text:
Is mammalian vision processed as a sequence of frames?
I often read that people believe that human vision has an inherent frames-per-second rate (FPS) that causes stroboscopic effects - such as seeing the spokes of a rotating wheel apparently rotating at a different speed or appearing stationary when moving.
For example: in a Physics.SE answer to Can a “superhuman” move so fast that an average person cannot see them?

The human eye-brain visual refresh rate has an "effective frame rate" of around 30fps.
Have you never watched the rims of the wheel in a car next to yours? I can clearly recall many times watching as the wheels sped up how it appears to stand still then move backwards.

This surprises me as I would expect there is no synchronisation of neuron firing in the retina, that neuron firing rates would vary widely depending on light levels and that the brain has no need to process the continuous signals in fixed cycles or in cycles whose length is invariant.
I believe this question, or a good answer to it, would differ from What is the equivalent of shutter-speed in Human eye?
Is human vision in any way subject to a fixed frame rate of 30 FPS?

Short answer: no, there is no fixed frame rate or frame-based processing in mammalian vision.
Photons arriving at the photoreceptors at the back of the human retina interact with photo-sensitive pigments called opsins, and modulate their release of the neurotransmitter glutamate . The level of glutamate released from a photoreceptor then changes the membrane potential of the other neurons in the retina connected to the photoreceptor (bipolar cells, for instance). Signals are processed within the retina, then passed through retinal ganglion cells (RGCs), along the optic nerve, through sub-cortical structures and in to visual cortex.
This process occurs continuously, but all of the elements along the way have intrinsic time constants and other temporal constraints (number of photons required for opsin activation; recovery rate of the opsins in the photoreceptors; membrane time constants and refractory periods of neurons; synaptic delays; etc.). Persistence of vision (the effect underlying the perception of a movie as a continuous stream rather than a series of distinct frames) probably relies on the conjunction of many of these time constants.
Concretely, a flashed visual stimulus produces a response in (primate) visual cortex after around 30–50 ms (Maunsell and Gibson 1992). You can recognise and subsequently recall a lot of detail from a sequence of images flashed at around 100–150 ms per image [citation needed]. These are still not hard and fast definitions of the "speed" of vision.
Since we only learnt to produce movies as sequences of distinct frames, it's tempting to guesstimate the speed of human vision in those terms. Biology, as always, is more complicated.
As far as the "spinning rims" issue goes, there are many aspects of cortical and subcortical activity that tend towards oscillatory activity. In a system with an intrinsic frequency (for example, the neurons in the thalamocortical loop between LGN and primary visual cortex), providing an oscillatory stimulus can synchronise the system to the stimulus.
Many of the intrinsic time-constants I described above could result in a tendency to oscillate at some intrinsic frequency, and then be subject to phase locking due to a periodic stimulus close to that frequency.

While in human made cameras light sensor and any image processor are separate devices, in the living eye the first steps of image analysis begin in retina already as light sensing cells are part of the nervous system. The optic nerve carries pre-processed information and not the encoded original image to the brain. This pre-processed information is not segmented into frames.
The "image processing system" of the human vision would generalize a presented sequence of frames into logical continuous movement, even if the frame rate is as low as few FPS only. This does not mean the eye cannot see that is going on. Frame rates as high as 120 FPS are required to reach the inertia limits so that the flickering really cannot be seen.


text:
Common Ancestry of ETCs and ATP Synthase complexes
Rickettsiales are widely regarded as the ancestor of eukaryotic mitochondria through endosymbiosis.
Cyanobacteria are widely regarded as the ancestor of eukaryotic chloroplasts through endosymbiosis.
These two organelles bear striking similarities in terms of structure and mechanics. There seems to be plenty of information regarding speculation on the endosymbiosis that led from these free-living organims to the organelles. However I can't seem to find much on speculated relationships between these organisms in terms of common structures.
My Quesions : Are the electron transport systems and chemiosmosis simply ubiquitous phenomena in prokaryotes, or are these similarities evidence of highly conserved common ancestry? Or is there another answer?
Is there any information regarding the phylogenetics of Rickettsiales and Cyanobacteria. Do these two organisms belong to a single small clade or were these biochemistries (ETCs, ATP Synthases, etc) ubiquitous at some point and have simply been preserved in these two organisms today?

photosynthesis and respiration both use electron transport to generate ATP. However, in photosynthesis the proton is produced by photolysis of water whereas in respiration it is generated by oxidation of organic molecules, The ATP synthase is essentially the same. Also, the electron carriers like quinones and cytochromes are very similar. The different proton source in these two reactions must be a resultant of habitat among other factors.
Assuming that you already know these details, I am unsure of what exactly you are asking.

Rickettsia and Cyanobacteria are not part of a small clade that share these features.  ATP synthases are present across all domains of life, and they are all homologous, i.e. derived from a common ancestor.  The means its fairly likely that the last universal common ancestor had some form of ATP synthase.
ETCs and ATP synthases are part of the chemiosmotic theory put forward by Mitchell.  Whats beautiful about this mechanism is that you just need a single ATP synthase to make your energy, and it can be used regardless of your metabolism, be it a Cyano or a Rickettsia.  All you need to do is somehow couple your metabolism to a proton motive force across your membrane, and then you just let the protons fall back down their electrochemical gradient, powering the formation of ATP.
Organisms from all corners of the tree of life use this strategy, so this is not some special common feature linking the organisms that ultimately became eukaryotic organelles.  Its worth noting that there are alternatives to ETCs and proton motive force-based ATPases, you can make ATP by substrate-level phosphorylation like in fermentation metabolisms.

source: Stack Exchange

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

sort: votes


text:
Can all plants be reproduced through vegetative propagation?
I have learned that plants can be reproduced or propagated through vegetative parts but there is a question in my mind if we can each method for all  types of plants. I don't know if all  plants have cells which can proliferate and differentiate into other tissue types. Do these vegetative parts have such ability. Is it true for all of them?
Can we grow all type of plants from all vegetative parts( i.e, roots, stem and leaves)?

We ask that questions here show some evidence of prior research; as-is, your question is exceedingly broad. Can you share what you've learned already? What's the purpose of the question?

A point to start your research which challenges the assumptions that you're questioning would be chlorella - a single celled genus of algae with no differentiated cell types.

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


text:
How do mosquitoes know if they are going 'up'?
I have read articles that say mosquitoes detect humans through carbon dioxide exhalation and body odour. When we wave our hand around a mosquito, it usually flies away from ground (even if it initially moves towards it after immediate stimulus). How do indoor mosquitoes 'know' that they are moving 'up', that is, against gravity?
My hypotheses is that instead of detecting whether their direction of motion is against gravity, they somehow measure their distance from the ground but I doubt this because I chased a mosquito up the stairs and its distance from the steps remained almost constant. When I ran down the stairs, the mosquito still tried to swerve around me and move upwards.
If the above hypotheses is wrong, can you link to some experimental evidence as well? (Not necessarily experiments on mosquitoes)
What I could find

Honey bees
(Apis mellifica) were unable to fly normally and tumbled in weightlessness.
House flies (Muscus domestica ) mostly limited themselves to walking on the
walls.  When they did fly, they apparently could control motion in all three
axes, although flight only lasted for a few seconds.  Moths (Anticarsis
gammatalis) that developed in space, learned not to fly and preferred to float
without wing beat.  Whereas adults that were developed on Earth, then sent
into space, had problems controlling pitch.

This answer links to sources which directly consider the idea of the influence of Earth's magnetic field (not gravity) but looking at the comments, I am having second thoughts.

Invertebrate solutions for sensing gravity

Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.

Insects also use the skylight and horizon to maintain attitude. Did those experiments provide for that? Of course, it doesn't explain how insects fly indoors. They obviously integrate many methods.

Coordination between Cerci (on last segmet of body) to detect gravity; compound eye (can se 10-15 feet) ;vector memory of their home & surrounding and body organs (as mentioned in above comment of user:domen) to detect inertia (inertia inturn detects direction and acceleration)

We're looking for long answers that provide explanation, context, and include references to reliable sources. Don't just give a short answer; explain why your answer is right with appropriate citations. This is a good example of how to format references.

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


text:
What does it mean to say that egg derived vaccines are "cheap but slow to produce"?
A nature review of bird flu says:

currently available vaccines rely on inactivated strains of viruses grown in chicken eggs, which are cheap, but slow, to produce. Researchers are developing vaccines using mRNA technology...

A simple way to read this to mean something like "While egg based vaccines are cheap, the fact that they are slow means we should invest in developing vaccines using mRNA technology".
The timelime of egg based vaccine production is described here and summarised in the below graphic.  It takes about six months, but the first few are "Egg supply organisation", which could start now. and we can make billions of doses "cheaply".  We have a well established mechanism for selection and testing of the particular vaccine variant.  This timeline seems far preferable to anything involving developing vaccines using mRNA technology.
What does "cheap but slow" mean in this context?

Why would you think it is anything other than the reason you have in the last sentence?

This is a question and answer site about problems in biology. Your post, in contrast, is the expression of an opinion on methods of vaccine production, prefaced with a rhetorical question about the intent of an author in using a particular phrase. I therefore regard your question as it stands as off-topic.  You can make it on-topic by rewriting it addressing the question that concerns you directly: “Why is mRNA technology preferred to egg passage for producing vaccines for possible future pandemics?” or the like. Then it would be valid to suggest an argument.

