Beer, Chemistry and Marketing, a violently exothermic reaction of the brain.

Television advertisements.

Some of them can be absolutely ingenious. Some of them can be incredibly annoying. And some of them can be unquestionably, mindbogglingly stupid. The latest marketing campaign for Miller Genuine Draft beer belongs to this last category.

You've probably seen the commercials. They portray someone in a tough situation where they are uncommonly open, and consequently resolve the situation to their benefit. This is complete with their marketing slogan: "Miller Genuine Draft is in a clear bottle because it has nothing to hide", showcasing their unique clear bottles. And it's those damn clear bottles that make this marketing campaign so stupid. It would seem that the folks at Miller forgot to hire a chemist or two for their marketing department, because beer is bottled in dark bottles for a reason.

One of the key ingredients in beer is hops. Hops contributes much to the flavour of beer, through a class of chemicals known as isohumulones. Isohumulones are in all types of beer, and are perfectly fine. They are not a problem by themselves. Problems can arise, however, because of another chemical found in beer: riboflavin.

Ribovlavin (better known as Vitamin B2) is found in all kinds of foods and beer is no exception. Unfortunately, riboflavin and isohumulones don't get along very well. Riboflavin tends to break down isohumulones, so having them both in beer can be problematic. Normally, this is not a big deal, though, because the chemical reaction whereby riboflavin degrades isohumulones requires a catalyst, and that catalyst is light. This is the reason why beer comes packaged in dark-coloured bottles. The dark colouration keeps out light, and prevents the isohumulones from breaking down.

Why is isohumulone degradation a bad thing? Well, when these chemicals are broken down by riboflavin, they form a compound called 3-methylbut-2-ene-1-thiol. This compound gives the beer a very, very bitter taste: the beer becomes spoiled (unless you happen to enjoy very bitter beer, I suppose). If this happens to beer, then it is often referred to as being "skunky". Little wonder why: 3-methylbut-2-ene-1-thiol is very similar to the compound used by skunks in their spray.

So beer that is bottled in clear bottles like Miller Genuine Draft (as well as Corona, and beers bottled in green bottles like Heineken) will end up spoiling and becoming very bitter much quicker than beers packaged in dark bottles.

So does Miller Genuine Draft really have nothing to hide? I think the fact that their beer contains skunk juice is something worthy of keeping hidden.

EDIT: It's been brought to my attention that Miller uses a strain of hops that contains a more light-stable form of isohumulone to prevent their beer from skunkifying when exposed to light. Nevertheless, the chemistry remains the same and is still interesting. Take note all you home brewmasters out there.

Sex Determination and Lizards

Sex determination is a pretty hot topic in molecular biology. Trying to elucidate the underlying mechanisms that determine whether a fetus is male or female has been a productive field. Many species rely on a hemizygous¹ method of sex determination, and we humans are no exception (but rather, we are the rule). Males are XY and females are XX, and this is the way it works in all mammals² (even in monotremes like the platypus, though monotremes go to the extreme and can have as many as ten sex chromosomes; a male platypus is XYXYXYXYXY, for instance). Birds rely on a similar ZW system, but in this case, the females are heterogametic; females are ZW and males are ZZ. Some insects use an entirely different system, the XO system, where there is only one sex chromosome - X - and females have two (XX) whereas makes only have one (XO)³.

Despite the system used to determine sex, all the above examples have something in common: they all rely on genotypic sex determination (GSD). In these cases, it is the sex chromosomes (the number, presence or absence) which determines the sex of the resulting fetus. GSD, however, is not the only mode of sex determination. External environmental factors may also influence sex determination. Crocodiles, for example, have no sex chromosomes whatsoever. It is the temperature of the eggs which determines the sex; eggs laid in a warm nest become male and those in a cooler nest become female. Environmental sex determination (ESD) and GSD are not mutually exclusive, of course, and it has been known that many species of reptiles rely on both GSD and ESD. The interaction between ESD and GSD in these species was not thought to be a complex one; eggs at moderate temperatures use GSD, but the sex-chromosome method is bypassed and a temperature-dependant method is used if the eggs are at more extreme temperatures.

