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What causes the development of antibiotic-resistant strains of bacteria?
I understand bacteria have become resistant to antibiotics due to selection pressures, but how do resistant bacteria process antibiotics when exposed to it, compared to non-resistant bacteria. Also, what research is being conducted to combat bacteria resistant to antibiotics?

I suggested an edit for the title, the original one sounds like all bacteria are antibiotic-resistant.

Similar questions could be asked for resistance in insects, "weeds", fungi...

@J.M. + cancer as well

Bacteria usually gain resistance mechanisms through horizontal gene transfer (such as conjugation and phage infection). The four main mechanisms in which bacteria elude antibiotics are:

Drug Inactivation: For example, E. coli can produce beta-lactamase that inactivate many lactam based antibiotics such as penicillin.
Alteration of Target Site: Mutations in genes encoding for target sites can reduce drug binding affinity. Example: Random mutations in DNA gyrase and topoisomerase IV reduces binding affinity to fluoroquinolone.
Alteration of Metabolic Pathways: Many drugs target certain parts of metabolic pathways by inactivating enzymes or sequestering substrates. Bacteria can use alternative metabolic pathways or find ways to uptake the necessary nutrients from the environment.
Reduced drug accumulation: Caused by reduced drug permeability or the ability of the bacteria to transport drugs out of the cell (for example, tetA encodes for a tetracycline efflux transporter). They can gain these abilities through conjugation, phage infection (transduction), or uptake of environmental DNA (transformation).

Wikipedia has a pretty extensive and comprehensive article on antibiotic resistance. There's also a good list of references. http://en.wikipedia.org/wiki/Antibiotic_resistance

Also, what research is being conducted to combat bacteria resistant to antibiotics?

You've gotten some decent answers for how antibiotic resistance arises, so I thought I'd touch on this a bit. There's three major thrusts to anti-resistance research:

Finding new targets and mechanisms. Essentially, creating new antibiotics that are subtly different enough that they slip past existing resistance mechanisms (usually by tacking a more elaborate side-group onto an existing antibiotic) or an entirely new class that targets a different mechanism to disrupt bacteria. This is essentially a drug development task, and is hard.
Antimicrobial stewardship. This is largely clinical research examining how we use are existing antibiotics. Can we alter the duration/deployment/etc. of a course of antibiotics to minimize the chance of resistance. Can we minimize the number of times we use antibiotics inappropriately, giving rise to resistance with no gain to the patient?
Alternate antimicrobial techniques. Can we use non-antibiotic techniques to prevent bacterial infections in the first place, or treat them when they occur? Antimicrobial surfaces, like copper or silver impregnated surfaces, improved surface cleaning, etc.

Another one for antimicrobial stewardship: it is somewhat interesting that some of the antibiotics used in animals have some similarity with antibiotics used in humans. There is a concern that animal pathogens that gain resistance to feed antibiotics can pass their resistance factors to human pathogens that haven't had the time to develop their own resistance factors. One offhand example I have is quinupristin/dalfopristin (one of the antibiotics tried when vancomycin can't cut it), which has structural similarity to the virginiamycins in animal feeds...

The lead question you have answered yourself: bacteria become resistant because of the selection pressure caused by the antibiotic's effective suppression of the original non-resistant bacteria.  Those variants which resist the suppression are selected for as a natural consequence.
How do resistant bacteria process antibiotics?  It depends on the details of the particular antibiotic, and perhaps the kind of resistance.
Take the case of penicillin and related antibiotics, like amoxicillin.  These antibiotics act by inhibiting the formation of a layer of the cell wall which is essential for many kinds of bacteria.  This prevents multiplication of the bacteria and contributes to their distruction. Wikipedia gives some details on the action of these β-lactam antibiotics.
Bacterial resistance to drugs like penicillin usually takes the form of the bacteria producing an enzyme (called β-lactamase) which breaks apart a ring in the drug molecule, disabling it and thus removing its effect on cell wall synthesis.
This resistance has become common because of the widespread use of  penicillin-like drugs and because of transfer of the gene for it between bacteria species as by plasmids.
Researchers managed in the 70s to discover and develop an auxilliary weapon in this war.  This was clavulanic acid, which has a structure partly similar to the penicillins and like them is attacked by the bacterial β-lactamase enzyme.  Unlike the penicilins though, it forms a permanent bond with the enzyme molecule, disabling its activity.  This has led to currently effective drugs like Augmentin which include in the same pill both amoxicillin and its protector, clavulanic acid.

The other route taken, of course, was to find β-lactams that are not degraded by enzymes that affect penicillins and cephalosporins. Two of these β-lactam classes are the carbapenems (e.g. imipenem, meropenem) and monobactams (e.g. aztreonam, tigemonam)

@J.M. and the route taken by bacteria is to evolve/select for beta-lactamases that have activity against carbapenems, like some of the lesser-prevalent (at present) class-D enzymes, thus ensuring a continuing source of funding for our lab.

@Nick: Right. War never really ends, no? :(

@J.M. you're eluding to how calling it a "war" is a bit of a lie; reminds me of a guy on TotN talking about the "war on cancer"

@Nick, sure, but you have to admit that coping with infectious diseases was treated like a "war" for the past few decades, what with the escalation of "improved" antibiotics. Would we have had to use glycopeptides like vancomycin if β-lactams were sufficient to keep the bacteria down?

Most resistance is acquired by horizontal transfer by various means
Conjugation is the sexual transfer
Transduction is transfer by viruses that integrate into the  genome then when they are activated, they carry bits of the genome attached to their own to a new host
Transformation is the uptake of naked plasmid DNA into a new host
Transfection is similar to transduction and is viral mediated
And of course you have acquired which results from point mutations that alter the cells ability to be harmed by an agent, simple changes like change of the cellular membrane or receptor sites

thanks for your answer and efforts in the community... we always appreciate references to back up the information stated in answers as well as questions... do you thin you could add some links to help others follow your answer (I know some of this may be common knowledge to you, but citations and other sources - even webpages - are better than nothing). Also, you may want to check out the help site on "how to write a good answer" http://biology.stackexchange.com/help/how-to-answer


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What are the function(s) of Alu elements in the cell?
My 2008 biology book (1) states that some 10% of the human genome consists of relatively short (~300 nucleotides long) Alu elements which do not code for proteins but many of which are transcribed into RNA. Do these Alu elements have any function in the cell?
(1) Biology, 8th ed., Campbell & Reece, 2008

Alu elements are a type of transposable element. They possess the means for their own duplication and movement.  Alu is a SINE-like element that is transcribed by RNA Pol III, and so a single DNA copy can make multiple RNA copies, each capable of inserting into DNA, so it's no wonder they have a very high copy number.  Here is a picture of one means of insertion http://www.nature.com/nrg/journal/v3/n5/box/nrg798_BX1.html, although there are likely others.
They do not have "a function" per se, in that they are not selected for, they are just rarely selected against and there are so many of them.  They do not add functionality, but rather are one half of the "war" between transposable elements and viruses versus the genome's evolution to mitigate the damage they cause.  They are, of course, commonly used as sources of new DNA for sequence evolution, or can be used to create transpositions or other chromosome rearrangements, but mostly they just fail to cause too much damage and so tend to accumulate in the genome.

Because of the retrotransposon ability of Alu and other interspersed elements, insertion into parts of the genome can contribute to genetic diversity among the population. This can be analogous to random point mutations accumulated throughout a lifetime.
Some of these mutations can be beneficial and increase the overall fitness of the organism. However, many of these mutations and random insertions are harmful especially when elements insert themselves into essential genes or tumor suppressor genes (which leads to cancer).

I've really not studied this, however wikipedia does a good job talking about some of the functions, particularly the associated diseases that result from changed in those sequences.  Of particular interest is this sentence:

The discovery of Alu subfamilies led to the hypothesis of master/source genes, and provided the definitive link between transposable elements (active elements) and interspersed repetitive DNA (mutated copies of active elements).

The article goes on to discuss the effects of Alu changes:

Alu elements are a common source of mutation in humans, but such mutations are often confined to non-coding regions where they have little discernible impact on the bearer[citation needed]. However, the variation generated can be used in studies of the movement and ancestry of human populations[citation needed], and the mutagenic effect of Alu[9] and retrotransposons in general[10] has played a major role in the recent evolution of the human genome. There are also a number of cases where Alu insertions or deletions are associated with specific effects in humans:
Associations with human disease
Alu insertions are sometimes disruptive and can result in inherited disorders. However, most Alu variation acts as markers that segregate with the disease so the presence of a particular Alu allele does not mean that the carrier will definitely get the disease. The first report of Alu-mediated recombination causing a prevalent inherited predisposition to cancer was a 1995 report about hereditary nonpolyposis colorectal cancer.
The following human diseases have been linked with Alu insertions:
Breast cancer
Ewing's sarcoma
Familial hypercholesterolemia
Hemophilia
Neurofibromatosis
Diabetes mellitus type II
And the following diseases have been associated with single-nucleotide DNA variations in Alu elements impacting transcription levels:
Alzheimer's disease
Lung cancer
Gastric cancer
Other alu-associated human mutations
The ACE gene, encoding Angiotensin-converting_enzyme, has 2 common variants, one with an Alu insertion (ACE-I) and one with the Alu deleted (ACE-D). This variation has been linked to changes in sporting ability: the presence of the Alu element is associated with better performance in endurance-oriented events (e.g. triathlons), whereas its absence is associated with strength- and power-oriented performance
The opsin gene duplication which resulted in the re-gaining of trichromacy in Old World primates (including humans) is flanked by an Alu element, implicating the role of Alu in the evolution of three colour vision.

Of course, there is still a great deal to study on this.  For instance, the University of Iowa has a team studying this "junk" DNA.

