How does DNA work?

D@vid Asks:

Given that genes aren't the only determining factor in our makeup (we are 50% banana and 98-99% each other), and proteins account for (at least some of) the difference, what factors affect the proteins? are they just a random element? where do they come from? do environmental or genetic factors affect them?

Mitsy Answers:

Hi D@ve...

Yes, you're right there is one body part that does closely resemble a banana, and any guy who claims his body mass to be half "banana" is my kinda.... What?... Oh all right, he never lets me answer anything!

Schpat Resumes:

Sorry about that folks, Mitsy is a young teen who started her life in sex forums, what do you expect! Well now she's pouting so I'll let Mitsy answer a question after I'm finished with this one.

Let me start by correcting you: genes are the only determining factor in our makeup. I'm not throwing decades of nature vs nurture arguments out the window here, but your genes are entirely responsible for the way that your body has developed. Genes are the construction manual for the assembly of the wet and sloppy Mechano Set that is your body! Similarities in DNA between species, like most things, have been highly sensationalised by the mass media. let me quickly explain how they are calculated.

First of all everyone knows that DNA (Deoxyribonucleic Acid) has a "double helixical" structure. In fact this double helix is actually two strands of organic molecules called nucleotides. Each nucleotide on one strand is joined by a hydrogen bond to a nucleotide on the other strand. In Genomics each joining is called a "Base Pair". Genes are made up by patterns of base pairs.

When comparing DNA between different, or even the same, species it is actually the base pairs that are being compared. Now considering that there are only a very small number of nucleotides this really reduces the number of combinations possible and increased the chances of finding pattern matches. By the way the human genome consists of more than 3 billion base pairs, and only about 25000 genes. The number of pairs comprising these genes is accountable for less than 3% of our DNA, the rest has been termed "Junk DNA". Most of the similarities that have been found between us and other organisms are actually found in this "junk". If you did a comparison of relevant genes between humans and chips you'd probably come up with a much, much smaller number.

So why do scientists tout the 98% similarity figure for chimps? Well that's because they are trying to show a common ancestor, and thus prove evolution. Proponents of "intelligent design" (religious folks who have realised that the whole creationism thing is a total croc, but just cant bring themselves to take the next obvious step) say that this proves nothing.

So back to those proteins. Proteins are organic compounds that consist of amino acids joined by peptide bonds. Proteins, much like DNA, are components of cells and are responsible for almost all cellular functions. If DNA is the construction manual for your body, then proteins are the building blocks. DNA is self replicating and, in very basic terms, regulates the manufacture and coding of proteins, that's how it is responsible for how your body is built.

What factors affect proteins? Duh, DNA! What, weren't you listening? Seriously though, while DNA is inherited, in equal parts, from you parents sometimes mutation does occur, this is the basic premise of evolution. DNA is replicated whenever a cell divides, this is done through a complex process of translation and transcription and involves RNS (Ribonucleic Acid). Sometimes however transcription errors occur and DNA gets all messed up. This can cause good or bad things and when happening in the stem cells can be passed on to offspring. When happening in other cells, like skin and lung, it mostly results in cancers. It has been theorised that these transcription errors occur due to environmental factors such as free radicals and stellar radiation from old supernovas, normal radiation will also screw with your DNA.

If you're having a problem visualising all this microscopic stuff then just check out his site. It's very cool!


Ok over to Mitsy..........


Ork Khrist Asks

Why did clicking on these banner ads make me feal so dirty?

Mitsy Answers:

Well Ork, that's because you've only stared doing it. It gets easier with each one. This'll be our little secret! Practice makes perfect.

Thanks Mitsy


The Voice of Dissent:

Er, that would be 'helical', not 'helixical'. How much of this stuff do you paraphrase, and how much is copy/pasted? Or do you do something silly like manually type out everything?

"Now considering that there are only a very small number of nucleotides this really reduces the number of combinations possible and increased the chances of finding pattern matches"
Bollocks. The patterns matched are really really long, more than enough to compensate for the small number (4 in humans, but there are a few weird ones in other organisms) of base pairs. Sure, if you were looking for AGTT, you would find bazillions of matches, but when looking for a set long enough to encode a protein, the chance of finding a random, unrelated match drops dramatically.

