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Can extinct animals be cloned?
Scientists have found mammoth blood, and are planning to clone a mammoth.
How does one go from having its blood to a full blown living mammoth? Is it possible?
Why does it matter if the blood is frozen or not? Suppose one found dinosaur blood, could one clone a dinsosaur (as in say 'Jurassic Park')?

and I think the DNA will be too heavily degraded by now too get a copy of the full genome of one

Given that nobody has ever been able a clone, say, a frozen chicken out of a household freezer, I'm highly skeptical cloning mammoth is possible today.

My guess is that they might synthesize DNA, by sequencing fragments found in the blood. Once they have the DNA, perhaps implant it in an elephant egg?

DNA degradation half-lifetime within fossilized/frozen species is ~ 500 years., even when the conditions are perfect for preservation.
Thus, in theory, if we could sequence anything that is less then 13 000 years old (expected length of preserved nucleotide sequences ~30 bp, which is just enough to stitch together two unique regions). If we have several copies of DNA (several cells), we can go a little bit further by sequencing same reads several times. If we assume an average cell is 30 um in diameter, we have ~40 000 cells in a cubic mm of tissue samle. this will allow us to extend the sequencing horizon by another 8000 years. With a cubic sample of intact, perfectly preserved tissue (this is REALLY A LOT and REALLY RARE) we could get an additional 5000 years, limiting our possibility to know the genome, let alone reproduce it to 26-30 000 years.
By using a couple of sequence assembly tricks, such as existence of reference genomes of closely related species, we could either decrease the amount of tissue sames or allow the DNA to get a little bit more degraded. However, even with a cubic centimeter of tissue we won't be able to go beyond 50-100 000 years.
The furthest we have gotten now is a Neanderthal sequence (~30 000 years) and it was already tough. It would be impossible to get a hand on dinasaurus DNA sequence, let alone trying to clone it. Mammoth, Saber-tooth Tiger and Dodo should be ok, provided we can find their remainders.
Now, Once you get the raw DNA sequence, you have to get the epigenetic code right, find a compatible egg of a related spicies (that is quite hard), inject your DNA into it, and hopefully, with lots of ifs you can get your clone and hope it survives. However the part about getting the epigenetic code right and finding a compatible egg is really not easy. Personally, I won't parry on anything that doesn't have close related species still living.
UPDATE: as of June 2013 a genome of a wild horse 700 000 years old have been sequenced, which is the furthers we could get so far.

I'll just add that projects to clone a mammoth have been active for over a decade and privately funded projects are also underway.  While the precedent has not been set by actually doing this, the technology of reproductive cloning of animals is still very new and each new case is its own problems to solve but there's reason to believe that the technical difficulties can be overcome as new animals are constantly being added to the list..
For instance lots of hybrid experiments are underway where a modern animal's genome is used as a scaffold in which extinct animals genes are inserted, just as was suggested in Jurassic Park.  Its not clear how far this can go, but there's reason to be quite optimistic.
By the way, Ed Yong's blog post is a great place to start for a discussion of the details of inseminating an elephant successfully.

@GriffinEvo You shouldn’t add content like this to other answers – instead, post your own answer.

@KonradRudolph Apologies, here is my additional point but I am not going to write a whole answer because this isn't a complete answer: This TED talk (http://www.ted.com/talks/michael_archer_how_we_ll_resurrect_the_gastric_brooding_frog_the_tasmanian_tiger.html), from June 2013, is about such projects which are trying to rescue two recently extinct species and they seem to be making some progress.

How does one go from having its blood to a full blown living mammoth?
  Is it possible?

It is possible, but it is really hard with the current technology. The DNA in the frozen mammoth blood is heavily degraded, but with enough degraded DNA samples you can create a DNA sequence. After that you can compare it with elephant DNA, and you can genetically alter an elephant zygote. You can synthesize the whole genome too, but it's much harder.

Why does it matter if the blood is frozen or not?

The DNA degrades slower when the blood is frozen.

Suppose one found dinosaur blood, could one clone a dinsosaur (as in
  say 'Jurrasic Park')?

You will never find dinosaur blood, fossils are just rock, nothing more.

Welcome to Skeptics Stack Exchange! We require references for all significant claims here. Please edit your answer to include appropriate references.

The premise of Jurassic Park was that mosquitoes, with a meal of dinosaur blood, had been trapped and preserved in amber. This is distinct from fossilization - an answer needs to address this.

Ye, but you cannot preserve DNA for millions of years...

@Fabian Ok, I'll cite articles later, now I have to go...

“you cannot preserve DNA for millions of years” – any evidence for that? I know for a fact that plenty of respectable biologists think the opposite.

http://gnusha.org/~nmz787/instability%20and%20decay%20of%20the%20primary%20structure%20of%20DNA.pdf

Btw. you can preserve DNA for millions years if you use an energy source and repair mechanisms to maintain its structure. So you have to work against entropy. I don't think fossils contain such a mechanism...

Hmm maybe you are right, in the end of this article there is a section which describes, that maybe there is a chance to retain dna fragments from 20 million years old fossils. I tried to find more recent articles, but I have found nothing yet... :S


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Is there a practical upper limit to amount of nucleotides or genes in a transformed plasmid?
I'm currently working on a synthetic biology project which involves working with lots of different parts. I would ultimately like to integrate these genes by transforming a single plasmid. I've heard (casually) that 9-10 foreign genes on a transformed plasmid is often the practical upper limit for these types of experiments, without a real explanation other than "beyond that, it just doesn't work".
Is there a practical upper limit to size of amount of genes in a transformed plasmid, assuming all need to be expressible? What causes this upper limit?

I think the upper limit is more about the size of the plasmid and the efficiency of getting very large constructs into cells, at least in my experience working with mammalian systems. Beyond that you would need to start thinking about other vectors besides plasmids, such as viral delivery systems, Vaccinia vectors, artificial chromosomes, and the like.

I'll most likely be working with E.coli. Putting aside differences in transformation, would there be any reason to suspect differences in functional expression of each gene? (If there is, I've never heard of it. It would seem like genes should get expressed equally in no matter what lengths of nucleotide).

As long as you can get the construct into the cells in one piece without some kind of degradation or shearing, I don't see why they shouldn't get expressed. Most of my experience with E. coli is just using them as a tool to generate plasmids or proteins, and I know that some of their characteristics are quite different than eukaryotes. I was just thinking, though, would a BAC or something similar serve your purpose? 150-350 kb is a heck of a lot bigger than your standard pUC19...

A BAC might work. Thank you for the advice. You should turn your comments into an answer.

From my experience in the mammalian world (and this may apply to bacterial systems as well), it's not so much the number of genes in the plasmid as its actual size. The larger the construct is, the more difficult it will be to get it into your target cells in one piece, without degradation or shearing. Since the transformation efficiency is lower, you are getting fewer whole constructs per cell, so depending on how you've set up your promoters, the overall expression level can be significantly lower. The trouble with splitting your genes amongst two or more plasmids is that each will have different transformation efficiencies, and there will be a certain (perhaps large) number of cells that don't get the full complement of genes, interfering with phenotype analysis. And again, you'll also have to consider differential expression rates.
However, once you get your vector into the cells in one piece, theoretically they should all get expressed at approximately equal levels (assuming identical promoters). It's possible that steric hindrance among multiple transcription complexes may occur - I just don't know enough about bacterial transcription and the effects of circular plasmids to say.
One way to get around many of these factors would be to use a bacterial artificial chromosome or BAC. BACs are 7-10 kb vectors that can have inserts of up to 1 million bp cloned into them and are then electroporated into cells. One of (the many) cool things about them is they control their own duplication and partitioning at cell division, so succeeding generations should have essentially the same copy number as the original. They were heavily used during the Human Genome Project to amplify large sections of DNA for sequencing, but they are also used in many other studies, including synthetic biology. OpenWetWare has a list of some common ones, and NEB sells pBeloBAC11 systems.

Also bear in mind that being based on the F plasmid, BACs are low copy-number plasmids. This means you may have to take care with antibiotic concentrations, and if levels of gene expression are important in your work you shouldn't expect as much as you would get from a standard high copy number plasmid.

@AlanBoyd thanks for the edits - sorry about mitosis, like I said I'm a mammalian guy :)

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Identify this waterfowl species?
I've been unable to find anything on the Google resembling this bird. I took the photo in Virginia Beach, VA around 2010, October, I think...
It appears to be between winter and summer plumage but I'm not sure. I tried looking on whatbird.com but couldn't find anything that really seemed to match up well.
Edit
I've added some more photos since people seem to question whether or not the white is snow, for some reason. Also note that most seem to have a red bill with a black tip, while the one with more white on its breast has a largely black bill with just a red band. Do bills change colors when plumage does, is that a thing, or perhaps it's just an anomaly or a gender trait?

I don't think there's seasonal plumage change going on here.  The white patches seem to be driven snow.  The bird on the left is plastered like the tree on the right.

There is snow, but it's not all snow. Also notice that the bills are two different colors.

It looks like a male and a female with the female being smaller and read beaked.

They don't really look like different sizes to me(at least, not drastic enough that I'd think it was a gender distinction...) the one on the left just has its head up and the one on the right has its head down.

Yes, looks like Cairina Moschata - Muscovy Duck. Native to Americas, domestic/semi-wild in Europe.