@David My question is about the meaning of the particular phrase, used by the journal nature to justify a particular public health stance.  I added the details of egg based production because people thought my question was homework.  There is probably a reason for the use of the word "slow" when comparing these two technologies, whether that is related to the details of mRNA technology or egg based vaccines in this particular instance I do not know.

A question about the meaning of a phrase consisting of simple English words, and having no particular technical aspect is not an appropriate subject for questions on SE Biology. I am trying to help you present your concerns in an appropriate format, rather than just voting to close on these grounds, especially as you appear to understand quite well what the phrase means. It now seems that you wish to know how much slower propagation in eggs is than using mRNA and tissue culture. You might rephrase your question to make this your focus. But…

…first carefully re-read the article, which is not a review but a News item from one of Nature's correspondents. It does not attempt to "justify" anything, but reports the reasons given by various government organizations and associated scientists for decision they have made regarding vaccine development. As regards the advantages of mRNA technology given by one Scott Hensley, not only is speed cited, but the fact that "formulation can be updated to target emerging strains". Wishing to understand the reasons for such public health choices is fine, but trying to nit-pick a news article, is not.

In the context of a rapidly changing virus like Influenza (as that's what the article is talking about) the process is slow because no-one, including the experts, knows exactly which strains and variants are going to be around in the future.
The article notes that egg production takes some time to ramp up, but does NOT mention the work that is going on in the virology field of looking at the current strains of the viruses in the environment, both in humans and in birds and pigs. This work is carried out by a group known as the Global Influenza Surveillance and Response System (GISRS) at reference laboratories across the globe, including national influenza centres in each country, WHO collaborating laboratories, etc. In these laboratories the virologists determine the prevalence of strains of the virus that are present now, as well as which strains were present in the last year or more, and, critically, look at the immune patterns of the human population and how strongly viruses produce an immune response in people. These patterns are different in the Northern and Southern Hemispheres of the world. You can look at some of the information generated on FluNet.
This work involves screening millions of samples, determining the subtype (HA and N components), genome sequencing (now commonly done) or sequencing specific regions in the genome (previously), and then maybe looking at antigenicity of the virus itself if it is significantly different to ones not already looked at. This data is then shared globally through GISAID. The WHO teams will be discussing which viruses are looking like being present and developing stocks using GMP for distribution to the vaccine manufacturers.
With this information, the WHO vaccine team meets formally  to look at the virus and immune data and makes an informed decision on which viruses to include in the vaccine for the coming winter in each hemisphere. At this point, the exact virus component in each vaccine is released for the manufacturers to start growing it in the eggs (D0 in your graph), which actually takes about 6 months from the WHO vaccine decision meeting until release for the general population (note mid Feb to July/August in your figure), making it about a year in total (from D-6 to D0 to vaccine release at about D+6).
Egg production isn't as simple as mixing some virus with egg and taking the resulting mix to inject into people, it first needs to be purified (to remove egg components), made into subunits, tested to ensure that it has the right immunological response, etc. This all takes time. In addition, you need a LOT of eggs to make the amounts of virus needed for the vaccine. Some viruses don't grow as well as others, so you need to use more eggs. The eggs themselves also need to be the right age, with a chick of the right age (10-11 days post-fertilization) to produce a decent amount of virus; older or younger means less virus. Doing this sort of thing on an industrial scale is difficult!
In contrast, mRNA vaccines are in some manner simpler and more adaptable. First off, you are starting with pure substances for synthesis of the mRNA, this means that you don't need to go through a lot of the purification that an egg based vaccine does, and it can all be produced in a sterile environment, with much less of the messy biological side involved in eggs. In addition, these very pure inputs are often expensive to produce themselves, which adds to the cost compared to cheap eggs.
The adaptable bit means that you can change the mRNA relatively easily within the vaccine itself - say you had a variant with a specific mutation that gave a stronger immune response and you wanted to include that - simply plug that mutation into your pipeline and you have it shortly (in theory at least). Of course, you would still need to do the immune response testing etc, without the need to grow whole new viruses, generate stocks, distribute them, then grow new vaccine in bulk.


text:
Quantitative Traits Genetics

Can someone please help with this question? I'm not so sure whether part A should be 11 inches or something else. Also, is part B correct

Question a

The only possible genotype that brings a phenotype of 12 inches is: $AABBCC$. Similarly the only possible genotype that bring a phenotype of 6 inches is: $aabbcc$. In consequence the offsprings can only be: $AaBbCc$ which measure $2+1+2+1+2+1 = 9$ inches.

Question b

Now the question is: if we breed two $AaBbCc$ how many offsprings measure 11 inches? Because there are three bi-allelic genotypes you have $2^3=8$ possible gametes and therefore you have to draw a 8x8 punnett square. Doing so, just count the proportion of offsprings that measure 11 inches. You can reason slightly more logically and get a faster answer. To measure 11 inches you need to have only capital letters in your genome except at one position. In consequence, if your father gives the gamete $ABC$, you mother should give the gamete $ABc$, $AbC$ or $aBC$. You can inverse the role of the father and the mother and it works as well. Therefore, you have 6 possible combinations that give rise to an offspring that measure 11 inches. Because there are $8 \cdot 8 = 64$ possible combinations, the proportion of offspring that are 11 inch-long is $\frac{6}{64} = \frac{3}{32} = 0.09375 ≈ 0.1$. About 10% of your F2 individuals are 11 inch long.

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


text:
Need to make a library of mammalian coding sequences
I want to clone ~100 different coding sequences from human or mouse into an expression vector to analyze phenotypes in tissue culture. I can do all of the steps, but I'm not sure what I should use as the template for my reactions. Ideally, I would purchase a pool of full length cDNAs from a bunch of organs, and amplify from that. Less ideally, I can generate cDNAs myself, from multiple organs and pool them. Does anyone have suggestions on a template source?

If you plan to take one isoform for each one of the genes, then I see no point in amplifying them pools of tissues.

The goal is to do a miniscreen for proteins of annotated with a specific function (there are about 100 genes). The idea is to automate the task as much as possible, without spending too much time choosing isoforms or fusion points.  I just don't have experience doing this, so I'm not sure if such libraries exist, or if I essentially need to start from scratch from cDNAs and gene specific primers. I figures that by pooling cDNAs I would most likely amplify the most abundant isoform.

Verify where these transcripts are generally present (this should not be difficult for common organisms)
If they are all expressed in a certain tissue use cDNA from that tissue
If not then pool the cDNAs from different tissues such that all genes can be amplified
cDNA libraries (including whole organism) are also available and you may obtain them from the nearest repository (I guess NCBI also provides).

Some other things you can do:

Ask the primer synthesis company to provide primer sets it in a
96well format.
DNA synthesis is also a decent option (it takes something like $0.5
per base pair), but that can be expensive if your cDNAs are huge.


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

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

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

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

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

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

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

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

@Ohad Dan: glad you liked it!


text:
What is this freshwater microorganism?
Can anyone help us identify this microorganism?
Location: muddy pond water in the Santa Monica Mountains.
Size: For size reference, I think that's a euglena on its lower left.
Behavior: It was moving around, getting caught up on various other microorganisms and dragging them with it.
We are very new to this, and it doesn't look like anything else we've seen so far. Thank you!

Paramecium or Stentor? just a wild guess based on size

Thanks for the reply! We did see some paramecium and they looked different to me. The only stentor images I'm seeing have a different shape. Are there more oval-like stentors? This has that zipper-like groove all along the bottom of it, and a neat row of round brown dots along the groove.

Stentors can look oval sometimes. However, in case you saw them moving around, they should have their typical 'trumpet' shape. If you say it has a groove then I tend more towards Paramecium. What makes you think it looks different to the ones you saw?

The ones I think we saw on the same slide were more clear. We could see distinct vacuoles and an oral groove that went halfway across it. They also were less peanut shaped. And this unknown organism was rigid when it moved, so it just looked like a floating log, if that makes sense.

Thank you for the the new photo and descriptive comment. I think it is Euglena sanguinea. The color comes from astaxanthin. They are super interesting when it comes to light adaptation and their production of the toxin euglenophycin.


text:
Is there any running experiment to selectively breed non-human smart animals?
Is there any running experiment to selectively breed non-human smart animals?
I saw some scientists made overly tame and friendly foxes using fust selective breeding. Could it be possible to add the trait of intelligence to say giant rats?
Could it be possible to do so using gene modification?
Were there any attempts to breed such an animal.

There are a couple of interesting genetic candidates towards higher cognitive function. Here they produced transgenic monkeys to test this. I am not sure about any 'breeding' experiments. Depends on how you measure/define being "smart" in an animal model.

@MaximilianPress - The OP is familiar with the fox farm experiment; it was referred to in his question. Re. dogs, I think you're correct. OP: I used to breed Border Collies, considered by many to be the most intelligent dogs in the world (I'm a bit skeptical, but...). The majority of good BC breeders breed to improve the breed, not for confirmation (that's the AKC route). Intelligence is part of that. I have had some scary-smart BC's, including one who understood syntax. Look up Chaser, who had the largest recorded animal vocabulary and also understood syntax and concepts... wow!

