1

Cells, Microbes & Viruses / Re: How do our actions affect our genes?

« on: 13/04/2014 19:28:17 »

Yes. If your actions are damaging to DNA and mutagenic e.g. smoking. The damage done to the DNA can then lead to cancer

Your actions can also have an effect at the epigenetic level, and thus affect the expression of different genes. Diet and exercise are just two examples of lifestyle choices that can do this.

2

Physiology & Medicine / Re: brain methylation?

« on: 27/04/2013 23:04:59 »

Bisulphite sequencing is used to look at DNA methylation. Bisulphite will convert cytosine bases into uracils which will become thymines in the next round of replication, but it cannot do this for methylated cytosines. DNA methylation occurs on cytosines, so if you sequence the DNA following bisulphite treatment you're only going to see those sites that are methylated. To do this for the brain specifically then you'd need to take the DNA you use from brain tissue, which perhaps you could compare with methylation in different tissues.

3

Cells, Microbes & Viruses / Re: Can you resolve this disagreement about virus nature/RNA?

« on: 23/04/2013 20:59:39 »

Viruses can't really do anything by themselves, however they can carry functional enzymes e.g. reverse transcriptase in the case of HIV and other retroviruses. These enzymes are not manufactured 'in-house' by the viruses, but get produced by the host cell that is infected and are then packaged into the new viral particles that then escape the cell. This means that when the virus goes on to infect a cell there may be active proteins released to do some dirty work. The same thing applies to ncRNAs. These will be transcribed from the viral genomic material by the host cell machinery upon infection, and may affect other cellular processes to help out the virus.

I don't think the statements contradict each other, but it's just how the first quotation is phrased.

Hope that helps

4

Cells, Microbes & Viruses / Re: Does infection with one bug beget immunity to another?

« on: 14/02/2013 19:28:44 »

No, you may not have explicitly stated it but you did imply it.

And I also think you are wrong that being overly sterile in the home isnt harmful-I think it is harmful.  Not having the correct balance of gut flora leads to all kinds of metabolic and auto immune disorders and also has serious effects on mental health.  If peoples diets were optimal I would agree with you that being overly sterile in the home is not a problem but because gut flora is already badly unbalanced by a bad diet simple hygiene is better-wash your hands before you eat is enough.

You have stated, explicitly, that you think over-cleaning is harmful. You have then proceeded to mention that gut flora imbalances apparently cause certain issues. You have then suggested that 'over-sterilization' in conjunction with gut flora imbalances is a problem. I would like evidence showing that over-cleaning in ones home exacerbates problems caused by gut flora imbalances, or, as you explicitly stated, that 'simple-hygiene' is better under these circumstances.

Moreover, if I have taken something from your message that you did not intend (I apologise if I have) then it simply demonstrates the care that needs to be taken when talking about this. Hand-washing is, as you have said, very important. But, you have also said over-cleaning is a problem. Would excessive hand-washing be considered a problem? People might ignore washing their hands once in a while, because they've been told that 'over sterilization' could be bad for their health.

I may indeed underestimate the intelligence of the public at large. But, in circumstances relating to health it is far better to assume the worst than to assume the best. You must assume that the public will take a message to extreme levels, because then at least you're prepared for it.

5

Plant Sciences, Zoology & Evolution / Re: Cooperation or Competition?

« on: 11/02/2013 20:09:59 »

This is a science Q&A forum.  In that context, this is like shouting at a cow for not producing goats milk.


If you will indulge a hypothetical situation, would you class intentionally trying to get banned from internet fora (wasting the time of well meaning volunteers in the process) as a way of "finding pleasure in life"?  Would you describe this as a cooperative or competitive behaviour?

*Favourite post of 2013*

6

Cells, Microbes & Viruses / Re: Does infection with one bug beget immunity to another?

« on: 11/02/2013 20:04:05 »

Well-you cant worry about how every individual interprets the information they take in. Some will get it some wont-thats humans for you....   

