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how to close a severed artery/vein?
This is a medicine-related question that I've been wondering about. I've been watching medical lectures on YouTube regarding the human body and was wondering about how surgeons treat a severed artery or vein (think Juggular or Carotid)? Specifically I was curious about what kind of tools they use and what the technique is for performing this operation.
And before anyone asks, no, I don't need to treat someone with this kind of injury :).
Thanks,
mj

They use clamps and act very very quickly.

So they clamp the blood vessel, suture it, and then release? What happens if the vessel has been damaged such that know it's going to take a while? Do they ever put in a sterile tube to join the two severed ends? Thanks for your response.

Sorry, no idea, I'm a biologist not an MD which is why I only posted an answer. Perhaps someone else here has knowledge of surgical techniques but they are not a part of biology so I wouldn't get my hopes up. Also bear in mind that this will only happen if the vessel is severed during an operation. If this happens anywhere else the chances are that the patient will be dead long before a doctor can get anywhere near them.

I likewise don't know, but here's an oddly in-depth story about a hockey player who was cut on his carotid.  The relevant point to back up @terdon is that he was clamped for about 15 minutes, which apparently isn't that long (I beg to differ...).  But anything major and for much longer will leave you dead.

I'm not really how specific an answer you are looking for, there are literally text books on the subject.  In general we contain as fast as possible, isolate, and reconnect or close depending on the options.  It's also not really correct to lump veins and arteries together as they are treated differently. Was there under a particular condition that you were curious about?  The Juggular or Carotid are not good examples of what you would normally run into in a live pt outside of surgery.

I presume that arteries in the appendages are more commonly injured? I had no condition that I was curious about, just the general question about how they splice the artery back together w/out a patient dying.

My father has had a few surgeries where they put a catheter up his femoral artery. When they're done they close up the artery and then bring in the heaviest male nurse they have to lean on the surgical site for about 20 minutes to apply pressure.

I'm going to take a shot at putting a whole lot of information into a small answer, so let me know what parts need more explanation.  To any others experienced with closure, I am certainly skipping plenty of steps and ideas in attempt to convey the general.
******A general warning that graphic surgical images are used below.******

The Setup:
You asked about "severed" jugular and carotid injuries, so we will focus on neck injuries, with a focus on insults to the R/L common carotid arteries (CCA) and the R/L internal jugular vein (IJV).  To get everyone on the same page visually, we are talking about the large blood vessels in this image:

For the sake of simplicity, we will deal with injuries that are focused directly on these vessels.  In reality, there are so many different and important tissues tightly packed in the neck that there are often many complications and multiple vessels that need to be dealt with near simultaneously.  Further, we will suppose that our patient (pt) is unlucky to have a "severed" vessel in his neck, but lucky enough to have immediate access to ATLS.
Just like you should have learned in your basic neighborhood CPR/aid class, you address the ABC's (MD's add DE): A irway, B reathing, C irculation (D isability, E xposure).  In reality when presented with a pt bleeding from the neck, you will almost always begin by applying pressure at the wound site, while you address the airway.  When I say "applying pressure" I literally mean a nurse or medic putting their fingers up against where it is bleeding and trying to stop it like a hose.
We will assume that a clear airway is established, the pt is breathing normally enough, and under general anaesthesia.  We will also give us the advantage of having the head, and to a little lesser extent body, packed down with ice.  This will give us precious time, and help prevent brain damage.  All else is presumed to be well with the pt, and all we need to do is fix the bleed in his neck.

Identifying the problem:
Now that we have our idealized pt ready to fix, the first thing you have to do is to identify where the bleed is.  Assuming you have serious bleeding, like one would come from a "severed" CCA or IJV that normally means cutting open the wound quickly and in a controlled manner.  Again, the neck is full of tissue you don't want to damage, so a anterior sternocleidomastoid incision is normally called for when you are looking for where the CCA or IJV is damaged.  As opposed to coming from the top the way we would dissect a cadaver (as in the drawing above), the sternocleidomastoid incision will give us a side view into the neck like this:

The point at this stage is to gain control of the bleed.  You don't want to just go digging in where the vessel is bleeding, because you are likely to cause more damage than help (and in this case, loose the pt).  Instead you are going to clamp above and below where the vessel is bleeding.  This will let you suck out the blood and see what's going on.  If you happen to have a large wound in a large vein, there's a chance that a clamp won't give you sufficient control of the bleeding.  In that case you have to also use a catheter to stop the bleeding (in obtaining distil control to be specific).
In our case, this means dissecting the carotid sheath.  This needs to be done very carefully so that you don't damage the vagus nerve.
You may have noticed I kept putting "severed" in quotes.  That's because it matters how the vessels are damaged.  Were they crushed or ground apart? Cut jagged or cleanly? Transverse or longitudinal?  All of these change the exact procedures into how you go forward.  Clearly a vessel that has a small tear is easier to repair than one that has been totally separated with jagged shredding from a crush injury.  Veins and arteries won't retract from the insult in the same way either, so how you find them can be a bit different.  Here is a flow chart that shows the basic decisions:

Put it back together Doc: [warning of graphic images]
You may notice that there are basically two end points for either veins or arteries: repair it or ligate it.  There are many different technical/specific ways either can be done, but those are beyond the scope of this answer.  If the sight of open wounds bothers you, note I am going to start using actual surgical photos below.
When it's possible it's better to repair the vessel.  That means that you can close the artery where it is.  If there is just a small hole, you can suture the hole closed.  With the CCA or IJV it's more likely that you are going to need a patch.  This means that you take another piece of vein or a synthetic replacement, and suture it into the hole.  I always like to tell people surgery is a lot more tailoring than most people realize (not that this is as easy as sewing fabric).  Below is an example of where a patch would be used in the CCA:
First the tear in the artery:

And after the patch has been added:

Suturing and patching can only be used to close the vessels when tension isn't needed to repair the wound.  If the laceration or severing of the vessels are such that it has come mostly (not completely) apart, but you can still get the ends together with NO tension,  end-to-end anastomosis repair can be utilized.  This means that you take the two ends, with branches if there are any at the wound, and suture them back together.
Again here is an example of the opening in the artery (popliteal):

And here it is again after end-to-end anastomosis repair:

Now let's say that you really did get the vessel cut in half.  That's a bit of bad news for you, you're going to have to ligate the vessel.  That means sewing up the end of it to close it down.  You start above the injury in arteries and below in veins, and then you tie at least three loops--many prefer five loops--down on the vein, and make a clean cut leaving at least two loops on the part staying in the body.  Then you do the same thing on the other side of the injury.  I think this is best displayed by a video, unfortunately most of the good ones I know of are not available to the public.
This video certainly not the best technique I've ever seen but it get's the idea across.  I will search for a better video as I have time.
Now if it is possible, a surgeon will try to make a graft deal with the ligation.  The first choice is a interposition graft.  This means taking a larger vein graft and connecting the two ends of the severed vessel.  You do this after making clean ends with the ligations from above.
Here we have the femoral artery prepped for an interposition graft:

And here is interposition graft in place:

In certain cases, this is not possible.  As strange as it sounds, the ligation may just be left in place, depending on where it is.

Is that all?
No, not by a long shot, but that is the basics.  There are many different techniques that can be used, with new and better ones being invented often.  For example instead of suturing, chemical cauterizing of the ligation can be used and is quicker.  That also allows the surgery to be done through a scope.  But the basics remain the same:
Stop the bleeding, gain basic access, get full control of the bleeding, obtain full exposure/access, sew up the problem, put everything back, close up, give fluids, and send them to ICU.  Even after getting everything right in surgery, the recovery can be quite difficult.

Sources and Further Reading
Note: I will try to come back with primary sources, I started from knowing what to do and searched for sources.  Here are two great sources which contain more complete information:
1) Trauma.org  This is a great site for use by actual medical professionals when addressing trauma.  They don't really cover the basics, but they do give wonderful care write ups.  Here is the relevant reference for this answer:
Karim B, 'Peripheral Vascular Trauma' trauma.org 7:3, March 2002. http://www.trauma.org/archive/vascular/PVTmanage.html
2) Acssurgery.com  Even more than Trauma.Org, this site is designed for use by clinicians.  Relevant reference:
Wisner DH, Galante JM, INJURIES TO THE NECK acssurgery.com 7:4, 2010. http://www.acssurgery.com/acssurgery/institutional/getChapterByIDHTML.action?chapId=part07_ch04&type=tab

Great answer which deserves +1, but I'm not qualified to judge if it's accurate.

@fileunderwater I linked to many sources that will say the same thing, but I will come through with line citations later.  Answers like this take long enough to write as it is.

@mj_ Let me know if this isn't covering what you wanted to know.  You mentioned tools, and I could go as deep as to the size sutures recommended, but the spirit of the question doesn't seem to call for that.

@Atl_LED My comment wasn't in any way meant as a critique, if you saw it that way, rather the opposite. It is a great and informative answer. However, since the question was specifically asking for info on how surgeons work, I just didn't feel qualified to rate the answer - therefore my comment.

I'd give a +1 just for mentioning primary survey ;)  Great answer


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Mayfly identification - Oregon
Found in a web by a very small, slow moving stream. Douglas-fir forest in Gales Creek area, April 28.

Great picture -- it's reaching for the sky!

Approximate size?

source: Stack Exchange

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sort: votes


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Carbon Monoxide and High-Oxygen-Affinity Varieties of Hemoglobin
I recently learned about the concept of "affinity" in regards to hemoglobin. For hemoglobin in humans, carbon dioxide has a lower affinity than oxygen, which allows gas exchange to occur in our lungs.
Carbon monoxide is problematic for us because it has an even higher affinity to hemoglobin than oxygen does. This means that our red blood cells will not exchange carbon monoxide for oxygen in our lungs.
My question is: for high-altitude-adapted organisms such as the bar-headed goose, whose hemoglobin has a higher affinity to oxygen than ours does, is carbon monoxide still poisonous?

