text:
Remove RNAse from pipettes?
Our lab uses old Gilson Pipetman pipettes. I've been using some for making mRNA by in vitro transcription and started running into RNAse issues. I'm trying to clean everything up, including the pipettes. I'm not sure these old pipettes can be autoclaved, at least not in one piece, I think I can take them apart and autoclave the parts that might touch the solutions. Is there some way to wash the pipettes out effectively and remove any RNAses?
I use boxes of RNAse free barrier tips, do all my work on new pieces of aluminum foil, use commercial RNAse free water, gloves, labcoat, facemask, etc. However yields from the in vitro transcription kit have been reduced, and yields from the tailing kit are even worse, sometimes losing 90% of the RNA. There's only so much I can do, our building is old and full of dust and the damn pipes above my work bench leak ( all the pipes leak, had 2 major pipe bursts in the last 6 months ).
I'll probably have to get new kits. Just have to prove to my advisor that the kits are contaminated.

I'd disassemble the pipettes and put the appropriate parts in DEPC solution. I would also consider other issues aside from RNAses, reduced yield can have many different causes.

I took apart the pipettes and sonicated the lower parts in RNAse Away, rinsed in ddH2O, then 70% ethanol followed by autoclave. Reassembled with new seals and o-rings and checked the calibration. They seem ok so far. Been using this same kit for about 3-4 months, so it's had a lot of freeze thaws. Will have to replace soon anyway. Running denaturing gels shows smears instead of bands, suggesting degradation.

I'd also switch out all ingredients for your in vitro transcription if you have any RNAse problem. You might also want to aliquot the stocks further, to limit the damage contamination causes, and to protect the more sensitive stocks. Some stuff just gets bad quicker, DTT should be reasonably fresh, and NTPs also get noticeably worse if they're older. But we also don't use kits but prepare all the stuff in our lab.

wipe the pipette's neck with RNAseZap/RNAseAway and use filter tips for your experiment. Degradation is not essentially because of contamination by pipette- check your plasticware- tubes, tips, gel tanks etc. Also check the buffer that you use for your gels (was it autoclaved. is the pH fine). And if your building is dusty, you can perform the experiments in a laminar hood.

According to the Gilson Pipettman User Guide you can autoclave the following parts: Tip ejector, Tip holder and the connecting nut (have a look into the PDF linked above if you are not sure about the parts). All other parts can not be autoclaved. Gilson says the following conditions can be used (page 17 in the user guide): Autoclave for 20 minutes at 121°C, 0.1 MPa.
However, when you really have a DNAse contamination, you will not get rid of it with autoclaving, since RNAses are too stable. You can either try the various solutions on the market which made for killing RNAses or simply get a new set of pipettes used only for RNA work (on a different bench in a different lab with a completely different and fresh set of chemicals and plastic ware). And I would recommend filter tips for this work. They are more expensive but in the long run it will save money since you don't have to repeat experiments.
Regarding your leaking pipettes: The pipettes contain rubber rings and teflon seals in the inside which have to be replaced from time to time. The image below shows how (parts C and D), the ring can be purchased from Gilson. If you don't know how to do this work (and have no technician who does) you can also send in the pipettes for service. This costs a bit of money, but is ways better than to use unreliable, leaky pipettes.

And don't worry, Gilson pipettes are pretty good. I have used now more or less all brands on the market and I still prefer them. They only need some service from time to time.

The pipettes aren't leaking, the pipes are leaking. It's a plumbing problem. I'm cleaning the pipettes right now and I have replacement seals and o-rings, so hopefully this problem will be solved. Can't fix the pipes without a plumber.

Pipes. I somehow made this into pipettes here. Probably I had too much leaky ones as well :-)


text:
Total number of pleura in the exoskeleton of cockroach
Basically as far as i know cockroach consists of 10 terga and 9 sterna but what are the total number of pleura present in the cockroach.
Pleura are situated between tergum and sternum of a body segment and help in the articulation of terga and sterna.
What would that be in the case of the 10th abdominal segment in which sternum is absent ? Are pleura present there? If yes then what is their functions at that place?

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
Braquio-abduction illusion explanation and references
Illusion: Lying down on a hard flat floor move arms up and down (as when doing a snow angel) while keeping them touching the floor. While repeating it a few times the floor begins to appear concave, with the deepest part where the arms as perpendicular to the rest of the body.
Questions: What is the origin of this illusion?
My guess: I think it might be related to the arms being harder to extend towards the back when they are perpendicular to the body than when they are at other angles.
Note: The name above is only the way I like to call it. I found this illusion when I was a kid, but I am sure others might have noticed it as well.

It may be because, when we move our shoulders towards our the body, also know as abduction (Fig 1.) gives the central part of the body an elevation. when we rotate our arms more upwards (Adduction), the elevation will be lost.
So in other words, when we are making snow angels,

Start Normal position (hands near thighs) = Back and shoulders on ground
Middle position      (hands in middle)   = Back elevated and shoulders on ground
Final Position        (hands upward) = Back and shoulders on ground again.

Due to this motion, it seems as if the ground become concave.

Source:
Anatomical Terms of Movement
Articulating the Importance of Joints in Anatomy

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text:
DNA barcoding, querry regarding tree based (cluster) methods for species identification
I am working on success rate of DNA barcoding in identification of species using distance and tree based methods.
Regarding distance based method, I have used Adhoc and species identifier and confirmed species identification using best closest match criteria (BCM).
Please suggest program/software/method for tree based identification (using NJ, parsimony, bayes), exhibiting clustering (number of clusters formed for particular species) that will suggest singleton (=Ambigious) species.
(For more details: Attached image)
(Please Note: It is not possible to do it manually as iam having >4000 specimens)
Answers detailing methods or softwares appereciated! Thank you!

Are you searching for something like this: http://en.wikipedia.org/wiki/List_of_phylogenetics_software
this post is some what off topic.

@Devashish Das, thank you for your reply, to make it more clear, ive attached image. Pls have a look, keep posting.

You can try PHYLIP and ClustalW. You can run them from commandline and this can be automated.


text:
Do Ants have a sense of Direction?
Do ants understand which way is up or down?
Could they differentiate between uphill and downhill?

Actually No.
Amazingly there is this paper published on the motions on Ants which says:

The isotropic distribution of average speed appears as a surprising
  result since it would be expected, for instance, that ants progressing
  uphill should be slower than when moving downhill. For instance, Seidl
  et al. found lower speeds on steeper inclines in desert ants moving
  uphill, but indicate that desert ants progressing downhill displayed
  high velocities [42]. This is in contrast with our finding with Lasius
  niger in the present set-up where the velocity showed no dependency to
  the walking direction, even for the steepest inclination. However,
  Wohlgemuth et al. report, also in the desert ant, that speed was
  reduced in both their uphill and downhill channels (+540 ) compared to
  their flat channel, thereby excluding metabolic cost as a reliable
  means to gauge walked distance on various inclines [28]. In an attempt
  to determine the effects of inclination on the gross metabolic cost of
  locomotion in leaf-cutter ants, Holt & Askew report that ants
  travelled the fastest on a horizontal plane, and indeed moderated
  their speed with the inclination, both on the incline and the decline.
  They suggest that ants adapt their behavior so as to keep their
  metabolic rate constant despite changing mechanical demands.

Source: How Do Ants Make Sense of Gravity? A Boltzmann Walker Analysis of Lasius niger Trajectories on Various Inclines


text:
How Ants know about Earthquake?
How does an ant know about Earthquake is it because of an organ or due to other factors?

No, they may not sense Earthquake by an organ but due to other reasons. This may be any other physical factors which can be measured.

"...There is therefore
  little reason to believe that these ants react to earthquake
  precursors other, perhaps, than those that may affect colonies
  directly, by altering physical variables that can be directly measured
  by other means..."

Fascinating though the behavior and physiology of ants may be, they cannot be employed as reliable predictors or even sensors of earthquakes.
Source: Shaken, not stirred: a serendipitous study of ants and earthquakes

@Chris Is it better now?


text:
Will breathing through mouth result in any disorders?
My nose is slightly bent. When I was born, I had an issue with breathing. My mom said that doctors had inserted a breathing tube in one of my nostrils. This tube may have caused the deformation. From childhood, I breathe through my mouth. Will there be an any problems in the future? Do I have to take any treatment? Please suggest.

can you make the question little more general, it might be flagged for personal medication.

I don't think this can be generalised. To generalise, he'd need to understand his problem deeply, which he does not. @roarer should consult his doctor as soon as he can - I'm sure it's not a good idea to breath with your mouth. You'll get infections, which are normally filtered in nose.

@TomášZato I totally agree with that.

Yes, you become more prone to infections. Would be ideal to consult a doctor so as to get your nose sorted out. I wonder why they didn't try to fix it when you were a child as that would have been much easier than now.


text:
What is the name of this flower with purple leaves and orange inner part in NYC?
I've photographed this flower a few days ago in New York City:

Does anybody know the name of it? (and how is the orange part called?)

It's Echinacea. I've linked to one site but if you run an images search with Echinacea as the search term you'll see lots of examples.
And here is the WP page.
Supplementary
Echinacea are members of the Compositae. The flower (the head) in your picture is actually made up of lots of individual smaller flowers (i.e. it is a composite flower). The petals are formed by ray flowers, and the central part, the disc is made up of disc flowers. More details at the WP page I have linked to for Compositae.

And how is the orange part called?

@moose it is the head inflorescence which consists of ray florets and disk florets

@moose it is not a flower actually but an inflorescence which resembles like a flower. ray florets in general are situated at the peripheral parts of inflorescence and disk florets are situated in the centre which is a unique feature of asteraceae (other name for compositae)

@moose ray florets are the female flowers and disk florets are the bisexual flowers

The first link is dead.


text:
What is the name of this yellow bumble bee that I photographed in New York City?
Does anybody know the name of this bumblebee? (For categorization on Wikipedia Commons: 1 and 2)

Just to help prevent other non-native English speakers make the same common mistake, you cannot say “How is something called” in English (unlike French, German and most other Germanic or Romance languages). It is “What is it called”. However, in changing the title I used what I considered a more suitable construction.