Part of the answer to how and why primates differ from other mammals, and humans differ from other primates, may lie in the repetitive stretches of the genome that were once considered "junk."
A new study by researchers at the University of Iowa Carver College of Medicine finds that when a particular type of repetitive DNA segment, known as a Alu element, is inserted into existing genes, it can alter the rate at which proteins are produced -- a mechanism that could contribute to the evolution of different biological characteristics in different species. The study was published in the Feb. 15 issue of the journal Proceedings of the National Academy of Sciences (PNAS).
"Repetitive elements of the genome can provide a playground for the creation of new evolutionary characteristics," said senior study author Yi Xing, Ph.D., assistant professor of internal medicine and biomedical engineering, who holds a joint appointment in the UI Carver College of Medicine and the UI College of Engineering. "By understanding how these elements function, we can learn more about genetic mechanisms that might contribute to uniquely human traits."
Alu elements are a specific class of repetitive DNA that first appeared about 60 to 70 million years ago during primate evolution. They do not exist in genomes of other mammals. Alu elements are the most common form of mobile DNA in the human genome, and are able to transpose, or jump, to different positions in the genome sequence. When they jump into regions of the genome containing existing genes, these elements can become new exons -- pieces of messenger RNAs that carry the genetic information.

There is a paper by Srikanta et al entitled An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair (PDF).
Hope that helps.

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What triggers meiosis in gonadal cells?
What specific biochemical processes are involved in inducing meiosis rather than mitosis? Why are gonadal cells the only cells in the human body which do undergo meiosis?

What specific biochemical processes are involved in inducing meiosis rather than mitosis?

It's a difficult question because every step in the development of a germ cell is ultimately necessary for the final differentiation, which includes a meiotic division.  Meiosis requires a lot of specialized components to pair and segregate homologues, to induce and resolve recombination, etc.  What starts it all is still largely unknown.  There are plenty of mutants that halt the process, but these are required along the way, so damaging the pathway ultimately stops it from progressing.  At least one study has been able to initiate the program of meiosis in yeast:
Induction of meiosis in Saccharomyces cerevisiae depends on conversion of the transcriptional represssor Ume6 to a positive regulator by its regulated association with the transcriptional activator Ime1. I Rubin-Bejerano, S Mandel, K Robzyk, and Y Kassir
Basically, they turned on a transcription factor, which activated an entire suite of downstream genes necessary for meiosis.  In essence, they turned on the "meiosis pathway."  Bear in mind this is yeast, so does't have separate germ cells, but the concept is probably the same.

Why are gonadal cells the only cells in the human body which do undergo meiosis?

All other cells are diploid.  Only in germ cells does the organism induce reductional divisions (to make haploid gametes for ultimate fusion in the zygote of the next generation). Creation of haploid somatic cells would uncover recessive lethal mutations and cells would die.  In sperm and eggs, which do not express any genes until after fertilization and karyogamy, this is not a problem.

Ultimately, it seems that follicle-stimulating hormone (FSH), released from the pituitary gland, may be the direct signal for spermatocytes to enter meiosis [1]. It's worth noting, though, that these results come from in vitro studies, where spermatocytes were co-cultured with all cell types of seminiferous tubules in an artificial medium, which makes it a rather crude approximation of in vivo conditions: mimicking the complete spermatogenic cycle in vitro remains to be done [2].
It's a little bit more complicated with oocytes. They start meiosis during prenatal development, are arrested in diplotene stage of the first meiotic division, and then a surge of luteinizing hormone (LH), just before ovulation, makes them resume. But they are arrested again in the last phase, and only after conception do they finish meiosis. The pause occuring in prenatal development is thought to be induced by some kind of an "arrester" secreted by cells in the oocyte environment (specifically, mural granulosa cells) and sustained by high cAMP levels, that are produced in response to both intrinsic and extrinsic stimuli. [3]
Another matter, and quite interesting, is the issue of timing: meiosis starts in a distinct moment of a male mammal develompent, and then goes on continuously, but mammal oogenesis is a series of starts and stops. More on this can be found in [3] and [4].

[1] Tesarik, J., Guido, M., Mendoza, C. & Greco, E. Human spermatogenesis in vitro: respective effects of follicle-stimulating hormone and testosterone on meiosis, spermiogenesis, and Sertoli cell apoptosis. J. Clin. Endocrinol. Metab. 83, 4467–4473 (1998). PMID: 9851795. Free access.
[2] Sousa, M., Cremades, N., Alves, C., Silva, J. & Barros, A. Developmental potential of human spermatogenic cells co-cultured with Sertoli cells. Hum. Reprod. 17, 161–172 (2002). PMID: 11756382. Free access.
[3] Zhang, M. & Xia, G. Hormonal control of mammalian oocyte meiosis at diplotene stage. Cell. Mol. Life Sci. Epub ahead of print. (2011). PMID: 22045555.
[4] Albertini, D.F. & Carabatsos, M.J. Comparative aspects of meiotic cell cycle control in mammals. J. Mol. Med. 76, 795–799 (1998). PMID: 9846949.

Let's start by answering the second part of your question first. I can ask you a similar question like "Why do parietal cells secrete HCl?" or "Why are skeletal muscle cells multinucleated?". The reason why the cells in our body carry out different functions and undergo difference processes, despite having the same DNA, can be due to a multitude of factors. Here are some off the top of my head:

Differential gene expression
Alternative splicing
Regulation of gene expression at the mRNA level (silencing)
Chromosomal inactivation (as seen in XX females)
Cell-cell interactions
Environmental factors that influence all of the above

Now to answer what the specific mechanism in which gonadal cells undergo meiosis:
For one, histone modification (and therefore differential gene expression) has been implicated in the regulation of spermatogenesis. You can read about it in this paper:  Song N, Liu J, An S, Nishino T, Hishikawa Y, Koji T. 2011. Immunohistochemical Analysis of Histone H3 Modifications in Germ Cells during Mouse Spermatogenesis. Acta histochemica et cytochemica 44: 183–90.
At first glance, I didn't find anything on oogenesis; will update if I see anything.

This study really only shows that chromatin modifications are part of meiosis, not that they are causal.  For that matter, this study does't even show they're necessary, just that they happen.

@jp89: The link in your answer got broken, I've replaced it with reference via DOI, which should be more robust. Please, check that it is the same paper you originally referenced (since the link is broken I can't be sure).

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What's the maximum and minimum temperature a human can survive?
This is a question that has been in my mind since I was a kid. I'm not a doctor, nor even a biology student, just a curious person. What is the minimum and maximum temperature a human body can stand without dying or suffering severe consequences (eg. a burn or a freeze)? While at this subject, how much more global warming will the human body be able to take? Seeing as temperatures keep on rising, I'm just wondering how much longer until the temperature starts having drastic effects.
In my country the temperature is about 35-40-45 degrees Celsius in mid-summer (I live in Romania, eastern Europe, and the climate is supposedly ideal here) which is very unhealthy. Does the human body suffer more and more as the temperatures change?

Better to say climate change. "global warming" implies that eveywhere on Earth will heat up due to increasing atmospheric CO2. This is not necessarily the case. We will see be seeing regional variations some of which may even include localised cooling, greater precipitation etc.

Why would 35-40 degrees in mid-summer be unhealthy? It's way hotter in many part of the world...

@nico, have you even read my post? Have you ever been to Romania? The climate is soposed to be ideal with a maximum of 28 degress in mid-summer. It's in the paranthesis.

@ThePlan: you can say that it is uncommon for Romania, sure, still I don't see how it is unhealthy... are people getting sick because of that?

Yes, what people are describing in these answers are pretty similar. People faint on the streets here in my country, they report heart issues and the enviroment itself suffers, I watched the asphalt melt beneath the wheels of a bus a year ago. It's a very rough place.

@Bugster, are you asking about ambient temperatures surrounding the human, or the internal body temperature ? The way you formulated the question, it sounds like you are asking about ambient temperature.

The problem is not just temperature but the combination of temperature and humidity. A high temperature is survivable as long as the body can use evaporation (sweating) to keep the core temperature below ca 38°. At high humidity, evaporation is inefficient. The key quantity here is the so-called "wet bulb tempeature" which is the lowest temperature that can be achieved by evaporation, it's routinely measured in weather stations. If it is above 38°, you die. In practice, this doesn't happen because hot places (deserts) are typically also dry, so the wet bulb temp is much lower.

Hypothermia (when the body is too cold) is said to occur when the core body temperature of an individual has dropped below 35° celsius.  Normal core body temperature is 37°C. (1) Hypothermia is then further subdivided into levels of seriousness (2) (although all can be damaging to health if left for an extended period of time)

Mild 35–32 °C: shivering, vasoconstriction, liver failure (which would eventually be fatal) or hypo/hyper-glycemia (problems maintaining healthy blood sugar levels, both of which could eventually be fatal).
Moderate 32–28 °C: pronounced shivering, sufficient vasoconstriction to induce shock, cyanosis in extremities & lips (i.e. they turn blue), muscle mis-coordination becomes more apparent.
Severe 28–20 °C: this is where your body would start to rapidly give up.  Heart rate, respiratory rate and blood pressure fall to dangerous levels (HR of 30bpm would not be uncommon - normally around 70-100).  Multiple organs fail and clinical death (where the heart stops beating and breathing ceases) soon occurs.

However, as with most things in human biology, there is a wide scope for variation between individuals. The Swedish media reports the case of a seven year old girl recovering from hypothermia of 13°C (3) (though children are often more resilient than adults).
Hyperthermia (when the body is too hot - known in its acute form as heatstroke) and is medically defined as a core body temperature from 37.5–38.3 °C (4).  A body temperature of above 40°C is likely to be fatal due to the damage done to enzymes in critical biochemical pathways (e.g. respiratory enzymes).
As you mentioned burns, I will go into these too. Burns are a result of contact with a hot object or through infra-red (heat) radiation. Contact with hot liquid is referred to as a scald rather than a burn. Tests on animals showed that burns from hot objects start to take effect when the object is at least 50°C and the heat applied for over a minute. (5)
Freeze-burn/frostbite, which is harder to heal than heat burns(6) occurs when vaso-constriction progresses to the degree where blood flow to affected areas is virtually nil.  The tissue affected will eventually literally freeze, causing cell destruction. (7)  Similarly to hypothermia, frostbite is divided into four degrees (that can be viewed on Wikipedia).
As to the matter of global warming cooking us to death, I would imagine that it would be more indirect changes that got us first.  If the average temperature had risen  to the necessary 40°C to cause heat-stroke, sea levels would have risen hugely due to the melting of the polar ice caps.  Crops and other food sources would likely be affected too, therefore I don't think that global warming is overly likely to directly kill humans.