A new paper in Current Biology, however, shows that things might not be so simple.

Rajkumar S. Radder, David A. Pike, Alexander E. Quinn, and Richard Shine looked at sex determination in the eggs of the lizard Bassiana duperreyi⁴. They were examining how temperature effected the sex of the hatchlings when they noticed a correlation between the size of the eggs and the resulting sex: those eggs that were larger had female hatchlings and the smaller eggs had male offspring.

Of course, a simple correlation like this does little to prove an actual relationship and may simply be coincidence. So Shine and colleagues decided to try adding or removing yolk from the eggs during their development. What they found was pretty astounding. When they added extra yolk to the eggs, the hatchlings came out female, even if the sex chromosomes had already determined the sex to be male. And those eggs that had yolk removed switched to male even when the sex chromosomes had been set to female. This finding would suggest that sex determination in B. duperreyi is determined by a complex interaction of a minimum of three factors: sex chromosomes, temperature and egg size.

This also suggests that sex determination in any species may not be as simple as once thought.

------------------------------------------------------------------------

1. Hemizygous may not be a term you learned in Genetics 101. Whereas homozygous and heterozygous refer to having one or two different alleles, respectively, hemizygous refers to having only one of a set of two chromosomes. Female humans have two X chromosomes (XX), whereas males are XY; they are hemizygous with respect to the X chromosome. You could also refer to females as homogametic and males as heterogametic.

2. To be more specific, sex determination in mammals relies on a gene called sry (Sex-determining Region Y) located on the Y-chromosome. The gene encodes for a transcription factor called TDF (testis determining factor). When TDF is expressed, it influences the undeveloped gonad to develop into testes instead of the default state of developing into ovaries. If the SRY region of the Y chromosome is deleted or mutated, then the resulting child will be phenotypically female but genotypically male. Likewise, a translocation of SRY onto an X chromosome can lead to children who are phenotypically male but genotypically female. Interestingly, TDF does not begin to work, and consequently sex is not determined, until after the nipples have developed, which is why men have nipples that are pointless (beyond giving purple nurples, of course).

3. One interesting downside of this system is that it can lead to bilateral hermaphroditism. It is possible for the X chromosome to form a "ring chromosome" where the ends of the chromosome fuse together to make a ring. This ring chromosome is easily lost during cell division. If an embryo begins as XX (female), and very early on in development (at the 4 cell stage, say) a ring chromosome is formed and lost in one cell, the embryo will become split right down the middle, one side being male and the other side being female. This is rare, but not uncommon, in Drosophlia. Such flies are called gynandromorphs.

4. Rajkumar S. Radder, David A. Pike, Alexander E. Quinn, and Richard Shine. Offspring Sex in a Lizard Depends on Egg Size. Current Biology, 2009; DOI: 10.1016/j.cub.2009.05.027

Move over Boy Scouts, make way for the O.O.T.S.S.O.E.R.A.A.A.P

That is, the Order of the Science Scouts of Exemplary Repute and Above Average Physique. If you do science, this is the organization to be part of! And just like the Boy Scouts, you earn badges (to show off on your website/blog/whatever - along with a brief explanation how/why you've earned each one) for doing awesome sciencey stuff!

Here are the one's I've earned:

The "talking science" badge: Required for all members. Assumes the recipient conducts himself/herself in such a manner as to talk science whenever he/she gets the chance. Not easily fazed by looks of disinterest from friends or the act of “zoning out” by well intentioned loved ones.

The "I Blog About Science" badge: In which the recipient maintains a blog where at least a quarter of the material is about science. Suffice to say, this does not include scientology. Don't know exactly what porportion of my blog is about science but it's definately more than 1/4.

The "I’m pretty confident around an open flame" badge: Recipients have demonstrated proficiency around open flames in laboratory settings. I regularly use a Bunsen burner without disasterous consequences.

The "Destroyer of Quackery" badge: In which the recipient never ever backs down from an argument that pits sound science over quackery.