It's a Brown-belted Bumble Bee (Bombus griseocollis).

Details: http://bugguide.net/node/view/3538

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text:
Mesoporous silica particles as anti cancer drug delivery method
If this question is a little off topic for Biology, I'm sorry. I've recently read a lot about mesoporous silica nanoparticles as a promising drug delivery method. The huge range of customizability of the particles, coatings, contents, etc. can pretty much tailor them to be effective in delivering most drugs to most target locations in the body (or to specific cells). The research is not new, and all the articles hail the method as a very promising way to treat for example cancer. However, as far as I know, these methods are not widely used today. Why? Is there some catch that I don't see?
I'm no biology expert, but if this is so promising, and the research is at least a decade old, some companies would have produced this (they already produce the particles) in terms of drug delivery. So why not? Is it a case of null-findings not being published? Is it actually used and I'm blind?
Thanks for your help!
edit: for those interested, here is a good review

It's Nice question. But mostly Nanotechnology is not into health industry is because of side effects(and may be the cost of research) or toxicity. http://guardianlv.com/2014/07/nanoparticles-that-deliver-medicines-have-problems-that-may-be-solved/

Those are good points, but given the amount of research done, and the huge (I would believe) interest of the pharmaceutical industry, those problems are easily rectified. Negative surface charge (when considering targeting the brain), size to prevent endocytosis. It can target specific cells via antibody coatings. It can be used in MRI. You can control content release. I mean, whats not to like. Still we go on with systemic drugs and therapies (looking at you chemotherapy). The materials used can alse be designed to be biodegrable and non toxic.

I work in the pharma/biotech industry. Nanotechnology in general is a very active field of research. The issues with any new delivery system are two-fold - the first is being able to prove safety and efficacy, which is no small task, and the second is development time. It can take 10-15 years or more for a novel therapeutic to reach the market, and that's with a "standard" delivery system like a pill or infusion. Developing and getting approval for something entirely new like this would add even more time to the pipeline, which is why you haven't seen it on the market yet.

I think that pretty much answers the question. I would guess that this form of delivery method is indeed surging forward to the markets as we speak? Do you perchance have links or information about any specific solutions that are on their way to market, or nearing a point where they can be put to market?

Though I totally agree with your views towards nanotechnology, There is always two sides of a coin.
According to this article THE BAD (of Nanotechnology):

Health:
Nanoparticles have been shown to be absorbed in the livers of research
  animals and even cause brain damage in fish exposed to them after just
  48 hours.   If they can be taken up by cells, then they can enter our
  food chain through bacteria and pose a health threat like mercury in
  fish, pesticides in vegetables or hormones in meat.  The
  increasingly-popular carbon nanotube (20x stronger and lighter than
  steel) looks very much like an asbestos fiber – what happens if they
  get released into the air?  Being carbon-based, they wouldn’t set off
  the usual alarms in our bodies, making them difficult to detect.
Environmental:
If nanomaterials really are as strong as diamonds, how decomposable or
  persistent are they?  Will they litter our environment further or
  present another disposal problem like nuclear waste or space litter?
  In the distant future, will self-replicating nanobots – necessary to
  create the trillions of nanoassemblers needed to build any kind of
  product – run amok, spreading as quickly as a virus, in the infamous
  “gray goo” scenario?

Not only that Each country have a different point of view on the topic of nanotechnology in Health(or nano-medicine).
Government Response on Nanotechnology:
United Kingdom
In its seminal 2004 report Nanoscience and Nanotechnologies: Opportunities and Uncertainties, the United Kingdom's Royal Society concluded that:

Many nanotechnologies pose no new risks to health and almost all the
  concerns relate to the potential impacts of deliberately manufactured
  nanoparticles and nanotubes that are free rather than fixed to or
  within a material.

They want to change the existing regulation to be modified on a precautionary basis because they expect that the toxicity of chemicals in the form of free nanoparticles cannot be predicted from their toxicity in a larger form.
United States
Rather than adopt a new nano-specific regulatory framework, FDA convenes an 'interest group' each quarter with representatives of FDA centers that have responsibility for assessment and regulation of different substances and products. This interest group ensures coordination and communication. A September 2009 FDA document called for identifying sources of nanomaterials, how they move in the environment, the problems they might cause for people, animals and plants, and how these problems could be avoided or mitigated.
Berkeley, CA is currently the only city in the United States to regulate nanotechnology, which is still being opposed.
European Union
The European Union has formed a group to study the implications of nanotechnology called the Scientific Committee on Emerging and Newly Identified Health Risks which has published a list of risks associated with nanoparticles.
Consequently, manufacturers and importers of carbon products, including carbon nano-tubes will have to submit full health and safety data within a year or so in order to comply with REACH.
According to REACH(from Page 22, 4.2 Pharmaceutical regulation, PhD Thesis of Steffen Foss Hansen, DTU):
The application of engineered nanoparticles for medical use offers immense benefits
within areas like diagnosis, targeted drug delivery, and drug development and have been
marketed for more than 17 years (NanoRoad SME 2006, EGE 2007, Gaspar 2007).
Well-described and understood medicinal products containing nanoparticles in the form
of liposomes, polymer protein conjugates, polymeric substances or suspensions have
been given Marketing Authorizations within the EU under the existing regulatory
framework e.g. Regulation 726/2004 on authorization and supervision of medicinal
products for human and veterinary use, Directive 2001/83/EC on medicinal products for
human use, Directive 93/42/EEC concerning medical devices, Directive 90/385/EEC
relating to active implantable medical devices, and Directive 98/79/EC on in vitro
diagnostic medical devices (EP & CEU 2004, Council of the European Communities
1990, 1993, 1998, 2001).
There is no specific mentioning of nanomedicine in the EU legislation on medicinal
products and devices, tissue engineering and other advanced therapies. None of these
regulations or directives was written with nanomedicinal applications in mind and
although their scope covers nanomedicine they have been accused for being general and
non-specific and fraught with concerns and difficulties when it comes to dealing with
drugs more complex than traditional ones (Editorial 2007, D'Silva and Van Calster
2008).
The use of nanoparticles in nanomedicine has not been subject to much regulatory
scrutiny since existing laws and regulatory instruments are believed also to cover
medical products based on nanotechnology. The extensive testing requirements prior to
marketing of medicine may also contribute to the notion that the potentially negative
effects will be discovered prior to marketing, that patients are adequately informed
about negative side-effects, and that benefits outweigh the risks or the adverse effects,
should such be found to occur (EGE 2007, N&ET Working Group 2007) .


text:
Intuitive explanation for Kin- and Group- selection
It is known from theoretician in the field of kin selection that kin selection (inclusive fitness theory) and group selection are actually two sides of the same coin. In other words, these two concepts are actually only one single process.
Questions

Is group selection equivalent to kin selection for any evolutionary game or exclusively for the prisoner's dilemna?
Can you please provide an intuitive explanation of why kin- and group-selection are the same thing?

I found this http://www.pnas.org/content/104/16/6736.full , Am I in the right direction?

Yes it seems to be in the right direction, given the title at least. This paper however failed (at first look) to give me a intuition of why these two concepts are the same process. Thanks @DevashishDas

First of all, there is a very heated debate about this in the field of social evolution at present, and you aren't likely to get a conclusive answer. One theorist may give you one answer, but another will vehemently disagree. I'll start by logically answering your questions in reverse order!
Question 2: Can you please provide an intuitive explanation of why kin- and group-selection are the same thing?
The first formal 'proof' that they are the same came from a paper by Queller in 1992. Let me give you the gist of what he found without being ultra rigorous. I won't focus on relatedness, since that was answered nicely by @falsum, "Price's equation tells us that this happens when the genetic variance between-groups is higher than the genetic variance within-groups. This is equivalent to saying that altruists tend to interact with other altruists and, accordingly, that the coefficient of relatedness increases."
Queller explored the change in mean additive genetic (breeding) value for a trait over a single generation using Price's equation
$
\Delta \bar{G} = \mathrm{Cov}(W,G)
$
where $G$ is the additive genetic value, and $W$ is relative fitness. Now, the key question is, how should we define fitness? If we treat it as a random variable, we can do a linear regression of fitness on a set of explanatory variables. What should we choose for the explanatory variables? One natural choice might be to predict the fitness of a focal individual based on the phenotype of the focal individual itself, and the phenotype of the individuals the individual interacts with socially:
$
W_{i} = w_{0} + \beta_{direct} P_{i} + \beta_{social} P_{j}
$
where $w_{0}$ is baseline fitness, $P_{i}$ is the phenotype of the focal individual, and $P_{j}$ is the phenotype of the focal individual's social partner. However, another way to predict the fitness of a focal individual might be to focus on the average phenotype of individuals in the focal individual's group, and the deviation of the focal individual's phenotype from the mean phenotype of individuals in the group
$
W_{i} = w_{0} + \beta_{deviation} (\bar{P}_{group} - P_{i}) + \beta_{group} \bar{P}_{group}
$
These regression equations for fitness hold exactly (only for a single generation), independent of the 'true' form of the fitness functions (they can be as non-linear as you like). What these allow us to do, however, is partition fitness effects into those that are due to benefits of a behaviour, those that are due to costs of a behaviour (and unmodelled residuals or 'noise').
From a kin-selection perspective, it turns out that the benefit in Hamilton's rule is
$
\beta_{social} = B
$
and the cost in Hamilton's rule is
$
\beta_{direct} = C
$
From a group-selection perspective, it turns out that the benefits and costs in Hamilton's rule are distributed over deivation and group effects
$
\beta_{deviation} = C - B
$
and
$
\beta_{group} = C + (N-1)B
$
Thus, we find that it possible to write fitness equivalently in two different ways that relate the change in frequency of individuals to benefits and costs associated with a social phenotype.
Question 1 Is group selection equivalent to kin selection for any evolutionary game or exclusively for the prisoner's dilemna?
They are always equivalent no matter what game is being played or how the population is structured if you are happy use the regression methods described to define fitness, benefits, costs, and relatedness. Many people have issues with the regression methods though. See Allen et al for a discussion of this. Others argue that kin-selection holds in every case and that the problems with kin-selection stem from a misunderstanding of the methodology. See Gardner et al for a discussion of this.
Many biologists find the debates in social evolution about kin/multi-level selection unhelpful (at best), and choose either framework to work in based on the question at hand. A few are very partisan on either side. There is a great deal of misrepresentation floating around about both, so read papers making strong claims with skepticism and caution.