As carbon monoxide binds to the same place in the heme as oxygen, I would expect that. The question is if the difference between a "normal" hemoglobin molecule and one from a altitude adapted bird does really matter.

I don't know about the makeup of bar-headed goose haemoglobin, but fetal haemoglobin (HbF) has a higher affinity for oxygen and a lower binding of carbon monoxide than HbA (http://bloodjournal.hematologylibrary.org/content/bloodjournal/33/1/37.full.pdf?sso-checked=1). If the goose haemoglobin behaves similarly it may also have lower affinity for carbon monoxide.

My question is: for high-altitude-adapted organisms such as the bar-headed goose, whose hemoglobin has a higher affinity to oxygen than ours does, is carbon monoxide still poisonous?

Yes. To put out a few other facts from the Stritch School of Medicine:
CO has 250 times the affinity for hemoglobin than O2
Hb becomes 100% saturated with CO at PCO = 0.6 mm Hg
Hb becomes 100% saturated with O2 at PO2 = 600 mm Hg

What does that mean? Well, that means that when the partial pressure of CO is 1mmHg, you're well and truly dead. So if the bar headed goose could survive in an environment more than 1% CO its hemoglobin would have to bind to molecular oxygen very, very tightly below 1mmHg. If this was true you would expect their binding curve to reach a high % of O2 saturation below a partial pressure of 1mmHg. Does it exhibit that?

Nope. At 1mmHg (remember, CO has 100% binding at 0.6mmHg) the bar headed goose hemoglobin's saturation is less than 2%. In fact, they're pretty similar to humans:

Is this casual glance conclusive? Well... Not entirely. I couldn't find any carbon monoxide data for the bar headed goose, but to overcome the 250x higher affinity for CO the goose's hemoglobin would have to be very, very different from that of humans while still exhibiting a similar binding curve. I've not received the education to determine if that's possible or how it would occur, but it is a very remote possibility.
Erring on the side of "most likely", however, I think it's safe to say that given a room filled with 1% CO you'd end up eventually killing anything that relied on hemoglobin to move necessary oxygen to tissues.

Do you have references for your images and graphs?

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Do you produce more sperm after 1 week of abstinence vs 1 year of abstinence
Question: I was wondering if the amount of sperm increase with the amount of abstinence?
Side questions:

Is their a max amount of sperm?
What happens with the excess amount?

Orgasm does not necessary involve ejaculation in those wet dreams.

I have read after 8 days of abstinence an significant increase is noticed in the amount of sperm and the amount of little soldiers.

Excess/old sperm is broken down (by phages?) and is re absorbed in the body

There is an increase by abstinence.

The within-subject variability of the semen sperm count (n), volume
  (v) and the total number of spermatozoa (N) was studied on 220
  ejaculates from 36 normal subjects after an abstinence of 7 days or
  less.
The three semen characteristics for a given subject were highly
  correlated with the length of abstinence: for an increase in
  abstinence of 1 day there were mean increments of 13 × 106/ml for n,
  0·4 ml for v, and 87 × 106 for N.

1979 - Within-subject variability of human semen in regard to sperm count, volume, total number of spermatozoa and length of abstinence

Semen analysis was performed on six men after various sexual
  abstinence periods (from 2 to 18 days). The variations in semen
  parameters were analyzed statistically as a function of the duration
  of abstinence.
Lengthy sexual abstinence was found to affect all semen
  characteristics. Semen volume and concentration and total sperm count
  showed significant increases, whereas motility and normal morphology
  decreased significantly with duration of abstinence. Significant
  changes in the percentage of normal sperm forms were observed after
  more than seven days' abstinence.
The study indicates that the influence of long sexual abstinence on
  semen quality varies with the variable considered. With regard to
  fertility, a long abstinence period might induce senescence of
  spermatozoa.

1994 - Effect of long abstinence periods on human sperm quality.

Sperms can die of "old age", as the previous quotes mentioned long abstinence period induces senescence. It is hard to find anything about their lifetime, it is at least 7 days I think.

For humans, entire process of spermatogenesis takes 74 days. Including
  the transport on ductal system, it takes 3 months. Testes produce 200
  to 300 million spermatozoa daily.

according to wikipedia

So there is a constant rate of sperm production.
I think the following differential equation can describe the change of the sperm count:
$$ \dot{x} = μ - Dx $$
where

x is the sperm count
μ is the production rate regulated by testosteron (about 250 million per day)
D is the death rate which depends on the age of the population (depends on the lifetime, production rate, elapsed time)

So there will be a maximum amount by abstinence. By that amount
$$ μ = Dx $$
so
$$ x_{max} = μ /D $$

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How close to Earth's core can organisms live?
We don't to know much about organisms living deep below the Earth's crust. Recently a team led by S. Giovanni discovered some microbes 300 m below the ocean floor. The microbes were found to be a completley new and exotic species and apparently they feed off hydrocarbons like methane and benzene. Scientists speculate that life may exist in our Solar System far below the surface of some planets or moons. This raises some questions:

What is the theoretical minimum distance from Earth's core where life can still exist. Please explain how you came up with this number. For example, there are temperature-imposed limits on many biochemical processes.
Is there the potential to discover some truly alien life forms in the Earth's mantle (by this I mean, life which is not carbon based, or life which gets its energy in ways we have not seen before, or non DNA-based life, or something along these lines)?
What is the greatest distance below the Earth's crust that life has been discovered? I believe it is the 300 m I cited above, but I am not 100% sure.

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

Are you serious? I am in high school, and I don't take a biology class. This is not homework and I doubt any professor would assign a homework question like this? I don't know much about biology, especially about organisms living deep below the Earth's crust, which is why I'm asking the question...How in the world do you expect someone who knows nothing about biology to "show an attempt at an answer". In my opinion this is a totaly valid question and its not homework.

@JoshuaBenabou Homework does not mean homework in school. Homework refers to your personal effort in the sense "doing your homework before asking others". Showing an attempt means looking up or at least doing a google search. And please dont give this "I don't know biology" argument. When I ask questions in stackoverflow I make sure that at least I read the manual page once. If you don't know any biology then start by learning some.

It is a good question. If you can add some evidence for your research, it will not be closed. Please be polite too! The message by Matt is a standard format "one reply for all" sort of message.

Alright I've edited the question to include some background information. Is it good now?

@JoshuaBenabou Can you provide some link to that experiment done by Giovanni and colleagues

http://www.eurekalert.org/pub_releases/2003-01/osu-rfl123102.php

I think the second subquestion should be removed, since it is rather nonsensical. It can be restated as: "What is the potential of discovering something completely unknown?". Of course we can discover something entirely new and alien, but to evaluate the possibility of this is far too speculative.

I bet the closest life can get to the core is 6377.1 km plus or minus 1 km.

How do you figure?

That is the radius of the earth. If you get 6370 km into the earth, you will be almost in the center of the core

@user137: But extremophile life has been found several miles deep in mines, so knock at least a few km off your number.  One example here http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=928683 or search for "deep biosphere".

we have found life 7km down in the kola superdeep bore hole, the answer may well be as deep as liquid water can exist. which admittedly is not that far.

There's a lot we don't know about life in deep caves, but we can bound the deepest living organism to at least 3.5 kilometers down, and probably not more than 30 kilometers down.
The worms recovered from deep mining boreholes are not particularly specifically adapted to live that far down: they have similar oxygen/temperature requirements as surface nematodes.
The Tau Tona mine is about 3.5 kilometers deep and about 60˚ C at the bottom. Hydrothermal vent life does just fine up to about 80˚C, and the crust gets warmer at "about" 25˚C per kilometer. It's entirely reasonable to expect life to about 5 kilometers down, but further than that is speculation.
Increasing pressure helps to stabilize biological molecules that would otherwise disintegrate at those temperatures, so it's not impossible there could be life even deeper. It may even be likely, given that the Tau Tona life breathes oxygen.
I am certain no life we might recognize as life exists in the upper mantle.


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Rice left in water for several months - what biological reactions or growths would occur?
In an attempt to make a hair care product, uncooked white basmati rice was left in an air-tight container half filled with tap water for several months.
When opening the container, the smell was extremely foul and disturbing, one of the most revolting things I have ever smelt.  It was worse than the smell you would usually associate with yeast, alcohol, or mold.  This horrid smell immediately spread to the entire property and took many hours of fan extraction to remove.  It was worse than the smell of sewage.
I rinsed the container used and cleaned it in the dishwasher several times at 75'c.  After several dishwasher cycles, the disgusting smell remains.  It makes me wonder what kind of biological or chemical product has been created that even a dishwasher cannot neutralise or sterilise at high temperatures?  Is this a safe substance?  This is especially concerning as this recipe exists on several hair care forums; is it widespread misinformation caused through malice?
I believe this is a valid scientific question about microbial life so on that basis I would not expect it to be down voted.
The substance looked like water with rice or rice starches dissolved in it; it was murky with a whitish colour.  There was no air bubbles which could be visually observed, although the murky texture could have been caused by micro-bubbles. The smell was very strange, unlike anything I have smelled before.  The closest description I could give is that of sewage, yet it is more disgusting than the smell of sewage if that is relatable at all.

What did the contents of the container look like?

It depends on the microflora in your locality. Difficult to comment unless you describe the smell accurately. In general I would advise against doing anything (in the name of home remedy) of which you have no knowledge.