And I also think you are wrong that being overly sterile in the home isnt harmful-I think it is harmful.  Not having the correct balance of gut flora leads to all kinds of metabolic and auto immune disorders and also has serious effects on mental health.  If peoples diets were optimal I would agree with you that being overly sterile in the home is not a problem but because gut flora is already badly unbalanced by a bad diet simple hygiene is better-wash your hands before you eat is enough.

I dont want you to misunderstand me - I'm not advocating that people should go roll their children in entrails - far from it.  But I do think that sterilising every surface in the house all the time is very detrimental to health.

On the contrary, we must worry about what people will take away from this message. It is our responsibility because it is the scientific community that is sending the message. If you tell people that over cleaning is damaging, people will stop cleaning their homes. Sure, these people may rear children with a more developed immune system (which is all that the link is suggesting) but they will also be more likely to succumb to conditions associated with bad hygiene. I think it's fairly apparent that the problems associated with poor hygiene are far worse than those associated with overly zealous cleaning. So, I really have to question the point of blaring out to people that they shouldn't over-clean their surfaces when it's likely going to be more problematic than what's going on at the moment.

I'd also like to see the evidence for your claim associating over-cleaning with mental health problems and metabolic disorders. Has this been conclusively shown?

7

Cells, Microbes & Viruses / Re: Does infection with one bug beget immunity to another?

« on: 10/02/2013 20:36:53 »

I think you are right but only because people don't understand the difference between good and bad hygiene - mostly through scaremongering tactics of cleaning product advertisements. 

The difference is that being overly lax on hygienic practices is far more dangerous than overly cleaning your house. I really do not think that parents should feel the need to go to 'special lengths' to encourage the development of their child's immune system. The immune system will develop as they mingle with other children at school, walk to school and play outside. It's inevitable.

This message is one I that very much worry will get lost if care is not taken. People have to understand that hygiene is not a bad thing. Those arguing that parents should not overly sterilise their homes must also spread the message that this is not an excuse to toss hygiene in the bin. That is what frightens me.

8

Cells, Microbes & Viruses / Re: Does infection with one bug beget immunity to another?

« on: 10/02/2013 13:05:21 »

I've always had a problem with this idea, because I feel as though it encourages poor hygiene. Let's not beat about the bush here, the development of hygienic practices and sanitation over the past 100-200 years has been one of the top medical advancements of all time. The issue is that people take things into extremes -- living in an operating theatre is not great for your health, but neither is encouraging people to eat copious amounts of dirt in the name of immunity. Everything must be taken in moderation. Kids should be allowed to play outside and get dirty, but equally they should be made to wash their hands before meals and after going to the bathroom

9

General Science / Re: If the world came to an end what would you save?

« on: 03/02/2013 15:34:18 »

    I'm suggesting (rather cheekily) that this question is probably unanswerable unless we assume a baseline technology, which is probably at the hunter-gatherer level (basic tools, fire and shelter), which were also probably already present when our species evolved.

I'll establish your baseline: they have fire, spears etc. They are what we would consider to be primitive hunter-gatherers. Thank you for bringing this to my attention. I've edited my original post accordingly.

In addition you are the sole survivor of our time period. How you miraculously survive this cataclysmic event and end up completely unharmed in the future is not important. What matters is that civilization collapsed and all but our most basic technologies disappeared with it. You now have a chance to lead them all into enlightenment. Go get 'em tiger.

10

General Science / If the world came to an end what would you save?

« on: 02/02/2013 19:36:31 »

Hello all,

I had this idea and thought it might be interesting. Imagine if civilization came to an end tomorrow, and that you somehow were transported into the future where humanity survives but with none of our current technology or understanding of science.
What would you teach them? E.g. Would you teach them how to generate electricity, or about the germ theory of disease? How would you explain it? I am also assuming that the English language survives, or that you are able to communicate with them in their own language. The new future human civilization are what we would consider to be hunter-gatherers. They already possess the technology of fire, spears etc.

I couldn't find it having been asked previously using the search feature, but I'm sorry if it's been asked before. Anyway, I hope you enjoy. I'm looking forward to seeing some cool ideas.

11

Physiology & Medicine / Re: Do viruses hold the key to their own undoing?