I am not an ornithologist, but using identify.whatbird.com and a simple google search, this appears to be a Muscovy Duck. Try a google image search for yourself! Some of the birds pictured have more ostentatiously red or larger caruncles, but some look very similar to the birds you photographed. For example: http://www.birdinginformation.com/birds/ducks/muskovy-duck/
From muscovyduckcentral.com and identify.whatbird.com:
The domestic breeds can come in a variety of colors, but are primarily black and white with red and white bills. The males are larger than the females -- around 15 lbs for a male and only 8 lbs for a female. Females are duller colored than the males. Muscovy ducks are indigenous to Mexico, Central and South America, but are now raised in many different locations. They are considered a good duck stock because they are large, breed quickly, provide good pest control, and are quieter than many other duck breeds.

I used whatbird.com for VA and that didn't come up ... (as mentioned in my comments) Well, your google-fu is obviously superior to mine. Thanks :D

Aaaah, that'd be why it dodn't show up in VA. I would've thought it would take migration into account tho. Huh.

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How do fully dioecious plants determine sex?
I know that a minority of plants are fully dioecious, with adult plants producing either only male or only female flowers. When is this sexual differentiation determined? Is the seed of such a plant already male or female? Is it a simple genetic difference?

The short answer is that in dioecious plants the sex of an individual plant is determined by its chromosomes.
Several familiar crop plants are dioecious: asparagus, kiwi, hop, papaya, spinach and yam. The evidence indicates that dioecy has evolved independently in different plant families. I refer you to

Matsunuga & Kawano (2001) Sex determination by sex chromosomes in dioecius plants. Plant Biol 3: 481-488.

I have summarised below some of the introductory information in this review.
First some background for context: In mammals there is an XY system in which maleness is determined by an active Y chromosome i.e. the Y chromosome carries male sex determination gene(s). Males are said to be heterogametic. In Drosophila there is also an XY system, with heterogametic males, but in this case what determines sex is the ratio of X chromosomes to autosomes. This ratio exerts its effects through the Sxl gene. In this system the Y chromosome does not carry male-determining genes.
In flowering plants, in dioecious species, the usual situation is that males are heterogametic. However, there is variability in the underlying mechanism of sex determination.  So for example in hop (Humulus lupulus) there is a pair of sex chromosomes that can be distinguished by their appearance. However there is no active male determination but rather the X to autosomal ratio determines sex (as in Drosophila). Conversely, in asparagus (Asparagus officinalis), sex is determined by a pair of chromosomes designated pair 5. The two chromosomes are morphologically indistinguishable but genetic evidence indicates that there is active sex determination in this species - one member of pair 5 acts like the mammalian Y chromosome.


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What is a good review article source for Physiology?
I am looking review articles for Physiology.
For instance, Physiological explanation of steps of measurement of the metabolism by Douglas-Haldane.
There is no section for Physiology or metabolism in Advanced Search of Nature Review.
What is a good review article source of Physiology?

Annual Review of Physiology? http://www.annualreviews.org/journal/physiol However the Douglas-Haldane method was published in 1913, so I'm not clear what you are hoping to find in recent reviews, but then again its really not my field.

The Journal of Physiology
Annual Reviews Physiology
Journals from American Physiological Society
Frontiers in Physiology
Experimental Physiology
Often, notable research papers are published in journals with high impact factors, although being published in a journal with high impact factor does not mean the research is better over research in smaller journals. But it can be a rough indication.


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Removing bacterial contaminants from resin
We have a few Strep-tactin columns that had some growth in them and we would like to regenerate the columns back since the resin is quite expensive. Basic goal: remove the brown stuff.
So far, I've killed whatever living material there is with 20% EtOH and 0.5 N NaOH. After cleaning out the columns with Tris Buffer, I've tried regenerating the columns with Buffer with HABA and the resin is a bit redder than before (typical reflection of good regeneration). However, rinsing out the columns again still leaves behind a brownish color. There is also a good deal of black particulate in the resin.
I'm curious what methods exists to clean out a contaminated column.

I'd check the data sheet of the column for the limits of what the column can handle and just try the harshest of those conditions. They usually also specify cleaning procedures there. I'd try something with high salt to wash out that stuff, maybe also reverse the flow direction and run the column backwards.

I'm going to try the high salt. That's a good suggestion. The reverse flow probably won't work since I've repacked the column a few times by now

in the future consider azide is also sometimes used to keep columns sterile in storage.  Though it won't clear out the dead matter...its possible that the column was never meant to be this cluttered up.  In my wet lab days i'd be throwing that out... sorry to be a party pooper, but molecular purity is hard enough without whole cell fragments drifting about.

@Shigeta, alas it wasn't my column. I guess it's time to buy some new resin.

Yeah sorry, but remember your time is valuable too - don't spend 3 days trying to fix equipment that might ruin your prep...unless you want to be fixing equipment of course.

I am an engineer by training. The default option is always to fix it yourself. Usually with duct tape.


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Why is the bond between oxygen and iron in hemoglobin at a specific angle?
The bond between oxygen and iron in hemoglobin is usually drawn at an angle of about 120 degrees to the O=O bond. Why?

summary:
O2 could form a linear complex with the Fe atom, but then it would start to look more like a mineral Fe=O...O bond - a linear bond would be like a transition state to an iron oxide (rust).   An Fe-O-O bent bond preserves more of the electronic character of the O2 molecule and promotes strong but reversible binding to Hemoglobin.
The oxygen molecule forms a partial covalent bond with the iron in the heme (the flat molecule is a ringlike heme in the picture viewed from the side so you can see the oxygen molecule bound to it.)
The lone pair of electrons of the oxygen atom which forms the bond to the iron has a 120 degree angle with respect to the oxygen molecule itself.  In chemistry we say it is sp2 hybridized.  This implies a slightly greater than 120 degree angle between the Fe-O and the O-O axis would be energetically preferred in oxygen binding.
You can see on the other end of the oxygen, there is a histidine sidechain nitrogen which interacts in a similar way - crooked at a similar angle to the oxygen molecule.
As @MattDMo points out in the comments, it would not be 120 degrees exactly in fact even freshman chemistry molecular orbital theory would say that the double bond would take up more 'space' than the sp2 orbitals, widening out the angle Fe-O=O angle to be greater than 120 degrees.  Then the protein has its own geometry - the histidine and the heme iron are fixed in space and probably have their own location, so this is just an approximate, qualitative bond angle..
The claims of superoxide formation is because the oxygen is diamagnetic the iron and he oxygen, which are both paramagnetic, somehow pair to eliminate their magnetic moment.  The PNAS paper cited here goes in depth on this issue.  The article curiously just says the highly reactive superoxide is kept from being chemically consumed by the hydrophobic pocket around it.
The oxygen almost makes a superoxygen the iron sort of oxidizes but doesn't quite. Its also due to the peroxide like character of the oxygen molecule, partially bonded at both ends.
Still the point is that hemoglobin holds onto the oxygen by making a partial covalent bond.  After all when the O2 unbinds, its just O2 again.  A later study does detect some paramagnetism at low temperatures. In the last word on this that I could find, Pauling does a review and concludes that the electronic state of the heme iron and oxygen complex is a combination of three different electronic states - partly superoxygen, partly oxy-iron and molecular oxygen.
The reference also gives the Fe-O-O angle as 117 degrees.
[Just a note that the reference page I got the picture from refers to rational design of the hemoglobin molecule...in this case they are engineers talking about how they could change the amino acids in the protein to get other properties out of the hemoglobin system - rationally.]

Have you read the Wikipedia article on hemoglobin? In this section it claims that the O2 is really in the .O2 superoxide form, and the iron is Fe(III). They don't talk about the bond angle specifically, but I would imagine that it wouldn't quite be the perfect 120° sp2 orbital that our first-year chem teachers taught us about...

@MattDMo you are right - good points - let me address this in the answer since its a bit long a response....

ok had time to dig a little deeper tonight...see above.

Hello @shigeta, can you tell me if the hemoglobin binds gas O2 or another state of O2 please?

its O2 dissolved in the blood, but its the same as the gas really :)

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Optogenetics - How do microbial opsins work?
I'm just introduced to the optogenetics method and am having some trouble grasping the genetics (of the optogenteics) part of things.
So we have Retinal and Opsin that form Rhodopsin molecule that serves as a light-gated ion channel (which is, needless to say, very cool).
What is the process in which a cell population is targeted and implanted with these Rhodopsins?
And where does the microbial opsin gets into picture?
My main resource, so far, was - Optogenetics - Method of the year/Nature.
Thanks!

Before I venture into an answer... what is your background level in biology/genetics? Anyway, the idea is the same as that of making GFP expressed in a specific cell type, maybe you are familiar with that?

@nico Thanks for your comment, My knowledge of genetics and specifically genetic-biology methods is somewhat limited. I would appreciate a high level explanation, more of a popular science approach than a guide to the optogenetics fresh experimenter. Something like - a virus DNA is engineered to have desired rhodopsin and using a specific promotor, when injected to the subject, spreads this DNA to the target cell which as a consequence starts expressing these light gated channels. And if I may add another small question, what is Cre-dependent, I keep encounter them all around. Thanks!

There is nothing special about the use of rhodopsin when compared to making a cell express any transgene. This question can then be read as:

What is the process in which a cell population is targeted and implanted with a gene of interest?