Nice answer. I realize that the answer is under debate and is not as easy as I hoped it to be. At first sight, I don't feel like your explanation of Queller's article is a proof that Kin and group selection are the same things, but I'll have a look at the paper as well as to the other papers you linked. Thank you! +1

@Remi.b you raise a good point - it isn't really a proof in the mathematical sense, hence my use of apostophes! However, it is the paper most commonly cited as showing the equivalence of the two approaches. Let me know if you have further questions regarding the paper and I will update my answer accordingly. Thanks

Are kin selection and group selection the same thing?  Yes and no.
Yes:  These days people tend to use the "direct fitness approach" (Taylor and Frank JTB 1996).  It turns out that this is based on EXACTLY the same equation as is contextual analysis, which is the currently favored approach for measuring multilevel selection in natural populations (Goodnight 2013 Evolution 67:1539).  So, yes, at this level they are the same thing.
No:  Although they use the same equation kin selection theory solves for the optimum, whereas MLS theory solves for the strength of selection at the state of the current population.  In other words, they are asking two different questions.  kin selection is asking "where are we going" MLS is asking "how are we getting there"
No (2):  Kin selection is oriented towards genes.  MLS is oriented towards phenotypes.  This may seem like a trivial difference, but in structured populations the relationship between genotype and phenotype can become impossibly complex.

Welcome to Bio and thanks for your great answer. The citations are much appreciated. +1 To improve your formatting - could you add links to your citations? I added one link and that should get you going to add the Taylor&Frank citation. You can use the chain symbol, or manually key in the weblink.

Regarding the equivalence of MLS and kin selection, here is how I see the equivalence between these two approaches to selection.
MLS says that cooperation is favored when the response to
between-group selection outweighs within-group selection. Price's
equation tells us that this happens when the genetic variance
between-groups is higher than the genetic variance within-groups.
This is equivalent to saying that altruists tend to interact
with other altruists and, accordingly, that the coefficient of
relatedness increases.


text:
What is this discarded exoskeleton from?
This morning I was looking round the garden and found this sticking out of a pit in patch of soil, next to the wall of the house (in a trough sort of thing). I came to the conclusion it must be part of an insects exoskeleton that was discarded or part of a pupae. Can anybody identify what this belongs to? My location is in the south-west (Wiltshire region) of Great Britain. I'm just interested in what exactly I've found!

I can't be certain, but it is probably the pupal shell of a crane fly (daddy longlegs, Tipula palidosa). Here is an image to compare, and you can find lots more with a Google image search.
In the UK at least, these are colloquially referred to as leatherjackets and if you find one in soil before the adult has emerged it will often twitch.

I think it's a moth: http://www.uksafari.com/buried_treasure.htm

I very much doubt this specimen and the photo you refer to are tipulid pupae. They look more like this one


text:
How did these apples grow together?
I came through this pic while scrolling through facebook, and it was a bit strange to me.
As far as I know apples have a corymbose type of inflorescence, in which a single pedicel ends in a single thalamus.
And I am totally sure that the edible part, which is fleshy in the apple, is thalamus. How did this fruit came into existence?
I want a biological answer for this query.

They are basically conjoined apples which share a common stalk. They are rare but do happen. Here is an article of one discovered in a backyard.

conjoined apple discovered in a store (reference)
It apparently happens because of bad weather conditions, stress and insect damage. Fused fruits are also found in the case of cherries, watermelons, peaches etc.

Inadequate pollination because of heat and other adverse growing
  conditions causes that section of the fruit in which the seed did not
  develop to not grow and fill out. Also, the fruit primordium
  (embryonic growing point) can be damaged or altered by environmental
  factors and cause strange growth forms. Of course, Siamese twins or
  two fruit growing together is also rather common(reference).

Read more about them on article 1 and article 2.

that was very well explained thanks for this answer.


text:
Can you measure ECG from a single location?
I want to make a DIY bracelet to measure my ECG. All I need is the interbeat interval.
Can I design a bracelet on one arm only, with two electrodes slightly spaced from one another, and figure out the beat from the conduction timing differences down the arm?

I am afraid you cannot build the classic ECG using only 1 hand.
Probably, you can measure HR - heart rate accordingly to pressure detection and similar sensors and from that you can simulate ECG by picture. Simulate I mean you cannot build any reliably ECG curve on the monitor, but can show some waves after every heart beat.

I definitely want to stick with electrical activity for now-- it's proved more reliable than pressure or photoplesmograph sensors at the wrist. I'm curious whether you think it's possible to only extract the heart beat from 2 electrodes on a single wrist. We don't need the classic ECG waveform, only the heartbeat  .

With a single electrode, it is impossible to get an EKG as it has to have biopotential from two points (it is impossible to gett voltage from a battery using only one terminal).
Regarding EKG from single arm, yes it is possible to get clean EKG from shoulder.

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text:
Is there a durable surface that ants can't pass?
I'm looking for a surface, that will be impassable for ant's yet not poisonous or easily decaying.
One idea is water - they really can't cross that. But water easily dries and is quite uncomfortable.
Is there something their legs will find uncomfortable? Something spiky for example?

Fluon is a substance that people use to make artificial ant nests. It is similar to teflon in property and fluon coated surfaces are too slippery for ants to cross. See here.

I've found that ants do not walk through petroleum jelly. It is also convenient, as it isn't too messy, and can be whatever shape you want. I use it to keep ants from climbing into my hummingbird feeders. Make sure the area you treat is wider than the ant is long.

Vinegar is something that the ants will not walk through,due to the fact that the vinegar overwhelms their senses.


text:
Effect of steroid hormone on specific cells?
As steroid hormones can pass through the plasma membrane by simple diffusion because they are lipid derived hormones, it means that they are capable of passing through every cell of our body, BUT why are only specific cells responsive against steroid hormones?
For example, all of our body cells almost contains the genes for the development of secondary sexual characters but why do only specific cells show a response against these steroid hormones because the development of secondary sexual characters occur only in specific region of our body, that is, beard formation occur only in a specific region of the face, etc.
IN SUMMARY: When steroid hormones can pass through every cell of our body then why do they show only a localized response?

Unlike other types of hormones, steroid hormones do not have to bind to plasma membrane receptors. Instead, they can interact with intracellular receptors that are themselves transcription activators. Steroid hormones too hydrophobic to dissolve readily in the blood  travel on speciﬁc carrier proteins from their point of release to their target tissues. In the target tissue, the hormone passes through the plasma membrane by simple diffusion and binds to its speciﬁc receptor protein in the cytoplasm. The receptor-hormone complex then translocates into the nucleus where it acts by binding to highly speciﬁc DNA sequences called hormone response elements (HREs), thereby altering gene expression.
Hormone binding triggers changes in the conformation of the receptor proteins so that they be- come capable of interacting with additional transcription factors. The bound hormone-receptor complex can either enhance or suppress the expression of adjacent genes.
The DNA sequences (HREs) to which hormone- receptor complexes bind are similar in length and arrangement, but differ in sequence, for the various steroid hormones. Each receptor has a consensus HRE sequence  to which the hormone-receptor complex binds well, with each consensus consisting of two six-nucleotide sequences, either contiguous or separated by three nucleotides,
The ability of a given hormone to act through the hormone-receptor complex to alter the expression of a speciﬁc gene depends on the exact sequence of the HRE, its position relative to the gene, and the number of HREs associated with the gene.

The quick answer is that only certain cell types express the required steroid hormone receptors that are necessary to induce signaling and gene regulation when bound to their target steroid hormones, like estrogen, testosterone, cortisol, etc. If no receptor is present, the steroid doesn't effect any change.
The second part of the answer involves the particular signaling pathways induced by the ligation of certain receptors by certain classes of hormones. Testosterone, for example, has numerous effects across the body, from promoting the growth of hair to building muscle mass to effects on mental well-being. Testosterone and its primary metabolite 5α-dihydrotestosterone bind primarily to the cytoplasmic androgen receptor, which then translocates to the nucleus, binds DNA at hormone response elements, and alters the transcriptional activity of genes (either increasing or decreasing, depending on the gene and the cell type). Testosterone can also be metabolized to estradiol and bind estrogen receptors, which function similarly to the androgen receptor (although it can have DNA-independent effects as well).
So, depending on the cell type, receptor expression levels, other DNA regulatory elements, the presence or absence of various testosterone-metabolizing enzymes, and other factors like age, gender, etc., a single steroid hormone can have a multitude of effects throughout the body.


text:
When a thought 'crosses your mind', does it literally cross between left and right cerebral hemispheres?
I've heard that part of cognitive processing is information passing between left and right cerebral hemispheres.

This is what happens in the Cerebral Cortex which is divided into two hemispheres,
  left brain and right brain connected by a thick layer of nerve fibers called the corpus callosum. These nerve fibers allow messages to pass between the left and right brain
  hemispheres

My question is When a thought 'crosses your mind', does it literally cross between left and right cerebral hemispheres?
Assumptions:

I'm making a big leap from 'electronic impulses of neurons' to 'thoughts'.