Hey, thanks for the answer. That pretty much sums it up.

I don't think this is a good answer. Atmospheric temperature is being confounded with internal (body) temperature here. If the atospheric temperature in Romania is 45 C, you will not die (even given a fatal temperature of 40 C), because your body can thermoregulate (up to a point). Plenty of populations have existed for millennia where temperatures routinely exceed 40 C.

I should clarify that I think this is a good answer to the question: "What is the range of internal body temperatures at which a human can survive?"

I do believe that though temperature above 40°C is alarming many children survive it when they are ill.

Surely these numbers are supposed to be negative, right? I can't imagine how 35°C would result in shivering...

@Mehrdad those numbers refer to the core temperature of a person (how warm they are rather than how warm their environment is.

@RoryM: Ohhhhhhhhh

As Rory explained, internal body temperature needs to be highly regulated.
Sweating is the main built in mechanism for removing excess heat from the human body. According to my biology book, in (100%) humid conditions humans cannot survive in heats of above around 45C, but in a dry environment can survive in heats of over 100C just through sweating.

45C = 113F, 100C = 212F

Some 200 years ago Dr.Charles Blagden, then secretary of Royal Society
  of London, went into  a room that had been heated to a temperature of
  126 degree Celsius ( 260 Fahrenheit) , taking with him a few friends ,
  a small dog in a basket and a steak.The entire group remained there
  for 45 minutes. Dr.Blegden and his friends emerged unaffected.

This shows the power of homeothermy.
Source : Helena Curtis ( 5th edition) Chp. 38

What happened to the dog? (It died because it could not cool down efficiently enough?) I guess the steak was cooked?

@WoJ The dog was ok, one of the steaks was overcooked.
https://publicdomainreview.org/collections/experiments-and-observations-in-a-heated-room-1774/

Yes, we can survive temperatures above 100 F (38 C) but surviving such temperatures requires continuous fluid intake.  Since sweat evaporates quickly in an arid (dry) environment we tend to be unaware of how much water we're losing.  This leads to heat exhaustion, then heat stroke, then death.  Survival time depends on how well hydrated you are and whether or not you can replace the lost fluid.

Can you add a reference to the statement on continuous fluid intake (and in what range it is valid)?


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How does laser surgery correct accommodation problems?
When someone undergoes laser surgery to improve eyesight, how does it correct accommodation problems?
Why does it not help presbyopia?

Overview

Laser eye surgery works by altering the shape of the cornea.  The cornea works together with the lens to focus rays of light onto the retina.  The cornea accounts for two-thirds of the optical power of the eye (1) (i.e. the eyes capability to focus light), however unlike the lens is of fixed power. It is the lens that changes is shape by the action of suspensory ligaments and ciliary muscles in order to focus light by the correct amount depending on how far away the light originated from (and consequently the angle of incidence with the cornea).  I'm sure that you are aware of all this, however for the benefit of future readers this is fully explained diagrammatically on this webpage.
Specific Conditions
Three forms of accommodation problems can be treated by laser surgery:

Hypermetropia (long-sight) is where light focusses behind the retina:

Laser treatment is used to make the cornea thicker, resulting in a greater degree of refraction of light and correction of the focus.

Myopia (short-sight) is where light focusses before the retina:

Laser treatment is used to make the cornea thinner, resulting in a reduced degree of refraction of light and correction of the focus.

Astigmatism is where the cornea is not the correct shape - it is closer to a rugby ball rather than the sweeping curve demonstrated in the first diagram.  This results in multiple focal points therefore a blurred image.

Laser eye surgery is used to alter the shape of the cornea until it is more normal.

Presbyopia is an age related condition where the lens becomes more rigid and is less able to change its shape to accommodate the light.

As this is a problem with the lens rather than the cornea, it can not be treated with laser eye surgery.  It must be corrected with glasses, as shown in the above diagram.

(1) Cassin, B. and Solomon, S. Dictionary of Eye Terminology. Gainsville, Florida: Triad Publishing Company, 1990.


text:
How does a brain distinguish stimuli?
If all the brain ever "sees" is action potentials, how do we know that one set of action potentials denotes a flash of light, another one signifies a loud sound, etc ?

The fundamental way in which this works is by geography: signals triggered by different stimuli travel by different pathways to different regions of the brain that are specialised for dealing with the sorts of information they contain.
For example, visual signals from the retina pass down the optic nerve and (after a few interesting twists and turns that, inter alia, send the left and right halves of each visual field to different brain hemispheres) wind up in the visual cortex, which contains neuronal networks adapted for recognising different structures and regularities in the image. Whereas sound information from the ears, after an even more tortuous sequence of processing steps, winds up in the auditory cortex.
Along the way, the signals will typically be split up across many neurons and reintegrated into new signals that pick out different kinds of information. So a particular stimulus will result in a complex spatio-temporal pattern of action potentials firing across many regions of the brain.
Conceptually, the further along this process you go, the more abstracted the signal probably becomes, so that it stands for a collection of events and ideas and thoughts rather than for excited photoreceptors or vibrating hair cells. But exactly how this parsing of the sensory content eventually turns into perception and conscious recognition is essentially unknown.

In short, one action potential denotes a flash of light and another one signifies a loud sound by occurring in different neurons.

Also, the frequency and the pattern of the action potentials are very important for information processing. A neuron firing short bursts of action potentials is not the same as one continuously firing.

For a human brain to differentiate signals from different locations of the brain, it must be able to perceive itself. And you commented how it is done is essentially unknown. But do you know any papers that attempt to figure out this how?

@jachilles it doesn't have to perceive itself, the brain is not homogenous, a signal entering the brain from one pathing is entering a different part of the brain and a different network of neurons than one entering from a different pathway.  there is no homunculus.

Just adding some metaphors in support to the excellent answer by walkytalky.
Our brain is like a huge processing center that can be seen from techni's prospective as a sort of a data center with parallel processing of hundreds of thousands of inputs with processing cores scattered throughout the complete brain.
Human brain (medulla) is connected with the rest of the body through special types of nerves that convey the information to brain (sensory, centropetal nerves) or deliver information from brain to the target organs (motor or centrofugal nerves) or both (mixed nerves).
I intentionally use the term "medulla", because this word comes from origin where it is applied to somwwhat more than brain: the spinal cord is also "medulla" (medulla spinalis), as well as the part that connects the spinal cord with the brain itself (medula oblongata).
The nerves that come directly from the brain are called cranial nerves. There are only 12 pairs of them in humans, numbered using Roman numbers (from I to XII) and every pair has a specific function: I bringing olfactory information (about smells), II -- the optic one, III -- moving the eyes etc.
The counterparts of these nerves in spinal cord are spinal nerves, which go through the holes between single vertebrae.
Brain and CNS in general can locate the information input and determine the information type judging by the input source using these nerves.
Besides the classical sensory information, like those from eyes coming via optical nerves into CNS, there is also some sensory information that is conveyed through autonomous nerve system, that is less specific and can not be localized as well as in case of sensory information coming via sensory input. Pain, for example, or the feeling of pressure belongs to the type of information coming via vegetative nerves.
The complete brain surface (so-called cortex) is mapped into special zones, called Brodmann zones, depending upon prevailing neuron types and (secondary) role in information processing.


text:
A good book for history of biology/biotechnology for lay people
I have many friends who are interested in Biology and want to know more about the subject in general (like a history of biology, from Darwin's theory, to DNA structure discovery, to the human genome project). Of course, I cannot suggest to them to read Alberts or Lenninger. Do you know whether such a book exist? I guess that a book that covers most fields of biology cannot be compiled, but even more focused book would do.
Let me try to narrow it down: something like the greatest discoveries in the field of biology (like this article) would be an interesting book to read.
I am not sure how appropriate this question is for SE, but I am sure that I will get the best answer here. Besides, it would be great if lay people can be more excited about biology and contribute to the site growth.

I think that this question is too broad, book recommendations about very specific questions are fine, but these very broad ones tend not to work all that well on SE sites. This is really something that chat would be good for, though our chat is somewhat deserted right now.

@Mad Scientist: pretty much any SE site I've been on has a few questions like this. And they are generally CW.

@Mad Scientist Didn't editing my question make it more specific?

It doesn't have very many reviews, but The Epic History of Biology sounds like it's perfect.
Flipping through the first chapter in the preview, it doesn't seem overly technical in any way, so secondary school-level knowledge is probably enough.  If your associates have absolutely no biology experience, perhaps a run through a popular press book would provide all of the background necessary.

I don't think the accepted answer should be a book that no one has actually read. I appreciate the "flipping through" that was done, but can anyone who has read the full book weigh in? If not, I'm uncomfortable that the community's best recommendation is based on a skim of the first chapter on Amazon.

@yamad I accepted this answer because the content of this book was the closest to what I was initially looking for. But the votes to the other answers should give you an idea of how good or well known the other books are.

@GerganaVandova, I understand. But isn't the critical question how good this book is? I'm interested to know if any of the upvotes know more about this book and could give their thoughts.

@yamad Her operative question here was: "Do you know whether such a book exist?"  I offered this based on the diverse list of topics it contains, I never claimed to have read it, and I was quite clear about that.

@yamad Unfortunately, I haven't read any of the recommended books, so it would be nice if people upvoted because they did. I am also happy to change my accepted answer as soon as someone recommends something else. I also recommended a book which fits what I was looking for but I haven't read it as well.

