Keep your eye on the ball

For all purposes, our nervous system has one hell of a difficult task to accomplish – it needs to take in numerous stimuli all occurring either simultaneously or in some sort of temporal order and determine if there is a pattern worth responding to. While other tissues only need to make a few hormones or make some polymer twitch, neurons need to be constantly opening and closing protein gates to balance various ions. In other words, your brain does a lot of work, and therefore uses the lion’s share of energy your body takes in to do so.

Change blindness is one of those classic demonstrations of the gaps that exist in our perception where our nervous system has evolved to take a bit of a gamble. While the specific neurology of it is still questioned, it is an indication that sensing visual information isn’t the same as observing it, and our short term memory isn’t always as reliable as we might believe. A flicker, or momentary change of attention, is all it takes to reset our comprehension of what sits in front of us in plain sight. Take this aircraft, for example. It might take you a while to notice what is missing*.

Psychologists from Harvard University have demonstrated a rather interesting illusion which goes further in showing how easily overwhelmed our perception can be through simple change and movement. There findings are due to be published in Current Biology.

Watch the clip below by paying close attention to the cross in the middle. The dots will change colour for about five seconds before the surrounding ring begins to rotate back and forth.

Now, watch it again, only this time watch one of the coloured dots. Where before they appeared to cease changing, on closer observation they do nothing of the sort.

Why?

The phenomenon has been termed ‘silencing’, and describes how it’s difficult to recognise change in a moving object. There could be two reasons this happens. One is that the observer sees the original state of an object and simply doesn’t update it with the new information (termed ‘freezing’). The other possibility is that the observer sees whatever the current state is, but doesn’t mark a change between the two therefore isn’t aware of any moment of difference (known as ‘implicit updating’).

Both explanations are shown to occur with other forms of illusion. But the results of the study indicated that the illusion is a case of seeing different colours without seeing them change.

The likely reason for this has to do with how our retina maps onto our brain. As a moving image drifts across the back of our eye, it proceeds to activate a line of photoreceptors, which in turn send those messages to a corresponding line of tissue in our brain’s visual processing system. Normally, a static, changing image will prompt a nervous reaction that says ‘this pattern isn’t like it was before’. But, if it moves quickly enough from one patch of neurons to another, the same resources aren’t capable of performing this act of recognition.  To do so would demand something a little more complicated than we currently have.

If the eye tracks the changing object, however, the object remains on the same section of retina, allowing it to persist long enough in the corresponding section of the visual processing system for a variation to become apparent. The take-home-message from this is that if your eye isn’t tracking it, change simply isn’t important enough for the brain to waste energy on bringing it to your awareness.

Yet another example of how our circuitry isn’t wired for truth, but rather for economy.

*Check out the engine beneath the wing.

For additional illusions used in the study, see this Harvard website.

Published in: on January 9, 2011 at 10:37 pm  Leave a Comment  
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All aboard the science roller coaster!

Henry thought he'd try the religious haunted house ride next.

Welcome to the science roller coaster. More loops and inversions than any other philosophical theme-park attraction and guaranteed to make you dizzy.

I won’t review the hype. If you’ve been living on Earth for the past week, you’ll already know how the world’s date with NASA started in a low-cut dress and mini skirt, but ended with a stoic hand shake and a pained smile. Speculation of life on Titan shifted to misrepresentations of evidence supporting a shadow biosphere on Earth, to be quickly replaced by a challenge to the defining elements of biochemistry, only to end with a shrug as the previously exciting results sustain cracks under closer scrutiny.

There’s no shortage of discussion on the topic on various science blogs, bulletin boards and the Twitter stream, with emotions running wild as lovers of science are left with the academic equivalent of blue balls.

What happened? Nothing, really. Or a lot. Depending on your angle.

On one front, it is science as usual. NASA funded the study of a species of an extremophile bacteria which might reveal something about how life can be sustained in environment we would normally consider hostile, thereby possibly broadening the range of extraterrestrial habitats worth investigating. The research came back promising, although the method was found to be too messy for such a revolutionary conclusion to be taken for granted. In time somebody will try again, modifying the method to close the gaps, and either give the thumbs up or will admit they failed to replicate the previous results.