You haven't really defined "a thought crossing your mind" at all. People without functioning corpus callosa have fleeting thoughts too, so at first glance, the answer is probably no.

Neuroscience doesn't really have a clear model for what a "thought" consists of exactly. Certain processes that are involved in thought have begun to be mapped--for example, this recent paper talks about a model for how the brain associates location in space with it's own mental map (http://www.ncbi.nlm.nih.gov/pubmed/24462102, I'll try to find something related that's not behind a paywall...). This one doesn't address your particular problem though, they only measured activity on one side of the brain. So basically, it might be possible to partially answer your question for more specific brain processes, but different kinds of "thoughts" are processed in different ways.
And of course I am also conflating impulses crossing the corpus callosum with the thoughts themselves, but I don't think this is really accurate. The most popular models in the labs I'm familiar with suggest that a "thought" is composed of a bunch of neural activity taken together rather than the activities of a few neurons on their own. But that might ultimately just be arguing semantics.


text:
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 can you explain the origin of life out of nonliving matter (abiogenesis)?
According to biochemist Robert Shapiro, the "primordial soup" theory is as follows:

Early Earth had a chemically reducing atmosphere.
This atmosphere, exposed to energy in various forms, produced simple organic compounds ("monomers").
These compounds accumulated in a "soup", which may have been concentrated at various locations (shorelines, oceanic vents etc.).
By further transformation, more complex organic polymers – and ultimately life – developed in the soup.

From: en.wikipedia.org/wiki/Primordial_soup
I don't understand how in step four life forms out of nonliving organic polymers. Could you explain this process? Can it be reproduced in the lab?
Louis Pasteur already disproved Spontaneous Generation: The law of biogenesis

I think my 'answer' to this question may give you something to think about: http://biology.stackexchange.com/questions/19720/how-is-the-origin-of-life-out-of-non-living-matter-explained-by-evolutionary-the Also, I'm sure this is a duplicate of many questions that have been asked here before. The simple answer is: we don't know.

Btw, the life-history tag indicates questions related to life-history traits and not with the "history of life".

Welcome to Biology.SE!
Your question has nothing to do with evolutionary biology
Evolutionary Theory does not explain the origin of life just like the Theory of Gravity does not explain the diffraction of light! In other words, explaining the origin of life is not within the scope of evolutionary biology. You should edit your title. But still, your question is within the scope of Biology so that your question is totally on-topic. This question would probably also be on topic on Chemistry.SE.
Some other posts may interest you
You may want to look at other posts on this site. This post for example explains what are our issues in order to select which of our hypotheses really explain the origin of life. This post, this one may eventually interest you as well.
Your question might be too broad. You may want to start with some introductory readings
Abiogenesis is not my field and I know very little about the origin of life. But at first sight, I am a bit afraid that your question is too broad and inaccurate and a good answer would ask for writing a lot. This post will give some good source of reading to further your knowledge. It may be good to start there and come back to this site with a more accurate question.
Hope I could help you a bit.

Some might think that this is a chemistry question, and indeed most of the work is done in chemistry departments, but that isn't because its not biology.
As far as evolutionary theory, there is a well-established definition of life as self-replicating systems and very little else.  Richard Dawkins' theory of the Replicator  is not always completely accepted (the link is to Stephen Gould's essay, who was usually in the opposition to Dawkins until he passed away).  Nonetheless, its logic is hard to completely dismiss: Once and only once chemical systems can self replicate then evolution happens - selection, variation and replication.  Dawkins thought springs from the pretty justifiable position that DNA is the center of all inheritance and variation in living things.  I'm not going to get into the arguments for and against but suffice to say that the replicator model might not be entirely true, but its not entirely wrong.
As far as the fourth step you mention, there are theories which are very credible but its reasonable to say that we are short on details... they may not satisfy and they certainly have not duplicated step 4...  The most detailed and credible theory is the RNA World Hypothesis.  At some stage, RNA polymers were able to self-replicate, pretty much by themselves it seems.
The evidence for RNA world is compelling but its more molecular archaeology than a series of coordinate events as we see it.  The ribosome and other RNA genes show that RNA could be fundamental genes.  In particular the ribosome consists of RNA whose structure are supported by protein, but RNA does all the chemical work.
Consider the odds.  The prebiotic soup may have existed for the better part of a billion years and covered all or a good part of Earth during much of that time.  As such, its exceedingly unlikely that we will be able to reproduce self replication of RNA in the lab.  Lucky and intelligent guesses may produce an environment that is just barely pre-biotic and produce a replicator, but even that seems quite unlikely.  Almost all this work tries to show that compounds and processes that come close to life are possible in pre-biotic Earth.


text:
What is the role of lamellar bodies in lung cells?
Lamellar bodies have been found to be secreted in lung cells many of their associated proteins have been identified. What is the current consensus or research on the function that these lamellar bodies play in lung?
(Sourced answers, please)

Little too broad! Can you narrow it down?

@DevashishDas is it? The answer can just be a few words. Even if you asked me, what is the role of RNA in the cell, I could answer with a few key words even if the full explanation would take a whole book

Well, The paper published in Nature 2003:

Despite two decades of progress in understanding the role of LGs and
their contents in epidermal barrier function, almost nothing is known
about the mechanisms responsible for the assembly of these unique
organelles.source: http://www.nature.com/jid/journal/v120/n4/full/5601763a.html

Since then the word "Lamellar Granule" appeared only 5 more times in journals:

1: Sando GN, Zhu H, Weis JM, Richman JT, Wertz PW, Madison KC.
Caveolin expression and localization in human keratinocytes suggest a
role in lamellar granule biogenesis. J Invest Dermatol. 2003
Apr;120(4):531-41. PubMed PMID:
12648214.
2: Akiyama M. The roles of ABCA12 in epidermal lipid barrier formation
and keratinocyte differentiation. Biochim Biophys Acta. 2014
Mar;1841(3):435-40. doi:
10.1016/j.bbalip.2013.08.009. Epub 2013 Aug 15. Review. PubMed PMID: 23954554.
3: Sakai K, Akiyama M, Sugiyama-Nakagiri Y, McMillan JR, Sawamura D,
Shimizu H. Localization of ABCA12 from Golgi apparatus to lamellar
granules in human upper epidermal keratinocytes. Exp Dermatol. 2007
Nov;16(11):920-6. PubMed PMID:
17927575.
4: Lee WS, Oh TH, Chun SH, Jeon SY, Lee EY, Lee S, Park WS, Hwang S.
Integral lipid in human hair follicle. J Investig Dermatol Symp Proc.
2005 Dec;10(3):234-7. PubMed PMID: 16382672.
5: Kelsell DP, Norgett EE, Unsworth H, Teh MT, Cullup T, Mein CA,
Dopping-Hepenstal PJ, Dale BA, Tadini G, Fleckman P, Stephens KG,
Sybert VP, Mallory SB, North BV, Witt DR, Sprecher E, Taylor AE,
Ilchyshyn A, Kennedy CT, Goodyear H, Moss C, Paige D, Harper JI, Young
BD, Leigh IM, Eady RA, O'Toole EA.  Mutations in ABCA12 underlie the
severe congenital skin disease harlequin ichthyosis. Am J Hum Genet.
2005 May;76(5):794-803. Epub 2005 Mar 8. PubMed PMID: 15756637; PubMed
Central PMCID: PMC1199369.
6: Ishida-Yamamoto A, Deraison C, Bonnart C, Bitoun E, Robinson R,
O'Brien TJ, Wakamatsu K, Ohtsubo S, Takahashi H, Hashimoto Y,
Dopping-Hepenstal PJ, McGrath JA, Iizuka H, Richard G, Hovnanian A.
LEKTI is localized in lamellar granules, separated from KLK5 and KLK7,
and is secreted in the extracellular spaces of the  superficial
stratum granulosum. J Invest Dermatol. 2005 Feb;124(2):360-6. PubMed
PMID: 15675955.

According to the last mentioned paper[6]:

LG(Lameller granule) constitute a specialized secretory system within the epidermis.

LG are seen as isolated oval-shaped granules in post-embedding methods, whereas they appear as parts of beaded tubular structures in cryo-ultramicrotomy

Result highlights the biological significance of LG in regulation of protease activities.

LEKTI labels were aggregated and not evenly distributed throughout the LG system, indicating the heterogeneous nature of the LG  (Ishida-Yamamoto et al, 2004).

Biologically active fragments derived from LEKTI are released extracellularly (Bitoun et al, 2003).

LEKTI labels were seen in the extracellular spaces in the superficial granular layers and the first cornified layer with release from the apical side of upper granular cells. Aggregates of LEKTI immunolabels were also closely associated with the TGN46-positive trans-Golgi network .

Double labeling with antibodies to glucosylceramide, a well-known LG molecule, showed that each occupies a distinct domain of beaded tubular structure

The ultrastructural localization of LEKTI was compared with that of KLK7. As reported previously (Sondell et al, 1995; Ishida-Yamamoto et al, 2004), KLK7 was localized in the LG system but was not co-localized with LEKTI within keratinocytes.

This finding suggests that LEKTI is expressed and released earlier than its target proteases, which is consistent with a role in preventing premature proteolysis of extracellular matrix proteins or cell surface adhesion molecules, and in controlling the timing of desquamation.