It is likely a volatile organic compound (VOC) that is released as a by-product of microbial metabolism, although microbes can also produce some inorganic compounds, such as hydrogen sulfide (rotten egg smell). It could be any of a number of compounds, depending on the microbial species and the environmental conditions. The only relevant paper I could find based on a cursory search was by Yanqiang et al. (2013) on volatile compounds released from the anaerobic digestion of food waste in general; based on the results, the odor likely consists of a complex mixture of gases, and may be especially rich in aromatic compounds. Whether it could have any negative health effects is challenging to prove, but you would likely want to avoid exposure.
I presume that your container is made of plastic or at least contains a silicone ring. You can remove odors from metal or glass by washing them, but porous substances like plastics, rubber and the like will absorb volatile compounds, rendering them largely inaccessible to solvents such as water, and will release them slowly over time, which you can perceive via olfaction as you have noticed. If you want to eliminate the odor faster, you will need to accelerate this outgassing process. The way this is usually done is by baking in an oven (optimally in a vacuum, although this is not necessary). The rate of outgassing grows exponentially with the temperature, so you should use the maximum temperature that the material in question can withstand.

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How to obtain a list of proteins sorted by the ~1400 unique protein folds?
The databases CATH and SCOP both have around 1400 unique protein folds recorded from analysis of the PDB.  However, I do not see any method to access this particular data.

A list of each of the 1400 folds (just an id number, and/or a descriptor)?
For each individual fold (of the 1400), a list of PDB IDs for proteins which are known to adopt each individual fold?

Is https://www.rcsb.org/search/browse/scop suitable?

If there is a simple way provided to do this it is very well hidden. The tedious and stupid way to do 1 (get a list of folds) would seem to involve rolling your own:

Go to http://scop.berkeley.edu/ver=2.07 (or whatever is the latest version).

Click on each of the 12 classes in turn. e.g. (a) all alpha proteins will take you to http://scop.berkeley.edu/sunid=46456 .

Save the source of each page as text.

Write and run your own parser to pull out the sunid () from the http://scop.berkeley.edu/sunid= and the description line if you wish. (This assumes you program.) I think this sunid is the fold id.

If you can than find some database or table that has PDB and sunid values in it, you can write another program to find the answer to 2.
Alternatively… (appended January 2021)

Download dir.cla.scope.2.07-stable.txt (or the latest version)
Save as a text file.
Open in Mircorsoft Excel. (Just dragging onto the app icon formatted it properly on my Mac. Your mileage may vary.)
You can just select the column with the ids, paste into another sheet, and then remove duplicates to get all the different fold ids. (Alternatively, you have about 276,000 entries to do with whatever you wish.)

As this popped up again after about five years, and I have actually used this recently, I have added a non-programming method to get at the info, just using an Excel spreadsheet.

It looks like you can download the full database in SQL format or parse-able text files from here:  SCOP Download - Berkeley
The link has a link to the Schema as well:

Thanks for the answer, but it doesn't answer the question.  Being able to download the database doesn't help.  The schema might have been useful - except that none of the tables have around ~1400 rows, or at all mention folds/topologies in the table name or description.


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Stroke research question - has there been research in mirroring muscle electrical signals from a good limb to the bad one?
Transcutaneous electrical neural stimulation is an established tool to help stroke victims recover use of a paralyzed limb by engaging neuroplasticity. Has anyone here heard of research where you wear sensors on a good limb and mirror the signals from the good limb to the bad one as a sort of electrical mirroring? My search has been fruitless and I wanted to see if anyone knows of anything before I engage this further.

I would understand better what the benefit was if the same electrodes were the same on both sides, because they can already send electrical signals to one limb naturally and effect their own mirroring as a result.

Imagine the left arm is bad and the right arm is good. As the patient lives out his daily life and moves the right arm, sensors pick up the motion and send it to stimulators on the left arm, hence mirroring. The idea is to leverage activity in the brain for the right arm to create an association for the left arm.

What were your search phrases? You'd probably need to search the physical therapy literature. I'd start with physical therapy post stroke TENS and look for terms to narrow the field.


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What is a selective constraint?
I encountered the term selective constraint in Huber et al. 2015, page 4 (last paragraph) in:

If invariable  sites are included in the   analysis, then both the methods of
  Kim   and Stephan (2002)  and Nielsen et  al. (2005)  may be  sensitive
  to    assumptions regarding selective constraint  and mutation rates.

but the context does not quite help.
What it the definition of selective constraint?
Does it has to do with lethal mutations in non-coding regions? Does it has to do with selection interference?...

Please use the quote environment instead of the code environment (as far as I know most screen readers will start reading this character-by-character).

It is selective pressure that determines and limits the number of neutral/beneficial mutations that can take place. The more constrained a locus is under selection, the easier it is to generate deleterious mutations and the harder it is to generate beneficial ones; this can be reflected in low substitution rates at such loci in populations with time.
One widely used method to measure this is to compute the Ka/Ks ratio to infer if a locus is selectively constrained or not.

+1 Thank you. Can we associate a value to this concept? For example the  selective constrained could be $S = K_a/K_a$ or $S = mu_b/mu_d$, where $mu_b$ and $mu_d$ are the beneficial and deleterious mutation rates, respectively.

It is easier to measure Ka and Ks , so if something is under no selection (neutral) you'll see a ratio of 1 , less than 1 indicates purifying selection, more than 1 indicates positive selection. More here http://www.cs.mun.ca/~banzhaf/papers/ppsn08_evorate.pdf


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Nutritious protein substance for vitamin enhanced crop?
I am not a bio or science major, but we have a subject, like an elective on biotechnology and we were tasked to think of a product that hasn't been invented yet. My groupmates and I thought of a vitamin enhanced crop to help fight against malnutrition. As for the crop we thought of using sweet potatoes and altering its DNA to produce a more nutritious one.
Our plan is to use agrobacterium tumefaciens, cut its plasmid and insert a foreign DNA to it. Now we are stuck with what foreign DNA can we add to it so that we will produce a more nutritious sweet potato.
Our teacher gave us a hint that whatever we will add to the organism should be a protein because the DNA only codes for protein. So if we plan to add vitamins to the sweet potato then it should be protein-based.
Sorry but I am very confused with biotech terms because I am not a bio major. But any help would be very much appreciated! thank you in advance!

Proteins are not vitamins. It's plausible that you could add proteins to synthesize a vitamin. That  said, I think plants already make all the vitamins they need. I think you need to reevaluate your objectives.

Thank you for your reply! can you give example of proteins that could synthesize a vitamin?

This question is broad. There are many vitamins and each of them has a different biosynthetic pathway. You should also make an attempt to answer before asking others. If you have done so then please add it in the question.

You might want to look into http://en.wikipedia.org/wiki/Golden_rice

I'd start by looking at the nutritional facts for a sweet potato. What does it lack in? Now, look at biosynthesis pathways for your compound, and get a handle on what the precursors are, and what proteins are necessary. It could be just as easy as a Google search like "Vitamin C biosynthesis." There's also the Monsanto route ala Bt corn, but it'll take some digging through literature either way.


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What is the nature of plasmids?
What are the plasmids composed of? Are they composed of genomic or non-genomic DNA?
I guess the answer is "genomic DNA" but I'm not sure.

Is this a homework question? What definitions of "plasmid" and "genetic DNA" are you going by?

No...it's not a homework q...just one of my classmates was arguing about this....Actually I think you guys are just PARANOID about homework q....if it was a homework q. I think I have enough sense to put a 'homework' tag....

You probably mean genomic and non-genomic DNA - Plasmids are small rings of non-genomic double-stranded DNA in Bacteria. They replicate mostly indepently of the genomic DNA can can occur from a few to several hundred copies per cell. See the illustration from the Wikipedia:

Not only in bacteria.

@chris, yeah...


text:
Reason for different color perception in left/right eyes?
What could be the reason for a difference in color perception between the two eyes of an adult individual without any known eye conditions? In particular, a difference in the perceived color temperature in each individual eye and an average of the two when looking through both eyes.

It may be advisable to remove any reference to self. At Biology SE we explicitly discourage self-help questions, as we support seeking professional advise. However, we are happy to share information on general scientific questions :)

This is not a personal health advice question even though the OP has used a personal example. Therefore I suggest that personal references may be removed to avoid that confusion.

Edited accordingly, first time posting outside of code/math questions.

Most likely, tumor. Also, there is asymmetry between left/right hemispheres, so why not eyes, which are also central nervous system

@aandreev Why is tumor most likely? Folks can reproduce this phenomenon by lying down, and there's some variability in normal people (title: "Inter-eye comparison on the 100 hue test" if unavailable).

Good question. I've noticed this difference since my childhood.


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Book recommendation on mammal (or just primate) behaviour, especially in relation to child-rearing
I have a growing frustration with the lows 'new-age' parenting is reaching, along with asininity of so much of our public schools' (and summer camps') philosophies and policies in relation to our kids. Whatever the implications, this has continually lead me to the thought of

what the natural precedent is for how primates (or other mammals) raise their young, collectively or otherwise -- how they're guided, rewarded, chastised, and conditioned.

May someone please recommend a book that delves in to some of this? (Humans don't necessarily have to enter the picture, but something that does compare and contrast with the human condition would be a bonus.) (Preferably not a text book, but, by all means, please recommend those too.)

Please don't fall into the other new age fallacy that states that natural == good. Rape is perfectly natural for example (just look at cats) as is incest (most mammals) and war (chimps for example). That something is 'natural' or the way it is done by a different primate in the wild is no indication that is is a good approach for raising the young of our species. It might be, just not always.

Suggested Reads:
Evolutionary Psychology
By Lance Workman, Will Reader
Evolution of Human Behavior: Primate Models
edited by Warren G. Kinzey
Social Behaviour of Children: A Cross Cultural Assessment
By Ralph E. S. Tanner


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How does someone with red-green colorblindness see yellow on a monitor/television?
I recently watched the video This Is Not Yellow explaining how red, green, and blue pixels can be used to create images of all other colors. Since yellow is created with red and green pixels, how is a person with red-green colorblindness (me, for instance) able to perceive yellow on a monitor?