Oh, and before anyone goes '4 bases, but they come in pairs so only count as two', switching the order makes a difference, so an AT pair is different to a TA pair.

Synkronos.


Well Synk, stop nit-picking! Yes so I inadvertently made up a new word: "helixical". There, say it seven more times and it might even make it into the dictionary. I think you and everyone else did understand it to mean "helix shaped". So anyway, the protein coding patterns are really long, and it is very easy to find matches if are just comparing base pairs, and yes that is what they did when they found humans to be 50% matches to bananas, and yes that was my point, but thanks for clearing that up! I didn't really go into that too much because it was actually just background into the "what are proteins and stuff for" question?

schpat

What's up with the 'www'

Groundy asks:

I've noticed that some websites can be access both with the www prefix and without. Like http://schpatdope.blogspot.com/ or http://www.schpatdope.blogspot.com/ (which do you prefer?) Some sites force the www, and others force the lack of it. Some just flat don't work. What gives?

Schpat:

The answer is magical, mystical, internet fairy dust. Not buying it? Ok, settle in and I'll try to explain.

When Dan Quale invented the internet, way back in 1983, the www prefix was intended to show what protocol the document or 'page' used. A protocol is like a translation template and lets your computer know what to expect and how to read it. There are a number of internet protocols, or technically 'application level protocols' in the 'internet protocol suite'. Among them are HTTP, SMTP, SSH, POP3, IMAP, IRC, and FTP. If a user knew what protocol to use they would know what application would need to be used to access the information. So for instance a domain with the prefix 'mail' would use the 'SMTP' protocol and the user would know to use 'PegasusMail' to access it.

These days most application level protocols have been largely integrated into single applications such as Internet Explorer or Fire Fox. On windows machines the registry contains entries for prefixes that let these application know what protocol to use. This functionality is often abused by malicious adware to impose pop-up advertising on internet users. This practice is called browser hi-jacking.

Part of your question was that sometimes you can access a website without using the 'www' prefix, well that's because your browser is cleaver. You should actually be able to access any page that requires a 'www' without actually typing it in because if your browser does not find a page with no prefix specified it automatically tries the same page but with the default 'www'.

As to why certain domains require no prefix here's some more background: A domain name consists of three parts: the Top Level Domain, the Second Level Domain and the Prefix. The 'top level domain', or TLD, is the last part of the domain name, examples include '.com', '.org', '.net', and '.co.za'. The TLD lets your browser know where to start looking for the 'Domain Name Server', or DNS, that will eventually tell it what the IP (internet Protocol) address of the server that hosts the domain is, a DNS is a giant look-up table. Then there is the Second Level Domain, 'SLD'. The SLD is the part between the prefix and the TLD and can be made up of any number of clauses separated by 'dots'. The SLD and TLD together make up the Zone. When you register a domain name you are actually registering the zone, you can then run different applications on that zone by specifying the prefix. Most people default to 'www' for their public internet access prefix, as is dictated by standard, but some don't, 'www2' also sometimes seen. They could however just leave it off, if they do that a site name with the 'www' wont load.

So in short, when entering a URL you are more likely to get to the site if you leave off the 'www', but it will almost always take longer. I prefer to use the prefix because it's purer and lets users know exactly what to expect when typing in a URL. Domains that "just flat don't work" probably have been decommissioned or, probably due to inattentiveness, have a broken link in the DNS chain.

Mitsy says I should have just left it as magical, mystical, internet fairy dust, it's so much easier to understand. She likes internet fairies and asks me to remind you that every time you click on our sponsor's links, an internet fairy gets her wings.

Is Pluto being a planet just goofey?

Moonflake asks:

In serious news, an asteroid with multiple moons has been discovered. Adding to this the recent discovery of the as-yet-unnamed Planet X, a supposed 'planet' orbiting within the Kuiper Belt (a second asteroid belt beyond the orbit of Neptune, whose most famous member is Pluto), this begs the question: when is an asteroid just an asteroid, and when is it a planet? Is there some arbitrary line in the sand drawn by astronomers? The existence of a moon or moons can't be it, as the above article shows. Nor can size, composition or proximity to an established asteroid belt be a consistent qualifier as this would rate Planet X and Pluto firmly in the asteroid category. In addition, while Pluto is technically labelled a planet by the IAU, most astronomers would disagree with this classification. O SchpatDope, please help us on this one.

