ennui

There are some very good points about telomeres here. But another aspect of the age issue is the environment. While we may have it hard-wired in our genomes to have our telomeres shortened, etc. there is also the environment and how it affects our DNA. Our cells are constantly exposed to breakages and other kinds of damage. The mechanisms we have to repair the DNA aren't perfect. One of them, non-homologous end joining, can result in bits of the DNA being trimmed (e.g. by the enzyme Artemis, or other nucleases) or even bits of the DNA being added in a template-independent manner in microhomology sticky-ends (e.g. TdT and DNA polymerase mu). So as we live, we accumulate more damage to our DNA. Eventually, the damage is such that it escapes the cell's repair mechanisms (these being imperfect) and we get loss-of-function of certain proteins. This results in ageing and cancer.

Thank you! God, I've had no end of trouble with protein classification. My teacher has been away and journals haven't been a help. That's cleared a lot of stuff up. Gracias!!

Bioinformatics is giving me a headache! Lots of authors mention the terms 'protein fold', 'protein superfold', 'protein family', 'protein superfamily' and 'protein domain' interchangeably. How do you guys use these terms? What's standard in the protein community?

I'm wondering if anyone could help me with a genetics problem. I know that for RNA Polymerase II genes - you have a promoter, on which forms the preinitiation complex (PIC). As part of this apparatus, you have general transcription factors (GTFs) necessary for basal transcription in vitro. Things like TFIID, TFIIB, etc. But for efficient transcription in vivo, you need activators and co-activators, yeah? Activators bind to enhancers way upstream (or downstream!), which then bind to co-activators which can either (i) associate with the PIC directly, like certain TAFs and mediator OR (ii) remodel the chromatin to make things slide along easily. What I've just described is a model system. But can anyone think of any real examples of this? Something with clinical correlations would be awesome. I.e. if someone could point out an Activator & Co-activator for a certain eukaryotic virus which both associates with the PIC and/or remodels chromatin, that would be superb. Or perhaps some physiological process. It would be great to have a solid example which covers all the points of this model description of gene activator. Much appreciated.

Yeah it was hard to find in journals - even reviews. They were more occupied with explaining the mechanisms. But now I know everything I need to know - thanks!

The [math]\lambda[/math] bacteriophage has one of the most extensively studied 'molecular switches' in molecular genetics. The Cro/cI system appears to control the decision of the virus to go into a lytic or lysogenic cycle. cI is mainly responsible for lysogeny, and Cro [+cII] for lysis. I know that the occupation of the rightward operator (O[math]_{}R[/math]) and its three binding sites (O[math]_{}R[/math]1,O[math]_{}R[/math]2,O[math]_{}R[/math]3) determine the repression of P[math]_{}R[/math] and P[math]_{}L[/math], and hence halt Cro expression. They form an octamer with the leftward operator and 'bend' the DNA. But what is it in the bacterium that leads to a drop in cI levels, and hence a switch to the lytic stage? Some journals have hinted at cAMP levels affecting the transcription of cI, but I can't seem to find any detailed information about why the cI levels would drop and relax the repression of Cro transcription. Does anyone know a journal which points this out? Or could anyone familiar with this bacteriophage help explain it? Much appreciated.

For an exam I have to memorise things about Toll-like receptors. I should know (at the very least) their names, where they are in the cell, and what they detect (e.g. flagellin, ds-RNA or what-have-you). Anyone know any good mnemonics for this? Or does anyone know of a particularly good summary diagram on the Internet? Not sure if this belongs in the Homework or Immunology section - feel free to move.

There's a lot of talk on the news about tuition fees in Britain. The majority of university Vice-Chancellors want to raise the cap on fees to nearly double the current amount, while some want the fees to be limitless. How do you think this will impact the science sector in the UK? From my own perspective, I probably wouldn't have entered science if my total debt from university would be in the region of £60k. With some universities pushing for up to £20k a year, will this be reasonable for students from low-income backgrounds? I can't imagine that a prospective student from a low-income background would want to apply for a science degree if this happens. Imagine facing the reality of £60k for 3 years' worth of tuition, and then living expenses (£10-15k) on top of that. If you start off in a science company like GSK or Pfizer, you're looking at £22k a year when you start. Is this meagre salary worth so much debt? The salary will increase, sure, but to have £70k ($130-150k) of debt looming over your head in your 20s must be terrifying. What does everyone think about this? I'd be interested to hear some American perspectives, as I know that education is generally more privatised and expensive over there. How does a science degree 'pay-off'? Or do you see financial debt as more of a sacrifice for doing something you love? Personally I'm worried for the "next generation" of scientists. It would be tragic if aspiring medical researchers, engineers and ecologists were put-off by the spiralling costs of university tuition.

I'd say that peptides are polymers. Certainly as much as DNA is a polymer. Although you get different R-groups in a peptide (so it might not be an identical repeating unit), you get different bases on DNA. I work in amyloid research. It's a cross-beta repeat of a peptide unit to form a long, fibrous protein. Lots of the literature calls it a polymer.