There are many ways, which depend on the specific cell type and on whether you want to do it in vitro, in vivo and in which species, and it would be very complex to explain them all in detail here, so I will limit myself to two approaches that are popular when doing optogenetics in rodents: viral infection and transgenesis.
Viral infection uses an inactivated virus to deliver the transgene. Essentially you engineer a piece of DNA with the gene for the bacterial opsin of interest and you put it in a viral envelope, that is a series of proteins that form the "body" of the virus and that contain its genetic material.
You then inject the virus in the desired zone (e.g. in a specific brain nucleus) and wait for it to infect the cells around the injection site. A week later those cells will express the transgene.
For (at least, I think) historical reasons the first type of viruses used for this approach were lentiviruses. These, however, are a tad more complex to handle (especially as they require specialised rooms where they can be handled safely) so adeno-associated viruses (AAV) are becoming more and more popular.
Note that the virus is inactivated, that is, it cannot replicate, just infect the cells around the infection site, but it will not be able to spread around. This is both for safety reasons and because you want the infection to be confined to the specific region where you injected the virus.
As I was saying before, instead of putting a bacterial opsin you can put whatever gene of interest, the procedure is the same. As for the opsins, the first two that were used were the channelrhodopsin-2 (ChR2), a channel sensitive to blue light and that can be used to depolarize (=excite) the cells and the halorhodopsin (NpHR), a chloride pump sensitive to yellow light that will, conversely, hyperpolarize (=inhibit) the cells.
There are nowadays tens of variants of these and other opsins that can be used to drive cell activity with lights. Many of these are described in this (beware! Quite technical) review:
Optogenetics in neural systems - Yizhar et al., Neuron 2011
Transgenesis works instead by generating an animal that carries the opsin (or any other gene) in its DNA. This can be done in various way, such as by microinjection of embryonic stem cells carrying the transgene.
You can find a fairly detailed explanation of the process here: Transgenic Cells and Gene Knock-outs, well summed up by this figure (taken by the same page):
Transgenic mice generation http://9e.devbio.com/images/ch02/wt020302-2.jpg
But how do you get cell-type selectivity?
In front of the gene for the opsin you also will have to put another sequence, called promoter. The promoter is a sequence that is specific to each gene and that is used to determine which genes a cell will or will not transcribe. For instance, the promoter for the gene coding for a protein only present in muscles will be used by muscle cells but not by neurons. You can even get more specific, for instance by using promoters that are typical of a subset of cells and not other (e.g. glutamatergic neurons use a different set of promoters than GABAergic neurons, although these two sets will -at least in part- overlap). However, this means that if you want to change the cell type you are working on you will have to change the DNA vector you are using.
A commonly used approach to avoid this is that of using Cre-dependent vectors (note that this can be used both for viral infections or for transgenic animals).
Essentially you will have a mouse line which expresses a protein derived from the P1 phage, called Cre recombinase, only in the cell type of interest (again, using a specific promoter). Cre has the property of cutting DNA next to specific 34 base-pair-long sequences called loxP (with sequence ATAACTTCGTATAGCATACATTATACGAAGTTAT). Essentially, if you have loxP-[some sequence in the middle]-loxP and Cre recombinase is around, it will cut away the sequence in the middle, leaving only a loxP sequence.
Hundreds of different Cre-expressing mouse lines are commercially available nowadays, to target many different cell types in different organs.
Now, you just need a construct that allows you to express the opsin in a Cre-dependent manner. This is what was done by the group of Hongkui Zeng, and reported in this paper:
A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing. - Madisen et al., Nat. Neurosci. 2012
Without going into too much details, the idea is to flank a STOP sequence with two loxP sites. This will block transcription (that is what a STOP sequence does) unless Cre-recombinase is present.
Essentially:

Source: myself, CC-by-sa licensed, feel free to reuse it
Note that in the scheme, ROSA26 is an ubiquitous promoter, that is, a promoter used by all cells, so in this case the specificity is given by expression of Cre recombinase and not by the promoter of this construct. Also, a fluorescent reporter (e.g. GFP) is inserted to be able to visualize where the opsin is expressed.
By breeding these mice with the Cre-line(s) of your choice you can then express the opsins in the cell type of your interest.

Thank you very much! A thorough explanation that gets to the bottom of the subject on the one hand and is easy to understand on the other.

@Ohad Dan: glad you liked it!


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Would non-human carnivores be able to survive on farmed foods?
Certain creatures that are considered carnivores are non-obligate carnivores and are technically omnivores (such as wolves/dogs).  How different is the potential digestive ability of these species compared to humans?  If they theoretically developed sapience and the intelligence for agriculture, would they be able to survive on the same wide variety of plant foods that we do (i.e. could wolves survive on wheat, rice, etc)

The foods people in the developed world typically feed their carnivorous pets (including dogs and cats) are not made primarily from meat.  Instead, they are made from plants, specifically grains, such as corn, rice and wheat.
In order to get our pets to eat foods that are so different from the meat-rich diets of their ancestors, we add flavors to the food.
Check out this episode on the making of pet foods from the television series "How Its Made", http://www.youtube.com/watch?v=220PSFJWHao.
So, to answer your question directly-- yes, in places like the USA, domestic dogs and cats are already living on a diet that is almost entirely plant-based.


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Are we evolving to age slower, or to live longer aging at the same rate?
I wonder why most of us find senior people lovely and charming. Is it because to love grandpa and granny is vital to our survival as a species, in the same way as we love babies? If so, it would mean that we are either aging slower with time, or being selected somehow to love senior people despite their physical appearance, while they are aging at the same rate but living longer.
Update
Let's say every common characteristic among individuals of the same specie is product of evolution.
Many caracteristics are passed by the individuals to their offspring, but only those that were advantageous in some way or another allowed the offsring to survive and pass that caracteristic to their decendants in turn.
Our love for babies and elders is one of those caracteristics that we as indivudials of  a species have in common.
That make us to want our elders to be with us as much time as posible, just becouse our affinity with them.
This love for the elder have to be an advantaje that worthed to be selected by the evolutionary process, and this caracteristic is reflected in the tendency of the life expectancy to increase generation after generation.
One could say, that those elders that age slower would be more likely to benefit from the love of their offspring, than those that age faster.
On the other hand, to age slower may not make a difference at all, just because we love our elders despicte their physical appearance.
I'm considering the cultural and technological advantages that allow our elders to live longer to be a product of evolution too.
So my question is wheter we are evolving to age slower, or to live longer aging at the same rate?
As a side note, we are becoming more like what they call a super-organism, as most of os can only benefit of a longer life spam by living in society. Just like an anthill or a beehive. If that is true, we are not evolving to age slower.

Your premise is debatable and your argument is, frankly, nonsensical. Why does feeling affection for our elders imply that we are "aging slower with time" (whatever that means)?  Voting to close.

@terdon We feel affection for our elders, as a matter of fact, but that behavior has to be shaped somehow by evolution. Also life expectancy is increasing generation after generation, and we still feel such affection. The implication is obvious to me, we are evolving to love people that live longer. What I'm asking is whether we are being selected because we love people that age slower, or because we love elders despite their physical appearance.

Not all behaviors have to be shaped by evolution. We do plenty of things that are counter-productive to our continued existence as a species and/or as individuals, as a moment's reflection will tell you (nuclear proliferation, global warming, drinking and driving, etc.). Please read this question and its answers to better understand the terms "evolution" and "evolve."

@MattDMo I would say every behavior that is common among individuals of a species has to be due to natural selection, because it's being selected among many other behaviors that weren't. In the case of the love for the elder, it would mean that people that didn't experience such feelings in the same way was not favored by natural selection.

i wish we could be more tolerant of questions like this.

The question has a more or less official scientific name - the grandmother effect (or hypothesis).   In the rational world of evolutionary biology, children love their parents for the same sort of reason - the parents give them resources to gather their strength and develop as adults so they can have their own children with the most advantage that they possibly can.
Humans are off the charts in the amount of resources we invest in our children - our lives are 1/4 to 1/3 over before we sometimes leave our parents household (in some societies of course they never leave the house, but step into an extended family).  This may be one of the reasons we are so successful as a species - we live in practically every place we possibly could and have no danger of competition from any other living thing excepting ourselves.
The grandmother effect is essentially the idea that if women, who are more attached to the offspring in more cases than fathers, continue to live and help support the grandchildren and make them more successful, then this will allow post menopausal women to have a longer lifespan (which they do).
The evolutionary biologist Sara Hrdy, emeritus UC Davis, has written quite a bit about the nuances of the evolution of the role of motherhood - reading some of her articles or books might give you a deeper sense of how profoundly filial love has shaped human beings.
--- more answer this stuff may or may not be worth reading depending on how broadly you want to understand this question...
Its important to say that many of the expansions of human average human lifespan have not been genetic.  Its commonly cited that sewer systems, clean water, antibiotics and plentiful food are the three most important factors in human lifespan - and before modern developed world nations, the average lifespan of human beings was somewhere in the 30s.  And there are significant lifespan differences in regions where these factors and others (education of women, access to prenatal and early care etc) are available.
Studies continue to be published that examine environmental and lifestyle factors compared to genetics and it seems that environment and lifestyle can make an astounding difference.
But genetics undoubtedly has a role to play here too.  There are probably some individual humans and animals which have evolved to live longer.  This has been found to be genetically related in some humans by demographics and family lines.
Still there are genetic factors that are being identified.  I think its a common misconception that evolution changes the entire species, but its not really true.  There are some who have that tendency and others who do not - at times there will be more of say shorter lived people and other times longer lived individuals will be more common.  It depends upon whether the living conditions of the population really favor one tendency over another.  Usually shorter lived individuals can assume to have other advantages, say the ability to store energy more efficiently.

