The amazing “Thermodynamics by txt”

OK so this is a little compilation inspired by text conversations with Del last week, trying to deliver basic thermodynamics in the form of text message

What is a reaction?

Well, a reaction consists of a chemical change undergone by reactant(s) to form product(s). There are various different types of reaction from two molecules coming together to form one product to one reactant falling apart to form more than one product:

A + B → C or A → B + C or even A + B → C + D

The thermodynamics of a reaction are dictated by the energy held in the reactants or the products. Some reactions will result in a net release of energy; these reactions are known as exothermic and are characterised by the release of energy in the form of heat, light, sound, or even all of these (in the case of an explosion). Other reactions will require energy from the environment; these are known as endothermic and are usually identifiable by a drop in the temperature of the reaction mixture, in comparison with the surrounding temperature.

Are reactions always very fast/violent? Do solids react with other gases?

Solids may react with other gases, or even liquids, very readily depending on the reactants and reaction conditions. All gases may be reactive although the Noble gases tend not to react with anything. This can largely be explained with a brief description of atomic structure. The generally accepted model of the atom consists of a positively charged nucleus (made up of protons and neutrons) being orbited by negatively charged electrons. Electrons are very light and are arranged into energy levels or shells which are rather like the layers of an onion. Each energy level has space in its orbitals for a finite number of electrons, and atomic structure is most stable when all the shells are complete. As an atom becomes larger (as you go down the periodic table, for example from calcium to barium) the electrons are further from the nucleus and may be more easily lost to form positive ions, or gained to form negative ions, forming completed electronic shells. Noble gases begin with all electron shells being full so do not participate in reactions of this kind.

Is it possible for reactions to occur between solids?

Indeed, all that is required for reaction is for the atoms/molecules in question to come sufficiently close under favoured reaction conditions. When a solid becomes dissolved into solution, for example in water, this often enables molecules to get close enough to allow molecules to collide with enough force and in the right orientation for the reaction to take place. A solid dissolved in water may not, strictly speaking, be described as a liquid but rather as a solid suspended in liquid medium. As long as the molecules in question are able to orientate themselves correctly, dissolution in liquid may facilitate a reaction. Molecules must come close enough for reaction, in a manner similar to sexual intercourse between humans/animals. It is not possible to have sex without proper access to the relevant parts, from an appropriate angle.

are exothermic reactions more likely than endothermic reactions?

In theory they are equally likely although in practice it might be that exothermic reactions happen more frequently as energy does not usually need to be supplied to the system. The probability of a reaction happening simultaneously is determined by the free energy (G) of the system. The value for G is calculated by considering the energetic (H) and entropic (S) contributions of the system in the following equation:

G = H – TS (were T represents the temperature of reaction)

As G must be negative for the reaction to take place you can consider that it is most likely that an exothermic reaction (where the value for H would be negative) would give a spontaneous reaction. As the entropic contribution also takes into account the temperature of the reaction it is important to see that a reasonably large positive value for this component could give a negative value for G, and therefore a spontaneous reaction, even when H is positive (for an endothermic reaction, requiring energy from its surroundings).

The entropy (S) of the system considers the degree of disorder created during the reaction. As entropy always favours a more disordered system, increase in disorder results in a positive value for S, and often a favourable spontaneous reaction. I always (rather geekily) blame the usually diablolical state of my room on entropy.



Ok so this is just me messing with some explanations... feel free to question what you don't understand, or anything you want more detail on. more to follow

I think that at some point I would be interested in science journalism. My teaching duties have shown that I'm quite good at explaining concepts to many people and in different ways so I'm interested in building my communication skills and building a model portfolio type thing over the course of my PhD.

I will be requiring questions/subject areas in the bio/chem/health science areas that you might be interested in. I'm happy to read up on stuff for this. My subject areas for my research involve DNA/transcription/RNA/lipids/lipid-DNA self assembly/cellular processes. Any topics are relevant though. Would like to be encouraged to think.

So that is my task to you... come up with questions please

ok so i'm dropping off in my lecture this morning (probably because i have teh flu and should have been in bed but my boss needed me to tell him which reagents to add in which quantity and needed them getting out the freezer for him... but since i got up for that i decided to go to my one lecture of the week as i like ug molecular biology and it's good for me)... this is largely irrelevant but shhh i'm setting the scene. so yes, Del txts me with the following question:

"Is it possible to have a genetic mutation that isn't hereditary?"