Some that just come to mind, in random order:
One cannot skip reading:

Richard Dawkins - The selfish gene

And, obviously:

Charles Darwin - The Origin of Species

And, for those interested in the evolution of the brain (and its quirks):

David J Linden - The Accidental Mind
Oliver Sacks - The Man Who Mistook His Wife for a Hat

Not very DNA/evolution-oriented, but wonderful science books nonetheless:

Primo Levi - The Periodic table
And the neveraging must-read:
Isaac Asimov - A Short History of Chemistry

Most if not all of Sacks's books also appeal to lay people.  "Island of the Colorblind" is particularly good.

I agree that Sacks is a great author to dig into. Such great first-hand experiences. I am a big fan of Dawkins, and think his 'Selfish Gene' is excellent, although, I think his rigor might turn casual readers off in this volume. However, I find The Greatest Show on Earth  much more readable - and available as an audiobook read by himself. (Selfish gene is also on audible, but I can't imagine it translating as well)

A good recollection of the early days of micro and molecular biology is "The Eighth day of Creation"
It covers the early use of e. coli, the discovery of phage, transcriptional elements and the impact that DNA structure had.  It's very comprehensive and really useful if you are doing molecular biology today.

I had not heard of this - thanks for the recommendation.

I don't know about useful, but it certainly brought things into perspective - it was required reading for our first year in the molecular biology PhD program.

I think somewhere in your PhD you can stop and try to figure out how we know things and how the process of discovery happens in a broader sense which is really useful and fun.

A fantastic book that covers the evolution of modern science since the Renaissance (including a great deal of biology) is The Scientists by John Gribbin. I found that by focusing on the people doing the science in the context of the society in which they lived, I got a much better understanding for why early scientists thought the way they did and researched the questions that they did.
Here's the blurb from the publisher:

In this ambitious new book, John Gribbin tells the stories of the
  people who have made science, and of the times in which they lived and
  worked. He begins with Copernicus, during the Renaissance, when
  science replaced mysticism as a means of explaining the workings of
  the world, and he continues through the centuries, creating an
  unbroken genealogy of not only the greatest but also the more obscure
  names of Western science, a dot-to-dot line linking amateur to genius,
  and accidental discovery to brilliant deduction.

I don't know very many books that might be referred to as the Grand History of Biology or anything like that. That's...a big topic. Really big. How about some suggestions for good Biology/Medical History books accessible to lay people:

And the Band Played On, by Randy Shilts, an account of the beginning of the AIDS epidemic in the U.S.
The Great Influenza, by John Berry, which is about the 1918 influenza pandemic.
The Demon Under the Microscope, by Thomas Hager, which is about sulfa and the development of early antibiotics.

Finally, I believe James Watson wrote a somewhat popular science-oriented account of the discovery of DNA, which would no doubt be interesting, though likely somewhat skewed in favor of his own awesomeness.

Hmm, thanks but I was mostly thinking about Cell Biology or Molecular Biology oriented books. Watson wrote "The Double Helix", but this book is focused only on the discovery of DNA, which, although very appealing to me, is too narrow-scope.

All of Watson's books are mostly about how many pretty girls he saw or met, and then secondarily about how he worked with lots of famous people. At some point he usually mentions a bit of biology, but it's tangential to the main theme of pretty girls.

I just came across Understanding Biotechnology. There is one very positive and one very negative review. I haven't read the book myself, but it looks that it is exactly what I was looking for: the table of content includes topics like small history overview, genetic engineering, gene therapy, pharmacogenomics, etc. It might be even useful for people with biology background.
Has anyone heard about this book?

By far the best book I've read on the history of biology is A Guinea Pig's History of Biology, by Jim Endersby. It tells the history of the field by focusing on experimental organisms and the contributions which were made by studying them. It has an engaging narrative style and the idea of focussing on organisms' stories is an excellent and original one.
However, the best resource there is on the history of science is the TTC History of Science lecture series. It comes in two parts:

Antiquity to 1700 by Lawrence M Principe of Johns Hopkins University
1700-1900 by Professor Frederick Gregory of Harvard

The lecture series are VERY expensive - around $200 each. However, most good libraries will have them, and I strongly recommend getting hold of them if you can.

This book, although a little dated, has given me an incredible appreciation of biology that I never gained in school:

What is Life? by Erwin Shrodinger

I am not a biologist, but I occasionally work on mathematical-biology and have training in physics and theoretical computer science. This book was much more accessible to me that other books on biology. Before reading the book I perceived biology as a collection of fun facts (what Rutherford would call "stamp collecting"). Shrodinger's presentation was well tailored to the typical reductionist and "everything must have a reason" thinking of a theoretical physicists.
I think the book does a good job of explaining the basics and providing intuition and grounding. The excited reader can then move on to more orthodox treatments.

My two favorite books are Molecular Biology made simple and fun and Biotechnology for Beginners. Both are well written and fun to read. As their names suggest, the former covers the basics of biology and the latter covers the basics of biotechnology.

There is a free video course "Modern Biology" at Carnegie-Mellon University's Open learning initiative. This is very technical and does not cover history of biology.
I quite liked D.A. Sadava's non-free video course Understanding Genetics: DNA, Genes, and Their Real-World Applications. This is Genetics and Molecular Biology oriented, but also not a book. It is suitable for a reader with high-school knowledge of chemistry. Maybe it contains too few basics, so it is also not for the absolute layperson. He starts with Mendel and mentions many other 20th-century researchers.
The author has co-authored one of those thick, expensive college-level biology textbooks as well.


text:
How does a veggie-less diet affect the human body?
I have some question, which I'm sure would fit better in the fitness section but proper answers should probably come from someone that knows biology.
My question is rather simple. How can a person that doesn't eat any vegetables at all be affected by such a diet? By no vegetables at all, I mean not eating any ever.

You mean something like the Anti-Vegetarian?

I don't know if it has a name. Just a person that doesn't eat any vegetables at all.

Including or excluding fruits? The difference is purely culinary...

Excluding fruit. A noemal diet with fruits but no vegetables.

@ThePlan: well that renders my answer useless...

I would have thought that most nutrients that would be found in vegetables could also be found in fruits somewhere?

-1, vague question. There are other ways of obtaining all nutrients in vegetables. This would be better fit for fitness.SE.

Yeah, the Carnivore Diet does have a name.

There is a list of several implications of not eating vegetables (references 1, 2, 3):

Weight gain (by eating fat-rich products);
Malnutrition (not reveiving enough vitamin A, C, D, K, etc);
Digestive problems (low fiber intake leads to digestion disorders, which could lead to health problems);
High risk of heart disease;
High risk of certain cancers.

I also pulled up the nutrition fact sheets for vegetables, fruits, and seafood created by the US Food and Drug Administration.
In order to obtain all the necessary vitamins, one can substitute vegetables for fruits. For example, to obtain 100% of the daily value of vitamin A, one should eat as little as one carrot a day. In order to get the same amount of vitamin A from fruits, one should eat 134g of cantaloupe, or 462g of grapefruit, or 50 large apples a day. Although this could be difficult but possible, the sugar content of the above-mentioned fruits should be taken into account.
Something else which needs to be considered is that vegetables are richer in minerals (iron, potassium, calcium), compared to fruits.
All this in mind, perhaps all minerals and vitamins could be acquired from a source other than vegetables.

It's not just the vitamins, of course. By eschewing vegetables, you are depriving yourself of helpful phytochemicals (e.g. sulforaphane in broccoli and other crucifers, flavonoids in most other vegetables), which are helpful in staving off the onset of degenerative diseases. Not even most multivitamin supplements can give you those phytochemicals.

FYI: this guy doesn't eat any vegetable: http://robrhinehart.com/?p=298

Weight gain? You can't possibly gain weight if you're consuming an equal amount of calories you're expending. Regardless of what you're eating.

@Memming: Almost all the people who promote meal replacement products are bogus, and so are most of the products. Even the established brands like Nestle make it clear that their meal replacement products are only to be used under guidance from medical professionals and not for long-term. Not eating real food will cause problems in the long run.

You'd be deprived of the vitamins and minerals which are found only in vegetables, but you'd live. There are vitamins and minerals in meat and other foods, plenty of them, and your metabolism would adapt to produce the proteins which are missing. Human body is a wonderful organism.
You wouldn't have a higher risk of cancer because cancer is a byproduct of life (the DNA repair mechanism and programmed cell death) and you can't get it by consuming meat or by not consuming vegetables.
You wouldn't gain weight if you're not consuming too much food. The math is simple, if you need 2000 calories, you'll gain weight if you're consuming 2050 calories of vegetables and lose weight if you're consuming 1950 calories of meat.
Your risk of heart disease wouldn't increase.
The only things which would change in this case would be the ones directly related to the nature of carbohydrates, proteins and fat. The carbohydrates in vegetables release energy slowly over a longer period of time, so if you'd eliminate vegetables you'd possibly be hungry more often. However, fat - and the glucose produced from it - would keep you going.
And you might have digestion problems because of lowered intake of fibers until your metabolism adapts.

Do you have any reference/s to support your claims?

Not saying a pure-carnivore diet is a good idea, but there are no vitamins or minerals that are only found in vegetables (assuming you include organ-meat, etc - the entire animal). There are compounds such as phytonutrients, only in plants, but those aren't vitamins. In fact, it's really the other way around, there are vitamins in meat that are, at best, extremely hard to get from plant-based diets only (no supplements).


text:
Why do some mammals not have testes in a scrotum?
Coming from an evolutionary approach, Is the only purpose of a scrotum to regulate the temperature of the testes?
Knowing all mammals are warm blooded, shouldn't all mammals have testes in a scrotum?