@anongoodnurse fair enough, reading comprehension is always a challenge. deleting.

The question is rather hard to answer as the measure of intelligence can be defined within many different aspects. I am not aware of specific 'breeding' approaches in this context.
Moreover, it also differs depending on the animal models. What I basically want to say is that intelligence is an emergent phenomenon from vastly complex molecular and environmental factors.
One example of a 'measure' is the cogntivie factor (g) both in humans and animals.

Could it be possible to do so using gene modification?

Nevertheless, there are genotypes related to cognitive function. Famously FOXP2 was coined the "language gene". (Spoiler: it's not that simple).
In humans, this article summarizes such aspects from a genetic basis.
To give another example – as I commented before – researchers looked at transgenic monkeys to study brain development. In this study, the transgenic monkeys showed better short-term memory and shorter reaction time compared to the wildtype.

I think you will have to take an answer here that is not the answer you wanted.  I truly believe that there is no secret base making an army of intelligent dingo soldiers.
We are currently at the point where we have a bunch of different approaches to even answering what intelligence is. Each different theory of intelligence have created a different effort, each with its own flavor.
Here are some examples:
Domesticated Foxes.  Socializing with human beings is not exactly intelligence but Russian biologist Dmitry Belyayev wanted to show that evolution of new traits could happen with selective breeding.  Starting with some wild type foxes , he would test foxes for their calmness or interest in people.  Animals who were did not score well in tameness were put in an anti-social group (this is social to people) animals who were tame were put in a social group.  After 10 generations the animals were showing significant signs of social acceptance of human beings, seeking their company.
A lot of work assumes that some animals are intelligent and try to ask them about that.
Talking Chimpanzees. Early efforts to get an ape to talk were successful but limited by the physiology of the vocal chords in primates.  Studies with primates focused on teaching them sign language.  The champion to date is Koko who had 1000 signs in her vocabulary and could talk about what happens after life.  it was estimated her IQ was 70-95.  Kanzi, a bonobo used a symbolic keyboard and was able to use 400 symbols.
Conversant Parrots. Alex, a grey parrot was the subject of a 30 year study where he was able to communicate with researchers and passed cognitive tests such as identifying objects on command.
Talking to Dogs
There is a lot of research on how humans interact with dogs and cats. They can hear and understand language. They watch humans for social cues.  A lot of the researchers think they are capable of cognition.  More recently many pet owners are using panels of buttons (like used with primates) to get the animals to try talking.  its eerie.


text:
Happiness from sunlight is from IR or UV?
I found this study that shows that UV light makes our skin release feel-good endorphins. This is the pop-sci writeup.
On the other hand, it seems like IR is what causes the sense of warmth in the skin when you feel sunlight.
So are there two effects that make us happy when we see the sun? One being physical - IR heat - and the other chemical/biological - endorphins from UV? Is one more important than the other in that feel-good sensation?


text:
Why don't we see new diseases more often? Or, ever?
It seems like every disease we ever hear about is something that's been around since ancient times, since thousands of years ago. Of course new diseases were catalogued over the course of the past couple hundred years, but they weren't actually new diseases-- they just hadn't been previously classified/identified.
Given that (in my understanding) viruses and microbial lifeforms can evolve and change considerably more rapidly than higher order organisms, why don't we often/ever hear about completely new diseases that have never been seen before? Diseases that may have only just been born.

You might find this interesting: http://royalsociety.org/events/2006/plagues-parasites/?gclid=CLD5yoOTs70CFedV4godnwUA1A#

Evolution doesn't really work like that, everything is a slightly different version of what we had last year, it's only on the very long term that you can see major change. New flu arrives every year, but we still call it flu because it's only a little different

HIV anyone? It's new in the sense that it only came to infect humans recently.

The terms about we are speaking are relatively long. There are a number of pathogens (mostly viruses) which are relatively new. Among them are SARS and MERS, HIV, Ebola, Marburg, Hendra and so on. These are mostly viruses which spill over from their reservoir hosts into humans. There is an excellent book on that topic, which I can really recommend. It is "Spillover" by David Quammen.

I think the answer is completely given in the comments. One could group these comments to make an answer and add some link to seasonal flu or to new pathogens.

Zoonosis is another term for spillover. BTW @Chris, I loved reading spillover :)

@WYSIWYG I know :-) Another interesting reading: http://stories.weather.com/virushunters

The first thing to note is that nothing is truly new, everything is a slightly different version of what existed previously, it's only on the very long term that you can see major change. Mutations occur continuously and new variants arise often. For example you need a new flu shot every year due to the high mutation rate of the influenza virus but we still call it flu because it's only a little different.
While disease causing organisms evolve at a relatively slow rate new diseases can appear suddenly when the effect on humans suddenly changes; the most obvious example of which is when a disease changes host species. For example the sudden appearance of HIV when Simian immunodeficiency virus (SIV) "jumped species" to infect human, most likely through the consumption and processing of Primate meat. While HIV appears new it is again ancient in the sense that it has caused a similar condition to HIV/AIDS in many African non-human primates for a significant period.

New diseases appear all the time. Some of them have been around for ages but are detected due to improved surveillance, while others appear due to shifts in host. Others are detected because they spread geographically into a region where they are either more conspicuous or just more highly reported/investigated, or because new hosts are introduced into their original range.
For example, in the last few years alone both the snappily-titled arthrogryposis hydranencephaly syndrome (caused by Schmallenberg virus, a previously unknown bunyavirus) and bovine neonatal pancytopenia (aka 'bleeding calf syndrome') have been discovered. Both were first detected in Europe, where veterinary surveillance is among the most intense in the world; Schmallenberg was detected because of syndromic surveillance in use in NL and DE. When bluetongue first emerged in Europe a slight difference in primer sets used in Switzerland detected a novel related virus that was called Toggenberg orbivirus (later classified as a new serotype of bluetongue virus). This may have been circulating in Europe undetected for many years and it's only by chance that it was detectable by the Swiss primer set (although it doesn't appear to cause clinical disease).
Incidentally, bluetongue and two other high-impact livestock diseases originating in sub-Saharan Africa (African swine fever and African horse sickness) appeared at the end of the C19th when European settlers introduced 'improved' breeds of livestock into the region; before that the pathogens were circulating subclinically in the natural hosts (warthogs for ASF virus, zebra for AHS virus and various ruminants for BT virus).


text:
What causes a small bump in the arterial pressure plot?

In my book there is a plot of the arterial pressure against time.
From the plot, during heart contraction, there is greater pressure on the artery and during heart relaxation, there is lower amount of pressure on the arteries.
This makes sense because P = F/A, the surface area of the heart is smaller when it is contracted versus when it is relaxed, hence greater pressure.
But why is there a small bump while the pressure is decreasing from systolic pressure to diastolic pressure?

This bump is related to the closure of the aortic valve as a reaction to the retrograde blood flow which in turn gives small change in blood pressure.


text:
What is a complex?
In my text book it says that "Troponin" is a complex of Troponin C, I and T. In this sense, what is the relation between Troponin complex and C, I, T?

http://en.m.wikipedia.org/wiki/Multiprotein_complex

Even a simple "google question" needs to be answered (ref). Also, it is not necessarily easy to go from the word complex that is used everywhere the the biological concept of protein concept. Let's not be too harsh :)

This is a homework question, please elaborate.

How about a question from a robotic engineer who does not know anything about biology but wish to understand how the muscle works so to make better robot arms?

Sounds like a very exciting project! $\ddot \smile$

@Remi.b no, they do not need to be answered. If they are answered, they should be answered correctly, which I agree to, instead of posting a link to LMGTFY. However, I think canadianer's comment is a completely sufficient answer, and after it the question can be closed as homework. I don't think this site should be for explaining every single piece of terminology (especially extremely common terminology) that is come across in a paper or textbook. A very important part of learning is being able to find answers for yourself, and not just asking someone to answer it for you.

@Remi.b - how on earth did you generate that smiley?!

ha ha \ddot \smile gives you $\ddot \smile$

The word complex in your sentence designate a protein complex, also called multiprotein complex.
A protein complex is a group of two or more polypeptide chains that bind together to make up a functional unit. A complex can be made up of similar polypeptide chains or totally different polypeptide chains. Proteasome, Metabolon or hemoglobins are examples.
For more info, have a look at wiki

Are they binded through electrostatic attraction or some sort of chemical compound? How are the "polypeptide chains" connected to each other? i.e. intertwined together

@IllegalImmigrant For all complexes, various intermolecular forces play a part: electrostatic, van der Waals, hydrophobic. For some complexes, the polypeptide chains are connected by disulfide bonds (covalent). Technically this makes the polypeptide chains one molecule, but they are still called complexes because the individual chains are produced and can sometimes act independently.

There is this sentence in the introduction of the wiki link: Proteins in a protein complex are linked by non-covalent protein–protein interactions. Also, there is an assembly category in the wiki link. I would expect that different kinds of forces leads the the binding of different pair of proteins. I don't think there is a general rule for that but I know little about biochemistry.

@canadianer This is pretty mind blowing to think about these tiny little chains in our body is arranged in a way that it binds to other chains in a manner that forms a larger structure called a complex without being pulled apart by trillions of chains, molecules and atoms. Hard to believe that something like this exist but this is the human body after all.