The "Sexing Up Science" badge: In which the recipient has had experience with things such as selective breeding, crossing, mate selection, prokaryotic conjugation, fertility studies, STD related microbiology, and/or any other acceptable interpretation of the badge. I vowed never to breed Drosophlia

again but at least it got me this badge.

The "has frozen stuff just to see what happens" badge, levels 1-3: In which the recipient has frozen something in the freezer (I)/dry ice (II)/ liquid nitrogen (III) for the sake of scientific curiosity.

The "I’ve done science with no conceivable practical application" badge. Perhaps this should be known as the "basic research" badge.

The "I know what a tadpole is" badge: In which the recipient knows what a tadpole is. Basically, an easy way to get a badge that looks a little like the semen one above.

The "Cloner" badge: In which the recipient has cloned something or other. I've done more cloning than you can shake a stick at. A cloned stick, even.

The "totally digs highly exothermic reactions" badge. Because who doesn't enjoy a fanciful display of exothermic activity?

The "somewhat confused as to what scientific field I actually belong to" badge. I'm trained in genetics, but I do molecular biology in a biochemistry lab. You tell me what my field is.

The "Works With Acids" badge. Usually only HCl and acetic acid, but hey, DNA

is technically an acid too!

The "Non-explainer" badge (Level 1): Where the recipient can no longer explain what they do to their parents.

My take on accomodationism.

Lately the science blogosphere has been abuzz with discussion about accomodationism. It all started off with a piece by Jerry Coyne for New Republic on the subject, which has since stirred the pot and prompted Chris Mooney, Jason Rosenhouse, Ken Miller and P.Z. Myers to give their two cents on the issue (a chronological list of postings and replies [as of June 12th] can be found here). There is alot to read about accomodationism but it all revolves around one question: is there room in science for religion - that is, can science and religion get along, or are they diametrically opposed?

And if you ask me, no, they can't and yes, they are.

The simple reason why is because science deals with the observable, the empirical, the testable; while religion deals with the metaphysical, the unobservable, the untestable. To be a scientist requires, then, a certain mindset - one that forsakes reliance in the intangible and deals wholly with physical reality. For one to have this scientific mindset and still hold a belief in religion requires a measure of doublethink in the true Orwellian fashion.

Much of the accomidationism discussion has talked about Gould's Non-Overlapping Magisteria (NOMA). In his 1999 book, The Rock of Ages, Gould proposed that science and religion attempt to explain different aspects of life: science attempting to explain how the world works and religion attempting to explain how we should act. If kept separate, then, the two magisteria should never conflict with one another. Accomidationists tend to use NOMA to suggest how science and religion can co-exist: if people keep them separate then there should be no problem with believing in both. Unfortunately, there is a big problem with using NOMA to justify accomodationism: the two magisteria DO NOT stay separate. Religion constantly makes an attempt to explain how the world works - take creationism for an example. Religion makes many claims about the physical world, which is supposedly science's realm. And many times, what religion claims and what science posits conflicts. To believe BOTH means you have to twist one to fit the other - usually twisting religion to fit science. The usual way is to claim that certain Biblical statements are just "symbolism". This poses a question: how do you decide which aspects to take "for real", and which are just "symbolism" (the answer is, of course, there is no criteria for deciding this). And if ANY of the Bible is symbolic, then what reason do you have to believe that any of it is real?

But there lies a bigger problem with accepting NOMA as a basis for accomodationism. If one is able to keep the magisteria separate, the very fact that one accepts the religious magisterium means that one accepts the idea that there are intangible, untestable entities and processes in existence. As a scientist, how could you ever divorce that idea from explaining the observable world? What keeps you from invoking the metaphysical to explain the physical? Again, there is no defined criteria for this judgement. One is resigned to proposing that there might be some unknown, intangible - in other words, unscientific - entity/process behind the physical world. And at that point, one ceases to be a proper scientist.