One could say that cultural and technological advantages are part of being human, if so they are being shaped by evolution too. In the other hand that could imply that our species is becoming more like a superorganism, like an ant-hill, where one organism  can't have the benefit of a longer live span by itself, but only if one live in a colony.

that's true, though in terms of biology and evolution that's language that needs careful discussion - superorganism sounds a little like group selection and not everyone is into that idea ;)


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How does injecting low doses of allergens cure allergies?
Allergy shots (aka. allergen immunotherapy) help people adapt to allergens by injecting a gradually increasing doses of one or more allergens.
Does this procedure tell the body that this allergen is safe and there is no need to mount a response to it? In other words, does this mean that there will be no reaction at all rather than just a reduction in the allergic reaction.

These question is obviously off-topic as it is asking for theoretical suggestions for curing a medical condition. Answers to this must, of their nature, be off-topic. This is a question and answer site, not a discussion site.

@David — I tried to fix the question since it has a decent answer, do you think that helped?

@tyersome — OK but what are “allergy shots”. Are they low doses of the allergen? If so I would make that clear in the question. I would also change the title to something simpler like “How does treatment with low doses of allergen cure allergies?”

@David — Thanks for the suggestions. Good enough now?

@tyresome — Fine. Thank you for your effort. I still think it is too medical, and I'm not sure the answer is really more than superficial. But it's rather water under the bridge.

But are there ways to tell the body that this allergy is safe and there is no need to amount a response to it?

Yes, that's what allergy shots (Exposure Therapy) does. Exposure Therapy is an effective, albeit sometimes imperfect, method of letting the body know that a substance is common and that it shouldn't mount a response to it. Over time the body re-calibrates itself to accept the allergen, although in some cases it's never fully accepted.
A complete "cure" can be attained via allergy shots, but the extent of the therapy's success will rely almost exclusively on the individual's immune system. Some people can be cured completely, others will never be cured.

If not, why not?

There will probably not be a general "allergy" cure anytime soon because we're still not 100% sure why the body responds in such an overprotective matter sometimes and not others. Even if we fully understood at some point, there are many ways which the immune system can go awry that result in allergies.
There isn't a single, double, or triple point of failure along the line - just about any immune cell, whether Mast, Eisonophile, T-Cell, T-Reg, B-Cell, etc. can misidentify a substance and contribute to an allergic reaction (although some are more likely candidates than others). More than that, just about any substance can become an allergen for people. There's a well-studied case of a woman who became allergic to Copper because of repeated exposure via an early version of IUD that she had implanted.
So with nearly every immune cell capable of mounting a response, and nearly anything in the world capable of provoking a response, the best route - at least thus far - has been repeated, increasing exposures to teach the body what is "OK" and what isn't. The absolute best way to avoid allergies later in life is to simply promote outdoor playtime and a widely variable diet to children while the immune system is operating at peak efficiency and learning capability.

Immune Amnesia
I have a speculative idea of how someone might start to turn off allergic reactions in the immune system.
I've read that the measles virus can cause "immune amnesia".
If biologists had a deep understanding of why this happened, then maybe they could use that understanding to wipe of immune memories that cause allergic reactions.  Maybe they could use a genetically modified measles virus, maybe something else inspired by this.
I'm sure someone else must have thought of this before, but I haven't seen anything when I searched.
I think it would be an interesting beginning for a research project.  But I'm not a biologist, so I wouldn't really know.

This is a question and answer site about biological problems that allow objective answers. Only answer questions that conform to this type. This question invites speculation and is clearly off-topic. Ideas — especially not crazy ones — are not suitable answers to any question.

I have been thinking about this topic as well. A theoretical way (as you asked for) would be to kill all the immune cells which hold the (mistaken) memory of the specific allergen being dangerous. I haven't looked into it yet, but it would be interesting to see if post-chemotherapy patients had any changes with their allergies.
A future way of going at it might be to design specific killer cells to find and destroy only those immune cells with matching receptors (bait and kill).

This is a question and answer site about biological problems that allow objective answers. Only answer questions that conform to this type. This question invites speculation and is clearly off-topic. Your answer is such speculation and is only suitable for a discussion site which this is not.

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


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How do animals perform detailed active camouflage?
We often see videos of octopuses and chameleons changing their color to suit their surroundings. If it was a simple color change from white to red, it'd be understandable, but some of these animals can change colors while incorporating a lot of detail.
How do they process so much information and mimic it. Is this a subconscious action, or do they actually draw a picture in their head and then 'print' it on their bodies? Does this ability come from birth or does it get better over time?

Some of it is voluntary and some involuntary and is detailed in this book. Chameleons have chromatophores (pigment containing light reflecting organelles in cells) which help in their colour change and many factors like age, health, etc does affect it. And no, they do not form a picture on their head and print it on their bodies.


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What is this insect?
These photographs were taken today in Marseille, in the Mediterranean coast of France. My French friends inform me that these beasties are called cousins because they are "cousins" of mosquitoes (whatever that means).
The thing is, we are absolutely infested by them. They seem to be more active at dawn and dusk (like mosquitoes) but we have dozens flying around the house every evening. I would like to know the species' name to see if I can learn anything about them. Do they have cycles like cicadas? Are they linked to stagnant waters like mosquitoes? Why are there so many of them this year?

Here's one with my hand next to it to give you an indication of their size:

Some kind of crane fly (http://en.wikipedia.org/wiki/Crane_fly)

I agree it must be a Tipulidae. I also call them "cousins" in French, or "tipules".
I think their larvae live in the soil, not in stagnant water.
I'd bet their abundance could be related to the anormally long "winter".

i have also seen this guy roaming around in mosquito hiding places.. i used to think that it is a mutated mosquito :P

It is indeed a Crane fly, superfamily Tipuloidea, which is part of two-winged insects (Diptera). There are >15000 species worldwide. Their systematics is somewhat uncertain (used to be a single family, now a superfamily). They are placed in the same suborder as mosquitoes (Nematocera). The adults feed on nectar or not at all (they do not prey on mosquitoes), and the larvae usually feeds on litter, roots, fungi etc, but some aquatic species are predatory. Larvae of some species develop in soil and others in water. Adults of many species are attracted by light, which is why you often find them inside houses. I dont know why you find so many this year where you live, but winter conditions affecting survival is a possible explanation.

In many areas of the United States the predatory versions that prey on mosquito larvae are purposefully bred and introduced in large numbers as a non-chemical method of mosquito control. Since the predatory versions don't prey on much else (and do not prey on anything as adults) they're found in large numbers in the Summer, but are otherwise harmless. Perhaps the French government did something similar?

Didn't know that they were used as biocontrol. In the US, some introduced species are also consided pests, e.g. the European crane fly (pdf)

Nematocerans are not monophyletic, and are therefore not a valid suborder. Other than that, I agree with the answer.


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Food Intake versus ability to flee among birds, particularly the hummingbird?
Logically speaking, if a hummingbird drinks too much nectar, it will be temporarily overweight and less able or unable to fly to escape danger. However if the same hummingbird doesn't drink enough nectar, it will suffer the same problem of not being able to flee danger, but for the different reason of it wouldn't have enough energy to do so. Hummingbirds are incredibly small, so I would assume they would have the most problem with this issue due to the fact it would have very little margin for error. I am not sure how much that margin is though or the marginal percent of body weight, so I'll ask that question too.
What mechanisms do (humming)birds have to regulate and control their body weight and their energy needs and scouting and timing the acquisition of their next potential food source? What is their margin for error and how do they meet it and how did they meet it in the past?
EDIT: I want a more concise question, so hopefully this is answerable:
Alternatively and optionally, Can you describe to  me a general day in the life of a Hummingbird? I want to know what good decisions it makes over the course of its "perfectly average" day to survive. Such things as what it does to avoid dangers, and how it finds its time to eat and how much it eats and at what intervals, and what it does with the rest of its time?

Okay someone who knows a bit about this told me that like shrews, hummingbirds are always less than two hours away from death. If they do not find a meal in that two hour window they die.

It is not specific to hummingbirds, but this topic is treated in the book Modelling for Field Biologists and Other Interesting People by Hanna Kokko: http://www.cambridge.org/us/academic/subjects/life-sciences/quantitative-biology-biostatistics-and-mathematical-modellin/modelling-field-biologists-and-other-interesting-people


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What determined the evolution of different faces in humans?
The most distinctive characteristic of a human is it's face - it is unique among each individual (with the exception of identical twins). It is uncertain to me if whether we best identify other humans by their face due to special brain parts developed for this (there are people with disease that cannot recognize faces) or for actual very distinctive physical face forms; maybe it is a combination of this.
Anyway, the question is about evolution. Why would distinct faces (or ability to recognize distinct faces) be something useful that would be retained by evolution? How is this better at survival?

I've read that penguins are also pretty good at identifying family members(visually and/or vocally) amongst hundreds of other similar looking birds.

Speculation: It seems that identification would be important in society.  Having a distinctive appearance means one gets credit for good behavior and being able to distinguish would allow giving credit only where due.  Helping gene-sharers (similar appearance) and breeding with dissimilar others could have selective advantages; both require recognizing similarities and differences.  Distinctive aspects of appearance may also accentuate, honestly expose, or disguise fitness markers, with obvious selective advantages, and discerning actual fitness markers would be advantageous.