Below is a summary of the information found here and from how Enchroma glasses work (although, I've tried the glasses and the effect is too subtle for me to wear them regularly).
Human color vision works because there are three different color-sensitive receptors called cones that detect short-wavelength light (bluish), medium-wavelength light (greenish), and long-wavelength light (reddish). The charts below show the sensitivity of these receptors in people with different genetics.

Chart taken from Color Art and Science, edited by  Trevor Lamb and Janine Bourriau
The bottom chart, marked (c), shows the sensitivities of eyes of people with normal color vision. Short-wavelength (blueish) cones detect a distinct patch of light while the medium- (greenish) and long- (reddish) wavelength cones overlap, but are still separated enough to reliably distinguish between the two color ranges.
The middle chart, marked (b), shows mild protananomaly or deutananomaly color blindness in which the color regions that medium (greenish) and long (reddish) cones react to are more overlapped than in people with normal vision. This can lead to trouble distinguishing these colors since the overlap causes both receptors to light up for more colors.
The top chart, marked (a), shows complete protanopia or deutanopia, where the long (reddish) and medium (greenish) receptors completely overlap in their sensitivity ranges. This can also happen if one receptor is entirely missing from the retina.
I was under the impression that all red-green color blindness was of the protanopia/deutanopia type, meaning that the yellow generated on a computer screen should look red because the green light wouldn't be activating any of the non-functional medium (greenish) cones. In actuality, I only have a mild protananomaly/deutananomaly, so my eyes are still sensitive to the differences between red and green light, just less so than normal people. The yellow I see may be subtly different than other people, but I can still differentiate.
Enchroma glasses work for mild colorblindness by filtering out light in the overlap region of medium (greenish) and long (reddish) cones. This creates more separation in the detection region of those cones, thus making some colors more distinct at the cost of blocking some light.

Normal people see color due to the bellow mentioned combination of red, green and blue:

But due to genetic factors, The graph Distorts:

Now,If consider the normal Color code for yellow:
Yellow = R(255) + G(255) + B(0)
Or in other words
Max. Red + Max. Green + no Blue = Yellow
That means even if you can see a little of Red and Green, you can still a little deeper or lighter shade of yellow.
So Summing it up in the images:

Normal

Red ColorBlind

Green ColorBlind

Blue ColorBlind
Source:
Coblis — Color Blindness Simulator
A quick introduction to colorblindness

What is the effect of having mutated green cones? Are they non-functional, of reduced sensitivity, or something else?

@MarkH: Can you ask it as a separate question?

@MarkH: Hey, hope my answer solved you query, if so, please mark this as answer.


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Do humans have a "dominant" neurotransmitter system/sensitivity within their brain?
I've recently heard a podcast, in which Dr. Helen Fisher suggests that there are "4 broad personality types", and each one is associated with a particular neurotransmitter:

The corresponding Platonic thinking style, Keirsey temperament type (according to some readers, not Fisher herself), and color can be seen in parenthesis.

Explorer (creative; Artisan temperament, yellow) = dopamine
Builder (sensible; Guardian temperament, blue) = serotonin
Director (reasoning; Rational temperament; red) = testosterone
Negotiator (intuitive; Idealist temperament; green) = estrogen/oxytocin

I'm interested if there's indeed scientific evidence to support that for different people their affinity for a certain neurotransmitter is increased to such degree that it manifests in a noticeable difference in personality?

Dr. Helen Fisher's conclusions are plain bunkum. What does it even mean when she says associated with a particular neurotransmitter? The sheer work required to even get at this question is vast and difficult so it is unsurprising that she is venturing as much as a guess.There is scientific evidence to support different neurotransmitters systems can go awry in diseases but Fisher is overinterpreting the literature. Take a look at the neurotrasmiter table and you can see what each does and how malfunctions can result in certain diseases.
http://en.wikipedia.org/wiki/Neurotransmitter
Also testosterone and estrogen are thought of primarily as hormones not neurotrasmiters.So Fisher is saying women(who have more estrogen) are better negotiatiors whereas men(more testosterone) are directors. Even these banal conclusions are contentious and debatable.

I know that the Keirsey model itself is rather unsubstantiated. It's a sort of simplified version of MBTI. So I am not sure if relating the neurotransmitters to Keirsey temperament would work due to the fallibility of temperaments.
However, different neurotransmitter levels certainly contribute to different moods. That has been proved. Does that translate to personality? Don't know.

This just equivocates. Not a helpful answer.


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What is meant by "neurotransmitters flooding the brain"?
I frequently hear expressions like "Dopamine flooding the brain" or "X neurotransmitter flooding the brain" used to communicate with general audiences. For example: "Following [orgasm]? oxytocin floods the brain, causing feeling of deep connectedness between people"
What exactly do they mean by "Oxytocin flooding the brain"? I'm interested in where and how it happens. Do they mean that excess neurotransmitters are released in the synaptic cleft? Is it localized to some brain areas, or is it indeed throughout the brain?
If they are indeed talking about the synaptic cleft, then I'm interested in how such "flood" triggers the change in state - the answer to this question suggests that the half life of dopamine is only about 2 seconds in prefrontal cortex. Assuming that the half life of oxytocin is similar, in the "oxytocin floods the brain and produces feeling of connectedness" example, does it mean that a single burst of oxytocin(x seconds in synaptic cleft) is enough to produce such feeling, or are they talking about sustained release or some kind of release loop mechanism?

WOW! Whenever I have read about drug addiction, I have come across"flooding" but never wondered what actually it meant ! +100000000000

I'm pretty sure the answer is that it's a sensationalistic media term with no specific meaning. It probably covers a variety of different underlying biological mechanisms.

@octern I disagree, my answer elaborates...

It is very likely what they mean by "neurotransmitters flooding the brain" is the phenomenon called Volume Transmission.
I paraphrase from this source:

When a neurotransmitter is released at a synapse, it reaches its
  highest concentration inside the narrow space of the synaptic cleft,
  but some of it is certain to diffuse away before being reabsorbed or
  broken down. If it diffuses away, it has the potential to activate
  receptors that are located either at other synapses or on the membrane
  away from any synapse. The extrasynaptic activity of a
  neurotransmitter is known as volume transmission. It is well
  established that such effects occur to some degree, but their
  functional importance has long been a matter of controversy.


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Why do we age? or Do we have a theory of senescence?
There seem to be a number of ideas about why we age. Hypotheses include the gradual accumulation of cell metabolic products affecting organism function and the reduction of telomere length during cell division.
My hand-wavey idea would be "wear and tear".
Are we anywhere near a consensus theory of senescence?

This is one of the subjects where -- in my opinion -- there can't be just a single dominating theory, at least not now. As in many other areas of biology, many different theories do co-exist here and the reality seems to be a mix-up of them all.

Can you explain why there can't be a single dominating theory? Your comment suggests that in the future we might have one. I find this a fascinating subject - since so many pathologies are age related, surely a "theory of senescence" should be one of the primary focuses of medicine..?

The 'wear and tear' argument is most likely true but it is also interesting to reason about ageing as inevitable from the evolutionary point of view.
To set up the argument, we need two things:
First, each individual has got a 'reproductive potential' which is realised throughout life. This means a deleterious mutation which has an effect in early life, will affect reproductive value more than a mutation which manifests itself in later life, after the individual has already had offspring. Thus selection will act strongly on genes which are expressed in early life than on those which are expressed later. For that reason, there's no strong selection against diseases such as diabetes or cancer. This argument can be applied not only to occurrence of disease but also to decay of ordinary functions of the body.
Secondly, cells in the body are constantly renewed and defects such as telomeric breaks are repaired. Mutations in the soma are taken care of by the immune system and can be in principle avoided. The fact that they tend to accumulate in later life can be explained by the first point: selection is weaker to oppose telomeric breaks and mutations in later life.
I was trying to be brief here, but there are more sides to the argument (e.g. Williams' antagonistic pleiotropy). Modular Evolution (Vinicius, CUP 2010) provides a good overview of the evolutionary aspect of theory of senescence (and many other interesting evolutionary arguments).

Thanks @Greg Slodkowicz. Would it then be true to say that all sexually reproducing species age? I ask this because some bacteria do not exhibit senescence.

http://en.wikipedia.org/wiki/Turritopsis_nutricula is a famous example. In case of bacteria, they are said to be immortal as a colony, since they can divide indefinitely. But for single-cell organisms which reproduce asexually even the notion of an individual is blurred, since each cell splits to form two identical daughter cells.

I’ve never been completely convinced by the wear & tear argument: germ cells (and all unicellular organisms) are direct descendants of the “arch” cell. Not just genetical, but cytoplasmatic, through cell division. If the wear & tear argument were naively true, germ cells would long have ceased working. Now, it may be that preventing wear & tear is so expensive that metazoa have disbanded it in somatic cells (where it’s expendable). But I’ve never heard that mention.

Maybe recombination prevents the accumulation of defects that you would expect from germ cells by providing other alleles that may be functional.

Once could argue that we die because it is advantageous to get rid of mature individuals once they have reproduced.  Because mature individuals have no more offspring to convey beneficial genes, those offspring which will benefit from knocking off their ancestors will have an evolutionary advantage.

Actually, you want them to stick around long enough to take care of their offspring.

But not too much longer ofter that.  Any post-reproductive beneficial traits will not be selected for, and will die out.

@dar7yl Except for post-reproductive lifespan in women. Not sure how strongly it is selected for, but it clearly has an advantage. See here. Awesome results!

That doesn't explain why we don't just reach sexual maturity and then stop aging - it can't be the primary explanation, although it would be a selective pressure once aging existed in the first place.

There is a pretty good discussion on this topic in chapter 2 of Geriactric Medicine - An Evidence Based Approach (4th ed) by Cassel. This is the main reference for the info below which can hopefully add something to the answers already given.
In terms of views on ageing, there's evidence to support both:

general principles that may apply to it; and
it being a consequence of a collection of degenerative processes (this is apparently the more supported view).