Now, I want feel I should say that this does not mean you cannot be a good scientist and be religious, or that being religious necessarily makes one a bad scientist. What matters is whether or not you incorporate your religious beliefs into your scientific activities. Once you try mixing the two, you cross the line from "good scientist" to "poor scientist". This is what separates the Ken Millers from the Michael Behes; Miller, while openly Christian, leaves his religion out of his science, and Behe, also openly Christian, insists on mixing the two. The problem lies, as I said above, in that to do this requires a measure of doublethink. You have to ignore (or attempt to explain away) the areas where science and religion are in disagreement, and you have to use the metaphysical for religious purposes and the physical for the scientific despite having no clear reason why they should be kept separate in the first place.

No doubt the accomodationism debate will continue. One wonders if it will ever be settled.

Why Biorad is one of my favourite companies.

If their first video wasn't awesome enough, this one is:



I also think it's funny how they made a 70's-esque video about a technique that was not developed until the mid-80's (unless you coun't Kleppe's paper as describing PCR¹).

--------------------------------------------------------------------
1. Kleppe K, Ohtsuka E, Kleppe R, Molineux I, Khorana HG "Studies on polynucleotides. XCVI. Repair replications of short synthetic DNA's as catalyzed by DNA polymerases." J. Molec. Biol. vol. 56, pp. 341-61 (1971)

Creepy-Crawlies and Conservatives

A new study has purported to find correlations between political alignment and the degree to which things disgust you.

The study, conducted by David A. Pizarro, Yoel Inbar and Paul Bloom, and published in Cognition and Emotion, surveyed 181 American adults by subjecting them to a "Disgust Sensitivity Scale" (DSS), to assess their level of disgust in various situations. The subjects were then assessed on a political ideology scale. They found that those who tended to be easily disgusted also tended to be political conservatives.

Pizarro and colleagues followed this up by surveying 91 undergrads by giving them the DSS and then asking them their opinions on issues like abortion, same-sex marriage and gun control. Again, they found a correlation between conservative views and being easily disgusted.

This is a pretty interesting find, but it raises a major question: if conservatives are easily disgusted by creepy, slimy things, then why do so many conservative politicians turn out to be complete slimeballs?

----------------------------------------

Yoel Inbar; David A. Pizarro; Paul Bloom. Conservatives are more easily disgusted than liberals. Cognition & Emotion, 2008; 23 (4): 714 DOI: 10.1080/02699930802110007

A more in-depth article about this study and a related one can be found at ScienceDaily:
http://www.sciencedaily.com/releases/2009/06/090604163620.htm

Bill O'Reilly caught lying once again.

If there is anything that annoys me more than fanatical right-wingers who inanely babble on about topics they know nothing about, it's fanatical right-wingers who inanely babble on about topics they know nothing about and then lie about it. Bill O'Reilly fits nicely into that latter category.

By now, everyone has heard about the absolutely tragic murder of Dr. George Tiller, who ran a women's health clinic in Kansas that provided late-term abortions for women who needed them due to dire medical complications. Dr. Tiller has been a target of radical pro-lifers for years, having been shot once before, and had received a constant barrage of death threats and pointless lawsuits.

The man who shot and killed Dr. Tiller acted alone, and one should not judge the entire pro-life movement on the actions of one deranged individual, though I can't help but feel that his malicious deed was in part due to the movers and shakers in the pro-life camp; had they not spilled their hate-fueled campaign against Tiller, then he would likely be alive today. And one such person who specifically targeted Tiller was Bill O'Reilly.

In fact, O'Reilly held such disdain for Dr. Tiller that he commonly referred to him as "Tiller the Baby Killer". And after Tiller's death, do you think that O'Reilly felt any remorse about making him a constant target for the right-wing media? Of course not! He just lied about ever calling Tiller a "baby killer" in the first place:

"It took just minutes after the report of Tiller's murder for the far-left loons to hit the websites. Postings on the Daily Kos and The Huffington Post immediately blamed me and Fox News for inciting Tiller's killer. Even though I reported on the doctor honestly, the loons asserted that my analysis of him was "hateful."

Chief of among the complaints was the doctor's nickname, "Tiller the baby killer." Some pro-lifers branded him with that, and I reported it. So did hundreds of other news sources. But the bigger picture here is the glorification of Tiller."