Given the prevalance of myopia in humans I would have thought that facial recognition was secondary to other indicators such as gait recognition which is also unique to individuals though can be copied to an extent. Voice and shape are also used to identify people.
Being able to recognise individuals would allow the formation of groups, allow for structures of trust, reciprocal altruism to develop as well as punishing transgressors. Repeat interactions with other people require some kind of identification, but I dunno if facial recognition is the only/primary one.


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Can any species be bred selectively/engineered to become as diverse looking as dogs?
I've done some research and it appears that dogs are the most diverse looking single species of mammals. The questions that interest me is - are dogs special in respect to genes/gene activation mechanisms related to appearance? Or does this dramatic difference in appearance have something to do with dog anatomy and how they give birth?
If dogs are not special, this makes me interested if other species of mammals can also be bred selectively (or genetically engineered) to produce such dramatic variation?

good question.. no idea, as of now, about what are the genes in dog that give morphological diversity.. i think another species that has been selected for morphological features is pigeon.. you can check this paper out.. I shall also go through it..

Dogs have a genomic structure that allows breeding with high variation in size, shape, coat quality, color and other qualities particular to each breed as well.
Other domesticated animals can be bred for as many qualities, but dogs in particular show a wide level of morphological traits - varying in size from just over a pound to the size of a wolf, from which dogs are derived and genetically are still compatible.  But more interesting than just size or coat color/texture and even their intelligence and personalities, the proportions of their bodies, of their skull length and breadth, are remarkable.
There are over 160 registered breeds of dogs, but this is only a measure of how much time people have put into them.  I think its possible to get nearly anything you want with animals, if you are patient enough - its not clear what is and is not possible with enough genetic manipulating. For instance, horses can be bred over nearly as great a size range for instance (the miniature horse the size of a large dog, the Shire is 3,300 pounds), but it would not be as easy to get both the size and muscularity and shape of a bulldog in a horse.  Breeding a mouse of various colors can be done, and so can interesting behaviors, but body shape seems to be harder: a Weimaraner mouse could take a tremendous amount of time and animals.

Great answer, from your first link, it appears that dogs have smaller number of genes that strongly morphology, while other organisms, like humans have larger number of genes that have only mild to moderate effect

thanks for saying that outright - i should have said that in the answer... :)  This is the reason that there is such an interest in dog genetics.

Good answer, and there are other animals bred for weird stuff. Pigeons and rabbits, etc. Pigeons in particular we've pretty thoroughly reshaped.

Also chickens have been bred into many different varieties.  The size range doesn't seem to be as great as with dogs, but feathers give a larger range of color & form.

Its true nearly any animal can produce many breeds with behavioral, colorful and fascinating variations.  dogs seem to have a remarkable variation in body shape and size in particular though.

its really more about the kinds of genes and how sensitive they are to mutation - i'm sure dogs have a similar number of genes that control development, but with other animals (such as cats) they are not as sensitive to breeding.

Rabbits have been bred domestically since at least ancient egypt.
Rabbits vary in size from > 15 kg (35lb) for a Continental Giant to .5kg(1lb) for A small Netherland Dwarf.
The American Rabbit Breeders Association recognizes 47 different breeds of rabbit for shows and there are a number of breeds that are either not recognized or are being developed for acceptance.
Breeders break the rabbits down by type of body, size, fur, and ear type.  Each breed is then broken down into Groups and Varieties.  It may be hard to believe but each of these rabbits share the same basic DNA.  Though interestingly some breeds will express the genes in manners that are often not the same visually.

Interesting, I didn't know there were so many rabbits. It would be interesting to know if the genes for "floppy ears" are similar between dogs and rabbits

There is not actually a single gene for floppy ears.  It is a number of genes that go into the expression of their ears.  One part that is especially important to the display of their ears is the crown, which is the muscle and tendons that provide ear support.  In french lops you want a very strong and visible crown.  In English lops you want no visible crown at all.

Not a mammal. But goldfish have also been modified both in shape and colour
http://40.media.tumblr.com/ef8838366e4b7a51646b74b5330238e3/tumblr_mi60i8S52c1rmp9qqo1_1280.jpg


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Does precipitation influence the UV spec reading?
I have been checking my sample for Hydroxyl radical scavenging activity. I have dissolved Hydrogen peroxide in Phosphate buffer. My sample is clear and reagent is also clear but when I have mixed my sample extract with Hydrogen peroxide reagent a precipitant is formed. Control is very less than solution that is kept for reaction to proceed. So I am getting an answer in negatives (230 nm). Is that formation of precipitate affect the absorbance of the solution? Does precipitation increase the OD value compare to clear solution?
 Mine is mushroom powder. It is extracted with Ethanol. Extract is dried and finally it is dissolved with solvent above said. That has been used for Hydroxyl radical scavenging activity. Hydrogen peroxide 0.01 milli molar reagent is prepared with Phosphate buffer. First i have taken reading for H2O2 and added extract kept for ten mins and took reading. in 230 nm..

what is your sample and how is it stored ? Is it DNA dissolved in TE/water or cell extracts ?

also.. please describe your protocol so that the problem can be understood better

this question would be much more suited to Chemistry.SE

@MattDMo UV spectroscopy is a very common technique in the biolab, so this is certainly on-topic here. Migration is rather disruptive, so we try to avoid it for questions that are not actually off-topic on the source site.

Perhaps you could help us by explaining the basis of the assay? Am I correct in thinking that UV promotes OH radical formation? And that hydrogen-bonded OH radical absorbs at 230 nm? So is the UV beam from the spectrophotometer both promoting radical formation and also allowing the measurement of how much there is of it? And finally, do you get the precipitate if you leave out the peroxide?

No.. precipitate is forming when sample is added..

Yes UV promotes and it can be read in 230 nm as I have referred earlier.

The answer to the question as asked is that yes, any precipitate will affect the value that you are reading in your spectrophotometer. The basis of spectrophotometry is that light passes through a sample, and less light emerges than the amount which entered. The amount of light that has "disappeared" is used to deduce something about the solution in the cuvette. Light can be absorbed by chemical groups (this is the basis for e.g. DNA having an absorbance value) or it can be scattered by particulate material (this is the basis for measuring the cell density of a bacterial culture). If you are trying to make a measurement of the first type (absorbance) and you get a precipitate your reading will be distorted by the light scattering effect.
Precipitates are incompatible with spectrophotometry.
As the comments have noted: if you give more details of your protocol someone may be able to help. Phosphates are, of course, notorious for generating unwanted precipitates.

Thank you for response. Mine is mushroom powder. It is extracted with Ethanol. Extract is dried and finally it is dissolved with solvent above said. That has been used for Hydroxyl radical scavenging activity. Hydrogen peroxide  0.01 milli molar reagent is prepared with Phosphate buffer. First i have taken reading for H2O2 and added extract kept for ten mins and took reading. in 230 nm..


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Superposing DNA
I have a series of protein models with DNA docked. I now want to superpose the DNA on a reference DNA molecule and extract the translational distance applied and the rotation angle used.
I can superpose DNA molecules with Chimera, but I can't extract the translational distance and the rotational angle that was applied to superpose.
I have also had a look at MODELLER but it seems MODELLER cannot not superpose DNA.
Does anyone know of software/code by which I can extract the information I want?

Try this out with BioPython:
from Bio.PDB.PDBSuperimposer import PDBSuperimposer as superimposer
from Bio.PDB.PDBParser import PDBParser

parser = PDBParser()
sup = superimposer()
struct_1 = parser.get_structure("XXXX","first_pdb")
struct_2 = parser.get_structure("XXXX","second_pdb")

atoms1 = struct_1.get_atoms()
atoms2 = struct_2.get_atoms()
sup.set_atoms(atoms1,atoms2)

print sup.rotrans #print the rotation translation matrix from the SVD

#then to complete the alignment
sup.apply()

You can look here for further details. SuperPoser


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Evolution after the development of sexual reproduction
My understanding of evolution is that genetic mutation occurs in individual members of a species, and they become a new species.
Isn't a definition of species a group of genetically similar organisms that are pretty much exclusive in breeding ability?
Wouldn't there have to be a male and female with the same genetic divergence at the same time to make a new species?  What is the popularly accepted mechanism for the splitting into a new species in organisms that require sexual reproduction?

er, not all mutations "create" new species. also, as a side point, the definition of a species is still under debate. You might take a look here and here

My understanding of evolution is that genetic mutation occurs in individual members of a species, and they become a new species.
Isn't a definition of species a group of genetically similar organisms that are pretty much exclusive in breeding ability?

Well, no.
You are correct in that the origin for any new species lies in mutations which occur in individuals and are then passed down through DNA.
You are misunderstanding that simply because a mutation exists in an individual that they become a new species. Take Lactase Persistence as a widely studied example in humans. The majority of the world is lactose intolerant after they stop drinking their mother's milk, but a single point mutation results in the ability to consume dairy products into adulthood. It does not make people who are lactose tolerant a new species, but it does open up a potential new nutrient source, which benefits the people who have it and thus it was passed down successfully over other variations.
In addition to that example, the definition of "Species" is NOT exactly defined. There are many variations, including (but not limited to):
1) A group of organisms that cannot interbreed in the wild.
2) A group of organisms with significantly different phenotypes (appearances).
3) A group of organisms with sufficient* genetic divergence.
*There is absolutely no scientific consensus on how much genetic divergence is necessary to create a new species. We share >95% of our genetics with Chimpanzees, so it's not much - it could be as little as a few key genes out of the entire genome.
So where you define the boundaries of species is up for grabs to some extent, but the most common is what you delineated - when a member of one group cannot interbreed with another group.