Schpat answers:

Mmm, toughie. Actually Moonie it doesn't beg the question, "begging the question" refers to flawed logic requiring circular reasoning, this discovery instead raises the question. I don't mean to be pedantic about this but when you make as many leaps of logic as I do you'd better know what they are called! Don't feel bad, this usage has been commonly accepted since about 1983 so I'll let it slide.

By the way have you seen the size of Pluto? It's almost microscopic in relation to the five gas giants. It's smaller than our moon. If you were driving to Icon and back you would have travelled far enough to pass directly though its centre by the time you got back to Beufort West.

Back to the question at hand, what is the difference between an asteroid and a planet? Well astronomers have not in fact drawn an arbitrary line in the sand, none of them are brave enough... yet. While the matter was under discussion for some years over at the IAU no decision was ever made. The discovery of 2003 UB313 (or Planet X) has forced the IAU to review the matter as people are asking them to finally come up with and answer.

In order to define the rules for planetary classification let's first investigate the meaning of the word planet. Planet is derived from greek and not-so-literally means "wanderer". The Greeks thought that planets were a specific subset of stars that wandered across the sky for some reason known only to themselves and the gods after which they were named. So by greek standards a planet is anything that wanders across the sky, this isn't really going to help us is it?

While looking into this I came across a site describing how star trek weaponry was way cooler than Star Wars weaponry because they could vaporise a large asteroid with a single photon torpedo but it took the entire death star to destroy a planet. I didn't really look into that too much, but it did give me the idea to see if maybe Starfleet had some kind of defining rule that we could use. Their definition: "Planets are large objects orbiting a star [...] size-based distinctions will prove somewhat arbitrary". Gene, I can't believe you whimped-out, Starfleet is just as indecisive as the IAU.

The best idea I've seen was from Mike Brown of Caltech. He proposes that a planet be defined as any body that has a mass greater than the sum of the masses of all other bodies in a similar orbit. This seems like a good idea to me. I'd make a few minor tweaks, like saying 'approximately' the same or greater mass, and allowing for double planet systems like the ones described in Anne McCaffrey's Pern and another very cool sci-fi book I lent to zenstar and can't remember the name of.

If the IAU decide to go with this definition then Pluto may have to be relegated from the planetary league. There is precedent for this. The first few asteroids discovered were considered planets for quite a while, almost 40 years. Later, once more and more of these bodies were discovered, they were reclassified as asteroids. Pluto has been considered a planet for about 75 years and now that more and more of these plutonoids are being discovered demotion would seem to be a logical decision. However logic is not always the prevailing factor when it comes to decision making.

When Pluto was originally discovered by Clyde Tombaugh in 1930, totally by accident I might add, there was debate by the IAU as to whether or not it should be awarded planetary status. Active lobbying ensured that the only "planet" discovered by an American got the status it truly deserved. Demoting the planet now may be considered a serious affront by the American public. Already letter writing campaigns have been started at primary school level to stop this from happening.

As to whether or not Planet X, or the latest incarnation thereof anyway, should be designated as a planet the following may play a part in the decision making process. Currently interest in space is at almost an all time low. If it wasn't for a few failed shuttle missions the general public would have all but forgotten about actual space exploration. The discovery of a new planet would without a doubt result in a renewed interest and probably in increase in funding for NASA. That is possibly why NASA has already tacitly accepted 2003 UB313 as a planet and is putting pressure on the IAU to declare it as one.

Mitsy says that all this sciency stuff is making her head hurt and has found an alternate criteria on her teen forums. One poster says: "The 'planet versus asteroid' debate isn’t too tricky for me [...] I can personally attest to the strength of Pluto’s influence [...] therefore, Pluto is a planet [...] this new one is bigger than Pluto so it's a planet too". In case you didn't realise this commentator is talking about proving that 2003 UB313 is a planet based on astrology. Well, at least it's decisive.

Submit your own questions for the SchpatDope by leaving them in the comments. Help us to help Mitsy by supporting our sponsors and clicking on their links.

SchpatDope on SchpatDope??!??

Mark Asks:

Hey schpat!
Have you got an RSS or Atom syndication feed for your blog?