Having descended testes is a derived characteristic within mammals; monotremes and the Afrotheria (including elephants) all retain the ancestral character state (Kleisner, et al., 2010)2. Among those mammals with descended testes, these can be ascrotal or scrotal. Testicular descent is hypothesized to have only occurred once within Mammalia, with the ascrotal Laurasiatheria. Descended ascrotal testes are found in cetaceans, phocid seals, hippos, tapirs, rhinos, and some bats. Descended scrotal testes are found in horses, pigs, camels, and Carnivora.
Since basal mammals would presumably have to regulate testicular temperature just as much as derived mammals, the temperature regulation hypothesis seems to not hold up. So the real question is: why have a scrotum? One hypothesis has to do with evolution of fast locomotion (e.g., galloping).
According to Frey (1991, 40)4:

The strong flexions and extensions of the vertebral column during
gallop should cause intense fluctuations of intra-abdominal pressure.
Fluctuations of intra-abdominal pressure severely impede continuous
flow of blood in the abdominal veins. Periodically reduced venous
drainage resulting in fluctuations of intra-testicular pressure would
impair the process of spermiohistogenesis, which is dependent on an
absolutely constant pressure within the testis.

Chance (1996)5 suggests that the temperature hypothesis might represent a secondary adaptation:

Because in the human male, scrotal testes function optimally at
temperatures below that of the body, much speculation, and a
considerable amount of research, has gone into attempting to see what
(metabolic) advantage might accrue from this lower temperature,
without considering the possibility that this is a secondary
adaptation to an enforced external position.

Kleisner, K., Ivell, R., and Flegr, J. 2010. The evolutionary history of testicular externalization and the origin of the scrotum. J Biosci 35:27-37
Frey, R. 1991. Zur Ursache des Hodenabstiegs (Descensus testiculorum) bei Säugetieren. Z Zool Sys Evolut-Forsch 29:40–65
Chance, M.R.A. 1996. Reason for externalization of the testis of mammals. J Zool 239:691–695

What about dolphins or marine mammals? Do they have ascrotal testes?

@GabrielFair This has more than you will ever want to know about mammalian penises and testes, but the answer is no, cetaceans and seals do not have scrota, presumably an adaptation for being streamlined.


text:
Is the squid giant axon the fastest conducting unmyelinated axon known?
The conduction velocity of the squid giant axon can reach 30 m/s. Is there any known example of an even faster conducting unmyelinated axons?

The conductance velocity in the unmyelinated axon has been calculated and measured to be proportional to the square root of the axon diameter (see for example: Rushton, 1951). Since the giant axon is, well, giant, it conducts much faster than others. AFAIK, all other large neurons studied are myelinated. Maybe try to find bigger squids! ;)

Did he show that the diameter is the only factor?

No, that's just one factor, but thought to be more variable than others, such as membrane capacitance or cytoplasm resistance, that are less variable among different cell types.

+1 for answer and making me laugh. Giant axons are giant, man!


text:
In C. elegans, why does knock-down of cco-1 in some tissues increase lifespan, and knock-down of cco-1 in other tissues decrease lifespan?
Full question: In C. elegans, why does knock-down of cco-1 via RNA interference in specific tissues like body wall muscle decreases life span, whereas knock-down in the nervous system and intestine increases life-span?
http://www.wormbase.org/db/gene/gene?name=WBGene00000371;class=Gene
Also from paper 'The Cell-Non-Autonomous Nature of Electron Transport Chain-Mediated Longevity'
Supposedly, it's through hormesis. But why is there a differential effect from tissue to tissue?

Let us first answer the question: what is the effect of cco-1 knock-down in C. elegans. Durieux J., Wolff S. and Dillin A. in their paper "The cell-non-autonomous nature of electron transport chain-mediated longevity". Cell 144:79-91 (2011) provide the following explanation:

The life span of C. elegans can be increased via reduced function of
  the mitochondria; however, the extent to which mitochondrial
  alteration in a single, distinct tissue may influence aging in the
  whole organism remains unknown.

So, by slowing-down the mitochondria function you manage to slow-down the normal wear-and-tear of the mitochondrial enzymes, which are normally responsible for the so-called respiratory chain -- one of the fundamental biological process for storing energy in cells (despite the common belief, ATP is rarely to store energy, but mostly to transfer it to the target!).
If we group the tissues where the knock-down leads to similar effects we will get muscle cells opposed by neurons and intenstine cells.
This is just my suggestion, but if we approach those groups with the idea of energy storage and re-use in mind, we'll see that muscle cells have much higher turnover of energy (for contraction and even more for dilation), whereas nerve and intestine cells are not that dependent upon energy and have much lower baseline of energy consumption and turnover.
Now we can suggest that cco-1 knock-down decreases the functions of mitochondria in muscle cells below the acceptable level and the decreased life span is due to depletion of mitochondrial energy storage under light stress conditions which would have been easily coped with under normal conditions. And vice versa, nervous/intenstine cells requiring a constant energy source at a much lower level just help the animal to cope with stress more effectively even during old age, leading to increased life span.


text:
What portions of the brain have drastic changes in activation when we "sense" someone is there?
I was watching an old Arnold Schwarzenegger movie ("Commando") where he plays an elite soldier (surprise).  An enemy tries to sneak up on him, and Arnold says that he smelled the other guy approaching.  While this is possible, I find it to be more hyperbole than truth, but what modalities and areas of the brain would he would harness for this detection task?
All of us not being super soldiers, we do occasionally get a feeling when someone has entered a room silently behind us.  Is it audible clues that fall below a certain threshold, is it the sensation of air moving in a the room, some sort of vibrational or proprioceptive sensation, or a combination of all three of these?

First of all one should tell that one can attribute the activation of certain brain zones with some indepent events only when the activation takes place along the signal input (receptors, sensory pathways towards the cortex and the sensory areas in cortex) or motor action (=output) (along the motox cortex => motor neuron => target organ). Those zones in brain are also termed as primary ones, for there is a clear mapping between the event/action and the activity here.
In case of your "sneak feeling" as you describe in your post, there seems to be more not the sensory input from some unknown type of receptor, but rather a subconscious processing of the complete sensory input that reveals some potential danger and is percepted as a kind of "smell of danger". Since this processing happens in secondary zones and can be well distributed throughout the whole brain, there is no possibility to find a single focus with high activity change here (in my opinion, of course) -- those changes in activity are beyond the measuring/imaging capabilities of modern examination methods.
Possible sensory inputs here might include (but not limited to):

Optical (some shades, moving asyncronously etc).
Acustic (some sneaking sounds, normally disguised by the background sound).
Air move, air stream blocking sense etc (tactile feeling).

So, everything you suggest might apply here.


text:
Why would stablising selection ever happen?
If the aim of evolution is to allow an organism to better compete against rivals, why would stabilizing selection ever happen? If you're not selecting the most highly adapted competitors at either end of the spectrum then how would a species progress?

Evolution has no aim. Surviving of the fittest is only the way how it works.

As @MartaCz-C says, evolution is not purposeful or goal-orientated, it's a logical phenomenon that just occurs.

It occurs when a beneficial characteristic has been developed over time and it would be harmful to stray from it.  In these cases it is not the individuals at the fringe (as you put it the most adapted) who are the best adapted.
I think it may help if I answer with an example that is widely promoted by AQA in their A2 Biology syllabus.
Stabilising Selection in human birth weight
It is harmful for an infant to be born with a very low birth weight. They are much more vulnerable to heat loss due to their high surface area to volume ratio and consequently their respiratory demands are very high.  Pre-term babies (which account for 67% of low-birthweight infants(1)) are particularly susceptible to respiratory problems (lack of surfactant in the lungs), cardiac problems (Patent ductus arteriosus - the lungs are still bypassed when the umbilical cord has been cut) and dangerous intestinal problems (Necrotizing enterocolitis) amongst many other conditions can all be fatal (further information on mentioned conditions) and are reflected in high mortality rates at these low birth rates.  It is therefore not beneficial to be on the extremes of birth weight.
Similarly, delivering a child of too high birth weight can cause complications with delivery if the head and shoulders are too wide to pass through the mother's hips.  Therefore the other extreme of high birth rate is also not beneficial and will not be selected towards.
This leads to selective pressures in both directions, stabilising towards a mean birth weight as shown below:

This is an example of evolution not pushing a species forward but ensuring that individuals have the best chance of getting to reproductive age themselves.
(1) Martin, J.A., et al. (2007). Births: Final Data for 2005. National Vital Statistics Reports, 56(6).

this a great answer Rory.

Evolution has no aim, you seem to be repeating a caricature of what the theory of evolution really says.  Evolution works by a mechanism where pressures on a population select for the traits that are best suited for that environment.  If there are no pressures on a population, then the selection of specific traits will be slowed down, as all members of the population have an equal chance at reproducing.
Now to wax a bit philosophical on the issue.
As John Rennie said in Scientific American:

"Survival of the fittest" is a conversational way to describe natural selection, but a more technical description speaks of differential rates of survival and reproduction. That is, rather than labeling species as more or less fit, one can describe how many offspring they are likely to leave under given circumstances. Drop a fast-breeding pair of small-beaked finches and a slower-breeding pair of large-beaked finches onto an island full of food seeds. Within a few generations the fast breeders may control more of the food resources. Yet if large beaks more easily crush seeds, the advantage may tip to the slow breeders. In a pioneering study of finches on the Gal pagos Islands, Peter R. Grant of Princeton University observed these kinds of population shifts in the wild [see his article "Natural Selection and Darwin's Finches"; Scientific American, October 1991].
The key is that adaptive fitness can be defined without reference to survival: large beaks are better adapted for crushing seeds, irrespective of whether that trait has survival value under the circumstances.

Michael Shermer states:

Living fossils (organisms that have not changed for millions of years) simply means that they evolved an adequate structure for a relatively static and unchanging environment, good enough to maintain a niche.

