target siaylation of a specific glycoprotein in a cancer cell. Not only would that likely require cancer cell specificity, it would require activation of some metabolic pathway that would only sialylate EGFR--in otherwords subcellular accuracy. I don't think I've ever read of a way to specifically control glycosylation of a targeted single protein. I guess I simply don't agree with the authors' conclusions where they state that shutting down transferases might be a "bad" thing because it would promote EGFR dimers.

I know many people have long been trying to create glyco-transferase inhibitors to try to inhibit things like sialyation of cancer cell surfaces to prevent metastasis.  This paper alludes to the idea that this might be bad because it would promote EGFR activation.  I can't see why the authors would reach such a conclusion based solely off the study of just 1 glycoprotein when there are many others on the surface that may have negative influences if excess sialylated.

@GPI - that's why I put "specific over-sialylation of EGFR could turn out to be very useful, if we can learn how to modulate and target it" in there. It's a pretty big if.