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Is it me or has New Scientist gone completely fucking shit?
Hadn't noticed it being particularly shit of late, but then I'm not a regular reader. It doesn't seem to have as many of the divine Kate Charlesworth's cartoons in it as it used to. I spotted a letter from Pete Carroll a few months back.
Here's a big chunk of the New Scientist article:
"All the bonds affecting water molecules are ultimately caused by quantum effects, but hydrogen bonds are the result of one of the strangest quantum phenomena: so-called zero-point vibrations. A consequence of Heisenberg's famous uncertainty principle, these constant vibrations are a product of the impossibility of pinning down the total energy of a system with absolute precision at any given moment in time. Even if the universe itself froze over and its temperature plunged to absolute zero, zero-point vibrations would still be going strong, propelled by energy from empty space.
Quantum lifeline
In the case of water, these vibrations stretch the bonds between hydrogen atoms and their host oxygen atoms, enabling them to link up with neighbouring molecules more easily. The result is the highly cohesive liquid that keeps our planet alive.
Felix Franks of the University of Cambridge has a nice illustration of the vital role this quantum effect plays. Just take some water and swap the hydrogen for atoms of its heavier isotope deuterium. You end up with a liquid that is chemically identical, yet poisonous to all but the most primitive organisms. "The only difference is in the zero-point energy," says Franks.
A growing number of researchers are now investigating the consequences of this deep link between quantum effects and life. Recent advances in theoretical methods, experimental techniques and brute computing power have allowed them to study how water interacts with DNA, proteins and cells in unprecedented detail.
The results are often unexpected, and challenge simplistic assumptions about how life works. Certainly the fashionable view that the secret of life can be summed up in a catalogue of genes and the proteins they code for looks risibly simplistic. It is becoming clear that they cannot carry out even their most basic functions without direct help from molecules of the colourless, odourless curiosity that comes out of the tap. "Without water, it is all just chemistry," says Franks, "but add water and you get biology."
Some of the most impressive evidence is emerging from studies of proteins. Created from chains of amino acids linked up according to the instructions of DNA, proteins are the workhorse molecules of life. They perform a host of key functions, from fighting off invaders to catalysing reactions and building fresh cells. Their precise action depends largely on their physical shape, and water molecules have long been known to be vital in ensuring amino acids curl up in the right way. Only now are researchers discovering the mechanism.
What they are finding is an astonishingly delicate interplay of proteins and water molecules, orchestrated by those all-important hydrogen bonds. In January, Florian Garczarek and Klaus Gerwert at the department of biophysics at the Ruhr University of Bochum, Germany, reported on the role water molecules play in a protein called bacteriorhodopsin, which is found in the outer walls of primitive life forms (Nature, vol 439, p 109).
Bacteriorhodopsin undergoes a simple form of photosynthesis, using light to create a source of chemical energy. Researchers have long suspected that this process relies on the incoming light shifting protons around the molecule, creating a charge difference that acts rather like a battery. An obvious source of protons is the hydrogen nuclei of the water trapped within the protein's structure, but no one had shown how this could work.
Enter Garczarek and Gerwert. They exposed bacteriorhodopsin to infrared light, and found that the behaviour of the water molecules trapped within it was far from that of idle captives. Once struck by photons of light, the shape of the protein changed, breaking some of the hydrogen bonds between the trapped water molecules. The pair found that this triggered a chain of events in which fragments of some water molecules and clusters of others interacted to move protons through the protein.
This sophisticated process is all made possible by the quantum behaviour of the hydrogen bonds in water. "Having bonds that can easily be formed but are not too difficult to break is a big advantage," says Garczarek. The results suggest that it is no accident that chains of amino acids trap water molecules as they fold up to form a protein.
Hydrogen bonds are also turning out to have a profound role in the functioning of that other key constituent of life, DNA. As with proteins, new findings suggest it is time for a rethink of the familiar thumbnail sketch of DNA as a double helix of four chemical bases.
To perform its biological functions, DNA has to carry out various manoeuvres, twisting, turning and docking with proteins at just the right place. No problem for a metre-long stringy molecule like DNA, one might think. Yet on the far smaller scale where the real action takes place - typically a few hundred bases - DNA is pretty rigid. And then there's the mystery of how proteins meet up with just the right parts of the double helix.
