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Humans are almost unimaginably complex, with trillions of cells organized into hundreds of different tissues. But we have scarcely more genes than a fruitfly or a worm, and only about four or five times as many as brewers' yeast or some bacteria. Surprising then that the human genome is 250 times larger than the yeast's. It comprises about 99% 'junk DNA' — genetic code that is not used to make the protein building blocks of life.You know what's coming next, don't you? We're going to hear about one of the seven silly excuses for why we don't really have junk DNA (see The Deflated Ego Problem). Here's how Martin Pagel sets up his choice of excuse.
Junk DNA gives every appearance of fulfilling the metaphor of the selfish gene. It accumulates in organisms' genomes simply because it is good at accumulating; it can even be harmful. Why we put up with it has long been a mystery.Astute readers will see where this is going—he's going to use the "regulatory DNA" excuse. All this will accomplish is to demonstrate; (a) Martin Pagel's inability to reason like a scientist by considering evidence that has been accumulated over four decades, and (b) Nature's inability to recognize good science from bad science.
Increasingly, it seems that the genes that do code for proteins may recruit some or all of this junk DNA to regulate when, where and how much they are expressed. Because nearly every cell in the body carries a complete copy of the genome, something has to tell the genes that make eyes not to switch on in the back of the head, or genes for teeth to stay silent in our toes. Something has to instruct genes to team up to produce complex structures such as hearts and kidneys, or the chemical networks that create our metabolism and physiology.
Genes, in effect, use regulation to promote their interests within the bodily phenotype: it is how they vary their exposure to the outside world. Regulation is how we can have over 98.5% similarity to chimpanzees in the sequences of our coding genes, yet differ so utterly from them.This is, of course, complete nonsense. We know for a fact that large amounts of the human genome are really junk. We know for a fact that you can have complex regulation by using only a small percentage of the genome (1000 bp per gene, or less than 1% of the genome, per gene is more than sufficent [Junk in Your Genome: Protein-Encoding Genes]. We know for a fact that some single-celled species (amoeba) have huge amounts of junk DNA and some some complex multicellular species have genomes that are much smaller than mammalian genomes (Drosohila melanogaster.
Indeed, the huge quantity of junk DNA in the genomes of most complex organisms may act as a vast digital regulatory mechanism. Until recently many common machines, such as aeroplanes, clocks, and even computers were analogue devices, regulated by levers, springs, heat or pressure. Aeroplanes were flown with a stick, springs drove clocks. Digital regulation — instructions encoded in strings of binary numbers arbitrarily long, and hence precise — enabled complexity to increase. Stealth fighters and space shuttles are so complex that they can be flown only by digital computers, not (analogue) human pilots.
Similarly, the emergence of digital regulation derived from unused stretches of junk DNA may have precipitated the transition from single cells to complex multicellular organisms. Long runs of the four chemical bases that make up DNA can easily act like binary strings. How these stretches bind to a gene can regulate exquisitely the degree and timing of that gene's expression. Tellingly, bacteria and some other single-celled organisms have negligible amounts of junk DNA. They rely far more on analogue systems of gene regulation that are protein-based and less precise.
I do think there's a problem in making science appear frightening and linked to a laboratory activity. As comments you've already heard suggest, science really is a process. A process by which you have ideas, you test them out, you look at evidence, you measure things, and you draw conclusions. And that's a process that applies to almost any phase of life.Science is a process. It's a way of knowing. That's what we should be teaching.
Believe it or not, there was a time when I didn't consider acupuncture to be a form of woo.None of us have time to investigate every form of superstition and irrational thinking. Sometimes we have to rely on trusted experts to do the required homework. Orac is one of those.
I know, I know, it's hard to believe, given the sorts of posts I've done recently on acupuncture, but it's true. Certainly, I didn't believe the whole rigamarole about needles somehow "restoring the flow of qi" or anything like that, but I did wonder if maybe there was some physiologic mechanism at work behind acupuncture that produced real benefits in terms of pain relief above that of placebo. Sure, I may have dismissed homeopathy as the pure magical thinking that it was, but acupuncture I wasn't so sure about.
Obviously, that's changed.
The reason my opinion has changed and now I place acupuncture firmly in the "woo" category is that I've actually been reading the scientific literature on acupuncture over the last year or so....
Your Majesties, Your Royal Highnesses, Ladies and Gentlemen,
In the days of Alfred Nobel, the learned academies used to entertain and educate the public by holding open demonstrations explaining the latest scientific advances. This tradition has been largely – and perhaps unfortunately – forgotten. So let us try to revive the public demonstration of science, if only for a brief moment.