« on: 31/01/2013 18:22:06 »

"The Texas-based team discovered that the HIV-1 Nef locks onto just one part of the beclin-1 protein, so they produced a soluble, synthetic version of this small region."

Whilst this is really interesting I can't help but wonder how long it will take HIV to worm its way around this. It binds to a 'small region' of a protein receptor. How long until it mutates to bind to a different region of the same protein? This is obviously having a direct impact on the survival of HIV, it will introduce a selection pressure and HIV is extremely responsive to such things.

12

Physiology & Medicine / Re: What cancer therapies are available?

« on: 27/01/2013 16:53:19 »

I absolutely despise posts with an agenda, and over the past couple of days I have seen quite a number of them. Post after post of 'beware of the evil big pharma'.

I'm talking about stuff like this:

The advantages from a profit point of view is that any company can make a drug,hire a couple of "reviewers" showing marginal improvement,discard,hide,suppress negative results,milk a few billion out of the drug and then move on to the next one.

No names named, no proof, pure conjecture. If you know something then you should be taking it to the authorities. I cannot stand this drivel. If you have something to add about cancer research then by all means go ahead. But this is not a forum for discussing conspiracies. Keep them to yourself.

13

Physiology & Medicine / Re: Will the result always be a human as we know them?

« on: 24/01/2013 20:24:35 »

The answer to 1&2 is no. This idea was put forward by Jean-Baptiste Lamarck, and was called Lamarckism or the inheritance of acquired characteristics. This is the idea that offspring would inherit characteristics acquired by the parents over the course of their lives e.g. the lost thumb or extra finger idea. This hypothesis was ultimately destroyed as we learnt more about genetics and how traits are passed on.

As for 3&4 it depends. It depends upon where and when the genetic modification took place in the parents. There are two broad types of cell in the body: somatic and germline. Germline cells are cells that go on to produce the gametes, whilst somatic cells are everything else. If the modification occurred within somatic cells then the answer is no. But, if a modification was induced within the germline then this modification would subsequently be passed on to all of the gametes produced by the parent and would be passed on to their offspring.

14

Plant Sciences, Zoology & Evolution / Re: Cooperation and Competition

« on: 14/01/2013 20:22:37 »

Mere survival is no reason to live, does not provide sufficient motivation to get animal or person out of bed in the morning; you need to have a reason to want to survive.  Animals and people must WANT to live, and they will only want to live if life has something to offer by way of fun/pleasure/interest and so on.  So the most important thing is that life should be good.

As far as I'm aware humans are the only organisms capable of actively wanting to end their life. What you say may hold some grain of truth in that respect. However, for other organisms that is absolutely not the case. The vast majority of organisms on this planet are not 'self-aware'; they don't know what they 'want' or 'like'. Yet many of these same organisms are able to compete and co-operate. Ants, for example, are extraordinary in their ability to co-operate with each other. They don't do it because they like each other though, they do it because that is how they've adapted to survive.

Living beings are hardwired to survive and pass on their genes to the next generation. Survival is difficult and different organisms have different methods of attaining it. Some have evolved to compete, others to co-operate. Humans have developed from organisms that have required the ability to both co-operate and compete with other organisms. So whilst we now have the ability to decide whether or not we enjoy life, and have the ability to affect our own survival, our traits of co-operation and competition have their roots within the quest for survival.

15

Physiology & Medicine / Re: Can 'junk DNA' have a purpose?

« on: 27/10/2012 17:43:34 »

Some viruses, particularly retroviruses like HIV, incorporate their genetic code into the genome of the host cell. This means that every time the cell divides the viral genome is also being replicated. When external conditions are favourable for the virus to re-emerge it will produce all the proteins needed for new viral particles and kill the host.
To do this they need an enzyme called reverse transcriptase. The DNA in your cells is being transcribed into mRNA, which is then in turn translated to produce proteins. As its name implies, reverse transcriptase does the opposite, so RNA is converted into DNA which can then be incorporated into the genome of the host.