Source: [6]. http://www.nature.com/jid/journal/v124/n2/fig_tab/5602696f4.html

(source: nature.com)

Caption: Lympho-epithelial Kazal-type-related inhibitor (LEKTI) is
transported through the lamellar granule (LG) system. Post-embedding
immunoelectron microscopy using Lowicryl HM20 resin (A, D) and a
cryo-ultramicrotomy method (B, C, E). (A, B) LEKTI signals (black
arrows) are detected in the LG using polyclonal antibodies against
D8–D11 in (A) and D1–D6 in (B). Note that LG are seen as isolated
granules in the post-embedding method (A), but appear as beaded
tubular structures in the cryo-ultramicrotomy (B). Lamellar internal
structures are seen in both methods (white arrows). (C) LEKTI is
secreted from the apical side of upper granular cells (arrows). d,
desmosomes. Polyclonal antibody to D8–D11 and desmoglein 1 monoclonal
antibody were used and were labeled with 5 and 10 nm immunogold,
respectively. (D) LEKTI antibody to D8–D11 labels are closely
associated with those of the TGN46-positive trans-Golgi network. (E)
LEKTI (monoclonal antibody, 5 nm gold labels) and glucosylceramides
(GlcCer, 10 nm gold labels) are localized within the same continuous
beaded tubular structure of the LG system.


text:
Inductance in cell
In an animal cell, especially neuron and in particular its axon, while there is electrical resistance and capacitance mechanism in the cell, which play essential roles in the cable theory model of neuronal action potential transmission, is there a prominent self inductance mechanism in the sense of electromagnetism?

i don't think there are any magnetic effects in a typical animal body. I can't think of any inductive effects.

@WYSIWYG: Magnetism is a by product of electricity. Is it not strange that animal does not or produce magnetic field while use electricity extensively?  I can think of one instance of magnetic field use in animal, their perception of orientation based on the earth magnetic field. See this NOVA article http://www.pbs.org/wgbh/nova/nature/magnetic-impact-on-animals.html.

Well moving charge does produce magnetic field but if you do the calculations you would need quite some current to generate a significant magnetic field. Yes animals can sense magnetic field but it is limited to some. Nonetheless, I still cannot think of any inductive effects in the cell (where is a coil?)

@WYSIWYG: I am not quite sure how you define "significant" magnetic field. Two parallel lines of current exerts forces on each other in close proximity. Circuit has to be designed carefully to eliminate the unintended inductive effect. Coils are to make the geometry better generate the inductance, but they are not necessary, since other shapes can generate inductance as well. Of course I do not know what structure in a cell would be able to generate sufficient inductance, hence the question.

What one thinks, no matter how intuitive it may appear is not particularly relevant in science.  The inductance associated with a neural axon has been well documented since Cole (1966).  Its role in the propagation of neural signals is developed extensively in http://neuronresearch.net/hearing/pdf/7Projection.pdf#page=39 .  The actual development begins earlier in Section 7.4 on page 322 of that document.
Failure to consider the inductance associated with any alternating electrical signal passed along a coaxial cable leads to disaster.  The first undersea cable based on the ideas of William Thompson,Lord Kelvin, and described as an RC cable by Hermann (page 322 in the above document) was a technical and financial disaster.  Two years later, a more sophisticated RLC cable based on Maxwell's Equations for a coaxial structure was laid with great success.  No RC cable has ever been used in practice since that time.  For unknown reasons, the biological community keeps trying to ignore the inductance of the coaxial myelinated axon (leading to ridiculous modeling data).  This appears to be the result of introductory courses in electricity for non-engineers trying to avoid the necessary mathematics to understand electromagnetic signal propagation through space and along various types of cables and waveguides.

So you are saying there is indeed inductance in myelinated axon. So should the correct equation for action potential be the telegrapher's equation http://en.wikipedia.org/wiki/Telegraph_equation rather than the cable equation http://en.wikipedia.org/wiki/Cable_equation? Is this the main difference between the myelinated and unmyelinated axon other than the insulation provided by the myelin?

There surely is inductance in neurons. This inductance is introduced by two different mechanisms.
1. The coil structure of myelin sheaths can introduce a real electrical inductance. The solid evidence for this is the opposite spiraling directions between the adjacent myelin sheaths.
Here I quote the description on Wikipedia:At the junction of two Schwann cells along an axon, the directions of the lamellar overhang of the myelin endings are of opposite sense. You can also check the details in this paper:  Uzmman B. G.; Nogueira-Graf G. (1957). "Electron microscope studies of the formation of nodes of Ranvier in mouse sciatic nerves". Journal of Biophysical and Biochemical Cytology. 3 (4): 589–597. doi:10.1083/jcb.3.4.589
The opposite spiraling directions can introduce a positive mutual inductance between adjacent myelin sheaths then further enhance the propagation speed of the neural signal. Meanwhile, it is easy to predict that the myelinated nerve can be stimulated by a magnetic field because of this coil inductor. Because of this opposite spiraling direction, the stimulation result is determined by the spatial gradient of the magnetic field. This phenomenon was validated by years and can be easily understood now.

The piezoelectric effect of the plasma membrane. If you check the molecular structure of the lipid bilayer of the plasma membrane, you will find that it is naturally a piezoelectric layer. The definition of the piezoelectric layer is a layer consists of two crystal layer with opposite polarities, which is exactly the same as the lipid bilayer. The equivalent circuit of this piezoelectric layer will be a RLC circuit, which contains an equivalent inductor. Since the inductor is not a real one, the value is only used to match with the mechanical resonance frequency. When the mechanical resonance frequency is very low, which is the case for a soft and thin plasma membrane, this inductance will be huge. This is why in Cole's paper for measurement of the squid axon, this inductance is 0.2H. Then as a direct prediction, there should be a mechanical wave accompany with the electric signal of the action potential.
This mechanical wave has been measured in this paper: Gonzalez-Perez, A., Mosgaard, L.D., Budvytyte, R., Villagran-Vargas, E., Jackson, A.D. and Heimburg, T., 2016. Solitary electromechanical pulses in lobster neurons. Biophysical chemistry, 216, pp.51-59.

I think here I already give a comprehensive answer to this question. You can check all the details in this paper on bioRix:https://www.biorxiv.org/content/early/2018/10/22/343905
Here I may talk something more, but these things will make most of the people in neuroscience unhappy.
If this inductance introduced by the coil structure of myelin and the piezoelectric effect is true, then the whole neuroscience is wrong from the Day 1. The H-H model is built based on a RC circuit and so many people have developed their theories and models based on this H-H model. But ridiculously, everyone claims his model or theory is correct and can explain the data when tha basis is wrong. I have seen so many absurd explanations to bypass this inductance, such as the frequency-dependent capacitor, virtual cathode, negative resistor, and even negative capacitor.
And indeed, more and more people begin to realize the so-called neuroscience is a complete failure. You can see in the homepage of Neuralink(https://neuralink.com/), they officially claim that they do not need any neuroscience experience, quote here:No neuroscience experience is required
Also, there are many groups now only use deep learning or machine learning to study neurons.

Well I might just be falling into your prediction as someone unhappy in neuroscience, but "the whole neuroscience is wrong from the Day 1" sounds like a gross exaggeration. The inductive effects you are describing are not all that important for understanding neuroscience.

I also have no idea why Neuralink has anything on-topic to do with this question and I feel like a good part of your answer is just a rant.


text:
How to measure Na/K channel activation at the membrane level?
Assume that there are two different signals occurring on the ECG - during depolarization and repolarization in the standard ECG.
I was advised not to use the standard ECG in measuring the exact electrical events during:

stages 0-2
3-4

We can get data about the electric activity of neurons in vivo in Fig. 1 where some data about the electric activity of neurons is present.
So my thought is that a similar technique could probably work with cardiomyocytes.
Fig. 1 Example of measurement for electric activity of neurons in vivo

I estimate that there is about 18% uncertainty when using the standard ECG because of the peak in the stage 1 (Gibbs phenomenon) and those two complete different phases.

This is probably not possible in vivo, but there are various methods (voltage clamping, channel blockers) that you can use in vitro with individual cells and perhaps correlate the results with the aggregate activity of a larger piece of heart muscle.

@jonsca I found that we can get data about the electric activity of neurons in vivo. So probably the same technique has been used with cardiomyocytes.

@Masi Neurons are easier because they aren't moving that much.

@NickSandor Can you please make your comment an answer and support it with evidence and/or sources. It is very interesting, but true. Can you say how much neurons and cardiomyocytes move, please. - - I am really interested in on any estimates about the topic because I have overlooked it for long time. - - Can you please state what you expect to be seen in cardiomyocyte activity? What is their metric in time-frequency plane or time-potential plane? I get mostly cloudy areas but different from neuron areas when studying spectrograms and other distributions.

I searched Pubmed for cardiomyocyte+"patch clamp", and read the first ~10 abstracts. Everyone measures plated cells. At best, these cells came from from hearts freshly minced in collagenase / EDTA. See PMIDs 27364017, 27076034, 26142302, 26241168, 26378152, to mention the most recent search results.

@NickSandor Please, see my new question here about the topic http://biology.stackexchange.com/q/50630/86 - - Why are they measuring exactly plated cells?


text:
RNeasy Mini Kit low 260/230 ratio -- can I purify this RNA for further use?
I used Qiagen's RNeasy Mini Kit to isolate RNA from 5*10^5 C28/I2 (immortalized human chondrocytes). However, my yield is low (~25 ng/ul), but my 260/280 ratio is great (~2.3), and my 260/230 ratio is tragic (~0.06). I have already thrown the spin column away, but I would like to know 1) if I could raise my 260/230 ratio for the 40 ul of RNA I extracted, and 2) if I could precipitate the RNA out of solution so as to make a more concentrated solution.
Please let me know if further details are necessary.
Thanks!

You can easily precipitate the RNA using either Ethanol or Isopropanol. I would do a Phenol-Chloroform extraction before that, too. But does this make sense? When you are working with a cell line, I would rather make a fresh prep than wasting time and money into saving the poor quality RNA.

These cells grow really slowly and I have some simple PCR that I need to run within the next couple days, so I'd ideally like to spare it. I've just never had these issues before. How do I precipitate the RNA using ethanol?

did you modify the amount of RLT buffer in the Qiagen RNAeasy mini kit? If yes, how much did you use?