The answer is but of course, although some context is needed. Anyway, it turns out that the topic at hand is homosexuality and whether the cause, for want of a better word, is genetic (or indeed a mutation) or down to environmental factors. The classic nature vs nurture debate. So ever since I have been pondering this, and while I am not in any way claiming to be right, here are some of my postulations that result from this:

I am going to use the analogy of a computer as I think it is fitting. Basically computers have 2 main bits; hardware and software. The hardware doesn't vary all that much from machine to machine, the same main pieces are required and are all related to function. With homo sapiens (or people if you like) the basic functions and functioning parts do not change all that much from person to person be they male, female, black, white, homosexual, heterosexual. We all need the same parts in order to be fully functioning (I mean a heart, lungs, brain, digestive system, etc). So this is the hardware of a person. Like computers people have hardware problems... and these are largely genetic, say for example, cystic fibrosis which is caused by a recessive mutated allele (both parents must be carrying a mutated copy and both copies passed to the offspring must be mutated for the disease to be present). This doesn't stop a person being alive, but it may well affect their quality of life and how well their hardware functions, in this case the lungs. You also get mutations of dominant alleles, where only one faulty copy of the gene is needed for the offspring to be affected. An example of this would be Von Hippel Lindau Syndrome (a disease where excess hif factors in cells cause increased blood supply and formation of benign tumours all over the body) or Huntington's Chorea. Interestingly, not all characteristics like this will be apparent from the beginning. The BRCAI gene for breast cancer often doesn't start to be an issue until around 40 years of age for most people... the chloride ion pump that is encoded within the gene is only produced incorrectly at a relatively late stage of life. But you get the picture, as in computers, hardware issues tend to be less common and more "serious"; the implications of them tend to have an overall effect on the function of the organism.

I guess this means that we have to define homosexuality and heterosexuality as being "software issues". If we use the term software to define all the things that make up a personality, then I think we're agreed that by and large these things have no impact on whether or not a body is able to function physically. There has always been talk of them being hormonal, which i guess could have a genetic aspect but is not such a be-all-and-end-all factor. For example, if we take the notion that varying levels of testosterone in the uterus causes differences between chromosomal gender and apparent physical gender then it's clear that these factors can appear somewhere on a sliding scale. Anatomically males and females are reasonably similar: testes and ovaries are very similar organs, the female clitoris is essentially a miniature penis and where women have a uterus men have a prostate. It is feasible that we all originate from the same thing. Hormonal control may be responsible fro variations in this development; all embryos start biologically off male or female, obviously, dictated by whether they inherit an X or Y chromosome from their father, although the idea of internal and external gender being different is not a new concept. The variation in degree of gender duplicity must stem from the fact that hormones are subtle, there are ranges of "normal" hormone concentrations and most people will remain between these somewhere. Some women will have more testosterone than others, just as some men naturally have more estrogen in their system. So this begins to get interesting; we have one "yes or no" option for being male or female but this can clearly be, at least in part, overridden by those pesky hormones. I guess this suggests that hormone production is controlled by many genes (and, given the six possible reading frames of any piece of double stranded DNA, this is reasonably plausible) resulting in individuals making varied amounts of said hormone. So that would be a genetic control of sexuality, and it does appear to be true that some people are just "programmed" to like boys while others are "programmed" to like girls, while of course other people are "programmed" to like both. The reason I liken this to a software issue is that well, for my computer, at least, there are plenty of things that don't work in quite the same way as on my other machine (for example entourage has stopped making sounds) that i have no explanation for but it doesn't stop the function of the computer, I can still send and receive emails.

Of course, then we have environmental factors... the largest of this being the introduction of estrogens and estrogen related compounds into the world around us. Many fertile women are on the pill, we're all (myself included) excreting estrogen which ends up in the water supply. Other sources of estrogen include many cleaning products used commonly; washing powder (i would switch to ecover but it doesn't actually work) and fairy liquid are just 2 examples of this. So the water supply appears to be being filled with estrogen, not such a problem for us girls but it sure is an issue for all you guys. Research has shown that fish are now having gender issues, males are developing female characteristics, suggesting that they're just swimming around in a whole vat of girly hormones. the health implications of that is as yet unclear although it does raise concerns for male fertility (though looking out of my window at the number of pushchairs in this part of the world suggests we don't have to worry just yet), perhaps the scenario in Children of Men (at least, I hope that's tghe film I mean, the one in the future where humans are infertile) is not as far fetched as it seemed. Lower sperm counts have been seen in men; my dad was practically firing blanks, as a result of working with pyridine i believe.

The nurture argument is still considered to be reasonably valid, if we return to the software analogy it's fair to say that whether or not a piece of software will do what it is supposed to depends largely on how it is used. If a child with homosexual tendencies is repressed then I guess that could (and has in the past) cause at least a delay in readiness to "come out" if you will. By the same token, a child who is brought up to be happy in themselves may be happier in revealing their preferences without fear of scorn. Though we are still talking about "programming" here. In my opinion the worst thing a parent can do is be too heavy handed. Everyone likes to get in the dressing up box at nursery and cross-dressing shouldn't be discouraged, will just cost somebody a whole heap in therapy in later life and is not necessarily indicative of later life choices. This is along the vein that camp doesn't necessarily equal homosexuality, although sometimes associations are made; small boys who like to wear dresses are not necessarily gay. it is interesting to ponder what the outcome of this would be though, while i laugh incredibly at green wing, when harriet makes pink brithday invites for her son Robbie with the response "he's gay" one has to wonder wether being too "ok" about thinking your four year-old is gay can be just as unhelpful. I imagine at this age it's simply important to love your child as i'm sure it's when the hormones at puberty kick in that these things are decided. And actually, then, it's important to love your child too.

Basically after making you read all that I really don't know. and these are just my musings on the subject. *sigh* it's an incredibly complex one really.

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