"Oh, I didn't call him "Tiller the baby killer," O'Reilly claims, "I just reported that other pro-lifers called him that." Well, not according to Media Matters:

"However, O'Reilly has not only "reported" on the term's usage by "pro-lifers," but he has adopted it himself, repeatedly referring to Tiller as "the baby killer" on his Fox News show:

• On the May 15 edition of The O'Reilly Factor, O'Reilly stated that Kathleen Sebelius, who was then the governor of Kansas and is now secretary of health and human services, "is the most pro-abortion governor in the United States. Based upon Dr. Tiller, the baby killer in her state, and all of that. All right? So there's no doubt."

• On the May 11 edition of The O'Reilly Factor, O'Reilly said Sebelius "is pro-abortion. She wants the babies done for. This is -- she supported Tiller the baby killer out there."

• On the April 27 edition of The O'Reilly Factor, O'Reilly said that Sebelius "recently vetoed a bill that placed restrictions on late-term abortions in Kansas. The bill was introduced because of the notorious Tiller the baby killer case, where Dr. George Tiller destroys fetuses for just about any reason right up until the birth date for $5,000."

• On the April 3 edition of The O'Reilly Factor, O'Reilly said, "Tiller got acquitted in Kansas, Tiller the baby killer."

• On the March 27 edition of The O'Reilly Factor, O'Reilly stated: "Now, we have bad news to report, that Tiller the baby killer out in Kansas -- acquitted. Acquitted today of murdering babies. I wasn't in the courtroom. I didn't sit on the jury. But there's got to be a special place in hell for this guy.""

How does it feel to have your own words come back and bite you in the ass, O'Reilly?
Bill O'Reilly is a vile, little man - vile for his moronic, loud-mouthed attitude, vile for his asinine ideology and vile for constantly lying through his teeth.

On Assumptions and Conclusions

One of the things that creationists often say that really annoys me is that evolution and creationism are not all that different in that they both rely on the same facts and observations, but come to different conclusions because they use different starting assumptions. Biologists, they claim, begin with the assumption that natural selection, common descent and descent with modification are all real phenomena, while creationists begin with the assumption that the Bible is the inerrant word of God. They posit that, because the two groups use different starting assumptions, they interpret the data differently, in a way which confirms their preconceived views; when a biologist looks at a giraffe, she sees the byproduct of billions of years of evolution, whereas a creationist sees obvious design.

This claim is absolute rubbish. Anyone who makes such a claim is exposing their incredible ignorance of the scientific method. In fact, such statements run completely contrary to the way the scientific method is supposed to work!

Generally, the scientific method works like this: you gather observations and empirical data, and from analysing the observations and data, you draw out general conclusions which explain all of the data. In other words, science does not start with any unfounded assumptions; it begins with the data, and from the data determines general principals on how the world works. Scientists do not begin by assuming the nonexistance of God - God doesn't even factor into the equation for the most part. In the case of evolution, biologists do not begin with assuming God does not exist and then interpret the data in a secular manner; instead, biologists determine from the data that species arise from a purely naturalistic process, and God's non-involvement follows as a natural conclusion.

Creationists, on the other hand, follow such counter-scientific principals to the tee. They start with their supposed conclusions - goddidit - and then ask "What facts can we find that support our conclusion?" To creationists, facts follow conclusions and not the other way around. They begin by assuming that the Bible is the inerrant word of a supernatural entity, and then stretch, skew and distort any facts they find to try and make them fit into their biblical beliefs.

The idea that science and religion simply begin by making different starting assumptions is antithetical to science. This is a big part of the reason why "creation science" is such a huge joke.

New Answers in Genesis Ad: Godless Heathens will Kill You / We Kill Godless Heathens

Answers In Genesis, the very same group of know-nothings that brought you The Creation Museum and the pitiful attempt at "real science" known as the Answers Research Journal, are starting to branch out with new advertising. Check out their new ad below:



Their little slogan makes me wonder: "If you don't matter to God, you don't matter to anyone", said while a wife-beater clad youth points and cocks a gun at the camera.