RNAeasy kit will not usually give phenolic contamination. Your poor 260/230 is perhaps because of low yield; check the absolute absorbance values. Low 260/230 (and low yield) also happens because of improper lysis. I would advise that you do the cell lysis using more effective methods. I would not advise another phenol-chloroform or alcohol precipitation step- you will lose your RNA. With what you have now, run a little bit on the gel to see the integrity. Also try heating the dissolved RNA at 65-70deg for 10-15min and measure OD again (use nanodrop or a similar device)

The low 260/230 ratio is indicative of guanidine contamination I believe. The RNeasy "RLT buffer" contains guanidine to my knowledge.

It does. but column based purification generally doesn't leave these contaminants..

How did you lyse them? WYSIWYG is probably onto something here.


text:
Lost Ability to Regenerate Body Parts during the Transition from Amphibians to Mammals
Why have higher-order animals lost the ability to regenerate body parts during evolution? Wouldn't it be better for survival? What is the evolutionary theory behind it?

the liver regenerates.. The regenerative ability of which animal are you talking about?

My question is about Limbs and other body parts. Like lizards can regenerate a whole limb but crocodile can't(just an example).

How do you deduce that higher animals lost the ability to regenerate during evolution? Can you please give me an example of such an animal which lost its ability to regenerate?

Like I said in my last comment, Limbs of Lizard and Crocodile.

Rephrase your question to "lost the ability to regenerate body parts during the transition from reptiles to mammals."

Sounds Better!!

You might want to rephrase your question just a little more and add some background. First, there was never a transition from reptiles to mammals. They share a common ancestor but evolved within their own clades. And do you know if the common ancestor of mammals and reptiles is believed to have limb regeneration? In other words, are the examples of regeneration in nature mostly conserved or have they evolved independently? Why do you think they were lost instead of never evolved?

I changed Reptiles to Amphibians in the title, because there is no reptile to mammal transition.

Regeneration of limbs in amphibians is an adaptation where new limbs are generated by dedifferentiated cells. This process is tightly linked to the embryonic program which, in most animal cells, is a difficult program to access once terminal differentiation has occurred (but it's possible, e.g. induced pluripotent stem cells).
Of note, amphibians have a unique life cycle that includes metamorphosis. It is thought that organisms with more diverse stages in their development may have increased potential for regeneration. Mammals, after birth, do pass through multiple stages of development, but these stages are largely continuous.
So the quick answer is: mammalian limbs are made up of terminally differentiated cells (and specialized stem cells) with high barriers of reprogramming. They're difficult to reprogram because there hasn't been strong selective pressure to do so. Limb regeneration might seem like a great adaptation, but it doesn't seem to be that important for the success of mammals. Additionally, selection for "maintaining a full set of functional limbs" could evolve many different ways. For example, primates may have evolved behaviors or reinforced anatomy that reduces their risk of injuring a limb. Also, larger animals are probably less likely to have limbs removed just given their size. And if they do, it may have little effect on their reproductive fitness. A legless amphibian probably finds few, if any, mates.
Yun Gates, and Brock. Regulation of p53 is critical for vertebrate limb regeneration, PNAS 2013

Wow, great answer. Can you add some references?

Thanks! I've added a reference. The introduction and citations in the linked paper include the relevant information.


text:
Start studying mathematical biology from basics
I am really passionate about theoretical and quantitative biology and I would like to build my future career around this topic.
I've just got my bachelor's degree in biology (ecology) but scince I've had only one math class through the years, my math skills are very poor, so I have problems in understanding even simpe models. My main interests are population dynamics, adaptive dynamics and game theoretical models of social conflicts.
I would like to improve my skills, but I have just no idea where/how to start. Could you give me some advice about textbooks or online resources?
I have almost no knowledge in the field of math, I am interested in resources for complete beginners. And I would also appreciate any suggestions about skills/topics I should master if I am interested in these biological phenomena.
Thank you!

There is one book that will perfectly suits your needs:
A biologist's guide to Mathematical Modeling in Ecology and Evolution, by Sally Otto
It is a very good book that is very easy to understand and in the meantime goes pretty far (It ends with the use of diffusion equation in Evolutionary Biology). I highly recommend it.
It covers:

How to create a model
Function approximation
Find general solution with $n$ variables for discrete and continuous model
Stability analysis
Find equilibrium
Analyzing cyclic behavior
Gives very good introduction in linear algebra and probability theory
Class structured population
Stochastic modeling (birth-death processes and diffusion approximations)
Transformations
All examples are from the field of ecology and evolution and the author derives many of the most important equations in ecology and evolution.

Online ressources
Also I think that Khan Academy is a very good and easy source of information for improving your math skills but it takes quite a bit of time to go through all these lectures.
For a good and complete introduction to probability theory, I'd recommend this MIT Opencourseware but again, it takes time to go through all these videos.
For further recommendations in population genetics, you should have a look to this post.
If you are interested in theoretical biology, you may also want to learn about programming (if you don't already know much about it). $R$ is used for data analysis purposes, $Mathematica$ or $Matlab$ for deal with mathematical modeling and $Python$, $Java$ or $C++$ for individual-based simulations.
Note: A bit less than 2 years ago, I had the same interests than you and had to face the same issues than you.

Thank you so much for your answer. It is most helpful. May I ask, if these resources were enough for you to get on well in this field?

@Alana Well..At the moment I just finished my Master degree and am starting my PhD (in theoretical population genetics at UBC, Vancouver) in early September. It is a bit hard to compare myself with specialist in this field but anyway these references allowed me to learn a lot and helped me to be creative and develop my own research projects. I feel I should still learn more about mathematics. I learned to program with online tutorials.

I edited my other answer here to add a new important reference. Wish you all the best in your readings and self education! Don't hesitate to ask further questions.

Thank you so much! Your answer really helped me a lot. I'll have only one more question: what programming language do you use? I've read aboutthe ones you recommended, but I've only used R so far.

I mostly use R (data analysis and some very simple simulation), Mathematica (for mathematical modeling) and Python (for Individual-based simulation (Object-oriented programming) ).

I can program in Java but I prefer Python and I know nothing about C++. Python has the advantage to be very easy to learn and to be good-looking as it uses much less special characters such as curly brackets than many other languages. You may be able to start simulating some fairly complex population (individual-based simulation) with Python after only 1 or 2 days of reading tutorials (The tutorial I used was in french, I am afraid I can't suggest you a given tutorial but you will probably find recommendation on other SE sites).

Thank you so much! I couldn't decide so far, what language to learn. I started practicing Java and C but both seemed complicated. I've just a find a nice Python tutorial at codacademy, and I think it is just for me. Thank you again, it was a great help for me! :)

My pleasure $\ddot \smile$


text:
Sugar as a defence against bacteria?
An answer on another SE site mentions that sugar "at a certain level acts as a preservative". I've always been taught that microorganisms eat sugar and expel acids, that is why sugary food are damaging to teeth. How is it that sugar acts as a preservative, then?
Googling the question I've found conflicting answers though I don't credit the sources as being especially reputable. What is the real reason that sugar can act as a preservative?

Sugar in high concentrations acts osmotic. This means that the water available in the cells is drawn towards the high concentration of a solutant (sugar), like in the image below (this is demonstrated with a plant cell, but the principle is the same for bacteria and other microorganisms):

Since microorganisms can not survive without water, they are not able to grow or reproduce. This effectively safes food. The same mechanism works when salt is used to conserve meat or fish.

This is also why quite large amounts of sugar (or salt) is needed in order for it to work as a preservative. With too little sugar there will be no osmotic effect (or too little) killing of the microorganisms spoiling what you're trying to preserve. Which in turn is why e.g. jam always is so sugary.

Sugar participate in food preservation only at high concentrations. When microbes are introduced to high sugar concentrated environment, water inside the microbial cell diffuses out to the high sugar concentrated solute due to the phenomenon called osmosis. As water is very much needed for cell functioning and metabolism the dehydrated cells fail to perform its function and eventually die. This is called sugar curing, a food preservation technique. Also hard sugary sweet is less susceptible to microbes than soft sugar sweet because of its high sugar content that makes it intolerant for microbial growth and also the absence of moisture (important factor for microbial growth) in the hard sweet as compared to soft sweet makes it less susceptible to microbial attack.


text:
Why doesn't honey spoil quickly?
Why is it that honey can last for decades and not spoil like other foods? Is there any chemical in honey which gives rise to this amazing feat?

see http://biology.stackexchange.com/questions/19744/sugar-as-a-defence-against-bacteria

Based on Alan Boyd's link I think this is a dupe.

One reason is that sugar has a pH of 7, while honey has a pH of 3.26 to 4.48, a killing field for bacteria. Also, bees process honey by means of an enzyme called glucose oxidase, AKA 'Penicillin A' (formerly) or 'Notatin', which reduces atmospheric O2 to H2O2 (Hydrogen peroxide), forming an antimicrobial barrier on the honey surface. Also, bacteria become desiccated in honey because of the hygroscopic effects of the sugar (mostly supersaturated in honey). Basically, related, but not a duplicate question.