Schpat Answers:

This is kinda a strange question for the SchpatDope to answer. It's not weird or sordid or anything, but I'll do it anyway. Hey questions are sparse!

The ScpatDope is inspired by Cecil Adam's The Straight Dope, it's just not as well researched or funny! Well it might be as funny sometimes, but I'm not promising anything!

I'd like to do a SchpatDope once a week, but that all depends on whether or not people actually ask me questions, it's really though work making them all up myself! When posts are made you can pick up the full contents via our Atom feed http://schpatdope.blogspot.com/atom.xml .

Remember that I'm fine with syndication, in fact I love the idea, as long as the post appears in exactly the same way as it was sent. That means no editing, especially not to remove the ads. Also all work is copyright to me and shouldn't be passed off as your own, always include The SchpatDope in your assignment under list of references. Although if you are using this site as a reference for an assignment, I'd think again.

Also if you do subscribe to the blog feed, or syndicate it to millions, I'd really appreciate it if you let me know. It's just so that I can see how many people are reading it. There have been 475 site view since friday, and if people subscribe it'll be difficult for me to keep track of that.

Also remember to support our sponsors by checking out their websites, even if they are only offering credit checks and free golf balls. Our newest researcher, Mitsy, really appreciates it!

So make with the sending of questions already and please don't be scared to comment on the posts.

thanks
schpat

The Sounds of Sex

Zenstar asks:

what noise does the average teenager make during sex?

Schpat answers:

Thanks to you Zenstar I had go deep undercover into the seedy world of teen sex, man the things I have to do for this column! In order to successfully infiltrate their world I chose an alter-ego: "Mitsy", a sixteen year old Catholic School girl from Southern California. I figured this would good cover. Having joined many online forums on teen sex, ignoring the gross NAMBLA type sites, I settled in to observe these teens in their natural habitat.

I'm pleased to report that teenagers are no less confused about sex than previous generations were. They still want to know things like whether or not having sex in a pool is an effective contraceptive. Another interesting question demonstrating the average teen's understanding with regards to issues of a sexual nature was:

"what exactly is a pussy whip, and how do I use it? My boyfriend tried a riding crop but it really hurt!"

About five or six posts valiantly attempted to answer this question but failed in varying degrees. Eventually an obviously more worldly poster was able to give a pretty concise definition including the fact that the term was in fact "pussy-whipped", to which the response from the original poster was: "but I still don't understand". Someone then suggested that it was a bondage item made of "extremely soft leather" and should be used with caution. A flame-war ensued. Eventually the last three pages of the topic were devoted to William Shatner and Star Trek. You gotta love that teenage attention span!

I found out many other interesting things like for instance there is a clear bias in tits vs arse preference among teenage boys. 55% of teen boys preferred boobs vs. 45% preferring arse, this makes total sense because they have their own arses! There is a much clearer bias when it comes to teen girls preferences on penis shaving. Of those polled 40% prefer shaved, 20% prefer unshaved, and 40% are undecided; although why teenage boys would need to shave thier penises I don't know!

The internet may just be the enabler in the next phase of the sexual revolution: "the Sexual Revolt". The anonymity of the internet has allowed teens to be completely open about their sexuality, I mean would you have told your school friends how many times a week you masturbated? This openness is leading to teens becoming more accustomed to sex than they have ever been before, many of them now see sex as just an everyday entertainment to pass the time. In fairness I'm sure it's not just the internet at fault, video games with hidden sexual content must surely also be to blame! ;)


Anyhoo, in an effort to answer your question our intrepid "Mitsy" posed the question about noises heard during sex and received the following responses:

"Make me a sandwich, bitch"
"It's Table Time Bitch!" *slam*
"She made goat noises so I could get turned on."
"umm my hand doesnt have a mouth:("
"I hear horseys."
"none, im a virgin! "
"Ouch"
"Stop"
"No"
"Not there"
"No that hurts"
"Lower"
"You suck"
"I'm getting a real man"
"Get off me"
"Your penis is too big, I'm scared"
"Whuubgggahhhhbahhhhjoooooobo!"
"I like sex"
"Those are boobs not stress balls"
"Just pretend it's a sandwich"
"It's razor burn, I swear"
"I'm calling the police!"
"i need a hug ;_;"
"mine says "oink" "

And Mitsy's personal favourite:

"I hear that weird rubbing noise you get when you sit on a leather couch. It might just be im not using enough lube with my inflate a date."