Wouldn't there have to be a male and female with the same genetic divergence at the same time to make a new species?  What is the popularly accepted mechanism for the splitting into a new species in organisms that require sexual reproduction?

Nope. Assuming everything necessary for the gametes to produce fertile offspring is present (aka - the chromosomes aren't significantly altered and the gametes are compatible) then a new species emerges through successive generations.
One mother or father gives their mutation to their children, which pass it on to their children, which pass it on to their children, etc. If the mutation is significantly advantageous it will allow the children with the mutation to better survive in the environment, and over time it could become the dominant phenotype that could lead to the creation of a new species as further mutations build in the new group - further differing the generations of the mother/father from the original group the mother/father were born into. Good examples are the HAR - Human Accelerated Regions which are sets of genes that are pretty much the same throughout all other vertebrates, but startlingly different in humans. The HAR did not create humans, but it's thought the mutations contributed greatly to our intelligence - which allowed other mutations to be taken advantage of (like the humble opposable thumb) as our lifestyle changed due to the increased intelligence.
Not all mutations need to be advantageous, though. There's lots of fuzzy areas. If a mutation isn't beneficial, but also isn't that detrimental, it can also stick around in a population. These mutations might not lead to the creation of new species, but can certainly contribute to genetic divergence.

It should also be added that allopatric speciation is arguably the most common form of speciation (compared to sympatric speciation). This means that, often, the only thing needed for speciation is lack of gene flow, time and genetic drift. Add to that the different selection pressures at different locations. However, the different mechanisms of allopatric, sympatric and parapatric speciation are probably better seen as a continuum (Butlin et al. 2008). Generally, speciation is a gradual and incremental process, even though distinct mutations can sometimes surely be important. For a review on the genetics of speciation see Noor & Feder (2006)


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Why is epinephrine not part of the somatic nervous system?
I learned that the adrenal medulla releases epinephrine, which is a vasodilator of the vessels that lead to the skeletal muscle.
I also learned that somatic nervous system only uses Achetycholine as its hormone (not epinephrine).
I also learned that the somatic nervous system controls skeletal muscle.
So, why is epinephrine not considered a part of the somatic nervous system hormones, if it is controlling the skeletal muscle? What is wrong here?

You are confusing different functional systems. Epinephrine released by the adrenal medulla circulates in the blood and indeed dilates the blood vessels in skeletal muscle. This ensures that enough oxygen and nutrients are available for the muscles to perform in a fight/flight response.
The somatic nervous system utilises acetylcholine not as a hormone but as a neurotransmitter. It is not released into the blood but only into the tiny (about 10nm wide) gap (synapse) between the nerve cell's axon terminal and the next nerve cell or muscle cell respectively.
This release by the somatic nerve cells causes an electrical potential in the muscle which makes it contract.
In summary:
The somatic nervous system controls the muscles because it stimulates the contraction which makes e.g. your arm move. Epinephrine released into the blood by the adrenal medulla serves to ensure the muscles have the blood supply they need in a stress response (e.g. a dangerous situation).
Along with muscular blood vessel dilation, epinephrine in the blood for example also stimulates the heart to beat faster and stronger, and dampens down mechanisms involved in digestion - essentially it does everything necessary to allow a quick escape or a strong fight.

Ah, yes, thank you. Confusion between hormones and neurotransmitters. Thanks!


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How do changes in temperature affect body weight in humans?
What would be effect on weight of individuals if we bring a fully adapted (to cold climate ) human individual and a fully adapted to very hot climate individual to a moderate climate region?

Can you expand your question some? Are you only interested in weight changes? Your title mentions metabolic rate, which is related to weight gain but certainly not the only factor. "What would happen" is very broad. What kind of animal(s) are you thinking of?

You would see moderate weight gain in both subjects.
Since humans thermoregulate and aren't terribly "adapted" to any extreme for either very hot or very cold climates, anything outside of short range of temperatures will cause us to either sweat or shiver.
Sweating or shivering will cost kcals ("Calories", "Joules"), and the extra energy expenditure will keep the subjects' weights lower than they would otherwise be.
Once the subjects enter an environment where they no longer need to sweat, shiver, or basically maintain a wide gap between the outside temperature and their body temperatures (which is the real driver here - the difference between the two), they will no longer expend as much energy maintaining human body temperature.
How much energy are they saving? Not much. I wish I could find the article again, but you're talking an extra 50kcal or so an hour saved - or a few pounds until the energy required to maintain the extra weight reaches equilibrium with the energy saved.
There are a few assumptions built into the above, which sees the question as more of a physics-oriented hypothetical than real-world example. In reality you have some large complications - getting anything done in cold temperatures is going to require a much larger energy expenditure, as you're usually carrying 30-50lbs of gear to not freeze to death, for example. A person used to wearing a dozen kilograms of animal furs during their weekly routine would gain a lot more weight than hypothesized above if they suddenly entered a mild climate with similar food intake, but without the constant load on their muscles.


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Excretion of monovalent and divalent ions in sharks
I have heard that sharks excrete $\ce{Na+}$ and $\ce{Cl-}$ by their gill surfaces but divalent ions like magnesium are excreted through feces. What could be the reason behind this?

You want the reason as in why such a behaviour would have been evolutionary beneficial or adaptively useful or as to what anatomical mechanisms make divalent ion removal through gills (or vice versa) not possible?

@SatwikPasani I actually want the physiological mechanism but I'll love to learn any evolutionary advantage.

divalent cations tend to form less soluble salts than monovalents, such as calcium phosphate. If you tried to excrete these through the gills it would probably lead to the build up of calcified deposits on the gills and damage the tissue and decrease gas transfer surface area. This isn't a problem if you dump the cations into solid waste.

@user137 Thanks. Why dont you convert this into an "answer" and add some references ?

The main reason seems to be a mechanism to save water and allow the excretion of higher concentrations of the ions. See the image (from here):

The urine enters the glomeruli at a relatively low rate and with a low magnesium concentration. The paper cited below mentions a concentration of 1.5mM. First organic compounds as glucose are recovered actively, water follows the molecules passively. Then more ions as Ca$^{2+}$ enter in the proximal segment II. In the distal segment finally sodium and chloride are actively transported out while water passively leaves the segment. The divalent ions (magnesium, calcium) are left in high concentrations (the paper below says that the Mg concentration is now around 130mM). This helps concentrating these ions for excretion while loosing as little water as possible at the same time. Sodium and chloride are actively regulated in the gills.
For a short overview, see the link at the image above, for a detailed view, have a look at the following publication: "Kidneys sans glomeruli".

Could there be a reason why this happens for calcium and magnesium not for sodium and chlorine ?

I have only found a hypothesis. First it seems a matter of energy (the transporters actively use ATP) and the nutrition. There is a paper about this, but I haven'T got hands on it.


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How to convince suspension cells to adhere more tightly?
I'm developing a cell-based assay in 96-well plates that requires adherent cells, as they need to be washed at least twice during the protocol. I'm using in-house strains of HT1080 cells (some overexpressing a certain protein of interest) that unfortunately have been selected for suspension growth in chemically-defined media (50/50 CD-CHO/CD-293). I can convince them to adhere by culturing in DMEM with 10% FBS and growing them in CELLBind flasks, but they still tend to pull away if there is very much shearing force, such as during the wash steps, or when they're in PBS during the assay wash and incubation steps (maybe 2 hours total for now, I'm still optimizing that).
Unfortunately, the parameters of my experiments don't allow me to keep the cells in serum-containing media during the assay, as it would interfere with the uptake of my drug. Like I've said, when in PBS they start detaching, and I would assume the same in HBSS, which I don't really want to use anyway due to its low buffering capacity in CO2 incubators.
Might DMEM alone (without FBS) provide a little more impetus to stay attached during the assay? What would the effect be of increasing the amount of FBS to say 15 or 20% during culturing - would that promote stronger attachment? I'm a little hesitant to coat the wells with poly-D-lysine, as my readout is on a fluorescent imager, and I'm worried it would substantially increase background. I don't really have enough time to re-select the cells for adherent growth (although if I'd known about these issues from my predecessor 3 or 4 months ago I would have started right away...), so are there any other tricks I can try in the meantime? Are there any media supplements I could use to promote adherin expression or something like that? Any tips or advice at all would be appreciated.

I'd suggest splitting out your edit into a new question, it looks like it would be a fine question on it's own.

@MadScientist - that's true, I hadn't thought of that. Coming right up!

I don't remeber this anymore exactly, but weren't there cell culture plates available which had a membrane bottom which allowed you removing liquids by centrifugation while the cells stayed on the membrane?