Biochemists have long suspected water molecules are important: concentrations of them around DNA appear to correlate with biological activity. It turns out that water undergoes radical changes as it approaches the surface of DNA. As the molecules draw near the double helix, the seething network of hydrogen bonds within bulk water becomes disrupted, and the motion of individual molecules becomes more and more sluggish.
The latest research focuses on what happens around the "troughs" in the double helix formed by specific base pairs. It seems that water molecules linger longer and rotate more slowly around some base pairs than others. Suddenly that link between hydration levels and biological activity doesn't seem so perplexing. After all, the base pairs on DNA are the building blocks of genes, and their sequence dictates the order in which amino acids are stitched together to make proteins. If water molecules linger longer around some base pairs than others, the level of hydration will mirror the sequence of base pairs.
Monika Fuxreiter of the Hungarian Academy of Sciences Biological Research Centre in Budapest believes that this explains how proteins and DNA interact. She and her colleagues at BRC's Institute of Enzymology created a computer simulation of DNA and a protein called BamHI, which uses water molecules to cut DNA at very specific points.
They saw that adding virtual water molecules to the mix had a dramatic effect. "The water molecules report the DNA sequence to the protein while it is still some distance away," says Fuxreiter. "Then as the protein gets closer, the water molecules are ejected from the site until it binds tightly to the DNA."
According to Fuxreiter the water molecules relay messages to the protein via electrostatic forces, which reflect the varying levels of hydration on the DNA. They can even warn the approaching protein about potential problems with the DNA before it arrives. "If the DNA is distorted due to some defect it becomes more hydrated and the protein can't make proper contact," says Fuxreiter. "Instead, it moves to another site - which is very good biologically." Fuxreiter's team is now planning to test just how effective water molecules are in determining where and when proteins bind to DNA.
“It is time for a radical overhaul of the scientific view of water”
That there is more to water than hydrogen and oxygen is something many researchers welcome. But Rustum Roy, a materials scientist at Pennsylvania State University in University Park goes further. He thinks it is time for a radical overhaul of the scientific view of water - one which, he believes, has been dominated by chemistry for too long. "It's absurd to say that chemical composition dictates everything," he says. "Take carbon, for example - the same atoms can give you graphite or diamond." In a review paper published in Materials Research Innovations in December, Roy and a team of collaborators called for a re-examination of the case against the most controversial of all claims made for water: that it has a "memory".
The idea that water can retain some kind of imprint of compounds dissolved in it has long been cited as a possible mechanism for homeopathy, which claims to treat ailments using solutions of certain compounds. Some homeopathic remedies are so dilute they no longer contain a single molecule of the original compound - prompting many scientists to dismiss homeopathic effects as imaginary. For how can water with nothing in it act as anything other than water?
Roy believes this is too simplistic: "It is a naive, chemistry-schoolbook argument." He argues that water has proved itself capable of effects that go beyond simple chemistry, and these may imbue water with a memory. One way this may occur, he says, is through an effect known as epitaxy: using the atomic structure of one compound as a template to induce the same structure in others.
Hidden depths
Epitaxy is routinely used in the microprocessor industry to create perfect semiconductor crystals. And according to Roy, water already exhibits epitaxial effects. "The 'seeding' of clouds is the growth of crystalline ice on a substrate of silver iodide, which has the same crystal structure," he says. "No chemical transfer whatsoever occurs."
Roy and his colleagues also point to another effect they believe has been overlooked by mainstream scientists in their rush to dismiss homeopathy: the vigorous shaking of the mixtures used, a process called succussion. The team estimates that shock waves generated by the shaking can cause localised pressures inside the water to reach over 10,000 atmospheres, which may trigger fundamental changes in the properties of the water molecules.
Roy believes that by taking homeopathy seriously scientists may find out more about water's fundamental properties. "The problem is that much more research needs to be done to find the right techniques to probe the properties of water reliably," he says.
However, many scientists question the very idea of taking homeopathy seriously. The most recent review of the medical evidence found that homeopathic remedies were no better than a placebo in all but a handful of cases (Journal of Alternative and Complementary Medicine, vol 11, p 813). That is likely to put the brakes on research into this aspect of water. "Rigorous experiments need to be done to provide support for all scientific claims," says theoretical chemist David Clary at the University of Oxford. "I don't think it is worth spending time on this." Chemist Martin Chaplin of London South Bank University is more sympathetic: "I think there may be something in it, but we need good experiments - and the best researchers won't go near the subject." |
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