Since almost all biological systems in the body degenerates with age and this happens seemingly at random, it's been difficult to identify particular catalysts that cause this. Consequently, biologists apparently steer away from a general theory or mechanism.
However, there are two classes of theories that have been floating around. That is 'loose cannon' and 'weak link'.
Loose Cannon encompasses theories that support the 'wear and tear' proposition. Two popular theories under this banner are free radicals and glucose.
Weak Link suggests that particular physiological systems are vulnerable during senescence and if a system fails, the whole body begins to decline. It's suggested that the neuroendocrine and immune systems are particularly vulnerable.
There is also a limit on the ability of cells to replicate - this is called the Hayflick Phenomenon (or limit). The reduction of the enzyme Telomerase, which lengthens telomeres during mitosis, is implicated in limiting a cell's ability to replicate indefinitely.

"WHY" we age is a different question from "HOW" we age.  The "WHY" refers to ageing from an evolutionally standpoint, whereas the "HOW" refers to biology of ageing.  As for the "WHY" I would read a few papers on the antagonistic pleiotropy hypothesis (click here).  As for the "HOW", there is no definitive understanding of mechanisms of ageing.  However, the role of cellular senescence in ageing and age-related disease is a major player in the biology of ageing (click here for example).  When cells become senescent (due to either telomere shortening/DNA-damage) they can no longer divide to regenerate damaged tissue.  Additionally, senescent cells are highly pro-inflammatory and so have the potential to damage the surrounding tissue if the are not removed.  In younger organisms, senescent cells are most likely removed my the immune system, but as organisms age, the immune system also ages and can no longer effectively remove senescent cells.

I know this question has closed out, but I wanted add this recent reference.  The reactivation of telomerase (which inhibits telomere shortening) seems to have rejuvinated mice, including neuronal growth in the brain.  This is crazy awesome for a couple of reasons.
One being that we may all get to see our 140th birthday.
But since there were a reversal of aging from telomere extension, that implies that aging is adaptive and not a 'wear and tear' phenomenon, at least in animals like mice (and hopefully humans).  hard to believe.
i.e. If there was a mutant that turned on telomerase, why is it not a ubiquitous trait?

Interesting, but the Guardian article is not really a reference - better to go to the original  paper. Also, a concern with telomere-lenghtening strategies would be carncer surely.

cancer is mentioned in the article...

I was think about this. I have same idea, so i think to be immortal we should resolve cancer first. So i'm still researching about cancer...

are you aware of Aubrey De Gray?  His thinking is theoretical at this point, but well articulated. http://www.ted.com/talks/aubrey_de_grey_says_we_can_avoid_aging.html


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Is there any possible way that hybrids can mate?
I'm writing a book, and a a portion of it involves a society of humanzees. Now, is there any plausible way that a hybrid (such as a humanzee) could procreate either with one another, or with their father/mother species? I apologize for my lack of understanding of biology, any help would be much appreciated!

This is a hypothetical scenario which I think could be compared in parallel to hybrids like a mule (offspring of a male donkey and a female horse) or a hinny (offspring of a male horse and a female donkey) or zebroids (reference). In the case of the fertility of mules on wikipedia it is stated that

A few female mules have produced offspring when mated with a purebred
  horse or donkey.

with examples being given as

Since 1527 there have been more than 60 documented cases of foals born
  to female mules around the world. There are reports that a mule in
  China produced a foal in 1984. In Morocco, in early 2002, a mare mule
  produced a rare foal. In 2007 a mule named Kate gave birth to a mule
  son in Colorado. Blood and hair samples were tested verifying that the
  mother was a mule and the colt was indeed her offspring (reference).

In the case of a hinny fertility is much more rare but there is a documented case on Wikipedia

In China in 1981, a hinny mare proved fertile with a donkey stallion.
  When the Chinese hinny was bred to a donkey jack, she produced "Dragon
  Foal," who resembled a donkey with mule-like features (reference).

The wikipedia page on hybrids will also be of interest in your research. In short, hybrids can procreate and give birth in rare cases. However, I wouldn't vouch on the survivability of the offsprings. Since your work is fictional, it is entirely left to your discretion on that topic. Btw, humazee or humzee makes a more intriguing name maybe. Good luck with the book.

Recent genetic analysis of human DNA shows neanderthal ancestry, so inter-species breeding to produce reproductively viable offspring (humanderthals?) appears to be possible - at least between species of the same genus. But with Homo sapiens being the only extant species in the genus Homo you'd be really stretching the boundaries of plausibility to have a human/ape or human/monkey hybrid.


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How to make sure a stem cell culture is cancer free?
Say I take a blood sample from an adult, extract the white cells and apply to them the process described in <this article>. Assuming this actually turns the adult white cells into stem cells, which I then transfer to a culture in order to grow an arbitrary quantity, how can I make sure in the end this culture is free of cancer stem cells? Is there a last step that can be applied which would eliminate any potential CSCs leaving only healthy cells in the culture?
Thank you.

I doubt that this differentiation between these cells is possible. Stem cells are not expressing very much surface markers and are relative inconspicuous. So you can only cultivate them and look for the outcome.

HAT media additives?

The moethod described in this paper has never been reproduced outside the Riken Institute (which claimed to have to developed the method). The papers describing it have since then been retracted due to scientific misconduct (falsified figures, which of course only have been wrongly put in there and so on) which caused a major scandal.

It would not be possible to differentiate CSC from normal population non-invasively and select them out. You may do a single cell expression analysis to say if a CSC is present in a population or not but there is no magic bullet method for eliminating them. Also there are several oncogenes and some of them are also required for usual stem cell function. HAT kind of methods will not be able to eliminate potential cancer cells. Also, usual cancer chemotherapeutic drugs also affect other actively growing cell.
Bottomline: Not possible with the current level of knowledge and technology.


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How late in a human pregnancy can a zygote split?
This page indicates that the first two days is "very early" for a zygote to split, and that conjoined twins are the result of an "extremely late" split:

If the zygote splits very early (in the first 2 days after fertilization) they may develop separate placentas (chorion) and separate sacs (amnion). ... Most of the time in identical twins the zygote will split after 2 days, resulting in a shared placenta, but two separate sacs. ... Finally, the zygote may split extremely late, resulting in conjoined twins.

What I'm looking for is more specificity. At what time in the pregnancy does a split zygote result in twins who share a placenta and not a sac? What about conjoined twins (I'm most interested in the most common types of conjoined twins)?

This information can be found in the wikipedia Twin article, specifically in the degree of separation section.

Identical twins
Twinning occurring at the two cell stage or afterwards, up to and including the 16 cell stage, which translates to days 1 to 3 after fertilization, results in diamniotic, dichorionic twins.
Twinning at the 32 cell stage (day 4), up to  and including day 6 results in diamniotic, monochorionic twins. The majority of identical twins split at this stage.
Twinning from day 7 up to day 10 results in monoamniotic, monochorionic twins. This is rare and only accounts for about one percent of identical twins.

diamniotic: twins have separate amniotic sacs
monoamniotic : twins share one amniotic sac
dichorionic: twins have separate placentas
monochorionic: twins share the same placenta

Conjoined twins
This is where things get a bit fuzzy. While some sources say that conjoined twins occur when the twinning event takes place after day 10, others say conjoined twins are created when

the twinning event occurs at about the primitive streak stage of development, at about 13–14 days after fertilisation in the human

It is very likely that because of the rarity of conjoined twins (one in 200,000 live births) there isn't enough data available on the very early embryogenesis.
Sources and further reading:
The embryology of conjoined twins
Twinning
Conjoined twins


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What kind of microscope for ML/biological research?
I am a computer science student, focusing on machine learning applications. I have been always interested in biology but I lack any training in it. Now, I had an idea that I could introduce myself to biology more by buying a microscope, and doing some small (still serious, if possible) experiments.
Now, the problem one I am facing is what kind of microscope should I get? Preferred answer would outline what kind of research is possible to do with such and such microscope, and what is the typical price range for the system.
If there are any safety (e.g. does any of the UV leak from fluorescence microscopes?) or ethical concerns I would like to hear about them too. Thanks!

Initially I can invest about max. 1000€ ($1300) but if it need be, I can keep saving more.

There is a similar question, which I have provided an answer for (http://biology.stackexchange.com/questions/5470/what-to-look-for-when-buying-a-light-microscope/17313#17313)

Put it this way: if I come to you and ask "I am a biologist wanting to learn about ML. Should I learn about linear regression or about classification trees?". Surely you would reply "depends on what you want to do in the end". This is exactly the same situation :)

:) I see. Could you answer my comment in the answer below, where I outlined some possible materials for study (food, blood, plants, wine)?

This really depends on the application you have in mind. As with other precision instruments there is a huge range of qualities and applications.
If you just want brigth field illumination and look at relatively big things ( approx 100 microns) then you could find something decent for the price you mention if you buy used.
But if you want more complex imaging techniques like confocal microscopy or fluorescence microscopy to image smaler strutures and cell imaging then your budget is probably not enough. There you probably won't get a decent microscope for less than 2500 Euro.
I think you should figure out what you want to do with your instrument not just buy one and then get started.

Ok, I see. Thank you for the good advice! What kind of microscope I should I get if I wanted to study for example a) plants, b) blood, c) liquids such as wine, d) food?

A simple bright field microscope should be enough. Best look for one with Köhler illumination and x10, x20, x40 and if possible x100 objectives.