The demonstration I have in mind is a simple one, and only requires that you do something that is in any case particularly fitting for a Nobel Prize ceremony: to think. But only for exactly 5 seconds!
So, please start thinking, for 5 seconds ... Thank you!
Let us now reflect briefly on what has just happened, in each and every one of us. First, a sudden increase in the activity of the brain when you started to wonder what this is all about – should I really think at this point in the ceremony? – then, cascades of nerve signals when you were actually thinking, and finally a return to the normal resting state. And all this thinking ultimately relied on one of the simplest chemical compounds you can imagine: ordinary salt – sodium, potassium and chloride ions – streaming back and forth across the walls of your nerve cells, thereby generating the signals that activated your mind. And not even very much salt – a rough estimate is that the total amount of salt spent during these five seconds in each one of us was no more than a few grains. Only a fistful of salt to set a whole Concert Hall thinking!
And while all this brain activity was occupying our minds, our kidneys worked on quietly, as they always do, reabsorbing water from the urine to the blood. But in this case, the volumes of water transported are too big, even during five seconds, to be suitable for a demonstration from the podium.
This year's Nobel Prize in Chemistry is all about salt water, and the biochemical mechanisms that control where, when, and how often ions and water are let into or out of the cells in our body. Mechanisms that the two Laureates – Peter Agre and Roderick MacKinnon – have elucidated down to the atomic level.
Agre's was a "serendipity discovery": while working on a completely different problem, he stumbled across a protein in red blood cells that he could soon show was the water channel researchers had been looking for in vain for well over a century. His unexpected discovery opened a whole new field of study.MacKinnon, on the other hand, decided at an early stage that he should try to do what was then thought impossible: to determine the three-dimensional structure of ion channels at atomic resolution. He bet his career on this vision – and succeeded to an extent that probably surprised even himself.
There is a lesson here, I believe: There is no one way to do science, and our support system must be sufficiently well funded and versatile to prepare the ground for both unexpected serendipity and focused, often risky, attacks on central scientific problems.
Peter Agre and Roderick MacKinnon stand for decisive contributions to the biochemistry of cell membranes, but their discoveries also have an almost tangible aesthetic component. Their work has uncovered an amazing "economy of design" in the atomic structures of the water and ion channels that is breathtaking in its simplicity and perfection. Indeed, after seeing these molecular machines, you find yourself thinking, "Of course, this is how it must be, this is how it must work!" What more could we ask of science?
Professor Agre, Professor MacKinnon, your fundamental discoveries concerning water and ion channels are singular achievements that have made it possible for us to see these exquisitely designed molecular machines in action at the atomic level. The biochemical basis for the transport of water – the most abundant and primordial substance of life – and ions – these tiny, mundane and yet absolutely essential constituents of the living world – can now be understood in unparalleled detail. On behalf of the Royal Swedish Academy of Sciences, I wish to convey to you our warmest congratulations, and I now ask you to step forward to receive the Nobel Prize in Chemistry from the hands of His Majesty the King.
A limited nuclear weapons exchange between Pakistan and India using their current arsenals could create a near-global ozone hole, triggering human health problems and wreaking environmental havoc for at least a decade, according to a study led by the University of Colorado at Boulder.Wow! That sounds really bad. By the way, they forgot to mention one other nasty little detail—about 100 million people will die in the blasts and of radiation poisoning in the aftermath of the attacks.
The computer-modeling study showed a nuclear war between the two countries involving 50 Hiroshima-sized nuclear devices on each side would cause massive urban fires and loft as much as 5 million metric tons of soot about 50 miles into the stratosphere, said CU-Boulder Research Associate Michael Mills, chief study author. The soot would absorb enough solar radiation to heat surrounding gases, setting in motion a series of chemical reactions that would break down the stratospheric ozone layer protecting Earth from harmful ultraviolet radiation, said Mills.
The bombardier beetle, found mainly in Africa and Asia, is remarkable in that it can fire a powerful jet of hot, toxic fluid to fight off predators such as birds and frogs. While the chemical reaction that makes the venom has been understood for some time, the actual power behind the venomous squirt, which can travel as far as 20cm, has been cause for speculation.Note, there isn't a problem understanding the chemical reaction and how the beetles control it. That's been well understood for several decades. You can watch a young Richard Dawkins debunking the standard creationst claims in a video posted on Genomicron [Bombardier beetles].
Quantities of hydroquinone and hydrogen peroxide gases build up in the beetle’s abdomen but, when necessary for defence, get mixed together in a connected ‘combustion chamber’ to produce toxic benzoquinone. This hot fluid is then fired off at force in the face of enemy predators.
[Photo Credit: Institute of Physics]