@IllegalImmigrant Yes, biology is the most interesting and generally best science ;) When you step back and think about this stuff, it's amazing.


text:
What do you call that part of the muscle that connects directly to the bone?
When you open up a chicken leg or a clam and you remove the meat, there is this little part that is connected to the bone and is not easily scraped off.
What is this part called and what mechanism does it use to connect to the bone or the shell?

The tendon is the part of the muscle that connects directly to the bone.

A tendon (or sinew) is a tough band of fibrous connective tissue that usually connects muscle to bone and is capable of withstanding tension. Tendons are similar to ligaments and fasciae; all three are made of collagen. Ligaments join one bone to another bone; fasciae connect muscles to other muscles. Tendons and muscles work together to move bones.

The image was taken from the wikipedia link.

The part of the bone to which the tendon connects is called esthesis

@CRags you mean enthesis?

Sorry spelled wrong, you are correct, it's enthesis


text:
What is meant by drug tolerance?
What is meant by drug tolerance?
This question is in my biology textbook for IGCSE and I have no idea what drug tolerance is. It would be very helpful if someone could clarify. Thank you.

Have you read the article in the Wikipedia about it? http://en.wikipedia.org/wiki/Drug_tolerance Do you have specific questions about it?

Yes I did but I still couldn't get a clear picture of it in my head.

Would you happen to know another site with a clearer definition?

Can you tell us what you find unclear in this definition? This makes writing a meaningful answer easier.

"when a subject's reaction to a specific drug and concentration of the drug is progressively reduced, requiring an increase in concentration to achieve the desired effect."

Does this mean the more the user takes the drug, more of it is needed for him to achieve a high?

It basically means, that the body gets used to certain drugs and that you need to raise the dose to reach an effect. This is for example true for a number of anesthetics or pain medications as morphine.
Permanent application leads to a down-regulation of the drug receptor (for morphin this is the mu-opiod receptor) and the activation of counteracting signaltransduction pathways. To still get an activation you will need a higher drug concentration.
For more details have a look at these articles:

Opiate tolerance and dependence: receptors, G-proteins, and
antiopiates
Cellular neuroadaptations to chronic opioids: tolerance, withdrawal
and addiction


text:
Why are mosquitoes repelled by smoke?
A well known way to have a rest of mosquitoes during camping is to stand in the fire's smoke. Moreover, I learned recently that shepherds in certain regions of Africa use the same tactic for cattle. They make smoky fires and cattle gathers in smoke to get rid of mosquitoes.
Why humans and cattle can stand smoke, but mosquitoes can't? Does this technique work for other kinds of insects?

Remember mosquitoes have very sensitive CO2 sensors. They track their prey using CO2, and smoke has lots of CO2 which makes mosquitoes blind, I presume.

Sorry but mosquitoes aren't attracted towards the smoke. This is because they get attracted toward Carbon Di Oxide

There is little hard evidence on whether smoke acts as a mosquitoe repellent. A literature review done by the WHO (Biran et al, 2008) on smoke and malaria show that evidence is mixed, at least when it comes to long term protection and protection from blood meals from firewood smoke. Their review also notes that few scientific studies have been done on the topic, and they report results from one experimental and a couple of observational studies. However, they do note that burning particular plant materials (based on traditionally used plants) may be effective (see e.g. Pålsson & Jaenson. 1999).
These results also doesn't preclude that very heavy, temporary, smoke may be effective to get rid of mosquitoes ("... during camping is to stand in the fire's smoke...") - that this can be effective is certainly my personal experience as well.

I imagine almost all insects would be repelled by direct signs of active fire.

Mosquitoes have olfactory receptors. Certain chemicals acts as repellent.
See this wikipedia page for an explanation about insects repellent mechanism.

Can you possibly elaborate on the mechanism? And the linked page doesn't even contain any information about smoke or its constituents.

citronella oil page on wikipedia here says : Consists of geraniol (18-20%), limonene (9-11%), methyl isoeugenol (7-11%), citronellol (6-8%), and citronellal (5-15%) for one type and Consists of citronellal (32-45%), geraniol (11-13%), geranyl acetate (3-8%), limonene (1-4%) for an other. The mechanism can be elaborated by following the cited sources like [number 9 for example](http://link.springer.com/article/10.1007%2Fs00018-011-0745-z]()

Mosquitoes aren't actually repelled by smoke. They are repelled by burning citronella oil. Citronella contains certain chemicals that naturally repel the dengue fever mosquito.

that's a probable mechanism, but not the reason. Why are they repelled by citronella oil?

All insects have a mortal fear of smoke because it is a harbinger of flames and flames - for an insect - means instant death. They have no mechanisms at all that are capable of regulating their body temperature sufficiently to survive direct flames.
Added:
Consider a population of mosquitoes (or any flying insect for that matter) that successfully develops a smoke-avoidance response. In an environment where forest fires are common and smoke is therefore a clear precursor - would this population have a better chance of survival than another that does not? I think you could only answer yes.
It merely remains to prove that it is possible for a population I have described to develop. Well - the presence of this question on this board proves that it is possible. I realize this is a slightly weird form of proof by induction but you have to admit it works.
Sorry - no references or citations - just a "because evolution".

Is there any scientific evidence to back up this claim?  It's plausible, but "fear" is a bit of a stretch.

Less "fear" - more "death follows swiftly". Kinda like "I smell almonds ... should I drink this or put it down?"

Yes, but you (or the cyanide drinker) have more than just a couple of ganglia strung together and a lifetime of experience (i.e., would someone not knowing the fact about that odor actually be repulsed by it).  Anyway, again, like I said, a plausible explanation, but evidence always helps.

Perhaps my additions will help.

Lots of species of insects are attracted by fire and smoke (forest fires), since their larvae develop in burned wood, e.g. the longhorn beetle Acmaeops marginatus

Unfortunately, this is an example of a just-so story https://en.m.wikipedia.org/wiki/Just-so_story.


text:
Excretion of various wastes and water requirement
A common fact is that Ammonia, Urea and Uric acid are the most common excreted metabolites and their removal needs varying amount of water, highest for ammonia (hence suited only for aquatic animals) and lowest for uric acid (suited for desert animals). Why is this so? Is it because of different solubility of these compounds in water or their toxicity? If it is the latter, how would excess water reduce the toxicity of a compound? This is a bit over-simplistic question, but I want to understand the tradeoffs involved in selecting the mode of excretion, ammonotelic, ureotelic, uricotelic.

you can also look at it in a molecular point of view.. Uric acid has more atoms of nitrogen (4) per mole; then comes urea (2) and then ammonia (1)

Ammonia is more water soluble and also more toxic than either urea or uric acid but it is energetically less expensive. So, in regions where deficiency of water is not a problem, ammonia is an excretory product. Where water is scarce urea or uric acid is the excretory product but it is energetically more expensive to manufacture them. So, you can see an obvious trade off between energy expenditure and water conservation.
You can refer to any introductory biology book like campbell for further reading.
UPDATE :
Ammonia    : Most toxic , Easily Soluble , Less Energy Requirement
Urea       :Moderately toxic , Moderately soluble , More energy requirement(As needed to be processed from ammonia
Uric Acid:Least toxic , Least soluble , Highest energy requirement ( As needed to be processed from ammonia )
It is obvious now what tradeoffs are involved.
The only tradeoff not deducible from above is that of the eggs/youngs. In birds, eggs are not permeable for water so the best option is to excrete waste in form of uric acid so that high concentration of waste does not build up. Uric acid is excreted in form of solid palette which can stay in the egg without any harm.
We can also think of tadpoles which live exclusively in water and so they excrete ammonia but the frogs live both in land and water and so while on land they excrete urea as dessication is the main problem there.

it would be nice if you provide some references (or explain a little bit).

This was helpful, and settles the tradeoffs part. But, Can you elaborate on why ammonia is the most toxic, and uric acid the least?

@satwik pasani Well, I asked this here at stack exchange but couldn't get an answer.

By the way, I do remember reading about ammonia toxicity in Lehninger biochemistry. I will try finding more about it !

One more thing, I haven't ever even thought about  why  uric acid is less toxic. Interesting question ! Will search it out.


text:
Haploid eukaryotes?
I was wondering whether there are any eukaryotes which never have a diploid phase. I can't think of any. Fungi have diploid stages, and I know any sexually reproducing organisms will have at least transient diploid stages (I am not referring to such transient stages- I mean extended diploid stages so I am counting as a 'haploid' organism one that only ever has two sets of chromosomes for a very short time while it undergoes meiosis.)

what about bees, males are haploid from the gamete stage.

Some apicomplexans such as Plasmodium spp. are haploid during their asexual stages. The organism spends more time (at least in the human host) in the asexual stage than sexual. source

Plasmodium spp. are haploid in both human and mosquito hosts except for a brief stage in the mosquito midgut where two haploid malaria gametes present in the mosquito's blood meal fuse to form a diploid zygote. This zygote immediately undergoes meiosis to generate four haploid cells that continue in the haploid form, reproducing through mitosis, until several thousand are present in a small sac, the oocyst, attached to the gut wall.

“Sexual” Population Structure and Genetics of the Malaria Agent P. falciparum

Welcome to Biology.SE! This looks like a good answer, but answers are much more likely to receive a favorable response if you include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion. This is a good example of how to format references. ——— You may also want to take the [tour] and then consult the help pages for additional advice on [Answer] effectively on this site. Thank you!