This sort of thing happens every single day in science. It just doesn’t make ripples outside of select tribes of researchers.

NASA’s media division would have to have been pretty daft to have not predicted the impact an embargoed whisper featuring astrobiology would have had on the the public. Of course, this is how people imagine science works – a punctuated equilibrium of discovery, where an odd electromagnetic signal or a peculiar chemical reaction constitutes a revolutionary ‘Eureka!’ moment. On the back of this fantastic view of science, all it takes is a subtle suggestion for the excitement to spread.

Will the community have learned a valuable lesson here on how science really works? I doubt it. Rather, I foresee cynicism and decreased confidence in scientists. It’s hard enough explaining to people that science is a plodding process where ‘wow!’ moments are best appreciated with years of hindsight, and not in the first five minutes of a curious anomaly.

People like the thrill of scientific discovery and innovation. They have done ever since the industrial revolution gave them cheaper socks and fatter pigs. And in a competition for attention, there’s no use in sitting back and asking for the patience it deserves.

Microbial melodramas make for good soap

There might be no ‘I’ in team, but there is definitely one in ‘bacteria’. While microbes aren’t traditionally recognised for their altruism, James Collins and a team of researchers from the Howard Hughes Medical Institute have found individual bacteria can pay a price that ultimately benefits others in the colony.

The text-book microbe competes in a bug-eats-bug world, where a subtle physiological variation in a select few can make the difference between a population’s survival and its annihilation. As the mutants come to represent the majority, resistance to old threats increases. Whether it is antibiotics or plain old disinfectants, chemical warfare loses its punch when a few bacterial mutants come to represent the species.

However, these new findings (Nature, Vol467, pg82) demonstrate the bacterial struggle for mutant dominance might not be so selfish. In an effort to observe how genetically identical bacteria developed the initial variations, Collins and his team subjected a population of cloned Escherichia coli to a steady gradient of the antibiotic norfloxacin. Routine tests of sample bacteria were taken to record the minimum concentration of antibiotic that would halt their growth.

On comparing the samples with their home population it was revealed that the very act of removing bacteria decreased their resistance to norfloxacin. Stranger still, individuals gifted with the ability to deal with the chemical attack were in the extreme minority, making up less than a mere one percent of the colony. Their talent lay in their ability to produce tryptophanase, an enzyme that breaks the amino acid tryptophan down into the chemical indole. Fortunately for its less capable siblings, an increased concentration of indole in the environment helps switch on useful metabolic pathways that combat the antibiotic’s effect, allowing the rest of the population to benefit.

Of course, given there is no such thing as a free lunch, the production of this enzyme requires the devotion of precious energy. ‘Kin selection’ is one explanation for this behaviour. A process first suggested in the 1960s by the evolutionary biologist William Hamilton, it suggests individuals act altruistically to increase the chance of survival and reproduction for those with a close genetic relationship.

What, then, of their nefarious counterpart, the bacterial bum? Led by Steven Diggle at the University of Nottingham’s Centre for Biomolecular Sciences, microbiologists have found that individuals within a population of Staphylococcus aureus can opt to coast along for the ride when it comes to contributing to the costs of an infection.

After deliberately infecting waxworms with the bacteria, the researchers eavesdropped on the developing colony by observing a chemical coordination process called ‘quorum sensing’. They discovered those which lacked the means to engage in this microbial forum could also refrain from making toxins, saving them energy which could be devoted instead to reproduction. In effect, these bacteria were relying on their siblings to provide them with their nutrients. Seeding an infection with these freeloaders could present physicians with a novel form of treatment.

While this could be great news for the medical world, it does present a rather perplexing contrast to their more charitable cousins. Understanding how microbes interact with their host’s environment is vital if we are to find additional ways of controlling infection. Just last year, the World Health Organisation released a warning concerning the potential threat posed by the NDM-1 strain of E. coli – a potential superbug that is on the rise across the globe. It could very well join the likes of more familiar foes such as the vancomycin-resistant enterococcus and the rather formidable methicillin-resistant staphylococcus aureus.