Thanks Mitsy!

My foray into the world of teen sex has shown me that kids no longer have to get misinformation about sex fed to them on in small snippets on the playground, they can now have misinformation fed to them in large volumes via the internet. The only difference is that along with bad advice about sex now they also learn poor spelling and grammar!

Leave your own SchpatDope Questions in the comments and I'll get to them as soon as I can. Also please support our sponsors, internet alter-egos aren’t free you know!

SchpatDope Returns

Moonflake Asks:

In America, the average age of consent across all 50 states is 16 and in Hawaii it's 14, but the age restriction on GTA:SA is being upped to 18+??? So in the majority of US states, you can, in fact, have sex on your console, just not on your console. Of course, you also have to be 18 to enter most porn sites in the states... so you can record yourself having sex, you just can't watch it. Brilliant. What gives? Help us Obi-Schpat, you're our only hope!

Ok, I added the last bit, but I said if you folks didn't ask questions I'd have to pretend that you did!

Schpat Answers:

That's an interesting question Moonflake, I'm glad I asked it for you. The confusion here is probably because of subtle inaccuracies in your wording. You might think I'm being a nit-picker for bringing up wording subtleties, but this is a question on law, and law is all in the wording!
First a little background info and interesting facts:

The minimum age for sexual consent varies around the world. It is often dictated by the specific societal values and beliefs. In some Muslim countries there is no minimum age for sexual consent but no sex is legal outside of marriage. Other laws ban certain types of sex on religious grounds egg: sodomy is illegal in many african countries, and Kansas.

In my research I found that it is possible to categorise societal influence, and therefore sexual consent laws, into 4 major groupings: average, conservative, antiquated, and enlightened.

Average: These are your normal run of the mill countries like The States and our very own South Africa. The minimum age for sexual consent is normally set somewhere between 16 and 18. Sometimes homosexual consent can only be given at older ages. There are also communally "Romeo and Juliet" laws which allow for teen sex with the provision that both partners meet certain age criteria, most communally that they are both under 18 and with in four years of age. This means that 14 year olds could legally have sex with 17 year olds. These laws normally also provide that the older partner must in no way have coerced the younger (egg: with food or money) or be in a position of authority over the younger (egg: a teacher or priest).

Conservative: These occur mostly in religious states, like the Muslim examples above. Most conservative states are not quite as fanatical about the whole thing and only have very high minimum ages for sexual consent, typically 21.

Antiquated: These are those back-woods states that don't really have any laws that govern this sort of thing. States like Pakistan, Oman, Chile, Paraguay, and Mexico. These states common law differs vastly on the subject but as an example in Mexico the common law states that it is a crime to deflower an honest woman under the age of 12. That means that if she is already not a virgin, or a real big tease it's alright! This is also the country where rape charges can be dropped if the perp agrees to marry the victim! Oh and you may be asking yourself why so many South American Countries are listed, that's because their common law is inherited from Spain, which still has the same laws.

Enlightened: for the weirdest stuff you have to visit our European friends like Sweden, France and Germany. In Sweden and France the legal age of consent is 15, but then it's also legal to have sex with animals in Sweden as long as you cause them no distress or discomfort. In Germany the legal age of consent is 14 as long as the partner is no older than 21 and the minor is not enticed by gifts or money, unless of course the minor is a prostitute then it's ok if she's over 12! Oh Yes, prostitution is legal in Germany.

Anyway, back to your question (snigger): Why is a 16 year old permitted to record themselves having sex but not permitted to watch it? Like I said it's in the wording. A sixteen year old may record themselves having sex, but to be clear no one else is allowed to unless the teen's parents consent, due to the fact that they have not yet reached the age of majority. Then comes the watching of the porn. It's not illegal for a 16 year old to see porn, but it is illegal to show them porn, this is normally a crime under corrupting a minor or under child abuse laws. Seeing as how you can't corrupt yourself that paradox is cleared up. The hypothetical minor would not however be able to tape themselves having sex and then distribute it to other under 18s.

Send in your own Schpat Dope questions or schpat might just twist your words too!