I agree with @Jeremias Brand's answer.
Pretty much you will have to forget about fluorescence microscopy... you can probably find some dusty old one on eBay in your price range, but it probably won't be any good.
However, the good news is that seen that in your comment you mention

a) plants, b) blood, c) liquids such as wine, d) food?

transmitted light (white light) would be perfect for a start.
eBay is surely a good place for finding used objectives at a cheap price. You may end up with a good collection of objectives for less than 100€.
That is surely tempting, and it may actually be OK as a start.
However, I personally think that it is better to own a good lower magnification objective than a cheap high-magnification one, so be always be a bit wary about offers that look too good to be true (especially for new piece of equipment).
I would strongly suggest getting a binocular microscope (so with two eyepieces), rather than a monocular one. Makes life much easier.
Also, be sure to have a camera attachment. While a camera may not be strictly necessary, especially at the beginning, it's better to have an attachment so that you can add one in the future, if you feel the need of taking pictures. Although many microscopes have specialized attachments for microscope cameras, you can get away with using your own normal camera, or even your cellphone, if you position it correctly (may need some DIY depending on the situation).
This page has very detailed explanations on how to connect a camera to a microscope.
As for your samples, plants are a very good and easy thing to start observing. Onions are probably one of the best samples to start with.
You may also want to stain your samples. Probably the easiest thing to get is methylene blue, which should be a few euros for 20-30 ml. However, fountain pen ink works as well.
Whenever you use chemicals, remember to look for their safety data sheet (MSDS). Methylene blue is pretty safe to work with, provided you don't swallow it (doh...) and use gloves (standard latex gloves are OK). Be careful because it stains and can be a bit messy, which is true for pen ink as well!
Crystals are also pretty cool to watch under a microscope: take a coverslip, put on a drop of sugary or salty water and wait for it to dry!

With all respect I think the accepted answer underestimates the quality of current inexpensive instruments. What I have found comparing images on my recently acquired $400 scope to those produced by top-end Nikons is that it produces images which are aesthetically less appealing but nearly identical in detail.
Mostly I have used it for fungi, which are well-suited for optical magnifications. To get the full benefit you need a PC to run the imaging software, so that expense must be factored in. Here is I think a pretty clear  image of Aspergillus (tape mount) showing concave spores.

When I hit the Lotto I will get a $7000 scope but I am really amazed at what I can see with this very inexpensive scope (and there are several similar brands available).
Another example--here is a high-end google image of Trichophyton sp. showing the diagnostic macroconidium. Everything that is wrong and right with the inexpensive scope can be seen by comparing the photo below:

The color is a bit garish (the blue stain is intentional) and there is always a background color as opposed to a neutral field). But the detail is very good. I had borrowed a scope from a friend and did not hesitate to buy.
The claim that one is restricted to objects of about 100$ \mu$ is incorrect. I bought a decent calibrating slide and here is a snippet of an image showing Penicillium spores. The small divisions are 10 microns. I didn't bother to calibrate the slide but the order of magnification is amply supported by the sorts of structures I have seen.

Again, the clarity and aesthetic appeal of images captured with a $7000 scope cannot be achieved, nor can you do good phase-contrast or florescence. But the functionality is really pretty amazing.
Below is a group of very small Penicillium from potato dextrose agar. The spores are not much bigger than 1 micron in diameter. It's not a crisp image but conveys a good sense of what an intact structure looks like.

Amateurmicrography.net has some nice images that can give you an idea of what different scopes can do.
Edit: added an image 7/31/14.

I have mixed feeling about this. Sure, you can see stuff with a small microscope, but sometimes you want crisper images than those you posted (and maybe with less fringing). But I am probably spoiled by using expensive scopes :P

@nico: Yes indeed, I really get envious when I see a crisp image with minimal distortion. In time I will move up for just those reasons. The cheap scope is also good for getting experience spotting structure in a cluttered field and preparing slides, but ultimately there is no alternative to a good quality scope.

obviously there are many factors to consider. I wouldn't spend 2000 euros on a microscope if I just want to give it a try... better to start with a cheap one and see whether you like it, then move on if you really want to get serious. Unfortunately there are certain microscopes you just cannot afford to buy, but then get a job in an imaging lab if you want to play with those toys! It's lots of fun!

Very popular microscopes for bio work these days are the inverted style, These allow you to view samples without preparing slides.
http://en.wikipedia.org/wiki/Inverted_microscope
http://www.biotechequipmentsales.com/equipment-for-sale/details/564/14/microscopes/nikon-eclipse-ts100

If you have to prepare samples or not depends on what you want to see. Can you work out your answer a bit more? Actually it is more or less two links.

Although what you say is correct, remember that mounting, especially if using specific microscopy mounting media increases the quality of the image. See for instance: http://www.microbehunter.com/the-importance-of-mounting-medium-refractive-index/


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How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids?
How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids?
The book's answer is $20^{12}$.
However, I disagree. This result distinguishes the following two polypeptides even though they are exactly the same polypeptide:
(Met)x11-Glu
and
Glu-(Met)x11
Am I right? How would I otherwise answer this question? My background in probabilities is very weak.

Judging from what you have said, I assume that combinatorics is not a problem to you.
I believe your problem is that you think Glu-(Met)x11 is equivalent to (Met)x11-Glu, just turned around. However, that is not a correct mindset. Amino acids are not symmetrical molecules, therefore reversed linear combination does not create a turned-around (be it chiral or not) form of a similar amino acid. My guess is that you write amino acid names in consecution when representing peptides. This method has a small problem that it does not incorporate directionality of molecules. Drawing the whole molecule may be a solution, but that is too much chore.
My solution is to add a small mark (perhaps an arrow, or a > mark) to represent a specific side of the amino acid molecule (amine group or carboxyl group), so that mirroring the sequence (so that the mark would be at the "other" side of each amino acid) would actually create a peptide molecule different from reversing the sequence (so that the mark is still at the "normal" side of each amino acid). If you think that doesn't look good, you can draw a frame around each amino acid, where one side of the amino acid has a dent and the other side has a bump (to represent the amine and carboxyl groups) so that only a bumped side can connect to a dented side. Mirroring the sequence would also reverse the positions of the bumps and dents, thereby creating a different peptide molecule than merely reversing the sequence while keeping the positions of the bumps and dents in place.

Tricky indeed. Very detailed and visual explanation. I forgot about the difference between the C- and N- terminus. Thanks.

Think of the amino acid choices as 12 seats. In the first seat, we have 20 choices. In the next seat, we have 20 choices, and this continues. Therefore, we have that
$$
\underbrace{20\cdots 20}_{12\text{ times}} = 20^{12}
$$
For your question about the the polypeptides, (Met)x11-Glu is not the same as Glu-(Met)x11, order matters.

Up to this point, we have considered the sequence of amino acids that make up a protein. This is the first of several levels of protein structure, illustrated in Fig. 4.4. The sequence of amino acids in
  a protein is its primary structure. The sequence of amino acids
  ultimately determines how a protein folds [1].

The individual amino acids are not symmetrical. Thus, your two example peptides are not chemically equivalent, and the $20^{12}$ figure is correct.


text:
Can't resolve protein with native PAGE

This is a native gel. Let's call the left 2 lanes protein A and the right 2 lanes protein B. B is the same as A except it has a FLAG tag. They are both homotetramers of about 65 kDa. After purification, both appeared as single bands on SDS-PAGE. However, these are relatively old samples and I expect multiple bands due to degradation (which I've observed with previous samples). Either way, I cannot for the life of me resolve them with native PAGE. B is somewhat workable, though still atrocious. For each of A and B, I've loaded 5 and 15 uL (hence why there are two lanes for each) with 5 uL of 5X loading buffer. Yes, I know that's not the correct ratio; I can't imagine that being my problem but I'm running it again with the correct ratio. The rest of the conditions are pretty standard:

The protein was in PBS (50 mM dibasic sodium phosphate, 75 mM NaCl, pH~7.3) prior to adding loading buffer; I've also used TBS (50 mM Tris, 7.5 mM NaCl, pH~7.4) with similar results
4% stacking gel, pH=6.8
6% resolving, pH=8.8
Tris-glycine running buffer, pH~8.3, ran at 4°C with 23 mA constant current. I've also ran at 30 mA with similar results.
Stained with Coomassie

Let me know if any other info is needed. Any advice will be greatly appreciated.

@vajra78 Each sample is a pure protein.

what exactly do you mean with 'resolve'? "To get a clear band"? Why is B better (i.e., clear band) than A you think? Isn't A not just totally degraded?

@AliceD Yes, get a clear band. I have no idea why B is better than A, the only difference is the FLAG tag (ie greater charge:mass ratio). A is not totally degraded because I can resolve it with SDS-PAGE.

When I see a smear I suspect heterogeniety. Since the smear goes up, it suggests the proteins are heavier (though it's a native gel and you can't assume mass and migration are directly correlated). Is there some possibility that A is polymerized? And the FLAG tag on B somehow disrupts this polymer?

@user137 That's an interesting idea; I was thinking it was just a problem with my gel conditions. The protein should have no specific interactions with one another. However, each monomer has a free cysteine that could possibly form a disulfide bond with another monomer and link the tetramers together. The FLAG tag could just add some electrostatic repulsion to prevent close contact of the cysteines. It's kind of a nice explanation; however, I really don't expect it to happen readily. I'll add some mercaptoethanol to the loading buffer and see what happens.

@user137 Well thanks for the suggestion but unfortunately mercaptoethanol didn't fix the problem and I can't think of any other reason why these proteins would polymerize.


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Puffball mushroom species ID?
Found this mushroom today. It's a kind of puffball mushroom and I think pestle puffball but I hope someone can confirm that/point me to other likely species.
It was in Central Eastern Sweden (Uppsala) in a pine and birch forest. Autumn has been quite dry so the season may be a bit delayed. They were in bunches of 2-5 mushrooms, they are about 1-4cm across the ball and the stem is quite fat plus about 1-3cm long. They are white through the middle.

As an addition - we ate it, none of us are dead at present. It tasted quite good.

Gutsy on eating it.  Did it have a sour, bitter, or nutty flavor by any chance?