Or as a particularly brilliant writer that goes by the name of Calilasseia said:

The static species fallacy.
This is a particularly stupid canard, which the above discourse on inheritance, and variation brought about by meiosis, should flush down the toilet at a stroke. But, in order to reinforce how stupid this canard is, it is necessary to cover rigorously what a species is.
A species is a population entity, and as a corollary thereof, a dynamic entity. A species is defined in rigorous biological work, as a population of living organisms, whose members can produce viable offspring with each other, but whose members can not produce viable offspring with a separate, distinct population. Actually, this is only one extant definition, but it is the one that matters with respect to evolution, because once again, it points to the central role of inheritance.
Of course, part of the problem arises because of taxonomy. Because scientists need a reference point from which to launch further investigation, they have alighted, courtesy of our old friend Linnaeus, upon the process of cataloguing organisms and providing them with a unique, unambiguous identity. This, of course, has been most helpful in furthering our understanding of the biosphere, and indeed, Linnaeus himself, on the basis of comparative anatomy alone, alighted upon the idea that organisms were related to each other a hundred years before Darwin, which is why he constructed his taxonomic scheme in the manner he did. Yes, that's right, a creationist (though he was only a creationist because no other option existed in 1758) alighted upon the idea of biological interrelatedness, as a result of paying attention to reality. But the very same taxonomic practices that have been useful to science, have also led to a popular misconception. This is because taxonomists base their classification upon individually sampled organisms, one of which is chosen as a 'type specimen' that is henceforth declared to be the reference standard against which all others are compared. Other specimens are maintained in order to provide a record of likely variation in characteristics from that reference standard. The trouble is, of course, basing the entire classification system upon such reference standards promotes the illusion that those standards remain in place for all time. Scientists, of course, recognise that this is not the case, but it takes diligent intellectual effort to recognise that the taxonomic standards are merely particular snapshots of the state of the species at a given point in its history, which scientists then choose as their reference benchmark for current work. The species itself, however, courtesy of all that dissemination of variation across generations, does not stay still. It is NOT static.
I cannot reinforce this strongly enough. A taxonomic classification is merely a historical snapshot of the state of a species, used as a reference point for further work, and does NOT constitute "the species" itself. The species itself, is the sum total of all the living organisms comprising that interfertile population, and with each new generation, that population undergoes change, because in the new generation, each of the organisms comprising that population are genetically different from those in the previous generation.
So, if anyone wishes to erect the ridiculous idea that a species is a static entity, the simple retort is this. Look at your family album. Are you identical to either of your parents? No? There's your evidence for the dynamic nature of a species. Now replicate that evidence across millions of humans, and picture what happens with each new generation, remembering that across generations, inheritance is a dynamic process. There goes the static species fallacy.

I hope that clears it up for you.


text:
How, on a physical level, does ATP confer energy?
When ATP is used as the energy currency to make, say, reaction X + Y → Z happen, is what happens on a physical level down at the molecular scale that during the reaction

ATP + H2O → ADP + Pi       ΔG˚ = −30.5 kJ/mol (−7.3 kcal/mol)

that 30.5 kJ/ mol is conferred by ATP molecules physically bumping around the reactants X and Y, the kinetic energy of the above reaction being what does it?
I mean, is the energy coin of ATP conferred to reactions by molecular collisions, or is it an electric field effect in the spatial geometry the way the ATP molecule tends to break apart?

Usually in biology (and being ATP, it most probably is biology), it's one of two things.
The gamma-phosphate (the third one, the one farthest from the adenosine) is very unstable, meaning the phosphoanhydride bond is easy to break.  The cell "allows" it to break, but only at the cost of moving the phosphate to some other molecule, such as a serine or glycerol or fructose or whatever.  This phosphorylation creates a bond with lower energy than the phosphoanhydride, and so is overall favored.  Imagine the personification: the gamma phosphate hates being attached to anything, but hates being attached to an ADP the most.
Alternatively, if ATP hydrolysis is coupled via an enzyme, it is usually done through transient storage of the energy is protein conformation.  An enzyme binds ATP, which makes the protein structure "bend" or conform around the ATP.  This puts loads of strain (energy = A) on the protein which is offset by the stabilization of binding the ATP (energy = B).  This strain can make an enzymatic surface open up on the protein which itself takes a lot of energy to make (energy = C).  The surface can catalyze some reaction (X+Y->Z in your example) that costs some energy (energy = D).  The completion of that reaction alters the enzyme's catalytic site to something new and higher energy (energy = E), which can be alleviated by cleavage of the ATP (-7.3 kcal/mol).  Alas, ADP and P do not fit well into that site of the enzyme, so they float out, restoring that original ATP-binding surface to it's original state.  Provided A>B>C>D>E>-7.3, the cycle will continue until the ATP is exhausted or you have no more Z to make.
Typing "enzyme catalysis cycle ATP" gives a few examples. Here's a few:
DNA gyrase
Actin-myosin cycle

Another interesting scheme of the myosin functioning

@KAM You're arguing from the basis of a thermodynamic ensemble, which really makes your argument more "on a biochemical level" than "on a physical level". I want to know, electron by electron, particle by particle, exactly mechanistically how the potential energy inherent in ATP flows from point A to point B. Where do I go for that answer?

Chemical reactions are based on collisions, but only those with the right amount of energy and the proper orientation give rise to them. If just one of these parameters deviates enough, the reactants will just bounce off. Within a cell, collisions between reactants are likely to happen, as one molecule is likely to collide with its enzyme within a second,[1, p. 6] but not in the right orientations. Enzymes through a moderate affinity to the reactants, place them in the right orientations.
Now, where does the energy come from? The molecular "storm" of water molecules around does have quite a bit of kinetic energy, but as collisions with them come from all directions, they usually cancel each other. When ATP hydrolyzes, about 0.36 eV of energy are released (5.8·10^-20 J),[2] and the molecules around it vibrate. I suppose that this is because once the chemical bond is broken, the repulsive force between ADP and phosphate is very strong at such a close distance, violently pushing whatever molecule they find on their way. The amount of energy released has 14 times the average kinetic energy of the molecules around it, so it is the equivalent of locally heating a molecule to 3,900 ºC.[2] Naturally, if the hydrolysis happens within an enzyme, it vibrates like crazy and induces a conformational change. If the enzyme has reactants bound to it, they are likely to collide with the right amount of energy.
Interestingly, the molecular storm is powerful enough at 150 ºC to break down ATP. This is why scientists do not expect to find any hyperthermophile living at such warm temperatures. Currently, the archeon Pyrolobus fumarii holds the record, being able to survive up to 122 ºC, but its optimal temperature is 113 ºC and "freezes to death" at temperatures lower than 90 ºC [Wikipedia].
[1] Goodsell, D. "The Machinery of Life". 2nd edition. Springer. 2009.
[2] Hoffmann, P. "Life's Ratchet: How molecular machines extract order from chaos" Basic Books. 2012.

Please add a link to your references, preferably to the original publisher's website, but Amazon or Google books, if necessary. Saves anyone interested having to search themseves.

Don't worry, I'll add them for tomorrow; including the page and version of the books.

Researching quantum constituents in ADP energy transfer gives this page which describes the ATP reaction with some geometry, aside from electrical/proton transfer of the many energy-expensive reactions like of cells like F-actin filament molecule treadmill lengthening process:
https://pubs.rsc.org/-/content/articlelanding/2016/cp/c6cp01364c/unauth#!divAbstract
This page describes F-actin length and reconstitution using ADP: https://m.phys.org/news/2014-09-scientists-uncover-clues-atp-mystery.html
Video actin treadmilling simulation:
https://m.youtube.com/watch?v=VVgXDW_8O4U
Two parallel F-actin strands must rotate 166 degrees join correctly together. This creates the double helix structure of the microfilaments found in the cytoskeleton.  ATP  is well described on wiki in at that level.
It seems to imply that there is a "static/magnetic" electrical charge differential surrounding the actin molecules and transferred in the minuscule H2O medium which attracts rotates and bonds them.
The electrical differential of Actin is described as heterogenous with surrounding salt bridges and protonationdeprotonation, by this general research:
https://www.google.com/amp/s/www.researchgate.net/figure/The-charge-distribution-on-the-surface-of-F-actin-is-highly-heterogeneous-leading-to_fig5_7090136/amp
I'll try to synthesise some quantim articles of that kind for a coherant sequence of events, ill have to pause because im writing on a phone.
Some info on the H2O alignment involving a different view of ATP is here :
https://www.google.com/amp/s/phys.org/news/2017-03-atp-hydrolysis-energy-large-scale-hybrid.amp

I’d wait to post until you have an answer. A list of references is not acceptable as an answer, as you will see if you read the help. I also wonder whether it might be better to re-ask this six-year old question on SE Chemistry, where it might come under more rigorous scrutiny than here.

If i delete it temporarily will it dissapear after a day? A week?

If you delete it it will disappear immediately. Just be sure to go into edit it first and then copy it and paste it into a word processor document so you can read use the relevant material when you have your full answer ready.


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Why are amino acids in biology homochiral?
Why are nearly all amino acids in organisms left-handed (exception is glycine which has no isomer) when abiotic samples typical have an even mix of left- and right-handed molecules?

It's no answer, but Radiolab had a great discussion of chirality and the issue you've brought up. Worth a listen: http://www.radiolab.org/2011/apr/18/mirror-mirror/

@yamad.  The site you link to contains the line 'all living molecules are left-handed'. This, of course, is nonsense.

@TomD ha, fair enough. Oversimplifications aside, though, I still like the piece because my memory is that they do a good job giving an intuitive feel for what chirality is and its effects. Of course, its likely that they make more frustrating oversimplifications and I missed them or forgave them in my rapture that a popular show was willing to dig pretty deeply into an idea like chirality for entertainment purposes. Sometimes Radiolab makes major missteps, but in general, I think their stuff is pretty solid as far as popular accounts of tricky scientific concepts go.