This can be taken in two different ways:

1) "If you think that God does not exist - that you don't matter to Him - then you don't think life has any meaning. To atheists, your life and the lives of others don't matter. Godless atheists will have no moral qualms about killing you (and probably will)."

or

2) "If you think that God doesn't exist, then you don't matter to anyone. Especially not us Christians. So don't be surprised when we start shooting you atheists, because you just don't matter."

I wonder which message they were trying to send. Either way, it's absolutely appalling, not to mention completely untrue. Just because one does not believe in a bearded man in the clouds does not mean one cannot be a compassionate individual who cares for the lives of others. To suggest otherwise is a complete non sequiter. There is no link between belief in a deity and compassion for your fellow man. Once again, Answers in Genesis glows like a big, shiny beacon of ignorance.

Everything you wanted to know about Chromosome 2 and evolution but were afraid to ask.

I recently joined Yahoo! Answers to give me something to do on my lunch breaks at work by answering peoples' questions about molecular biology and genetics (a niche that needed filling because it only took me a week to become a "Top Contributor" in biology). Yesterday, there was a challenge put towards "evolutionists" (ugh, how I hate that term): give the one (1) piece of evidence you would put forth to a creationist to try and sway his/her opinion on whether humans descended from earlier primates. There is literally a whole boatload of evidence to support man's descent from earlier primates, but picking the single piece of evidence to sway a creationist's opinion was tough. I thought about it for a minute and decided to present the case from Chromosome 2. I thought I'd reproduce my answer here:

You want one convincing proof? Consider this:

I'm sure you've heard that humans and chimpanzees have the vast majority of our DNA in common. You're also probably not convinced by this argument ("I don't understand...so what if two organisms share the same genes? How does this prove that they came from the same lineage?"). But for now, forget about how very similar we are in our genetic sequence and let's focus on our chromosomes.

If you need a refresher, remember that the number of chromosomes a species has tends to stay the same from generation to generation. A fruit fly has four autosomal chromosomes and one pair of sex chromosomes; it's offspring will all have the same number. What about us humans? We have 23 pairs of chromosomes; 46 chromosomes in total. If you took a karyotype - that's a display of all the chromosomes in a cell - of an ape (I know you're skeptical of humans being primates, but lets call 'em primates for now) you'll notice something different from human chromosomes: there's two extra! Apes have 48 chromosomes.

You might wonder how this proves we evolved from an ancestral primate. You might even suspect that it is evidence against such a claim, since an ancestral primate would have had 48 chromosomes, and that number would have likely stayed constant down the generations, while in us, it's different. Well, this information alone does not prove much. But let's take a look at what the genome sequence shows us.

The sequence of the human genome showed an interesting fact about our Chromosome 2. The area around the very centre of chromosome 2 (known as a centromere) looked an awful lot like telomeric DNA. Telomeres are the regions at the very ends of chromosomes; what were they doing in the centre of chromosome 2? Furthermore, each arm of Chromosome 2 had what appeared to be their own centromeres. Chromosome 2 was looking to be quite an oddity. No other human chromosome displayed these characteristics.

Once the chimpanzee genome was sequenced, things got even more interesting. One of the chimpanzee's chromosomes was pretty much identical to the top half of the human Chromosome 2. Another chimpanzee chromosome was nearly identical to the bottom half of Chromosome 2. On top of this, the banding pattern of these two chromosomes (as well as the same chromosomes in many other species of primates) was a complete match to the banding pattern of Chromosome 2.

Coincidence? Not likely. What this is, is evidence of a chromosomal fusion. An ancestral primate, ancestor to humans, chimpanzees and apes, had 24 pairs of chromosomes. Eventually, this lineage diverged: apes and chimps went one way and we humans evolved along a separate path. But something interesting happened in the lineage that was to become humans: the two extra chromosomes from that ancestor fused together end to end to become human Chromosome 2. This is why our Chromosome 2 has what appears to be telomeres in its centre, and what appears to be two extra centromeres, one on each arm.

The only way to explain Chromosome 2's odd characteristics and similarity to other primates is with a chromosomal fusion. And the only way this could be possible is if we were descended from a common primate ancestor.

So, I put the question to you: if you could give only one single line of evidence for man's primate ancestry to change a creationist's mind, what would it be?