My first thought is Lycoperdon perlatum.  I don't suppose you took any photos as you cut it up to eat it?

@AtlLED It was eaten based on the conclusion it was either l perlatun or the pestle puffball, both of which are edible, I couldn't find anything poisonous that looked similar. Flavor was a little nutty. Are these perhaps a little too small to be pestle puffballs?

Strange mushrooms which I am seeing it for the first time ! Would it be 'Lycoperdon echinatum' ? I think genus 'Lycoperdon' will give some answer to this.

I've been reading on it a bit, and from descriptions of the way the spikes/warts came off the surface I'd agree that it is L.perlatum.

@AtlLED No pictures were taken of the inside, it was just plain white.

Given what you've said in the comments, and how much more common they are, I'm going with my first gut reaction of Lycoperdon perlatum.  The big give away for me was that you said there was a good taste.  L. Perlatum has a rich nutty flavor (my wife grows them), but Handkea excipuliformis (pestle puffballs) don't have much taste if any.  They are seriously notably bland.  H. excipuliformis can take on the flavor of what ever you cook them with, so if you cooked in a nut oil or with nuts, then you would have given the flavor that way.
Not that I support taste as a primary means of id...  In this case most of the puffballs are edible so you were in a low risk situation.  I just don't want to start a wave of fungus ID's that include taste info!

A taste based field guide to fungi, perfect for adrenaline junkies interested in foraging!

@GriffinEvo The business model is easy.  We give away the guide, and charge a "killing" for the anti-toxins.


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Why does meiotic recombination disrupt the independent assortment of genes on the same chromosome?
There are many sources that say that genes that are "linked" by being on the same chromosome assort with each other -- that when an allele is passed on that the gamete containing said allele will also contain every allele from the chromosome rather than simple allowing everything to assort independently.
There are also many sources that say during meiosis there is recombination, hence, why aren't all genes completely random?

The previous title of this post had a negative and some imprecise terms.  In the interest of clarity I modified it to read "Why does meiotic recombination disrupt the independent assortment of genes on the same chromosome." It originally said "Why doesn't gene recombination maintain the law of independent assortment for genes on the same chromosome?" Hopefully I have preserved the sense of the OP's query.

Recombination does not make any two genes completely independent because there will not systematically be a recombination event between two given loci (=position on the chromosome).
Distance between loci
Consider two scenarios that describe the position of two loci on a chromosome.

Tightly linked loci

Consider two very closely linked loci. Let's say that a recombination event occurs somewhere in the chromosome. It is very likely for this recombination event to occur somewhere else than between these two loci. These two loci are essentially linked and do not segregate independently

Distant loci

Consider now two loci on the same chromosome. Each locus (=singular of loci) is found at one end of the chromosome. If a recombination event occurs, it is pretty sure that it will occurs between the two loci. As a consequence, the two loci will segregate (quasi) independently.
Conclusion
As a conclusion, recombination allows to break down the linkage between two loci but it does so at a given rate that depends on the physical distance between the two loci and on the per nucleotide recombination rate.

Doesn't recombination always occur between two alleles on homologous chromosomes of the same gene? Also, doesn't a recombination of one gene not effect another?

I don't understand what you mean. You say "recombination of one gene". What does it mean? A recombination (or cross-over) is the process by which homologous chromosomes exchange genetic material. This process  allows for higher independence of assortment of linked loci. The more closely linked are two loci, the less likely it is that a recombination event will separate them.

Recombination has nothing to do with genes.  The genes happen to be genetic markers arrayed along the physical chromosome.  Meiotic recombination, in general, occurs after a double-stranded break has been formed in one of the chromosomes.  One way to repair this break is to form a crossover.  When crossovers are repaired by the cell this can result in recombination (alternatively it can result in gene conversion).  If you have several heterozygotic genetic markers on the chromosome then you can score the progeny and possibly map where the crossover occurred.

By "two loci" Remi.b means two loci on the same chromosome. Simple example: (a) ------------X--X----------------- compared to (b) -X----------------------------X- , if Xs denote genes, it is much more likely for the genes in (a) to remain on the same chromosome than for the genes in (b) assuming a random choice of recombination point. Although recombination is not actually random, this example holds in vivo.

Are you saying that when a recombination event occurs (I am assuming this is the same thing as a cross-over, please correct me if I am wrong), the actual genetic material being moved around is just a random contiguous chunk that has no bearing on the borders between genes? If so, then am I correct in assuming that two closer genes are more likely to be swapped together since a single recombination event will more likely encompass both of those genes? If so, I would think an answer containing that information would be best.

Yes, recombination has nothing to do with genes. Not however that recombination rate per nucleotide tend to be lower in regions of high gene density. Two closely linked loci (might be genes at these loci) are less likely to segregate independently as it is less likely that a recombination event occurs in between them (you seem to say the opposite in your comment).

Imagine that mom's chromosome is blue, and dad's is red.  If crossing over was happening hundreds of times per chromosome, sure, you could make chromosomes to pass into gametes which were very a very highly shuffled combination of paternal and maternal alleles.  It would be blue, red, blue red, blue, red, all up and down the chromosome.
But it doesn't.  It generally only happens once on a chromosome.  So you can get a chromosome where the "top" 30% is red, and the rest blue, or the "top" 65% is blue and the rest red.  When genes are unlinked, the odds of getting both alleles from the same parent is 50%, and the odds of getting one from each parent is 50%.  If two genes are close together on the same chromosome, the odds of the break happening between them is small, so the odds of one being blue and one being red is much lower than 50%.


text:
What is the role of glycine in the running buffer for SDS-polyacrylamide gel electrophoresis
We used pH6.8 in stacking and pH8.8 in resolving gel. In the class, the professor explained that the glycine change is like:
glycine+ <-------> +glycine- <------> glycine-

it is said that most of the form will be +glycine- and glycine-. Why? And why does it change the charge when it runs from the stacking gel to resolving gel? What is the role of glycine in the running buffer for SDS-polyacrylamide gel electrophoresis?

In your original query I believe that you are confusing/conflating the electrophoresis with the transfer to a membrane. The electrophoresis is abbreviated SDS-PAGE. After the electrophoresis is complete you have several choices, including: fixation of the proteins in the gel followed by staining to visualize the protein bands; autoradiography if any of the proteins are radiolabelled; or transfer to a membrane if you have an antibody that recognizes the protein of interest. I have edited the post to correct this. I believe you are asking about the composition of he Tris-glycine buffer.

Gly is an amino acid its charge depends on the pH. It is probably ladder component, but I am not an expert of this. http://gmwgroup.harvard.edu/pubs/pdf/951.pdf

The pH of stacking and resolving gel are set in such a way that one is above and one is below the pI of gly (5.97).Therefore, Gly has two different charges in stacking and resolving gel. That is in stacking gel gly has no charge (which will allow the protein to stack according to size in this part of the gel rather than separating because of presence of gly in between the protein molecules, constraint in separation of proteins) but in resolving gel charge is negative since the pH is higher (constraint in movement of proteins no longer present so separation of protein based on size possible).
Hope this was helpful..

Could you add a reference or link to allow for background reading?

since the stacking gel have a ph of 6.8 the glycine will attain a neutral charge(by the isoelectric point and ph relation)thus the chloride ions travel faster followed by the sample and then at the last glycine ions,thereby stacking the sample in between both.when it reaches the resolving gel the ph increases which gives glycine a negative charge.so they travel faster along with the chloride ions leaving back the sample to get seperated without any hinderence

Welcome to Bio. Could you add sources to your answer?


text:
Standard datasets for testing new multiple sequence alignment algorithms?
Are there any open and freely distributed standard datasets for testing new algorithms for multiple sequence alignment?

possible duplicate of What is the state-of-the-art algorithm for multiple sequence alignment?

Welcome to Biology Beta @msa!!! Thanks for asking the wonderful question but I suggest you close any on one of ones you asked as they are duplicate of each other.

I have always myself wondered about this so it would be great to get a detailed response! but for the moment, could you not look at a known protein or DNA sequence like Ras within a organism or different species and align them? The best way to do it is to go to UniProt (http://www.uniprot.org/) and type in a protein such as Ras. Once you select a particular Ras, then under the phylogenomic databases you can select OrthoDB and once you enter the page you can select get FASTA or Tab delimited on the top of the page!

@DevashishDas This question is not a duplicate of the linked question as it is asking for a standard dataset for msa to test a new algorithm on and the previous question is not answered as far as I can tell so it is not of much help!

@Bez: Ok. But they seems awfully linked they could be asked in single question. Anyway, I will try to answer both.

I would suggest you PAcAlCI or Prediction of Accuracy in Alignments based on Computational Intelligence, though the acronym in wierd the tool is good for testing new Sequence Alignments. They
But before you start testing your algorithm, I suggest take a look at these papers:
[1] Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence
Alignment
[2] Issues in bioinformatics benchmarking: the case study of multiple sequence alignment
PS: I haven't tested or used the tool myself.


text:
What is the state-of-the-art algorithm for multiple sequence alignment?
Which algorithm or algorithms are considered the standard or state-of-the-art for multiple sequence alignment?
How big is the need for better algorithms? How many sequences need to be alignment in a typical test? I am trying to understand how important problem this is in bioinformatics.

This would be better asked on https://www.biostars.org, the bioinformatics stack exchange. For the typical number of sequences aligned: you cannot say that. There are so many different uses of MSAs and too many different datasets one could have to be able to give one typical example.

@skymninge Bioinformatics are on-topic here, and Biostars is not affiliated with SE in any way now (it was a SE 1.0 site, which means they used the SE software but SE wasn't involved otherwise in running the site)

@Mad Scientist Still, the chances that this type of theoretical question will be answered on Biostars are higher. The answered bioinformatics questions on this site are usually more practical approaches/use cases/... I did not imply the question is off-topic otherwise I would have flagged it as such. I just wanted to be helpful.