I know that you are referring to the commonly ribosome-translated L-proteins, but I can't help but add that there are some peptides, called nonribosomal peptides, which are not dependent on the mRNA and can incorporate D-amino acids. They have very important pharmaceutical properties. I recommend this (1) review article if you are interested in the subject. It is also worth mentioning that D-alanine and D-glutamine are incorporated into the peptidoglycane of bacteria.
I read several papers (2, 3, 4) that discuss the problem of chirality but all of them conclude that there is no apparent reason why we live in the L-world. The L-amino acids should not have chemical advantages over the D-amino acids, as biocs already pointed out.
Reasons for the occurrence of the twenty coded protein amino acids (2) has an informative and interesting outline. This is the paragraph on the topic of chirality:

This is related to the question of the origin of optical
activity in living organisms on which there is a very
large literature (Bonner 1972; Norden 1978; Brack and
Spack 1980). We do not propose to deal with this
question here, except to note that arguments presented
in this paper would apply to organisms constructed from
either D or L amino acids.

It might be possible that both L and D lives were present (L/D-amino acids, L/D-enzymes recognizing L/D-substrates), but, by random chance the L-world outcompeted the D-world.
I also found the same question in a forum where one of the answers seems intriguing. I cannot comment on the reliability of the answer, but hopefully someone will have the expertise to do so:

One, our galaxy has a chiral spin and a magnetic orientation, which causes cosmic dust particles to polarize starlight as circularly polarized in one direction only. This circularly polarized light degrades D enantiomers of amino acids more than L enantiomers, and this effect is clear when analyzing the amino acids found on comets and meteors. This explains why, at least in the milky way, L enantiomers are preferred.
Two, although gravity, electromagnetism, and the strong nuclear force are achiral, the weak nuclear force (radioactive decay) is chiral. During beta decay, the emitted electrons preferentially favor one kind of spin. That's right, the parity of the universe is not conserved in nuclear decay. These chiral electrons once again preferrentially degrade D amino acids vs. L amino acids.
Thus due to the chirality of sunlight and the chirality of nuclear radiation, L amino acids are the more stable enantiomers and therefore are favored for abiogenesis.

BIOSYNTHESIS OF NONRIBOSOMAL PEPTIDES

Reasons for the occurrence of the twenty coded protein amino acids

Molecular Basis for Chiral Selection in RNA Aminoacylation

How nature deals with stereoisomers

The adaptation of diastereomeric S-prolyl dipeptide derivatives to the quantitative estimation of R- and S-leucine enantiomers. Bonner WA, 1972

The asymmetry of life. Nordén B, 1978

Beta-Structures of polypeptides with L- and D-residues. Part III. Experimental evidences for enrichment in enantiomer. Brack A, Spach G, 1980

Thanks Gergana. I'll follow some of this up. I can comment on the astronomy angle later.

Hope these papers are helpful. Let me know what you have found.

The difference between L and D amino acids does not affect the tertiary structure?

Because I was bored, I found and added links to the citations from "Reasons for the occurrence of the twenty coded protein amino acids"

The ribosome holds the peptide-bound tRNA and aminoacyl-tRNA in the right orientation to catalyze the peptidyltransferase reaction.
http://www.pnas.org/content/103/36/13327/F1.expansion.html
If the incoming aminoacyl-tRNA was the other enantiomer, the amino acid moiety would not fit properly into the ribosome active site.  In other words, the shape of the ribosome selects for specific amino acid enantiomers.  In abiotic mixes, the creation of amino acids and their polymerization is non-catalytic, and so there is no specificity or selection for certain enantiomers.
If you're asking the "biogenesis" question, then I think the answer is that we don't know the original selection, and it may just be chance.  But once biochemistry began making and using them, of course they were all the same.  But frankly "why not D-amino acids" makes about as much sense as "why not 22 amino acids, or 23, or 24, or 25?"  Because that's what happened.

Thanks for the answer @KAM. However, i don't buy your criticism of the biogenesis aspect to the question! Sure,it may have been that "by chance" L-amino acids got selected, but the fact that all life now only uses L-aminos is intriguing. Given an equal probability of L and D aminos, this suggests that life only arose one from L-aminos, or that L-amino life managed to outcompete and eradicate D-amino life. Either possibility sends us in interesting directions.

But, you still get an upvote ;-)

As far as I know, it is unknown why we only see left-handed and not right–handed amino acids. A recent article speculates that the weak force could be responsible for a tiny asymmetry in energy levels between the stereo-isomers. However, if the effect is tiny, its hard to see why it should have biological implications. In 2004, Tamura and Schimmel showed that RNA has a preference for L-amino acids, whereas mirrored RNA has a preference for D-amino acids. They conclude:

These results suggest the possibility that the selection of L-amino acids for proteins was determined by the stereochemistry of RNA.

So the next question is: Why do we observe only one kind of RNA? It could just be by chance, that a polymer of one RNA configuration became self-replicating.

The chirality of RNA enforces the chirality of amino acids, neat. I wonder if there is mirror RNA out there, because the penalty for being mirrored is lower? (is it lower?)

The normal results of an attempt to assemble proteins with mixed chiral amino acids is a protein that fails to fold.
The general assumption due to this result is a choice has to be made very early on to use all right-handed or all left-handed amino acids. There doesn't seem to be any particular reason to choose one way over the other except for prevalence.

Using only 1 chirality for the ecosystem simplifies protein formation and folding frameworks. In theory, you could have a codon system with 40 distinct values (and 24 redundant values): glycine, stop codon, and left/right variations of each other amino acid. However, the proteins and nano-"machinery" required to support this would be crazy complex. It's much more efficient to build around 1 chirality and stick with it.
Alternately, you could have enzymes specifically designed to flip proteins of the "wrong" chirality depending on species.
With that in mind, an ecosystem with different species having different amino acid chirality would be digestive chaos. If you eat a dextro-protein steak, your digestion will break the proteins into... dextro amino acids. Best outcome: they fail to absorb and get flushed down the toilet. Worst outcome: they get absorbed and your cells use them to make proteins - causing severe folding errors, nonfunctional proteins, and a host of untraceable health problems that would likely get misdiagnosed as a spirochaete infection (wide-ranging health problems that aren't limited to a specific region and have no discernible pattern).

Addendum: your immune cells might identify nonfunctional/malformed proteins produced from consuming dextro-amino acids as dangerous foreign matter/invaders, causing widespread allergies

Most answers to the question of homochirality have considered the reason (if any) for amino acids in proteins being L rather than D. i.e. Why L? I have nothing further to add to that discussion.
A couple of answers have addressed the question of why there is not a mixture of L- and D- amino acids in proteins, i.e. Why all L? Two distinct arguments have emerged. I shall consider them in turn, and attempt to develop them a little further.
@Joshua stated that “the results of an attempt to assemble proteins with mixed chiral amino acids is a protein that fails to fold”. I think one can cast this more precisely in evolutionary terms. The α-helical secondary structure component of proteins probably arose early as it involves only the protein backbone, rather than the particular amino acid side-chain. Nevertheless, it is not possible to substitute a D-amino acid in an α-helix of L-amino acids, without disrupting the structure. Hence one can suppose that homochirality was necessary for the creation of standard ‘building blocks’ for early protein development.
@KAM has considered the question of the stereochemistry of the active site, specifically that of the peptidyl transferase. The stereochemistry of the active site of the interaction of enzymes with their substrates is a strong argument for homochirality, but it struck me that this needs to be addressed before peptide-bond formation — in the synthesis of the amino acids themselves.
It turns out that I was late to the party. In the 2002 edition (I haven’t checked earlier ones) of the text book, “Biochemistry”, by Berg et al., section 24.2.2 of the chapter on amino acid synthesis is entitled:
A common step determines the chirality of all amino acids
Amino acids are synthesized, directly or indirectly, via reactions catalysed by transaminases (aminotransferases) which convert keto-acids to amino acids:
Oxaloacetate → Asp → (Asn, Met, (Thr→Ile), Lys)
Pyruvate → (Ala, Val, Leu)
Phosphoenol pyruvate → (Phe, Tyr, Trp)
α-Ketoglutarate → Glu → (Gln, Pro, Arg)
3-Phosphoglycerate → Ser → (Cys, Gly)
Ribose 5-phosphate → His
These transaminases have a similar active site involving a lysine and arginine residue and use the cofactor, pyridoxal phosphate. The reaction mechanism (below) may appear a little complex, but the step at which the chirality of the amino acid is determined is the conversion of quinoid intermediate to external aldimine:

To quote from Berg et al. (from which the diagrams are taken):

The chirality of the amino acid formed is determined by the direction
from which this proton is added to the quinonoid form. This
protonation step determines the l configuration of the amino acids
produced. The interaction between the conserved arginine residue and
the α-carboxylate group helps orient the substrate so that, when the
lysine residue transfers a proton to the face of the quinonoid
intermediate, it generates an aldimine with an L configuration at the
Cα center.

So it would seem more likely that the stereochemistry of the active site of peptidyl transferase was an evolutionary response to the existing homochirality  of amino acids, rather than vice versa.


text:
What are the different ways an exon gets spliced?
Exons are produced by more than one mechanism, e.g. splicing out introns after transcription, if I remember correctly. Please list all mechanisms.

When voting to close a question please take the time to explain your reasoning in a comment, particularly if you are the first to cast a vote :)

Is this homework?

Exons are not "produced" by splicing. What exactly are you asking here?

There are several ways splicing can occur, which depends on the RNA molecule to be spliced and the catalyst that performs the splicing:

mRNA splicing is carried out by spliceosome, which consists of small nuclear RNAs. There are sequences at the end of the introns and branch sties which indicate the splice sites. The so called lariat structure is formed when the 2'OH group of an adenosine residue in the branch site attacks the 5' splice site.
self-splicing of ribosomal RNA precursor - it is performed with the absence of spliceosome.
tRNA splicing - it requires three enzymes and ATP hydrolysis.

References:
Biochemistry, L. Stryer, 5th eddition
J. Abelson. tRNA Splicing


text:
The GUG start codon in E. coli: identity of initiating tRNA and efficiency of translation
Translation in E. coli is usually initiated at an AUG codon, which encodes the amino acid methionine. In some cases, however, the start codon is GUG, which normally encodes valine. If GUG is used as the start codon, is a tRNA charged with methionine used or one charged with valine, and does the use of GUG as a start codon affect the efficiency of translation?