@daniel pls reopen the post. as J. Musser mentioned, it's definitely not a duplicate.


text:
How to use Autodock just for (re)scoring
I have some protein-ligand complexed that I have been docking with some other software and just want to use Autodock to evaluate those complexes. So, basically I just want to use it as a scoring function to take a look at the energy components - I don't want to re-dock the ligands into the protein binding sites.
From what I have found on the internet, I came up with this procedure, but I am not sure if this is the right approach, and also I get an error in the last step saying that "atoms are outside the grid".
It would be nice if someone could take a look at it and tell me whether this make sense and if this is the right procedure (and maybe a suggestion for the error source)
1) Preparing the receptor

need to add hydrogens if not present
adds gasteiger charges to peptide

input

protein.pdb

output

protein.pdbqt

script:

prepare_receptor4.py -r protein.pdb [options]

2) Preparing the ligand

add hydrogens if not present

input:

ligand.pdb or ligand.mol2

output:

ligand.pdbqt

script

prepare_ligand4.py -l ligand.mol2 [options]

3) Generate grid parameter file
inputs

ligand.pdbqt
protein.pdbqt

output

protein.gpf

script:
prepare_gpf4.py -l ligand.pdbqt -r protein.pdbqt [options]

4) AutoGrid: generate maps and grid data file
inputs:

protein.pdbqt
protein.gpf

outputs:

protein.glg             Grid Log File
protein.*.map         affinity maps for different atoms
protein.maps.fld     Grid data file
protein.d.map         desolvation map
protein.e.map         electrostatic map

command:
autogrid -p protein gpf

5) Generate docking parameter file
inputs

ligand.pdbqt
protein.pdbqt

output

ligand_protein.dpf

script:
prepare_dpf4.py -l ligand.pdbqt -r protein.pdbqt [options]

**
**
6) Prepare .dpf file and run autodock for re-scoring
**
**
Remove seach parameters and append the "epdb" keyword, so that an
examplary .dpf would look like this:
autodock_parameter_version 4.2       # used by autodock to validate
parameter set
outlev 1                             # diagnostic output level
intelec                              # calculate internal
electrostatics
ligand_types C HD N NA OA            # atoms types in ligand
fld rec.maps.fld                 # grid_data_file
map rec.C.map                    # atom-specific affinity map
map rec.HD.map                   # atom-specific affinity map
map rec.N.map                    # atom-specific affinity map
map rec.NA.map                   # atom-specific affinity map
map rec.OA.map                   # atom-specific affinity map
elecmap rec.e.map                # electrostatics map
desolvmap rec.d.map              # desolvation map
move lig.pdbqt                       # small molecule
about 17.6 22.2 32.6         # small molecule center
epdb                                   # small molecule to be
evaluated
**
**
inputs

ligand_receptor.dpf

command:
autodock -p ligand_protein.dpf
Edit
I managed to use AutoDock Vina for re-scoring now, however, the output is not as detailed as the one that would be produced by AutoDock 4.2.
For example, what I get is:
Affinity: -2.06943 (kcal/mol)
Intermolecular contributions to the terms, before weighting:
    gauss 1     : 51.97697
    gauss 2     : 1133.84012
    repulsion   : 7.41516
    hydrophobic : 34.56441
    Hydrogen    : 0.00000
(what is also weird is that the prepare_ligand4.py script to generate the .pdbqt file from the mol2 file removed the hydrogens)
In AutoDock4.2, the output would be, for example,
epdb: USER Estimated Free Energy of Binding = -6.54 kcal/mol [=(1)+(2)+(3)-(4)]
epdb: USER Estimated Inhibition Constant, Ki = 15.95 uM (micromolar) [Temperature = 298.15 K]
epdb: USER
epdb: USER (1) Final Intermolecular Energy = -7.14 kcal/mol
epdb: USER vdW + Hbond + desolv Energy = -6.33 kcal/mol
epdb: USER Electrostatic Energy = -0.81 kcal/mol
epdb: USER (2) Final Total Internal Energy = -0.20 kcal/mol
epdb: USER (3) Torsional Free Energy = +0.60 kcal/mol
epdb: USER (4) Unbound System's Energy [=(2)] = -0.20 kcal/mol
Anyone knows if this might be available through VINA somehow?

Okay, I finally figured it out. Basically there are those following 6 steps:

Preparing a protein
Preparing a ligand
Generating a grid parameter file
Generating maps and grid data files
Generating a docking parameter file
Running AutoDock

Since the details are a little bit too lengthy for this post, I have written it up as a tutorial. A lot of people (like me) seemed to struggle to get it to work, so I thought this write-up could be a useful reference: AutoDock4.2 re-scoring tutorial

Thanks! Since I didn't find any complete documentation on the internet, I felt like writing it down once and for all: For myself as future reference, and for anyone else who wants to use AutoDock4.2 just for re-scoring

You can use Autodock Vina. It provides an option to calculate local score only.

displaying the individual contributions to the intermolecular score, before weighting (these are shown with "--score_only")

Autodock is better tool in speed and accuracy than Autodock itself.
For using it, you need :
1) Protein.pdbqt
2) Ligand.pdbqt
3) Config.txt (the confguration file):

receptor = hsg1/rigid.pdbqt
ligand = ligand.pdbqt
center_x =  2 # Center of Grid points X
center_y =  6 # Center of Grid points Y
center_z = -7 # Center of Grid points Z
size_x = 25 # Number of Grid points in X direction
size_y = 25 # Number of Grid points in Y Direction
size_z = 25 # Number of Grid points in Z Direction

Run your code as :
vina --score_only --config config.txt --log your_filename.log

for mmore information type:
vina --help_advanced

source: http://vina.scripps.edu/manual.html#faq
UPDATE:
Use:
prepare_ligand4.py   -A 'hydrogens'

for Adding hydrogen
For understanding the scoring of Vina:
AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading

Thanks a lot, this works. However, the output is unfortunately not as detailed as the one that would be generated by AutoDock. I will make an edit to the original question in a few moments - the formatting works better there.


text:
Why does skin sometimes suddenly itch when you stretch it?
Sometimes, when I bend over, areas of my skin like my back can suddenly itch quite intensely. Sometimes it may be another part of my body and the pattern seems to be a part of the skin organ that is not used to stretching quite that much in that spot, perhaps the skin not being so flexible there.
I realise that temperature, dryness, and a whole lot of other external and internal factors can come into play, but if my scenario is not too broad, and I'm pretty sure it's a universal trait in skin physiology, (and I don't have any skin allergies either), what is the basic science behind this phenomenon of skin stretching when it's not used to it, and you do it very suddenly?

Do you have stretch marks around the area that itches?

No the stretching is only minor and the itching momentary (though sharp). The interest is due to the idea that when you stretch the skin, new skin cells are created and it essentially starts expanding if you keep stretching it enough (consistently). So biologically, I wonder what is happening with skin cells when you are doing momentary stretches to skin that isn't already 'expanded' enough for the task, so to speak. I wonder what is happening with the skin cells, because the itch sure is interesting and prominent, biologically. I do think dryness of air/skin is a big factor though, but still.

you mean relationship between http://www.ncbi.nlm.nih.gov/pubmed/21767766 and http://www.humankinetics.com/excerpts/excerpts/anatomy-and-physiology-of-stretching

I suppose, yes! :) Though not a blanket topical enquiry, more a specific application.


text:
How can I tell if regulation is at the transcriptional or translational level?
I was reading a paper, http://www.pnas.org/content/109/8/E471.short, where the authors claim that (e475)

Translation of the TfR (Transferrin Receptor) is regulated through sequences in the 3′ and 5′
  UTRs (untranslated regions) of its mRNA. To study the regulation of TfR levels independently
  of translational control, we measured the levels of TfR-EGFP expressed
  from a plasmid lacking the regulatory sequences present in the
  endogenous TfR mRNA (Fig. 6A).
  Endogenous and GFP-tagged expressed TfR levels were reduced equally in
  response to Rabenosyn-5 depletion, ruling out an effect of this
  protein on transcriptional or translational control of TfR expression.

I believe I understand that the effect can not be post-translational, since TfR-GFP has no region for translational regulation and so it cannot be regulated by any translationally active regulating factor.
My question is: Wouldn't the statement above, that Rabenosyn-5 has no effect on protein transcription, require a proof that mRNA levels are not affected by this protein?

Fig. 6A, http://www.pnas.org/content/109/8/E471.figures-only

From the Methods section:

Human TfR in plasmid cDNA was a gift from Tim McGraw (Weill-Cornell
  Medical College, New York, NY). Human TfR cDNA was subcloned in frame
  with EGFP in the Clontech pEGFP-N1 vector at the XhoI and BamHI
  restriction sites.

This TfR-GFP fusion protein does not have the endogenous TfR promoter. So it is not likely to be regulated by any TF that would directly regulate TfR transcription.
So they conclude that Rabenosyn-5 does not specifically regulate TfR expression.

I see. I guess if the cDNA plasmid would have had any regulatory sequence, they would have stated it.

cDNA can have 5' and 3' UTRs but that is not the case here..


text:
Does fasting improves immunity?
I have heard that fasting causes regeneration of memory cells(B- and T-lymphocytes) thereby improving immunity.Is this true? If yes, how?

For those interested, i have found a study examining memory cell depletion in deer mice due to food restriction. The author considers energy cost of memory immune response and examines it in animal trials. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2727600/#!po=65.9091 Perhaps not counterproductive in autoimmunity issues.

Interestingly this effect seems to be true - there is one paper which claims that fasting for three days leads to the depletion of unused (and especially damaged) immune cells to save energy. When food is back at normal rates, the body starts to renew these cells which have been depleted before. This process also seems to enhance the self-renewal process of stem cells which start to replicate and further differentiate.
This works like in the figure below (from the paper below):

Although this renews a part of the immune cells, I wouldn't say that this improves the immune system. I think that here mostly naive cells (which haven't) come in contact with an antigen are shut off. If you deplete memory cells (which had this contact) this would be counterproductive, since these cells are important for a fast immune response.