My main concern here is why you are using suspension-culture selected cells for an adherent cell-based assay? Is it possible to obtain a clone of adherent HT1080? Depending on what you are assaying with your protein of interest, the cell biology may be altered changing from suspension/adherent culture systems.
Here are my experiences using PC12 cells in culture, which are weakly adherent cells, with a preference to grow in clumps, rather than monolayers. I have found that these cells have a preference for specific tissue plastic; (without mentioning names), these cells will adhere on some poly-D-lysine coated plates while they won't adhere on others. I routinely perform immunofluorescence microscopy with these cells, and grow them on glass cover slips which I have skim-coated with rat tail type I collagen. This coating provides minor background in the green range and only when imaging close to the glass. With a bright fluorophore (e.g., AlexaFluor or cyanin dyes for fixed cell; enhanced GFP for live cells), this backgorund is not a problem for quantitative microscopy.
Lastly, for secretion assays we use high-glucose DMEM supplemented with 1% dialyzed FBS. If memory serves, this retains all serum components less than ~15 kDa, which includes various growth factors. I have observed these cells continue to live for up to one day (and maybe longer?) in supplemented medium, while they die after a few hours without. This may also help with non-specific binding you may be worried about with drug addition.

Thanks for sharing your experience. The main reason I'm using the cells is because that's what everyone else in the company is using, and they've been adapted to suspension growth for scaled-up production of ... stuff (pharma R&D). Some of the lines are various clones overexpressing a certain receptor, although after talking with my boss we might be able to work around that in our experimental design. My budget isn't that big, so I'm trying to work with what I've got, although if what we've got doesn't work we'll need to get something else :)

Just for the record, I hate PC12 cells. You're exactly right about them growing in some vessels, and not others, and only with very specific media and at very specific densities. They'll pull off the plate just to spite you, and if they're not dying every third passage they're getting contaminated. Good luck with them, I don't envy you!

Thanks MattDMo, they took a good while to troubleshoot! The biggest challenge now is getting them at the right density for single cell imaging and not some gnarly unresolvable clump. ;)

try gelatin or collagen coating on the culture plates..

@WYSIWYG - I currently collagen coat the coverslips. The nature of PC12 cells is that they prefer to grow in close proximity to each other, and spontaneously form cell clumps as they grow.

Have you looked into trying the DropArray microplates? They're a new technology where you don't need to centrifuge your cells to wash them...an old colleague of mine works for the company and they're pretty cool about demoing the products/instruments for you. It's http://www.curiox.com/.
I think most people that use the system are using suspension cells- because of the challenges you listed above, so may be worth a look!
Good luck!

Interesting. I'll have to check them out a little more. I'm not developing the assay anymore (I posted the question a year ago), but I ended up switching platforms to flow cytometry, and just used round-bottom/v-bottom plates.


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Measuring sugar content of a tree
I would like to grow mushrooms on oak trees I can harvest from my property.  I've read that the best results will be when the sap is rising but the tree hasn't budded yet.  The mycelium feeds on the sugars in the logs.
I would love to be able to measure the sugar content so I could accurately asses the sugar content.  Here in Southern Oregon the winters are mild and the leafing out of the oaks varies quite a bit from year to year.
How can I measure sugar content of the sap in a tree?

Interesting, +1. If you don't get any answers here after a few days, try Chemistry.SE.

The soluble carbohydrate can get the mushrooms off to a good start, but it is the cellulose that will be most important for production. Another reason people innoculate logs in winter is because there are fewer spores from competitors in the air, and less work to be done in the field (for farmers).

Yes, @Abe, an excellent point. Also many fungi can degrade lignin so this would also be a carbon source.

@alan even if lignin degraders breakdown lignin and can utilize some of the products, I don't think the lignin itself results in a net benefit to the fungus (because ligninases are so costly to build) it is the cellulose inside the lignin matrix that they are after.

@Abe - I didn't know that - any references?

@AlanBoyd Moorhead and Sinsabaugh 2006 "Theoretical Model of Litter Decay and Microbial Interaction" gives a good summary (see Part 2: Lignin x
cellulose controls).

The difficult step will be getting samples of sap: have a look at the WP page for maple syrup for ideas about methods of tapping into the xylem of your trees.
You will then need to assay sucrose in the sample of sap. There are many commercial assay kits available (Google: sucrose assay), which rely on an enzyme, invertase, to convert the sucrose to glucose + fructose. The released glucose is then measured by a glucose oxidase assay. You would need some kind of colorimeter/spectrophotometer for quantitative results but there is a visible color change, so you could probably get a rough idea of what is going on by visual comparison with a set of glucose standards.
Supplementary
An alternative would be to measure sugar concentration by refractometry: see here and here.

Is sucrose the most common disaccharide in sap?

I can't say for certain. Here is a reference for pedunculate oak: http://onlinelibrary.wiley.com/doi/10.1055/s-2001-12898/abstract Sucrose is 2x more soluble than glucose or maltose, so may be the best choice for transport in aqueous solution. The assay would, of course, pick up glucose.

Seems as if you can collect sap from cutting the end of a twig.  http://tywkiwdbi.blogspot.com/2011/04/adventure-with-birch-water-birch-sap.html  I wonder if, for my purposes, I can just monitor the quantity of sap production?  I'm guessing that when the tree is producing the most sap would be the time that the most sugar will be in the logs I harvest.

A spectrophotometer is a great idea!  http://spectralworkbench.org/sets/show/207 shows spectrograms for various stages of reducing maple sap to syrup.  I'm guessing that a season of collecting and analyzing samples would show me whether sugar concentration varies over the course of the sap run.

Ah, yes, the refractometer looks like the way to go!


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What parts of the brain are involved in regulating blood pressure in mammals?
I'm reading this Wikipedia  article on blood pressure and its regulation, and it mentions that medulla is involved. however, I vaguely remember reading another article on Wikipedia and it mentioned that hypothalamus or hippocampus could be involved. So my question is - what other parts of the brain or neurotransmitters have significant effect on blood pressure regulation?

You may want to look at vasopressin

Thanks, vasopressin does appear to affect blood pressure a bit in healthy individuals. There is a duplicate mention of blood pressure in the part of the article that deals with nervous system, but I'm not sure if this is the same or different effect


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How do different tissue culture matrices affect background in fluorescent microscopy?
In response to my previous question, I've been reading up a little bit on poly-D-lysine, Collagen I, Collagen IV, laminin, and other tissue culture coatings that promote cell adhesion. I've always assumed that anything other than standard TC-treated plastic or glass would significantly increase background, but perhaps my views on background fluorescence are a little outdated. Does anybody have experience with these in a fluorescent microscopy/high-throughput screening environment?
Specifically in my case, I'm looking at endocytosis and trafficking of a labeled protein into the lysosome. I'm labeling the protein with the pH-dependent dye pHrodoTM from Molecular Probes, which supposedly has very little fluorescence at neutral pH, but becomes very bright as the pH drops when endocytic vesicles become lysosomes. This theoretically means that a final wash step is not needed, but with a matrix coating on the plates I'm worried about background.
So, what is the current thinking as far as background fluorescence of the various TC matrices is concerned? Does the background come from the matrix itself, or by the fluorescent dye becoming adsorbed to it? Is it wavelength-dependent? Fortunately I may not be stuck with my poorly-adhering cells, and I may not need supplemental matrix at all in the end, but I still want a better understanding of how it works.

Extracellular matrix (ECM) fluoresces, especially Collagen and Laminin. The maximum is in the DAPI and FITC channels and the fluorescence becomes weaker towards longer wavelengths. However, since the coat on the TC flasks is very thin, I would not expect this to be a problem. The best thing is just to try it. There is also a quite famous document available which might be of help:
Autofluorescence: Causes and Cures


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Just how light-sensitive is ethidium bromide?
One lab I was in was paranoid about keeping it in a foil-wrapped conical tube; my current lab leaves it out on the bench (and it works fine for staining gels). It's the same company/concentration in both cases, but this second lab uses it up much faster.

Good question.
I found this reference in "Molecular Biology: A Project Approach"

A phenomenon called photobleaching occurs when ethidium bromide (EtBr) -stained DNA is illuminated by ultraviolet light.... This decreased fluorescence is presumably due to the dissociation of ethidium bromide from the DNA.

Ethidium bromide fluoresces when it is in a hydrophobic environment, such as when its stuck between two base pair stacks in DNA- water quenches its fluorescence.
I also found this article citing the fact that sunlight can break down EtBr but only when a catalyst of iron and titanium dioxide is there to catalyze the reaction.
A lot of the original characterization of EtBr as a stain is very old, so I couldn't access it directly online... It looks like the compound itself is pretty stable, but UV can, somehow interact with it when its bound to DNA to bleach it out.

Thanks. So on the bench in its bottle, ethidium bromide shouldn't be light-sensitive, unless there's iron and titanium dioxide contamination (or some hydrophobic substance)?  (also, could you link to the article? I'm pretty sure I found it earlier but I can't find it anymore)

I should think not. Eppendorf tubes are UV absorbant anyway.   I added a link to the article - thought I had it there.. (UV reference: http://www.eppendorfna.com/int/index.php?l=131&action=support&sitemap=4.1&productpage=41&catalognode=28832)

In my current lab we just leave the bottle out (but use it up pretty quickly as we have 20+ people). But we do buy 5 bottles at a time and leave them in the same spot as the bottle that is in use (inside a hood, with the light always turned on) and we've never had a problem with degradation/expiration


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How to bind antibodies to study their properties?
I want to experimentally look at the behavior of antibodies. To do so, I need to be able to bind these antibodies to a substrate.
Eventually, I want to study the specificity of antibodies to know to what substrates they bind. After that, I want to study the biological activity of the antibody over time.
But my question is more basic, namely: to what material do antibodies bind non-specifically? It's not about antigens at this stage, it's just about non-specific binding of antibodies to a carrier material. Also of interest would be howw to get the antibodies of that carrier again.