Below I think is the most extensive study so far quantitatively comparing all codons as a possible initiation codon in E. coli for sfGFP and Nano-Ogra-luc ("Nanoluc") proteins (published in 2016): "Measurements of translation initiation from all 64 codons in E. coli"
Ariel Hecht, Jeff Glasgow, Paul R. Jaschke, Lukmaan Bawazer, Matthew S. Munson, Jennifer Cochran, Drew Endy, Marc Salit https://doi.org/10.1101/063800
https://doi.org/10.1093/nar/gkx070

There are two substantially different questions here. As this was posted 7 years ago (before I was involved) there may be little to be done. It would be better if they could be separated, and certainly others should be discouraged from doing likewise.

The NCBI translation table translates all alternative start sites as methionines. To my understanding, all translation is initiated by the fMet-tRNA. I don't know if there are any exceptions to this rule.
Regarding translation efficiency, I only found a 1985 paper in PNAS (Reddy et al, PNAS 82:5656-60), in which they compared the translation efficiency of adenilate cyclase's own UUG start vs GUG or AUG, obtaining a translation ratio 1:2:6 UUG:GUG:AUG, suggesting that AUG is the most efficient one, followed by GUG. Also, Romero and Garcia, FEMS microbiology letters 84:325-330 (1991) compared the efficiency of AUG vs AUC, AUA and AUU, showing a much lower efficiency for those codons, but they did not compare it to GUG.

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


text:
Intrinsically disordered proteins as potential drug targets
Intrinsically disordered proteins (IDPs) are a class of proteins that do not adopt a stable secondary or tertiary structure under physiological conditions in vitro, but still have biological functions. Many IDPs are implicated in cancer, neurodegenerative diseases, and diabetes, which makes them attractive drug targets. Are there any successful examples of that? Are there any drugs which disrupt protein-protein interactions (where one of the proteins is an IDP)?

IDPs are indeed attractive drug targets and there are ongoing efforts to develop drug molecules that block interactions between a disordered and a structured protein. According to this relatively recent paper, however, these efforts have not brought a drug on the market, yet.
A few promising studies have shown drug-like molecules that inhibit protein-protein interactions based on intrinsic disorder of one of the partners and target:

oncogenic fusion protein EWS-FLI1 and RNA helicase A. A small molecule has been found that targets the disordered region of EWS-FLI1, blocks the interaction with the helicase and inhibits growth of Ewing's sarcoma.
p53 tumor supressor and its interactor Mdm2. Mdm2, by binding to an intrinsically disordered region of p53, targets p53 for ubiquitination and also causes it to be transported out of the nucleus. Promising small molecules  have been found that associate with Mdm2 and thereby block its interaction with p53.
c-Myc oncoprotein and the interaction with its partner Max protein. This study demonstrates two small molecules that bind to c-Myc and stabilize its disordered conformation, which inhibits its interaction with the Max protein.

The challenge in targeting protein-protein interactions for therapies stems largely from the fact, that the protein-protein contact surfaces are much larger than those involved in protein–small-molecule interactions (1,500–3,000 Å2 and (300–1,000 Å2, respectively) [2]. They are often flat and have no defined binding pocket. Also, IDPs often don't bind natural small ligands, that could act as starting points in developing drugs.
You may find this paper helpful:
Metallo SJ, Intrinsically disordered proteins are potential drug targets, Curr Opin Chem Biol. 2010 14(4): 481–488.
BTW: for a comprehensive, manually curated list of disordered proteins and regions, please check the Database of Protein Disorder.

Thanks for your answer and the references. I will definitely look them up. I already read the Metallo, SJ paper, which is an excellent paper! What concerns me the most though, is that all IDPs can interact with multiple small molecules or other proteins, so they cannot be specifically targeted. That's why I am very interested whether specific interactions have been discovered.

I have been working on this problem for quite some time now and believe me getting specific binding is a real issue with IDRs. Also, since these regions don't contribute to the core structure of the protein, the residues are less conserved (more prone to mutations). So in the case of evolving drug-resistance contributing proteins this becomes a bottleneck.
I have done some work on IDPs as potential drug targets: Unraveling the potential of intrinsically disordered proteins as drug targets: application to Mycobacterium tuberculosis.
But the concept has been taken well by even the conventional structural biologists.
As the paper suggests, my work is focused on Mycobacterium tuberculosis. Multi-Drug Resistant (MDR) and Extensively Drug Resistant (XDR) forms of TB have added to the tuberculosis loads not only in the developing but also developed nations. Drug resistance has been associated with proteins (mostly those involved in transport and metabolism) that have helped this pathogen grow resistant to the first line drugs or more. I refer to such proteins as "Drug resistance associated proteins".

Thanks for your answer. I will definitely read your paper. I also saw a list of your papers on linked in. I am particularly interested in the protein-protein interactions. By the way, what do you mean by "drug-resistance contributing proteins"?


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Why do plants have pith and how is it useful to them?
Many plants have pith, from walnut trees to corn to ragweed, but I can't think of anything it does them. What is pith and how is it useful to them?

Strange question: did you try to google? The first entry in my search results provides more than complete answer to your question.

The pith (medulla) forms part of the ground tissue system of a plant, and specifically it is the ground tissue which lies interior to a plants vascular tissues (xylem, phloem etc.)
The ground tissue system is responsible for much of a plants metabolic functioning, and contains various specialized cell types which aid in photosynthesis and storage of photosynthesis products. The pith is made from parenchyma cells.


text:
Absorption ratios 260/280 and 260/230 for RNA
I extracted RNA from different cell lines, an I want to perform reverse transcription and then PCR. To get good results, in which range should the absorption ratios 260/280 nm and 260/230 nm be? And what is the idea behind measuring those ratios?
I got values for the 260/280 ratio from 2.1 to 2.13 and values for the 260/230 ratio from 0.98 to 2.01. Are these values acceptable, and what information can I gain from them?

DNA and RNA absorb at 260nm. Proteins absorb at 280nm. The 260/280 ratio is a good estimate of how pure your sample is. For RNA, the 260/280 should be around 2. If it is lower, this might be an indication from contamination or proteins, phenol, or other contaminants in your sample. The 260/230 ratio is a second measure for purity of the sample, as the contaminants absorb at 230nm (like EDTA). The 260/230 ratio should be higher than the 260/280 ratio, as it is usually between 2 and 2.2. Lower ratio might be an indication of contamination.
In your case, I would be worried about the purity of the sample which gave you 260/230 ratio of 0.98. If you are using nanodrop, looking at the plot can also be a good indication of the quality of your sample. For a pure sample, a well defined peak (no shoulders or wiggles) at 260nm is expected.
Take a look at the NanoDrop manual for more information.

Indeed I remember than the sample with the ratio 260/230 had two peaks. In my case the values for the 260/230 ratio are never higher than the 260/280 which indicate I have contamination. What can be the consequences not to have the correct values for these ratio for a PCR? I will extract RNA soon. How can I prevent a contamination next time? What is the good practice?

If you have two peaks is a clear indication of contamination. Don't look only at the ratios because this gives you some idea, but doesn't make a strong statement. The PCR might fail due to contamination but you might try it anyway. You might also try isolating your RNA again.

For the sake of completeness and relevant detail: The aromatic amino acids (Phe, Trp and Tyr) are the primary contributors to the ability of proteins to absorb at 280nm. Cysteine double bonds can also absorb but its both rare and the extinction coefficient is smaller in comparison to the aromatic residues.


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Reverse transcription PCR optimization
What is the ideal amount of RNA to use for the RT? and how much cDNA to use then for the PCR?
I did RT with a solution of RNA of 0.36 ug/ul. Then for my PCR I used 1 ul of the cDNA obtained and used 25 cycles because I was hoping to see a difference between an endogenous level and an overexpression. However, I detected no band at the expected height of 500 bp but a diffuse band at 100 bp. What can this 100 bp represent? primer dimer? I switched to 35 cycles and I used either the same amount of cDNA or add 3 times more cDNA. In both cases I got bands at the expected height (but stronger when I put more cDNA) and still big bands at 100 bp.

RT PCR refers to reverse transcription I assume? Not to real time PCR?

@Alexander Galkin Why did you remove the PCR tag? I think the question is really about RT PCR, and not RT in particular.

@GerganaVandova Do you think that we need a special tag for RT PCR? Isn't it too confined area? I wasn't sure whether to correct it "PCR" or to "reverse transcription" and chose the last one. If you feel it is wrong, feel free to retag the question, it is more than welcome in the community.

@Alexander Galkin Yes, I believe the question is more about PCR rather than RT. You are probably right that RT-PCR tag is too specific. The PCR tag is good enough.

I agree with Gergana, this is a PCR question. I also believe that a PCR tag should be enough for all its variations (RT-, Q-, nested, etc)

I see big fuzzy bands around 100bp as well. They're most likely RNA contamination. To get rid of them, digest your RT-PCR products with RNAse-H. But if you just need to visualize your band of interest, and the fuzzy bands aren't getting in the way, it shouldn't be a problem.
I usually input anywhere from 1-2 ug of RNA into my RT-PCR reaction using the Invitrogen Superscript III kit for a total volume of 20 ul. After the reaction, I use 1/10 the volume of that (2 ul) for downstream (PCR) applications. This usually gives me nice results.
To optimize RT-PCR for detection of a specific target, consider using gene specific primers (make sure to use only anti-sense primers) in your RT-PCR instead of oligo-dT or random hexamers. This enriches your target when you use them for downstream applications. When you use GSPs though, make sure to run a parallel reaction with control (i.e. beta actin) primers to prove that your RT-PCR reaction is working.

There is no single "ideal amount" of RNA. I would suggest you to do a titration curve to determine the best amount for your specific assay. The band at 100 bp could be a non-specific amplification. You could try to increase slightly the annealing temp to see if that removes (or reduces) the lower band. Alternatively, you can consider a different primer set or even a nested PCR.
Also, it is still possible that you may look at a splicing alternative in that band. Do your primers span more than one exon?