Prolonged Fasting Reduces IGF-1/PKA to Promote
Hematopoietic-Stem-Cell-Based Regeneration and Reverse
Immunosuppression

There is as well an article in Science Daily, which summarizes the original paper. It can be found here.


text:
Where are the evolutionary "inbetweeners"?
The problem I've always had with evolution is the actual lack of variation between animals. More specifically, the lack of observable gradual change between species.
Take for example the hammerhead shark. It obviously has a strong connection with a normal shark, but where's the "half-hammerhead" shark? Where's the species that only has a SLIGHTLY wider head?
I really doubt that a single mutation on a normal shark resulted in a head shaped like that, it had to happen gradually. Right? As far as I understand, evolution works by random mutation in a child being somehow slightly beneficial to that animal so it get's to live longer and reproduce more, eventually resulting in it's genetic material in dominating the inferior ones before it. But if it was for whatever reason beneficial to have a slightly wider head, why don't all the sharks have slightly wider heads now? On the other hand, if it wasn't beneficial, how come the hammerhead still exists?
Furthermore, I feel like some characteristics of a certain animal can't really have gradual benefits. There's a lizard that shoots blood out of it's eyes. The original ancestor certainly didn't, and I'm sure that if it's child only bled slightly from it's eyes it wouldn't really help if much in life. So for it to actually become beneficial, it seems to me that there had to be a ton of lizards that had a disadvantage of bleeding slightly. In fact, there had to be so many that they evolved even further in the same direction and kept doing that until they bled so much it's an actual benefit (sorry for this turning so gross). So why did the inbetweeners survive long enough to evolve even more, and why did they THEN die out?

The fossil record in general contains transitional forms for some animals and not for others. Since geology and other factors enter into this, I think one has to choose a specific animal and ask why the fossil record might be deficient. Where would we find a transitional hammerhead shark, for example?

My question isn't about fossil evidence. It's about why those species aren't here TODAY. Or if they aren't because they're extinct due to their inferiority, then how did they live long enough for the superior species to evolve from them?

Have you studied the variety of hammerhead sharks? Do they all have precisely the same proportions? Even checking the Wiki entry, it indicates the winghead shark has the most pronounced cephalofoil. That would mean others are much less so. So there are gradations. It may not be a perfect spectrum but it may be that intermediates were poorly adapted.

Obviously not, but are you claiming there are species species of regular head to hammerheads and everything in between? I've also mentioned the lizard. Again, I don't know if all of those lizards perform the same. That's not what my question is saying.

Remi.b asked my next question for me. If there were only two grades of hammerhead would you insist on the two intermediates? And if there were four would you insist on eight, one between each gradation?

I am surprised to see that messy, unanswerable and very broad questions in evolutionary biology are often easily upvoted! I voted to close expecting the OP to ask his questions more clearly in two separate posts as it has been discussed below

I'm closing this according to our policy on creationist questions. If you're interesting in understanding evolution you're welcome to ask here. Questions that simply state the common creationist talking points will be closed.

The rostrum of a dolphin is control by the duration of promoter activity of a single gene. The gene is identical. But the longer the promoter is active, the longer the rostrum (and number of teeth in it). It is amazing that the length of such a complex structure is not even cause by genetic mutation to a gene but a mutation to the promoter sequence of that gene, which is not protein coding.

More specifically, the lack of observable gradual change between species.

Most significant phenotype differences occur over several thousand generations, which means several thousand years on up. While we certainly can create experiments where a controlled form of evolution occurs within a very small time-frame, I'm going to assume that you're not interested in closed laboratory experiments given the nature of your question.

It obviously has a strong connection with a normal shark, but where's the "half-hammerhead" shark? Where's the species that only has a SLIGHTLY wider head?

The data below does answer you question, but in reverse. Hammerheads are much older than most of their relatives; so their cousins have actually grown smaller heads... but there are certainly intermediates.
From Andrew Martin (1993 - mtDNA data) via Elasmo-research.org:
*The circles represent the head-width vs. body-length ratio.

Martin's conclusion: "...the hammer appeared rather suddenly and fully formed, and was later optimized along different lines to suit various selection pressures."

I really doubt that a single mutation on a normal shark resulted in a head shaped like that, it had to happen gradually. Right?

Not necessarily. Single Nucleotide Polymorphisms (a.k.a. - "SNPs" - a change in one nucleotide) can have pretty wide-ranging effects.
The vast majority of humans, for instance, are lactose intolerant in adulthood. However, lactose tolerance evolved twice from two different SNPs in two different human populations: One European and one African. One gene. One regulatory mechanism change. Massive benefits (essentially opening up a whole new resource in adulthood).
Significant differences in phenotypes (the physical appearance of something) can require more gene mutations, or not. It depends on where the mutation is in the genome and what the gene does.

But if it was for whatever reason beneficial to have a slightly wider head, why don't all the sharks have slightly wider heads now?

The simple answer is because either there wasn't enough selective pressure that the rest of the shark phenotypes succumbed to that the hammerhead avoided, or that the hammerhead design doesn't give enough of an advantage to completely dominate the gene pool. An alternate, but more abstract answer, is that there simply hasn't been enough time for the hammerhead design to dominate the shark phenotype. Remember, evolution works by generations - not years. It would take unknown thousands of generations for a weakly-advantageous design to dominate an entire niche - if it ever would.
Also, it is worth it to point out that evolution doesn't only select for advantageous mutations. Mutations that aren't very detrimental can still exist within a population as long as the detriment doesn't prevent resource exploitation and offspring production. Think Huntington's Disease which severely restricts a person's survivability, but only after their mid-30's (in general) - plenty of time for the person to have sex and raise a kid into semi-adulthood. It is a genetic defect which sticks around only because it allows humans to reproduce before it seriously affects them.

The original ancestor certainly didn't, and I'm sure that if it's child only bled slightly from it's eyes it wouldn't really help if much in life.

Maybe, maybe not. Maybe it shot something else before blood, and then a mutation caused it to shoot blood instead - but the overall effect (deterring predators) was the same so it doesn't really matter.
You're correct that some traits might appear very awkward if they had evolved gradually, but the question then becomes: Did they evolve gradually? Sometimes we simply do not know.

So why did the inbetweeners survive long enough to evolve even more, and why did they THEN die out?

Like I said above, just because a trait is detrimental doesn't necessarily mean it will be eliminated. As long as the being can survive long enough to reproduce successfully with the trait, the trait might not be eliminated for a very, very long time- if ever.
As for in-betweeners dying out - it's difficult to think of it like that. You're talking bout LCAs ("Last Common Ancestors") of extant (currently-living) species. While some LCAs just die out for some reason or another, it's more common that the LCA simply continued to evolve and become a genetic relative due to some sort of isolation.
Think of it like the in-betweeners coming to a fork in the road. Some choose right, some choose left. There isn't anybody left behind - merely two populations that are changing over time that were once one group until they don't really mate between each other anymore (or can't). Heck, even Biologists have trouble deciding at what point a population is considered a different "species" because of discoveries in the last 50 years - so right now a firm answer like "It takes 15% of the genome to change for a new species to emerge" isn't possible as it doesn't really work like that.
We'll get to it eventually, but for the time-being, it might be easier to say that everything currently living on Earth is an in-betweener of something else in the future. Everything in its current iteration will eventually die off, but not before something else emerges from our offspring which may or may not be significantly different from us due to however many genetic mutations our offspring have from us. It could be one that opens up a whole new realm of possibilities (like lactose tolerance) or an accumulation due to selective pressures (like Phoemelanin production and pale skin in humans [Redheads] to produce more Vitamin D3 at higher latitudes).

Your shark head diagram sort of says it all.

This sounds like a very basic question in evolutionary biology that often ask for a very long answer. But I think that you may get the answer you're looking for just if we ask you back how many inbetweeners would you expect to exist between the hammerhead shark and whatever is the closest currently living species of the hammerhead shark? If you had one more inbetweener would you still be surprised to not have more inbetweeners?
Your question might actually be "Why are there species rather than individuals that show a long continuum of various traits?". If this is your question, then the answer would indeed need to be fairly long and explain about the process of speciation.
You might want to have a look at this related post as well.
Edit
Studying a bit further the question of the hammerhead sharks, I discovered that there are actually 10 species of hammerhead sharks! You can find them here on the french wikipedia page
Let us know whether this comment/answer helped.

This is a great question (in the first para.). I don't usually upvote comments but +1.

Actually, yes. I would ask the question. Why isn't there a continuum of species? Why are there species at all? If the answer is long I'd appreciate if you could point me to some useful links so I could read more about it.

But I'm still not sure if this answers my original question. How did the blood shooting lizard get to be if for it to exists there had to be lizards that just bled from there eyes slightly? Any intuition tells me that those species would die out in a generation, let alone thousands of generations required for evolution to make the bleeding even stronger.

So, basically your post can be decomposed into 2 questions. 1) Why are there species rather than a continuum? 2) How can a trait evolved while the intermediate trait seems to be deleterious (deleterious=negative effect on the reproductive success and survival of the carrier). Did I understand your post correctly? If yes, I'd suggest you to split your question into two new posts (vote to close the current post in parallel). Note: The second question being fairly common, there might already has a post on this site that answers it.

Yeah. That's exactly right. Thank you for organizing my thoughts.

I know how hard that is to ask good questions when entering in a new field of knowledge $\ddot \smile$. I vote to close and am looking forward your coming posts!

What about developing a standard answer for questions like this which are too broad? You have almost done this and I think this is the right approach. Otherwise someone tries to answer and others try to close. Better yet, a standard comment with a list of basic texts?

How would you create a standard answer that fit all these "kind of broad questions"? We may want to discuss that in MetaBiology.SE. I am leaving soon I may not answer quickly to this discussion! Cheers!

@Remi.b I have posted a new question here: http://biology.stackexchange.com/questions/19762/why-are-there-species-instead-of-a-continuum-of-various-animals
And could you point me to those other questions that ask about deleterious traits? Or at least, what to search for.

@Darwin, you should read about something called a ring species. ie A continuous gradient/chain of populations that freely allow gene flow between adjacent population. However if populations at the ends of the chains are brought together, they cannot breed. The ends of the chain are different species... yet so long as every population in the chain is alive we have a something that could be considered a single species as gene flow while slow, is possible between the population of two ends via the intermediate populations.

However once one or more population in the ring goes extinct, the ring fragments and you get two or more species.

If an inbetweener offers a slight advantage to survival, and if the full-fledged trait even more so, then once the full-fledged population becomes sufficiently large, they will have the advantage and the inbetweeners will die out.