All bioinformatics questions are on-topic. Just that if someone requires technical help then biostars has more people who can help.

having said that, this question seems quite broad to me. More details need to be provided.

btw if you want a good bioinformatics problem, come up with an assembler that assembles any paired end illumina run optimally de novo without any input parameters.

My Vote goes to Mafft(insi) as it have ~86% accuracy and results in ~1.2 hour. Though fastest will be kalign takes only ~3 minutes to finish with an accuracy of 74.3%.
For testing:

For each of the 218 reference alignments in the benchmark, we applied
eight alignment programs, resulting in a total of 1744 automatically
constructed MSAs. The overall quality of these automatic alignments
was measured using the Column Score (CS) described in Methods.

FIGURE 1: Overall alignment performance for each of the MSA programs tested.
(A) Overall Accuracy
(B) Total run time for constructing all alignments (a log10 scale is used for display purposes).
doi:10.1371/journal.pone.0018093.g003
Compared Tools

(source: plosone.org)
Source and Photo Credits:
A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives
PS: This is from an old paper of 2011. If you want the new statistics you can always test on your own, by the process described in the source paper.

Personally, I always use muscle + gblocks for proteins. Does the job well enough, IMO.

@5heikki: I agree. Muscle is actually good.

I dont think any of them has a parallelization option. I think parallelization is possible for pairwise distance calculation step atleast.

Bare in mind that the results from this benchmark are already very out of date.

The PRANK and PAGAN algorithms have both come out of the Loytynoja lab in Finnland, and are stirring up the pot a bit. They use inferred phylogenetic relationships as a parameter, and tend to yield a much more 'gappy' alignment, supposedly due to more accurate handling of indels. For easy alignments the method doesn't matter so much, but if the sequences are highly divergent it might be worth while checking out PAGAN and PRANK.

Clustal has reinvented itself as Clustal Omega using Hidden Markov Models, and is particularly suited to the alignment of very many sequences.


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optimization of density gradient centrifugation
I'm trying to isolate a ~320kD protein (in oligomeric form) using density gradient ultra centrifugation technique.
Can any one tell me that what gradient (sucrose or glycerol or trehalose or etc) I should use and why ?
Any references regarding the optimization of gradient cutoff for macromolecules will be highly appreciated.

Have you tried size exclusion chromatography (SEC)? It's a lot easier to set up, perform, and analyze than gradient centrifugation.

Yes it is. But if you are trying to separate between  240kD and 320kD then it is not proving to be much of a helpful technique as both is coming in void volume in Superdex column. I have tried but not helpful in this scenario.

Have you tried different columns? If your analyte is coming out in the void, try altering the particle size in the column.

Yes, but given the availability of columns it is not being possible to resolve in this range using SEC procedure. That's why I was trying for density ultra centrifugation.

OK, I understand. Unfortunately, the only experience I have with density centrifugation is in purifying white blood cells from whole blood using Ficoll gradients, so I'm afraid I can't help with this. Good luck, though!


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Is there a difference between endorphins that are released while physical activity and sex/masturbation?
I observerd myself and I can identify two different types of "happines".

First - called by me - After Pleasure :
Occurs AFTER (and last long) long activity that require from me engagement focus and effort  for example :

running 16KM
learning for an hour things that I think are worthwhile
reading book
generally any mental or physical activity

Second - called by me - During Pleasure
Occurs DURING (and last short time) activity that DON'T require any engagement, focus or effort, for example :

masturbation
eating sweets
eating tasty things in general
having hot bathing time
watching funny videos/TV

I wonder is there any scientific distinction between those two states of my body and mind. And assuming that endorphins are the hormones are responsible for the "oh-good" state, are different kind of endorphins are released while taking this 2 different activities (like studying for 1hour and masturbation) ?
Thanks for an answer in advance.

What kind of difference? Concentration, type? Can you clarify this?

@Chris I just suspect there is a difference between endorphins that are released during this 2 activities since the "oh-good" state is longer in the first one, and shorter in the second, because one is released after Activity, and second During activity.

The title is a bit overspecific and thus confusing. I guess you're asking about short-term and long-term rewarding system action. If so, then yes, there's a whole lot of things that differ between these, them are actually two different modes of rewarding, involving different mediators and subsystems. I won't give you any direct references, but you can search for yourself: look for dophamine receptor types and their action, oxytocine and other mediators. The main plot is that "during" pleasure is related to passion while "after, long-term" is related to stability, ensurance and persistance.


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Evolution theory - roses spikes - being more bulgy doesn't give you advantage
I've seen spike, huge spike. And I thought that development of such spikes could be contrary to the evolution theory.

Being „little more” spiky doesn’t give you any advantage... So those individuals having one won't have smaller mortality rate than those with smooth stem.
Even more, the individuals with bulgy (more spiky) waste resources their ruggedness and have more things to feed, which should mean that they would have higher mortality rate.
So I can see no way to develop spikes on the stems of roses according to the evolution theory which embrace "small improvement". Spike is only efficient (to deter aggressor) when it's very sharp, it's either sharp or it isn't - there is little in between.
Could anybody tell me that this is bullshit (and why it is bullshit), and that I should us believe in Darwin competence?;)

Being a gardener with 50+ varieties of roses, from thornless "Zephirine Drouhin" on up, I think I'm in a position to say that thorns of any sort do give a definite advantage - especially as I'm in the middle of their spring pruning.

If you're looking for a trait which is maladapted to the natural environment then you should be looking at the rose's flower, Their flowers are a product of generations of selective breeding. Wild types have such simple flowers with so few petals they would hardly be recognised as roses. So I find it interesting that you pick out the thorns, which have such obvious utility, and would so even if they were tiny.

I think that the most important point has been given by CactusWoman, when (s)he says "Just because you cannot forsee a use for more "bulgy" spikes doesn't mean there isn't a use for them."
In addition to that, I would like to say that several plants evolved traits that were beneficial at a time where other herbivores existed and that are now useless. Those lineages did not lose their traits (yet?) just because there is a relatively low cost to making the trait in question.

Your post shows several of the very common misconception about evolutionary processes. Evolution is not all about Natural Selection. It is more interesting than that.

"small improvement"

The conception that evolution proceed through "small improvements" is either partially wrong or totally wrong.
First, because of the loaded term "improvement". Evolution can yield a population to have a lower mean reproductive success or a lower complexity, things that you could eventually see as deterioration.
Second, because changes not need to necessarily be small. Some mutations have a very big effect.
Third, because even small deleterious mutations can spread in the population and reach fixation (=and all individuals carry this mutation), just because of the joint effect of other evolutionary processes such as genetic drift. This post may help you to get a quick grasp of what genetic drift is. There are already multiple posts that emphasize the importance of other processes than natural selection in evolution to layman. Here is one of them.

believe in Darwin competence

Evolutionary biology is not anymore Darwin's evolution theory. It is way more than that. We've been working on the subject a lot since Darwin and today we have a much much better understanding of evolutionary processes than Darwin at its time. Everything is not fully understood yet and therefore there are still many people researching to better understand evolution. Of course, not to better test if evolution is true as this has been known for a long time now.

Just because you cannot forsee a use for more "bulgy" spikes doesn't mean there isn't a use for them. Furthermore, natural selection isn't about producing perfect organisms, it's about selecting for traits that are "good enough". There is also more to evolution than natural selection. The phenomenon of genetic drift can cause a neutral or slightly maladaptive trait to become fixed in the population.
In short, not every single trait is adaptive. Check out the famous paper The Spandrels of San Marco if you want to read more. It talks about how we shouldn't focus on trying to come up with an adaptionist theory for every trait and instead consider that other agents of evolutionary change, such as genetic drift, can generate non-adaptive traits.

Notably this answer about spikes is delivered by CactusWoman...

I think it's generally believed that spines/thorns/prickles are adaptive in that they deter herbivory while still allowing for pollination.  But as Gould et al. rightly point out, this would need to be tested.

@augurar Yes, it is well-known that spikes themselves deter herbivory. But the question was whether or not "more spiky" or more bulgy spikes were better than slimmer spikes.


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Are there any structures in mammals that are used only by males?
There are examples of structures which only serve a purpose in females, but it seems like the opposite could also be true. Are there any structures which exist in both mammalian sexes and only serve a purpose in males?

but it seems like the opposite should also be true. Why?

@nico because a structure that becomes vestigial in females and still serves some purpose in males will have evolutionary pressure to remain intact in both sexes. Likewise, a mutation that serves a useful purpose in only half the population will still be a useful mutation as far as the population is concerned.

@Shep: my point is the fact that an example of a shared structure that is used only in females exist does not in any way imply that the opposite should also be true. It could, but there is definitely no causality here.

@nico ah, should --> could, I didn't mean to imply any causality there.

Some researchers consider the neural circuitry responsible for orgasm vestigial in women. I disagree with this for a number of reasons, but here is a book exploring the hypothesis:
http://www.amazon.com/The-Case-Female-Orgasm-Evolution/dp/0674022467/ref=sr_1_1?ie=UTF8&qid=1336286206&sr=8-1

Females of Rangifer tarandus have horns which only used by males in competitions. Other species of deer only have males with horns.
Apart from this, possibly, clitoris and vulvar lips have no purpose in women: the vulvar lips are underdeveloped halves of scrotum, and clitoris has no need to be so sensitive as it is because it plays no role in sexual reproduction in females.


text:
How much does a human brain's metabolic rate vary?

Possible Duplicate:
How does brain energy consumption depend on mental activity?

Our brains consume about 20% of our energy when we're at rest. How variable is a human brain's energy consumption? Will thinking harder consume more energy? Does this change significantly when we sleep?

Related: http://biology.stackexchange.com/questions/839/how-does-brain-energy-consumption-depend-on-mental-activity

maybe even duplicate.