Paying attention to the melodramas unfolding in these microbial ‘Days of our Lives’ is certainly better than any daytime soap. What’s more, it might be the key to turning the tide on the twilight of the antibiotic.

Published in: on November 2, 2010 at 9:46 am  Leave a Comment  
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How to make a strawberry

If Mother Nature was incarnated in today’s world, her wrinkled, battle-scarred old body would be photoshopped within an inch of its life and adorn every food package, beauty product and health item available. It’s a common trick of marketing to appear to be nature’s ally, relying on the unstated belief that millions of years of gradual evolution is a far safer bet than several decades of tinkering in the lab with a shaved lab rat and glassware full of smoking liquid.

Subtle hints are typically dropped through the clever use of language. Familiar words are safer than numbers and nomenclature, for instance. Glycerin is ok, but additive 422 isn’t (yup, same thing).

Some years ago I came across a paper on synthesising the flavour and aroma of the humble strawberry. It contained a list of chemicals that had been gathered from relevant literature that were present in this succulent, delicious fruit. It’s not even complete – they are simply the compounds researchers have managed to wring out of the plant and detect.

Somewhere below there lies the secret of what makes a strawberry tastes like a strawberry and not a banana or a grape. Of course, as always in nature, not only is it a question of the right combination, it’s as much the dose that maketh the poison. Or in this case, the delectable taste.

Next time somebody raises their eyes at the ingredients on a food packet and claims it looks like a chemistry lab, implying that is a good indication that the food must be worse for them than some other item, print out this page and hand it to them. Of course, being aware of the impact certain compounds have on our health is useful, regardless of whether you can pronounce it or not. But ‘long lists of big names and numbers, hyphens and greek letters’, as the strawberry shows, is not shorthand for unhealthy or toxic. By the same token, short lists and familiar words are no guarantee of being better for you.

Acids

  • Formic acid
  • 3-Hydroxyoctanoic acid
  • Acetic acid
  • 16 Nonanoic acid
  • Propanoic acid
  • Non-3-enoic acid
  • 2-Methylpropanoic acid
  • Decanoic acid
  • Butanoic acid
  • Dec-2-enoic acid
  • 2-Methylbutanoic acid
  • Undecanoic acid
  • 3-Methylbutanoic acid
  • Dodecanoic acid
  • 2-Methylbut-2-enoic acid
  • Tridecanoic acid
  • Pentanoic acid
  • Tetradecanoic acid
  • 4-Methylpentanoic acid
  • Tetradec-2-enoic acid
  • 2-Methylpent-2-enoic acid
  • Pentadecanoic acid
  • 2-Methylpent-3-enoic acid
  • Hexadecanoic acid
  • Hexanoic acid
  • Hexadec-9-enoic acid
  • Hex-2-enoic acid
  • Heptadecanoic acid
  • 5-Methylhexanoic acid
  • Octadec-9-enoic acid
  • 3-Hydroxyhexanoic acid
  • Octadeca-9,12-dienoic acid
  • Heptanoic acid
  • Octadeca-9,12,15-trienoic acid
  • Octanoic acid
  • Nonadecanoic acid
  • Oct-2-enoic acid
  • Eicosanoic acid

Alcohols

  • Methanol
  • Hex-1-en-3-ol
  • Ethanol
  • Heptan-1-ol
  • Propan-1-ol
  • Heptan-2-ol
  • Propan-2-ol
  • Heptan-3-ol
  • 2-Methylpropan-1-ol
  • Octan-1-ol
  • Butan-1-ol
  • Octan-2-ol
  • Butan-2-ol
  • Octan-3-ol
  • 2-Methylbutan-1-ol
  • Oct-3-en-1-ol
  • 3-Methylbutan-1-ol
  • Oct-1-en-3-ol
  • 2-Methyl-butan-2-ol
  • Nonan-1-ol
  • Pentan-1-ol
  • Nonan-2-ol
  • Pentan-2-ol Non-1-en-3-ol
  • Pentan-3-ol
  • Decan-1-ol
  • Pent-1-en-3-ol
  • Decan-2-ol
  • Pent-3-en-2-ol
  • Undecan-2-ol
  • Hexan-1-ol
  • Dodecan-1-ol
  • Hexan-2-ol
  • Dodecan-2-ol
  • Hexan-3-ol
  • Tridecan-2-ol
  • trans-Hex-2-en-1-ol
  • Pentadecan-2-ol