Medical microbiology is investigating pathogenesis and virulence. E.g. investigating the edema factor of anthrax and how the body responds to it with toll-like receptors. Clinical microbiology is working in a hospital lab diagnosing people. E.g. receiving a tissue sample and diagnostic methods to identify the pathogen.

That's an awesome quote. Hadn't heard that one before.

I didn't argue against three men or three women, did I? In fact I only wish to discuss same-sex marriages. If there's a thread started for polygamous marriage I'll happily contribute. But for now let's stick to the one issue, shall we? There's no strong argument against same-sex marriage. I suspect that's why you deflected to the issue of polygamous marriage. Some people have insightfully highlighted that it would be easier to first introduce civil unions which grant the full legal status of marriage, but lack the terminology. Also, there's another argument floating about in the thread saying that it appears to be the "people's will" that marriage should be defined to a certain traditional way. Although these points can be reproached (I've seen a lot of good argument/counter-argument surrounding them), you can see how this line of discussion is of a higher quality than taking leaps of imagination. I always think it mars a discussion when people start using devices such as hyperbole to make a point: "So you're gonna let two guys marry? Well why not let a guy marry a table? Why not let a guy and a dog marry? You think it's okay to let a guy marry a dinosaur!?" Please, please just stick to the topic at hand. Discuss the pros and cons of same-sex marriage first. Launching into alternative scenarios doesn't say anything about the subject. Asking "why not three men or three women?" doesn't say anything about gay marriage. If you were to say "I don't agree with gay marriage, because I believe it will lead to polygamous marriages" then you'd have to first say why polygamous marriage was bad, and then prove that it would.

I've answered these questions in my last two posts. What I think might help is if I use a hypothetical example. The central dogma in biochemistry is that DNA produces mRNA, which in turn produces a protein. So the scheme is: DNA [math]\leftrightarrow[/math] mRNA [math]\rightarrow[/math] Protein You'll notice that arrow linking DNA to mRNA goes two ways. This is because there's transcription and reverse transcription (such as in viruses). Let's invent a protein. We'll call it 'SFN'. This protein is a growth receptor on the plasma membrane. When a hormone hits it, the cell knows when to divide and grow. So if SFN was active all the time, the cell would divide exponentially. You'd get cancer. This is the gene for SFN: 5'-ATGCGACCCTCCGGGACGGCC-3' This is the protein it will produce: N-MRPSGTA-C Now imagine that this protein needed the R residue (arginine, I've underlined it) to bind a hormone and let the cell know when to grow and divide. If the DNA is exposed to damage (from U.V., oxygen, carcinogens found in cigarettes, or whatever) then there could be a mutation. The "CGA" part of the DNA (this codes for the arginine in the protein) could become CCA. What will this do? It will change the protein. Instead of getting an arginine as the second amino acid, you'll now get a proline. The protein now has a different shape. What does this mean? It means that now the protein doesn't have the right amino acid to bind the hormone. It's no longer controlled by the body and the endocrine system. The result is that it's active all the time. It will result in a cancerous cell. This is a simplified analogy. The sequence is actually from a real protein, EGFR1, which is hugely present in a LOT of cancers. The cell can normally cope with mutation events like this through repair mechanisms. But as we age (and as we're exposed to more mutagenic chemicals) we lose the 'safety nets' that our cells have evolved. The damage we get is cumulative. I hope this helps you to understand. And I'll repeat the sentiments from my first post: if you don't think that progress is happening fast enough, get involved in the field and help out.

There aren't any good arguments against gay marriage. Case in point: Scrappy starts talking about earthworms of all things when his argument fails. He might as well devise a puppet-show too; anything to divert attention from such a shaky, ill-founded position. Two men should be allowed to marry each other. So should two women. It doesn't hurt anyone, and both parties do so of their own adult consent. Furthermore it means that homosexuals have the same rights and legal opportunities as a heterosexual couple. This is clearly a logical, good thing. To say that two men or two women should not be allowed to marry is silly. Creating some new 'civil unionship' might be progressive, but ultimately falls short of the mark. Imagine the outrage if a government invented a separate marriage-like system for black people but failed to call it a real marriage. I don't understand why everyone can't have the same rights and status. What does it matter if the marriage has two people of the same gender? To invoke analogies of incest is particularly low. It's a cheap tactic. It's like saying "Women shouldn't be allowed to vote. If we let them vote, we might as well let them murder people." It's exaggerating a liberty to a gross and degenerate form for the purpose of polemic deceit. I disagree with the statements about marriage being a religious byproduct. On the contrary, in classical Western Europe marriage was more often than not a financial or secular arrangement. Even if it were a religious entity, I wouldn't hang on to that meaning at all since it's been changed so much in recent years. Let gay people get married, call it marriage. Problem solved. Sure, some religious people won't like it. But I wouldn't change something based upon that reason. Imagine if we applied that thinking to evolution.