To offer a more multicellular look on life: there are many Hymenoptera species that are haploids their whole life. Many Hymenoptera are haplodiploidy meaning that one sex's life cycle starts out as diploid zygotes and the other sex's life cycle starts out as haploids. Many male bees, ants, wasps, and etc start their life as an unfertilized haploid eggs and remain haploid until their death. Of course, these haploid males cannot be made without a diploid female so this example may technically break your rule.


text:
What are some uses of oxidative/reductive power inside cells?
I know respiration and photosynthesis are based on oxidation and reduction, and the formation of NADH and NADPH in them is very important for many cell processes. I know that NADPH, for example, is used in the CBB cycle to fix carbon. However where else are oxidation and reduction reactions needed in cells? I can think of an example for oxidation: getting rid of toxic products. For example, alcohol dehydrogenase in the liver oxidises alcohol to acetaldehyde. However I can't think of much else, and i'm especially stuck on ehy reductive power is useful in cells.

This topic is quite broad, excluding energetic metabolism, there are still many reactions that use redox equivalents, whether NADH, NADPH, or FADH. Here are some paradigmatic illustrations.
Xenobiotic metabolism

Oxydation of substrate : as you mentioned, alcohol to aldehyde to carboxylic acid. Generate reducing power. (The alkane oxydation shown below occurs in bacteria)

Mono-oxygenation : hydroxylation of a substrate with $O_2$, with the other oxygen atom reduced to water. This proceeds as follow with CYP450 enzymes :

Regeneration of oxided gluthatione

Anabolic metabolism
Basically every time there is a need to create/remove a double bond, or move from carbonyl to aldehyde to alcohol and back, redox equivalent are used.

Fatty acid elongation : as this proceeds with acetyl-CoA as carbon source, intuitively one sees the need to reduce the carbonyl to obtain an alkane chain.

HMG-CoA Reductase (HMGCoAR) catalyses the commited step in cholesterol synthesis.

Synthesis of prostaglandins from arachidonic acid. (More generally, any lipidic mediator)

There are many, many more examples. You may want to check out the Wikipedia page for NADH, NADPH, FADH, or the list of enzyme that use them (1, 2, 3)
All illustrations from Biochemical Pathways, G. Michal & D. Schomburg, 2nd edition, Wiley


text:
Retrograde/anterorade transport; kinesin/dynein; COP1/COP2; Endoplasmic reticulum/Golgi
I am getting slightly confused with all of the terms above and was wondering if someone could see if I have got this right:

I think transport from the ER to Golgi is almost always from the plus end of a microtutbule to the minus end, and therefore is carrier by a dynein. I think this is signalled by a COP1 protein, which can attach to the dynein for transport. I think that this is retrograde trnsport as it is from the plus end to the minus end, however this I am really not sure about.
Conversely, I think that transport from the Golgi to the ER, being from the minus end to the plus end, is carrier by kinesis and therefore the COP2 protein which attaches to the kinesis carries these vesicles. I think this is an example of anterograde transport.

My confusion lies in the fact that

I am not sure whether retrograde and anterograde transport refer to movement from plus and to minus end of a microtubule or vice versa (respectively) or whether they refer to general motion of cargo into and out of the cell (respectively). For example, if a vesicle was being transported from the plasma membrane to the Golgi and then to the ER, the first part of this journey would be along the plus end to the minus end of the microtubule, carrier by dyneins; the second part of the journey from Golgi to ER would be from minus and to plus and and therefore carried by kinesis. Would this transport therefore initially be retrograde and then anterograde, or do these terms simply refer to the general direction of motion of cargo into/out of a cell and therefore this whole motion would be described as retrograde?

Secondly, if I remember correctly my lecturer said that one of the COP proteins takes proteins from the Golgi to the ER and the other takes froteins from the ER to the Golgi to the plasma membrane. This is confusing me because it would mean that the same COP protein would take a vesicle from plus end to minus end of a microtubule from ER to Golgi, and then from minus end to plus end from Golgi to the plasma membrane, which surely can't be right as the same protein should not be recognised by the two different motor proteins, right? However if it were the other case, that say COP 1 takes vesicles from ER to Golgi and COP 2 takes them from Golgi to ER OR from the Golgi to the plasma membrane, what would distinguish whether the cargo was taken to the plasma membrane or back to the endoplasmic reticulum?

Thank you in advance!


text:
Chromatids in metaphase?
Please see the following picture:

In my book, the author claims that these chromosomes are in metaphase (a metaphase stopped by cholchicin).
I don't understand why they don't have two chromatids...A chromosome looks, by everything I've learned, like TWO chromatids (http://i60.photobucket.com/albums/h1/GameMaster57/Chromosomestructure.jpg) and should be together in metaphase. These chromosomes only look like chromatids to me (1 of 2 pairs).
Have they been separated?
I am also asked to specify which chromosomes are from the father and which are from the mother. How would I go by doing that?
Thank you.

I would have guessed it's metaphase of Meiosis II but there should be only 23 chromosomes in that case.

The chromosomes in your picture do have sister chromatids, they are just very close together. A chromosome needs to pass through replication before it can compact into the typical metaphase chromosome shape depicted above. When I prepare metaphase chromosomes, I usually see a mixture of chromosome sets where the chromatids are close together (like above) and clearly separated. I think this is related to the time each metaphase has spent in the colcemid block-the longer the cell has been blocked at metaphase for, the longer the enzymes that work to separate the two chromatids have acted on it. Also chromosomes keep getting more and more compacted during the colcemid block-if you leave them for too long, they become a lot smaller.  This paper has very cool pictures showing the links between the sister chromatids:
http://www.ncbi.nlm.nih.gov/pubmed/18461479

There are two important terms to note:
Sister chromatids
Homologous  chromosomes.
Sister chromatids are visible during most phases of mitosis, but not rest of cell cycle.
colchasine is an inhibitor of micro tubules so it prevents the chromosomes from 'liningstrong text up" during metaphase hence it arrests  at metaphase and the chromosomes are scattered all
Over the cell.
The spindle also helps withpairing up sister chromatids (for each homolog) so that each new daughter cell gets a complete genome. Since the spindle is not intact the chromatids are not localized.

is it "liming up" or "lining up"? I have never hear the word "lime" before, but it exists, so it may be just my ignorance (both English and chromatid processes).


text:
Why use creatine phosphate?
We use creatine phosphate as an energy storage to resupply ADP with a phosphate group as our muscle cells only contain about 2-5 mM ATP. But why doesn't the muscle cells just keep 20-30 mM ATP instead of 20-30 mM creatine phosphate?

Because all available ATP will likely be quickly spent by various cellular machinery.
If there was 20-30mM of ATP, what would stop muscle from contraction and how could you keep ATP level constant at rest, be ready for rapid movement? By blocking all myosin? This creates enormous regulatory problems for the cell.
Phosphocreatine buffers energy for a period of time when it will be actually needed. Having buffer allows for more robust control of energy spending, for example via regulation creatine kinases and other enzymes. Just by activating single enzyme you then start rapid conversion of ADT into ATP via phosphocreatine.


text:
Chromosomal translocation notation
A reciprocal translocation is denoted for example: t(4;12)(q32;q24) indicating that q32 on chromosome 4 being swapped with q24 on chromosome 12 if I understand this correctly.
My question is: How do I know whether this is a balanced or an unbalanced translocation?

This translocation is balanced: if it was not there was a specific sign for specific unbalanced event, for example "del" for deletion or "+" and "-" signs etc.

Chromosomal aberrations have defined notations you can find here.
The notation rule for multiple genetic abnormalities is to concatenate them. In the presence of an unbalanced translocation two abnormalities will be indicated as you have both a translocation and another event (e.g. deletion, duplication, ...).
In your example, as no other abnormalities/events are indicated, this is a balanced translocation.


text:
What is the result of meiosis?
Is the result of meiosis ONLY the sex gametes (male and female) which later meet to form a somatic cell?
Sometimes I feel as if my book is hinting towards meiosis is the process where sperm cells meet oocytes?? I'm a bit confused.

In principle, Meiosis is only the process in which the haploid egg or sperm are generated. Have a look at this figure, which shows Meiosis I and II (from the Wikipedia):

During Meiosis I homologous recombination between homologous chromosomes can happen, the chromosomes are then distributed normally among the daughter cells. In Meiosis II the cells split again and here the sister chromatids are divided and the haploid gametes form.
In the oocytes the process is in principle the same, but the cells get arrested in the so-called diplotene stage of Meiosis I (picture from here):

In the diplotene stage the chromatin is decondensated and transcriptionally active, this helps maintaining a correct chromosome structure, as the diplotene stage can last up to 50 years. When the cell receives the hormonal signal to enter the fallopian tube, Meiosis I is finished. The resulting cells are not divided symmetrical, building one big oocyte and one polar body containing the second set of chromosomes. Most vertebrate cells are arrested in this stage again until they are fertilized. Then another asymmetrical division is done, leading to a haploid cell with two polar bodies. This oocyte is then fertilized.
This process can happen almost at the same time in a lot of vertebrate species, including humans. This is probably what was meant by your textbook.
For further reading I can recommend: Meiosis and Fertilization from the NIH bookshelf.