Like any other protein, antibodies will aspecifically bind nitrocellulose or PVDF membranes, but any other protein present in your antibody preparation will also do.
Depending on the antibody class, more specific binding can be obtained with protein A or protein G, that recognize the Fc domain. It's usual to have protein A/G immobilized on a stationary phase like agarose.
If you know the antigen used to develop the antibody, you can also use the immunizing peptide crosslinked to CnBr activated sepharose as a probe to bind your antibodies.
Knowing something more about your antibody preparation and what exactly is the 'behavior' your want to study could help obtain better answers.

96-well plates made from polystyrene are routinely used to immobilize antibodies with excellent results.  The immobilized antibodies are then used for binding to antigens e.g. ELISA.  The antibody should be free of other proteins for best results as these will compete for binding (many are supplied with carrier proteins such as BSA  that will compete).
A good read here:
https://www.corning.com/catalog/cls/documents/application-notes/CLS-DD-AN-454.pdf


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Movement of stem cells from mother to fetus
Recent results from J Lee Nelson and colleagues (Sci Am. 2008 Feb;298(2):64-71; available as full text through Google) show that cells from the mother were found in a person aged 46. Logically, these cells should be stem cells, as any other cells would die in such a long period of time.
So, what stem cells could be transferred from mother to fetus?
Why doesn't the immune system reject those cells?

Please add a full reference and link to the paper.

They could also be immune system memory cells, as they are (by necessity) extremely long-lived

Yes, a link to the reference would be most helpful. In the meantime, I found some abstract from a conference where they apparently presented this work here: Chimeric maternal cells as T lymphocyte targets in pediatric SLE

Please don't include articles directly into your posts, firstly it's huge and makes your question pretty much impossible to read but also it's very very close to plagiarism and copyright circumvention.  Usually linking to a pubmed index or the journal itself will suffice along with fairly quoting any relevant sections.

There's a lot more out there on mother-child cell exchange now -
e.g. a nice plain-English explanation of microchimeras from the baby in the mother here. Anyone feel like having a stab at answering this one?

This is also child->mother rather than the opposite, but I was interested to spot that the earliest publication documenting "feto-maternal trafficking" is substantially earlier than 2008 - 1893! (https://www.ncbi.nlm.nih.gov/pubmed/16620961)

The link in the OP is now broken, but it appears to be a reference to this paper by the Nelson group: https://www.nature.com/articles/3700471

Since the maternal cells can be found in a number of tissues including

In second trimester fetuses the thymus, lung, heart, pancreas, liver, spleen, kidney, adrenal gland, ovary, testis and brain had maternal Mc (microchimerism)

it's clear that these are stem or stem like cells that are being incorporated into fetal tissue.
Since these cells arrive while the immune system is developing, they are considered as self and not foreign. But a breakdown of that immune tolerance is thought to be involved in a number of autoimmune diseases, especially systemic sclerosis which resembles a host vs graft disease where the patient's immune system attacks tissues holding the maternal cells.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516290/


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Prenatal Marketing
This is for a short story idea.
Is it possible to modify the DNA of a child to make their metabolism more susceptible (physical response, addiction, etc) to a certain type of chemical i.e. a chemical present in a fictional food. The idea being that their DNA is modified when in the womb (or before) and when they grow older (think teenager) they become addicted to said product.
This could be before conception, during pregnancy or after birth. What ways, in the future, could we go about doing this? Maybe chemical mutagens (http://en.wikipedia.org/wiki/Mutagen) or site-directed mutagenesis (http://en.wikipedia.org/wiki/Site-directed_mutagenesis)? Gene therapy?
Or is there a way to alter the regulation of the physiological processes in the human body to make someone become easily addicted to a particular product?
I'm looking to have this aspect of the story as scientifically accurate as possible so I can examine the ethical questions around it within the story.

Also, as an alternative I've been suggested Epigenetics. Suggestions?

To extend with a theoretical way such a method might be possible (though I really hope this will never work or be done!) This is essentially a gene-therapy approach.

Are you talking about psychological addiction (needing it to avoid running crazy), or physical dependence (needing it to avoid health complications)? The latter could be achieved in a cruel way for example by engineering vital genes of enzymes involved in cell metabolism in such a way that they require your substance of choice as a cofactor to work. The former would first require the identification of some genetic basis of psychological addiction. Though for science fiction you could stay vague (because scientific knowledge is vague) and say that the metabolism of their substance is genetically modified in such a way that it overstimulates reward pathways. This would not make them addicted, but rather susceptible to addiction after little exposure.
One of these methods will require altering an existing gene, the other may require inserting a new gene for a new enzyme, or altering the gene of an existing enzyme. The modification will have to be made at the very earliest stages of embryonic development to ensure that all cells carry the modification later. If in-vitro fertilisation is performed, this can be done before inserting the embryo into the mother's womb. In a normal pergnancy, there is a problem as the developing embryo does not become accessible from the mother's blood vessels until several days into development, when there is already a considerable number of cells. You could claim that a virus was modified in a way that it would be able to cross endometrial tissue and enter the embryo. If you want to go more "fancy" high-tech (even though successfully engineering such a virus would already be very high-tech), they could use a nanoparticle, for example made of silicon, gold, or pure carbon.
Whichever method you choose, they could use said delivery method to carry a short stretch of DNA with the desired gene and machinery to recombine it into the embryonic cells' genomes, either exchanging the old gene for a new, engineered one, or simple inserting their own gene.
As for how they manufactured their own new gene or version of a gene, this could be achieved by site-directed mutagenesis

As fiction this is a reasonable premise, but at this point you are talking about what is called Gene Therapy - intentionally modifying or adding the sequence of a functional gene to change a deficiency of the subject.
Gene therapy is a persistent goal of research, but it has only recent been executed - changing the DNA of cells in a living human being.  There have been some scary and unpredictable side effects of gene therapy.  In the mid 1990s an 18 year old boy developed multiple organ failure as the result of gene therapy to cure a genetic digestive deficiency.
This article describes a retrovirally mediated gene therapy to treat X-linked severe combined immunodeficiency (SCID) in 2003.   SCID patients (also known as bubble boy disease) have a single defective gene (yc) on their one X chromosome and the varicella–zoster virus infection inserted a functional copy into the patients.  Three of the four subjects responded well and at 3 years seemed to be effectively cured, but a fourth developed acute lymphocytic leukemia.
Most of the gene therapy projects continue to happen in mice, but there has been some encouraging progress recently, the devil is in the details as to how gene therapy would work.
Here is a decent feed of gene therapy goings on.
If and when gene therapy is safe and precise enough to use, then it could change a lot of characteristics in human beings - just about anything that genes do could be modified or modulated.


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Intracellular lipid transport
I know that lipids are carried around the body in the blood either as micelles or by lipid-binding proteins which allow them to be solved.
Lipids can't always be integrated in a membrane though, the phospholipids used in membranes have to be synthesised somewhere from a precursor which will also by hydrophobic.
Consequently, at some point there will have to be transport of lipids within the cell where the lipids will need to be in solution. How is this facilitated?

Like in the blood, intracellular lipid trafficking is facilitated by vesicular transport and lipid carriers like fatty acid binding proteins. In addition, intracellular membranes are densely packed and they can exchange lipids by collision and transient hemifusion. If you have access to Cell, a good review is from Prinz W. 2010 Lipid Trafficking sans vesicles, Where, Why, How?

I have got access to Cell when I'm on my uni's VPN but it appears I can download the PDF even without access that way. Thanks, very interesting!


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Comparing BLAST and the Smith-Waterman algorithm
I've been asked: how does BLAST improve dynamic programming accuracy?
I do know that BLAST is based on heuristic approach that approximates the Smith-Waterman algorithm and that the Smith-Waterman is too slow for large databases but more accurate.
Can someone settle my conflict?

It doesn't improve DP, is less accurate but usable for large databases with excellent results

So I got this answer from my lecturer:
Since Smith-Waterman algorithm is based on DP, we will get the best performance on accuracy, but there is a change that the homologous sequence is not with the highest probability (so better matching sequences will be "hidden" behind worse ones).
Since blast is based on the heuristic approach, it overcomes the disadvantage described above, by adding biological information, and therefore make it more accurate from biologist's perspective.

BLAST uses a heuristic, but mainly to cut down the time spent looking for homologs, not to produce better alignment. So BLAST is not more accurate than S-W, but often times accurate enough.

ok another constraint I forgot to mention which I believe is crucial - the two sequences are not homologous

As Michael said, this answer is wrong; actually the question itself is wrong. BLAST uses heuristic for speed up, not for accuracy. It is less accurate than DP. BLAST does NOT "improve dynamic programming accuracy". With DP, we can also find suboptimal alignments. If we had an extremely fast computer, we would use DP, not BLAST.


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What regulates these two methods of splicing?
Alternative splicing can shuffle the exon order and select from the exon sequence of a single gene site to provide a combinatorial selection of possible transcription products from the one gene. Can intergenic trans splicing can do this starting from multiple gene sites?
What regulates these two "non linear" gene combination, transcript-splicing processes?

Are you referring to trans splicing?

As Alan Boyd said, this process is called trans splicing where exons of different RNAs are joined together. Physical proximity is conducive for trans-splicing. This study shows that trans-splicing frequency is higher if the genes are proximal. Proximity not only means closer in the genome but also the 3D proximity governed by chromosomal interactions.
Now, what factors  promote trans splicing is not properly understood.