Oh dear. That's pretty depressing. I'm just going to tell myself that when I get drunk, the alcohol is thinning my blood, thus allowing more blood to reach my brain. Or something like that.

Hey all, People often tell me that drinking lowers your IQ. And that if you drink regularly, it will be a permanent effect. I even remember a biology teacher once telling a class this. Do you think that alcohol consumption has any permanent effect on intelligence? Can you drink heavily for say, 5 years, and still have the same IQ once you stop? I wonder if there's any research to shed some light on this issue.

You used to have one? Did it attract fundamentalists?

This thread will open a large can of worms, I'm sure! I did a poll asking if people believed in God (it was a very crude one, without any definitions or anything- I wanted to keep it protean) and was surprised by how many people said yes. For some reason, I always imagined that members of the scientific community would be overwhelmingly atheist. It was partly bolstered by some studies I'd found a few months ago (from New Scientist, to my recollection) on the religious demographic of scientists in North America. From my hazy memory of the data collected, they pointed to a 90% or above atheist population within the sciences. Shovels of criticism can be laid upon polls as a means to distinguish a certain population's religious convictions, or lack thereof. But from personal experience it seems to be roughly accurate: about 90-95% of the scientists I know are atheists. I'd be surprised to learn if this wasn't the case for most Western laboratories or scientific institutions. I disagree with the premise in the initial post that education is some sort of 'flaming torch' to vanquish the shroud of religious and mystical mental trappings that occupy the human mind. There are likely more factors at work in determining the religious attitudes of a person. My personal experience has demonstrated to me that scientists from religiously conservative cultures such as Pakistan, India or Italy still have deeply rooted religious beliefs that don't change. No matter how much they educate themselves about science, they still attend a Mosque or Church every weekend. I've only spoken about scientists because I know a lot of them (and this is a science forum). But to me, this signifies that the religiosity of a person isn't really linked to education. I'd say that culture and personal experience hold much more sway. I'm sure it plays a part - but perhaps isn't the primary player. In my own case, I am religious - definitely not an atheist. I also have education in science. These two things haven't correlated at any point. As I become more educated in science, my religiosity isn't waning. If anything, I'm becoming more spiritual as I age.

I was browsing Wikipedia the other day to look at impact factors. One of the highest was Annual reviews in Immunology - I couldn't understand why immunology was higher than other things.

Hey all, I have a quick question regarding scientific journals. It's geared towards Biology/Biochemistry/Genetics, but not completely. I've heard that being published in Nature is pretty prestigious. But what about the other Nature journals? E.g. Nature Cell Biology, Nature Methods, Nature Genetics, etc. Is it still good to get published in these? What kind of impact factor is regarded as decent for a journal?

They're very good points. Sometimes we all have stupid days. Does anyone else ever get that brain-state when you can't even remember how to spell basic words you've been spelling all your life!? The other day, I had to think for a while on how to spell 'tunnel'. Personally, I'm not a big fan of I.Q. tests. I'm even less of a fan of high I.Q. societies. They seem awfully pretentious. But I.Q. tests themselves probably have their value of being a rough measure of some kinds of analytical skills. In my last I.Q. test, I scored somewhere in the region of 72. According to some charts, that's borderline retarded. Oh dear.

Here in the U.K. a science PhD will pay between 15k and 25k. The 15k stipends are usually given by the universities themselves, or the Medical Research Councils. The higher-end pays are from charities like the Wellcome Trust and the British Heart Foundation. It works out to be effectively worth more than a salary of the same number, since the stipend is wholly tax free - and postgraduate students are exempt from paying council tax, too. So a 15k stipend is comparitively similar to a 20k job salary. When I was applying for a PhD studentship funded by an Alzheimer's Trust, I was surprised at how much they invest into just one PhD. For the whole three years, it was over 90k. This included tuition fees, stipend, travel expenses and materials expenses. From researching pharmaceutical companies like Pfizer and Novartis, it appeared as though the starting salary was 18-20k. Of course, this has an advantage over a PhD stipend, namely bonuses and salary growth. I agree completely with your points about financial security. There was a fantastic article I read in a newspaper the other week about how a PhD is really not a good way to 'get rich'. In fact, I'd say that science as a whole (whatever qualification) is overall not a great financial path. I'd much rather call it a 'labour of love' for the subject itself. But if someone has the financial stability, a PhD could be great for learning more and being challenged more. In my own case, I think a PhD is a great idea because a lot of the careers I'm looking at require one. I either want to be a research fellow/lecturer at a university or go into clinical sciences in the health sector. While the former is more risky and the pay is a scandal (as Charon said), it's what would make me the most happy. I'm in love with the idea of being a university lecturer and having my own lab to do research.

Reading this thread is making me wanna watch Deep Impact.

I agree, I'm in the soft c camp. Merged post follows: Consecutive posts merged When lecturers say "a-my-no" people usually giggle. It's because they're almost always the very posh, upper-class lecturers. It's like the old scone/scooooone thing.