It should be notes that meiosis is sometimes arrested in eggs until fertilization.

You are right and I should have looked into the Alberts directly :-) Thanks for the notification.


text:
Why does a "cascade" of events happen during signal transduction?
I've been watching some videos on signal transduction and it says that because there are enzymes being activated by the signal, then there is a "cascade" which happens afterwards...I don't understand why?
Thanks.

Is your question "Why a long cascade instead of more simple, shorter cascade?"

There is one main reason: Amplification of the signal. You can start a signal downwards the cascade with relatively few receptors which need to be activated which allows even for weak signals to be translated into the nucleus.
This figure shows this for G protein coupled receptors (from here):

For example one molecule of cAMP can activate many molecules of pKA until it's hydrolysed which in turn can phosphorylate many other protein molecules.
For more information you can read the references articles (at least the introduction) and follow the references in them.
References:

Ultrasensitivity in the mitogen-activated protein kinase cascade
Noisy signal amplification in ultrasensitive signal transduction

Ok I think I get it now. It starts with ONE ligand, the epinepherine.
However it says that after the ligand binds and thus activates the G protein, it has 100 molecules activated? I thought that 1 ligand activates 1 G protein?
I think I'm a bit unsure on what exactly the G protein is and what the G protein RECEPTOR is?

No, 1 ligand activates one receptor. The receptor in turn binds inactive G-proteins and activates these (as long it is active himself). The activated G proteins are released from the receptor and activate downstream targets of the cascade. This is the first step of amplification.

So the G proteins are not on the membrane already? Does the ligand bind the receptor, which in turn recruits G proteins in the cytosol up to the membrane or? The information is very blurry on this. It seems to assume the G proteins and the receptor as one unit.

It will be pretty hard to explain this in detail here in the comments (and is not well liked as well). I suggest you open a new question on this with detailed things you want to know about it.

@Chris Does this multi-step process allow for finer regulation of the event?

@jerepierre There are more potential points to terminate a signal. But it also allows crosstalk between different pathways and more noise. See here for some more information.


text:
Where do amino acids get attached to tRNA and where is it synthesized?
Some very basic parts of transcription/translation seem to be left out in various literature. I can't find the answer to this anywhere:
How exactly is tRNA synthesized? I realize that mRNA is synthesized through transcription and I know a lot about that. However tRNA is supposedly synthesized the same way but every time you read about transcription they just talk about how the mRNA then gets this and that...?
Where do the amino acids get attached? Is it in the nucleus or outside the nucleus?
Thanks.

Does this answers some questions? http://en.wikipedia.org/wiki/Transfer_RNA#tRNA_biogenesis

A pre-tRNA is transcribed from tRNA genes in DNA by RNA polymerase III. Processing occurs in the nucleus, where a 5' sequence is cleaved by RNase P, the 3's CCA motif is added, and ~10% of the nucleotides are substituted. The tRNA are transported out via the pore complexes. Aminoacyl-tRNA synthetase enzymes attach amino acids in the cytoplasm in a 2-step reaction that requires ATP. You'll find there's a unique splicing mechanism in tRNA that additionally splices out an anticodon intron which is abesnt in mature tRNA's:
The wikipedia article notes RNA Pol III generally recognizes internal control elements rather than upstream control elements as in a normal gene.

Source: Qiagen

Source: Molecular Cell Biology. 4th edition.
Addendum: I said in my post that tRNA is charged in the cytoplasm, this is somewhat true. In mammalian cells, we also see that tRNA are charged in the nucleus as well, and it might aid in the export of some of these charged tRNAs. (Source)


text:
Can human mRNA be translated in vitro by prokaryotes?
As the genetic code is universal, can mRNA from a human cell be correctly translated by a prokaryote in a in vitro translation system?

Short answer: Yes, you can.
Usually these are coupled systems for transcription and translation. For these you clone the gene of interest into a vector which contains a prokaryotic promoter which is then used to generate the mRNA in the tube. This mRNA is then translated in the second step into a protein. This works very well, but the protein is missing the typical post-translational modifications of eukaryotic cells like glycosylations, as these are not existant in the bacteria.
These kits can be purchased of the shelf from the usual biotech companies. Mostly these are based on E.coli cell lysates. They work like shown in the figure (from here):


text:
RNA polymerase question
In this question we are examining a bacterial RNA polymerase that elongates at 20 codons per second.
Question 1: How long will this RNA polymerase take to transcribe the Lac Z gene at 3510 base pairs?
My answer: A codon is 3 base pairs so I start by dividing 3510 by 3 and then by 20 to get 58,5 seconds.
Question 2: Your bacteria can produce a Lac Z mRNA about every other second. How can you explain this?
My answer: I am very lost on this one. I thought that the mRNA would be as long as the gene so wouldn't this be 58,5 seconds not roughly 2 seconds??

Multiple RNA Polymerase transcription complexes engaged on the lacZ gene at the same time, staggered along the gene.

Either the gene is present in multiple copies (especially possible if it is in a plasmid) or multiple RNA polymerases are transcribing it, each beginning from the start site one after the other with some amount of time delay, much like multiple ribosomes translate the same mRNA to increase rate of protein production.


text:
Pilot agricultural study terminology
What is the technical word for a single crop field trial which divided into different treatments? I have examined Field trial manual Principles, planning and Implementation of Agricultural Field Trials By Peter Kurt Hansen with staff of the Shifting Cultivation Research Sub-programme, without success
The answer is likely in Agricultural Field Experiments: Design and Analysis (Books in Soils, Plants, and the Environment) 1st Edition, but I don't have access.
In my case the crops are split between mycorrhiza inoculation versus non-inoculated crops.
To put the analytics in perspective this is famous case where ANOVA was developed by Ron Fisher where the different crop groups in the 2x2 matrix were subject to different treatment and assess where the treatment was having an impact on crop growth (Fisher 1921)
Fisher, Ronald A. (1921). ") Studies in Crop Variation. I. An Examination of the Yield of Dressed Grain from Broadbalk". Journal of Agricultural Science. 11 (2): 107–135.

Welcome to Biology.SE. As a site, we expect some evidence of an attempt to answer the question yourself, e.g. a quote and a link to your source. What did Ron Fisher call it in his famous experiment?

Thanks for the welcome, I have added references of the background reading I have performed.

There is no one word for it. The design is typically called by its statistical term of "Randomized block design". There's a good study design page that explains all this here from University of Georgia.
This is a basic statistics question - I would suggest you have a read through a text on design of statistical trials and on statistical analysis before you start anything. Graphpad Prism has a decent starter guide for analysis. If you don't get these right your whole field trial will be unusable. The pages I linked above are a start for these only, this is a very complex area and I suggest you ask your advisor about this too.


text:
How do colorblind people see the back of their eyelids?
When people close their eyes, they still see and they see the back of the eyelids, in colorblind people, they see the back of their eyelids differently, how do colorblind people see the back of their eyelids?

Welcome to Biology StackExchange! How do you see the back of your eyelids, and what makes you think that anything would be significantly different for color-blind people?

The eyelids are translucent, if we face the light, we a reddish color and if we don't face the light, we see a quite not black color, with colorblind people, they see the back of the eyelids differently.

So if the lit eyelids are "objectively" slightly reddish, then color-blind people perceive them the same way as they perceive other slightly reddish objects–given the type of colorblindness they have. Why would seeing the eyelids be any different than seeing other objects?

Color blindness varies as much as skin color, some have the genes from both parents, so the results vary. Generally, the difference in color balance can make a red seem more attenuated or brown compared to other colors in a scene, or a blue or green depending on the type of genes they have. It's a comparison of many individual experiences and interpretations of vision, including a psychological interpretative balance.


text:
Two-compartment model for depot intramuscular injections
I am trying to learn pharmacokinetics.
Let us consider an intramuscular depot injection of $5 \,\pu{mg}$ ($5\cdot10^9 \,\pu{pg}$) of a drug, whose half-time is 4 days. Let us say that the initial plasma concentration is $C(0) = 50 \,\pu{pg/ml}$. After 3 days a blood test was taken and showed the plasma concentration $C(3) = 170 \,\pu{pg/ml}$.
We consider a two-compartment model in which:

first-order absorption to the central compartment with rate $k_a$

first-order distribution from the central compartment to the peripheral compartment with rate $k_d$

first-order elimination from the central compartment with rate $k_e$

We plot the amount in the serum, by solving the system of differential equations:
$$
\left\{
\begin{array}{l}
\frac{dx_1}{dt} = - k_a x_1 \\
\frac{dx_2}{dt} = k_a x_1 - k_d x_2 - k_e x_2 \\
\frac{dx_3}{dt} = k_e x_2
\end{array}
\right.
$$
Where $x_1$ is the amount in the depot, $x_2$ is the amount in the central compartment, and $x_3$ is the amount in the peripheral compartment.
We find that the amount of the drug in serum reaches, say $0.15 \,\pu{mg}$ ($1.5\cdot10^8 \,\pu{pg}$) on day 3. If we divide that by the amount of serum (e.g. $2.8 \,\pu{l} = 2800 \, \pu{ml}$), we obtain $$C(3) = \frac{1.5\cdot10^8 \,\pu{pg}}{2800 \, \pu{ml}} = 53571 \,\pu{pg/ml}$$ However the real concentration is just $170 \,\pu{pg/ml}$. Where does this all drug amount go? Why is there such a large mismatch?
I feel that I am missing something very basic.