There are strange 'things' (I can't think of another word to describe them) called retrotransposons, of which the LINEs and SINEs I mentioned earlier are a type, and they are basically DNA that moves. Some of these are very similar to retroviruses (some even being referred to as endogenous retroviruses), in that they use reverse transcriptase to copy themselves and re-incorporate elsewhere. They aren't especially harmful, they don't produce viruses or anything, but they can cause damage if they re-incorporate into any crucial genes. They do make up a staggering amount of our genome as well: I'm not sure of the exact figure, but we're talking double digit % of our genome rather than single digit. It is possible that retrotransposons may have played a role in fuelling evolution, as they help generate genetic variation.

Viruses by their very nature are obligate parasites. They lack any way of replicating without a host. In that sense, they are only harmful. However, they can be used to our advantage too. Bacteriophage viruses infect bacteria with extreme specificity. In the Soviet Union they were utilised in place of antibiotics, and with the number of antibiotic resistant infections about they are being looked at again.

16

The Environment / Re: How do we balance economic growth with its environmental cost?

« on: 25/10/2012 18:51:18 »

As I've said on a topic like this before, the only way you are ever going to get the world to 'go green' is to make it profitable. No amount of Kyoto conferences or pictures of Arctic ice shrinkage is going to stop The Man happily burning coal over renewables, or releasing huge amounts of pollution. You have to give these people a cost incentive or they'll just stay with the status quo. Why on Earth should small businesses try to go eco-friendly, probably putting themselves at a cost-disadvantage, when the huge international firms do nothing of the sort?

Once you make it profitable for industries to favour environmentally friendly methods of production then the whole world will follow suit. How you do this is the problem, however.

17

Physiology & Medicine / Re: Can 'junk DNA' have a purpose?

« on: 18/10/2012 08:49:36 »

Yikes, settle down! He was just making a (valid) point.

Not all organisms achieve the same objective the same way. Some organisms may well be polyploid, whilst others aren't. There are evidently advantages and downsides to both. Bacteria tend not to have many introns, if any at all. This is quite possibly for the reason that CliffordK pointed out -- there's simply no need to process more genetic information than is strictly necessary. If there's an advantage to be gained that outweighs the downside of wasting energy and time replicating extra material then that's going to take priority.

18

Physiology & Medicine / Re: Can 'junk DNA' have a purpose?

« on: 16/10/2012 08:59:16 »

This is a bit tricky. It depends on what you consider to be 'junk', and what you consider to be a purpose or role to play. There's loads of stuff in our genome that doesn't code for protein, but is still very important. Things like promoters, operators, enhancers and so forth. These things help regulate gene expression. Then in genes themselves you can have non-protein-coding regions called introns. Their functionality is not well understood, but it is thought that they may play some role in the regulation of gene expression.

Then you have the SINEs and LINEs (Short/Long Interspersed Nuclear Elements). They make up a frighteningly large proportion of our genome, and don't really do much. SINEs don't code for protein, yet the Alu repeat SINE is one of the most common features in our genome (and is found in many other primates). For a long time they were considered junk, but some research points towards some SINEs and LINEs doing things for us. The more we learn about things the less junky they become, I suppose.

19

General Science / Re: Cells and chromosome number in humans

« on: 12/10/2012 16:25:48 »

Don't forget the gametes. Sperm cells and egg cells each contain only half the normal number of chromosomes  -- they only contain the haploid number (23) whilst normal cells contain the diploid number (46). This is so that when the egg is fertilised by the sperm the newly formed zygote has 46 chromosomes, half coming from your mother and the other half from your father.

20

Geology, Palaeontology & Archaeology / Re: Where in the world?

« on: 27/09/2012 21:57:38 »

Would this be Pendle Hill? It is associated with witch-trials. I seemed to recall something between a hill and some witch hunts back in the 17th century, and looked it up.

Seems the name Pendle Hill is also a tautology, as the word Pendle is derived from Penhul. 'Pen' is apparently Cumbric for hill, whilst 'hul' is also meant hill in Old English. 'Hill' was later added again. It means HillHill Hill. That's pretty cool!