Note: Here is an example of a two-compartment model.

You said you fit the model, right? What are you fitting it to? Can you plot x1, x2, x3 as a function of time?

@BryanKrause Yes, I fit the model using the method of residuals. Since I cannot measure x1 and x3 directly, I used x2 only based on my measurements (blood tests). The curve does fit relatively well. It's just the number on a different scale. This is where I have this problem.

Well, you have all the numbers you need to calculate x1 and x3. Can you plot them all (the predictions, that is)?

I suspect there's either a problem with units, or something weird is happening with your model because you don't have enough information to distinguish between kd and ke.

@BryanKrause Yes, I can plot them. They fit the curve fairly well. Most importantly, the model gives x1 + x2 + x3 = 5mg for t = 0 ... +Infinity. It is possible to distinguish kd and ke due to phasing. I.e. distribution completes before elimination and it's easy to estimate elimination. With absorption faster than distribution and elimination, the model (and reality) gives a hump (peak) after 1-2 days. Like I said, it fits well. Just the scale is very different, which is the question here.

@Julia, it is difficult to comment the outcomes without your data and fitting protocol. I suggest you add data together with fits to the question.

Can you add the plot to your question? It makes absolutely no sense that you say it both fits well and that the concentration on day 3 is different from what you measure. And, based on the differential equations you posted, there is absolutely no separability of those parameters if you only have x2 measurements, so either you're using different differential equations or making other assumptions not mentioned in this post.

@Domen Here's the fitting protocol. https://www.pharmacy180.com/article/two-compartment-open-model--extravascular-administration---first-order-absorption-2527/ I need to figure out how to add an image here.

@Julia, no need for images, post your data, for example upload it to pastebin.

@BryanKrause I'd love to have these experimental data (x1 and x3) and I agree, it makes perfect sense to have them to accurately validate the model, but really, there is no way to accurately measure the amount of a drug in a depot or tissues. If you saw any studies on how to that on a human body, please let me know.

@Domen What specifically are you looking for? 1) The experimental measurements of x2 2) ka, kd, ke 3) calculated curves for x1, x2, x3? I just want to make sure I do the right thing.

I know, I'm not suggesting you collect those data from x1 and x3, just pointing out that the model you present has no way to distinguish them. Kd + Ke is constrained, but not Kd and Ke separately. But yes, those three things: data, fitted K values, and plotted curves will help us figure out where the problem lies.

I think I found my problems. The experimental data I have are starting at the point in time when drug distribution is supposed to be complete (i.e. the beginning of the steady state). That is, at that time all the drug amount is supposed to be distributed to tissues (peripheral compartment). This is the 1st problem. The second problem is using the amounts in the system of equations, not the concentrations. The system of equations should use concentrations.


text:
Is household ammonia okay for plants?
My father-in-law claims that since plants need nitrogen to produce proteins, and since ammonia is NH3, that Ammonia should be fine for the plants, since it's just nitrogen and water and hydrogen, according to him. We were cleaning a rusty chain and a bunch of spilled into our garden. I'm talking about household ammonia.
Is that true?
I'm thoroughly convinced he is an utter idiot but then again he could be right since he does say he minored in Chemistry in his college days.

Plants need nitrogen in a form which they can take up. This is either ammonium ions or nitrate.

Okay, he's not wrong, technically speaking. Practically speaking never ever fertilize your plants with ammonia.
The ammonia you spilled will be converted into nitrates eventually, so it's not like you spilled lead into your garden. On the other hand the populations of nitrifying bacteria take a fairly long time to adapt to a bounty like "a bunch" of household ammonia (their idea of a banquet beyond their wildest dreams is 2-4 ppm ammonia) but they will eventually eat it all.
(Fishkeepers should know about the nitrogen cycle, because you have to set up a complete yet tiny version of the real thing, which takes at least a week to establish)
So your plants will be fine... next year. This year they might have a little bit of trouble considering ammonia is a base and can burn plants directly or indirectly. Don't fertilize your plants with ammonia. They will probably die.


text:
Is the quality of sleep dependent on sleep duration?
I've been facing this lately, where I will wake up in the middle of the night after sleeping for perhaps 2-3 hours and be wide awake, but when I go back to sleep, I wake up more tired than before.
Can anyone shed some light on this?

Sleep duration certainly affects the quality of sleep, but it is nowhere near a simple correlation. It is just one of many factors, and these factors don't work in isolation. Statistically speaking, it's a multivariate model - and one which includes a differential equation, because the way sleep duration affects your sleep today depends on the sleep quality (and also the sleep duration) from yesterday. For example, if you go several day with too little sleep, but keeping firm going-to-bed and waking-up times, the ratio of your sleep phases changes significantly, giving you much more deep sleep. This is what compression therapy is based on.
And beyond that, the way you feel upon waking is also dependent on sleep quality in very complicated ways, and other factors (for example the synchronisation of the time at which you woke with your circadian cycle) play a much larger role than the sleep quality you got. Also, there are some unexpected effects, where getting too little sleep making you feel good - it's a kind of lightheaded, giddy state, somewhat comparable to having had a small glass of champagne.
So yes, there is a dependence, but you cannot expect that having had lots of sleep will make you feel good in the morning.

My experience that it depends on it. You sleep in cycles, each cycle has about a 90 min duration. I think the quality depends on how many cycles you ended. It seems like you need to sleep more by an interruption.

Sleep was recorded on 10 nights in each of seven older subjects (mean
  age 55) and nine younger normal subjects (mean age 22). The duration
  of the NREM-REM (non-rapid eye movement—rapid eye movement) sleep
  cycles was determined, starting from the onset of NREM sleep.
In the older group an intra-individual comparison was made between the
  mean duration of cycles interrupted by one period of spontaneous
  wakefulness, within their NREM part, and the duration of intact
  cycles. The interrupted cycles were found to be on average 20 min
  longer than the intact ones, despite the mean duration of intervening
  wakefulness being only 10 min.
In the younger group an intra-individual comparison was made between
  the mean duration of intact cycles ranked as containing a large amount
  of stages 3+4 and the mean duration of intact cycles ranked low for
  stages 3+4. Similar comparisons were made in respect of the amount of
  stage REM, and also the summed amount of stages 3+4 and REM. The
  cycles containing higher amounts of stages 3+4, REM, and of 3+4+REM
  were found to be on average 9, 18 and 18 min longer.
The effect of cycle content on cycle duration was most manifest for
  the first cycle, and least for the third cycle of the night.
The results demonstrate that whereas there may be an average cycle
  duration of about 90 min individual cycles are very variable. The
  contents of a cycle influence its duration, and the onset of the REM
  period is not a strictly time-locked phenomenon.

1974 - Sleep cycle content and sleep cycle duration

If you wake up in the middle of a cycle or if you are interrupted often, then you will be tired. I think what happens by sleeping is much more complex, so this is just a short answer.

From experience I cannot say quality is dependent on duration. For example, you can take a 30 minute power nap and feel much more refreshed than sleeping 8 hours. It may have something to do with dehydration and hunger during the long periods of sleep that disrupt our REM sleeping, our deep-sleep.


text:
How does one determine intracellular concentration?
The TL;DR version
Is there a fast way to determine what the cell environment of a particular cell (E.g RBC) is? (in terms of solute/ionic concentration)

I'm not sure if the question belongs here, but hear me out. I was doing revision and I kept coming across the line "put the cell in a solution which has the same solute/ionic concentration to prevent the cell from bursting or shrinking"
I get that concept, basically it's sort of replicating the internal environment of the cell with the buffer/solution so that the cell feels "at home."
Then my question is, how does one go about finding out how much exactly for each cell? I would think different cells have different internal environments and I don't believe that scientists actually just have stock solutions of buffers ranging from 0.00001M to 100M and trying every single solution until they find the perfect concentration.

patch clamping is how it's done.also enriching the fraction you want to study, losing the cells and measuring conductivity would work

@rhill45 how does one "enrich" a fraction?

In this case you would want a cytosolic fraction: 1. Was cells well in pbs, pellet at low speed, sonicate at lowest setting to break membrane only, add wAter to dilute. Spin at 80,000 x g 4c fixed angle. The top fraction should be your cytosol. All measurements times 2 since you diluted in water once

In fact the line that you quote doesn't mean that the solution is formulated to be identical to the cytosol. All that it means is that the solution should be buffered to physiological pH (typically slightly alkaline); should contain a relatively high concentration of sodium ions and a low concentration of potassium ions; and should be isotonic (i.e have the same osmolarity as the cytosol) to avoid osmotic effects such as plasmolysis (shrinkage due to loss of water) or osmotic lysis (bursting due to uptake of water).
There are many such solutions, but a commonly used simple one is phosphate buffered saline. Another is Ringer's solution. If the aim is to keep the cells metabolically active these are often supplemented with glucose or lactate, depending upon the cell type.
Addendum in response to comment from OP
According to the WP entry for Ringer's solution, Sydney Ringer determined the requirement for Na, K and Ca salts in a specific proportion when carrying out experiments with perfused frog hearts. This was in the late 19th century. A  Google search measurement of intracellular ion concentrations reveals current methods.
This review starts off with a discussion of early measurements of intracellular pH (see page 298). Basically these all consisted of making cell lysates, with various attempts to prevent post-lytic changes. If you do a Google search determination of intracellular pH you will find lots of current methods.

as in how did scientists derive that- what sort of tests did they do?

Patch clamping
Or
Ultracentrifugation to get soluble fractions. If you get enough of it and u have validated its purity you could runs conductivity probe into your fraction


text:
What is the use of shampoo; is it for the hair or for the scalp?
Apologies for the confusing question; I did not know how to better ask it.
I was doing a search on wikipedia when I found this statement.
Wikipedia's entry on hair states;

"The hair that is visible is the hair shaft, which exhibits no
  biochemical activity and is considered "dead"."

With that being said, why does one use shampoo? Is it because of the scalp that requires nourishment and cleaning because skin is not of a "dead" nature? Or is it to maintain the silkiness and smoothness of hair? Because it seems really redundant to take care of and maintain something which is already "dead".

both..Depending on the shampoo components, it can help nourish and clean the scalp as well as maintain hair texture. It would be redundant to take care of your hair if it wasn't a part of personal cleanliness and grooming.

@thelastword so it's safe to say when one takes care of his/her hair; it's only for personal grooming and does not bring about any health benefit?

gair, maybe so because I can't find any positives of specifically cleaning your hair and not your scalp. But the scalp has to be clean to prevent or delay the onset of scalp acne, scalp bleeding and dandruff. You wouldn't be cleaning your scalp alone without your hair though.

I'm skeptical of any claim that shampoo "nourishes" your scalp…

@canadianer http://www.ncbi.nlm.nih.gov/pubmed/15303780 ; http://www.ncbi.nlm.nih.gov/pubmed/8245236 ; I would call these 2 trials as examples of scalp nourishment by different shampoos. Maybe not in the strict sense, but you still have to admit that they do help in scalp treatment.

I think maybe we have different definitions of nourishment.

Neither hair nor scalp, really. Watch the rpoerts of uncontacted tribes of the Amazon. They seem to still have scalps and hair. Modern Western shampoos are designed to remove the natural smell, provide mainly (food-like) unnatural, but socially desired smell, and boost volume. The trials you are listing are for people with health problems, and the intervention is not "nourishing". Getting rid of dandruff is not similar to eating.

We shampoo our hair because of sebum. In humans, sebaceous glands are most numerous on the face and scalp, with (on the scalp at least) several glands plus a hair follicle making up a pilosebaceous unit.
Each gland secretes sebum, initially a colorless and odorless fatty substance (plus dead cells) that spreads from the scalp outward over the hair, but that breaks down by bacteria producing strong odors.
Look at a person who has not washed their hair in a week and it will be easy to understand why we wash the "dead" stuff on our heads. It looks oily and it eventually smells bad as well.

So with this being said, the reason for shampooing is for the benefit of the scalp? Since the sebum control is essential to prevent hair that smells bad-

It's for your benefit. The scalp will be still alive and well, although with a socially unacceptable smell.

@NickSandor ohh I see- thank you for clearing it up

Poorly kept hair directly contribute poor scalp hygiene and may result in health conditions, like Polish plait.
Of course grooming plays an important role as well, and perhaps even dominant role in modern western culture. We can see it, for example, by the variation in frequency of washing hair - if in US it is customary to wash hair every day, in Europe it is considered that using shampoo once in three-four days is quite enough. Note that, if washed regularly at the same interval, the hair does not appear dirty, as it gets oily more slowly than if washed every day.


text:
How did cells survive before the first appearance of topoisomerases?
How did cells operate before the first appearance of topoisomerases to relax DNA supercoils during replication? I read a recent paper on the early phase of topoisomerase evolution, but it doesn’t discuss the actual origin of the topoisomerases, or how cells survived before the first appearance of topoisomerases. Here is the paper:
Villain, P. et al, “Expanded Dataset Reveals the Emergence and Evolution of DNA Gyrase in Archaea.” Mol. Biol. Evol. 39(8), https://doi.org/10.1093/molbev/msac155


text:
How to resolve the contradiction between the time required for the fixation of neutral mutations and the time available according to the fossil record
More than thirty thousand synonymous single-nucleotide-substitutions have occurred in protein-coding genes in the human genome since the human lineage diverged from the chimp lineage ~7 million years ago (Bakewell et al, 2007, p.7490). Since, by definition, synonymous substitutions don’t change the amino acid, these substitutions must be selectively neutral mutations. For neutral mutations, the rate of evolution is simply equal to the point mutation rate U, “irrespective of selection at other linked loci, changes in population size, or almost any other conceivable complication” (Lanfear et al, 2014, p.36). This is problematic because U is approximately 10 to the -8 power for humans, which means that it took about a hundred million generations for each of these substitutions to become fixed in the human genome. Since each generation is more than ten years, a hundred million generations is more than a billion years, which is much longer than the ~7 million years since the human lineage diverged from the chimp lineage. How is this to be reconciled?
Bakewell, M. et al, “More genes underwent positive selection in chimpanzee evolution than in human evolution.” Proceedings of the National Academy of Sciences USA, vol 104, pages 7489–7494, 2007
Lanfear, R. et al, “Population size and the rate of evolution.”
Trends in Ecology and Evolution, vol 29, pages 33–40, 2014

Comments have been moved to chat; please do not continue the discussion here. Before posting a comment below this one, please review the purposes of comments. Comments that do not request clarification or suggest improvements usually belong as an answer, on [meta], or in [chat]. Comments continuing discussion may be removed.

The parameters cited by OP are not in conflict.
The misconception relates to a disconnect between what the theory predicts and the type of observation we have available. This leads to an unnecessary assumption that the observed substitutions have become fixed, as well as a failure to account for standing variation at the time of divergence.
Lanfear et al. correctly states that "the rate of evolution at a site is $KU × 1/K = U$". To find the amount of (this type of) evolution between two populations over time, one would calculate $UTG$, where $T$ is the time in number of generations, and $G$ is the genome size. However, this is a calculation of neutral substitutions that have become fixed across two diverged populations, and is really most appropriate when $T$ is much greater than the expected time to fixation ($T>2N$, where $N$ is the effective population size).
To perfectly test the theory, one would need to census all substitutions in both populations in order to differentiate between substitutions that have become fixed and those that are polymorphic.
The observation we have here, however, is essentially a single individual from each population.
When one compares two individual genomes that have been separated, the SNPs observed between them will include:

sites with a SNP that originated since divergence and has become fixed (what the theory is talking about).
sites that are polymorphic, with SNPs that originated since divergence.
sites polymorphic in the original population, where a SNP became fixed in one lineage and lost in the other.
sites polymorphic in the original population that are still polymorphic.

SNPs originating since divergence that have become fixed
Even just applying the above calculation, considering only fixed SNPs (or those that will become fixed) provides the same order of magnitude as the observation of 30,000 substitutions in humans since divergence with chimps.
Bakewell et al. surveyed 5,215,415 synonymous sites, so we'll use that as $G$. Assuming 20 years per generation and 7 million years of divergence $7×10^6/20= 3.5×10^5$ generations:
$UTG = 10^{-8} × (3.5×10^5) × 5,215,415 = 18,253$ substitutions (though we don't know which of the 30,000 observed substitutions these are).
Sites that are polymorphic with SNPs that originated since divergence.
New mutations are entering the population all the time, with every individual.
Imagine this measurement was taken one generation after divergence, and where the ancestral population was all exactly identical.
The human genome is $3×10^9$ nucleotides, so $10^{-8} × 1 × (3×10^9) = 30$ substitutions. Humans and chimps are diploid, so an individual would have ~$30$ mutations on each set of $3×10^9$ nucleotides, or ~$60$ mutations compared to our hypothetical source population.
As Lanfear pointed out, each one of these substitutions is unlikely to eventually become fixed (they have probability $1/K$), but we're taking the measurement now, so we observe them. Many of them are likely to spread in the population at least a little bit, even if they eventually disappear.
We also know from Bakewell that both the observed human and chimp genomes contain sites that are not only polymorphic in the population, but polymorphic in the sequenced individuals.
Sites polymorphic in the original population, where a SNP became fixed in one population and lost in the other
Overlooked by OP is the fact that the most recent common ancestor of humans and chimps (which was a population, not an individual) was not full of identical individuals, but contained the standing genetic variation one sees in any species. This allows for the fixation of alternative alleles between the daughter populations, even in the absence of new substitutions.
We know in fact this happened. The gorilla genome showed us that ~30% of the gorilla genome is more closely related to human or chimp than the later are to each other. This is due to a phenomenon called incomplete lineage sorting, which occurs when two speciation events occur over a short span of time (again $T<2N$; the gorilla/human/chimp split is thought to have occurred ~10 million years ago). It is caused by variation in the ancestral population that gets differentially sorted into the daughter populations.
Sites polymorphic in the original population that are still polymorphic
It's possible there are still sites that retain polymorphism within the daughter populations that was present in the ancestral population. A wide survey of human and chimp genomes could find these alleles.
(This may be rare between humans and chimps. Estimates of the human effective population size are generally $<10,000$, so $2N=20,000$. Our estimate of ~350,000 generations probably means few sites in the genome have failed coalesce in that time.)