Aldehydes

  • Acetaldehyde
  • cis-Hex-3-enal
  • Propanal
  • Hexa-2,4-dienal
  • Propenal
  • Heptanal
  • Butanal
  • Hept-2-enal
  • But-2-enal
  • Oct-2-enal
  • Pentanal
  • Nonanal
  • Pent-2-enal
  • Decanal
  • Hexanal
  • Deca-2,4-dienal
  • trans-Hex-2-enal

Ketones

  • Propanone
  • 4-Hydroxy-4-methyl-pentan-2-one
  • Butanone
  • Hexan-2-one
  • Methylbutanone
  • Heptan-2-one
  • Diacetyl (Butan-2,4-dione)
  • Octan-2-one
  • Pentan-2-one
  • Nonan-2-one
  • Pentan-3-one
  • Decan-2-one
  • Pent-3-en-2-one
  • Undecan-2-one

Esters

  • Methyl formate
  • Ethyl 2-methylbutanoate
  • Ethyl formate
  • Isopropyl 2-methylbutanoate
  • Butyl formate
  • Butyl 2-methylbutanoate
  • 3-Methylbutyl formate
  • 2-Methylpropyl 2-methylbutanoate
  • Hexyl formate
  • 2-Methylbutyl 2-methylbutanoate
  • Methyl acetate
  • 3-Methylbutyl 2-methylbutanoate
  • Ethyl acetate
  • Hexyl 2-methylbutanoate
  • Propyl acetate
  • Octyl 2-methylbutanoate
  • Isopropyl acetate
  • Ethyl 3-methylbutanoate
  • Butyl acetate
  • Butyl 3-methylbutanoate
  • 2-Methylpropyl acetate
  • Methyl 3-hydroxybutanoate
  • 2-Methylbutyl acetate
  • Ethyl 3-oxobutanoate
  • 3-Methylbut-2-enyl acetate
  • Ethyl pentanoate
  • Pentyl acetate
  • Methyl 4-methylpentanoate
  • Isoamyl acetate
  • Methyl hexanoate
  • 1-Methylbutyl acetate
  • Ethyl hexanoate
  • 3-Methylbutyl acetate
  • Butyl hexanoate
  • Pentyl acetate
  • Pentyl hexanoate
  • Hexyl acetate
  • 3-Methylbutyl hexanoate
  • 1-Methylpentyl acetate
  • 1-Methylbutyl hexanoate
  • trans-Hex-2-enyl acetate
  • Hexyl hexanoate
  • cis-Hex-3-enyl acetate
  • Hex-2-enyl hexanoate
  • Hex-1-en-3-yl acetate
  • trans-Hex-3-enyl hexanoate
  • 1-Methylhexyl acetate
  • 1-Methylhexyl hexanoate
  • Hept-1-en-3-yl acetate
  • Octyl hexanoate
  • Octyl acetate
  • Decyl hexanoate
  • Decyl acetate
  • Ethyl trans-hex-2-enoate
  • Methyl propanoate
  • Methyl 3-hydroxyhexanoate
  • Ethyl propanoate
  • Ethyl 3-hydroxyhexanoate
  • cis-Hex-3-enyl propanoate
  • Methyl heptanoate
  • Methyl 1-methyl propanoate
  • Ethyl heptanoate
  • Ethylmethyl propanoate
  • Methyl octanoate
  • Methyl butanoate
  • Ethyl octanoate
  • Ethyl butanoate
  • Isopropyl octanoate
  • Propyl butanoate
  • Butyl octanoate
  • Isopropyl butanoate
  • 3-Methylbutyl octanoate
  • Butyl butanoate
  • Hexyl octanoate
  • 2-Methylpropyl butanoate
  • cis-Hex-3-enyl octanoate
  • Pentyl butanoate
  • Methyl nonanoate
  • 1-Methylbutyl butanoate
  • 2-Methylpropyl nonanoate
  • 3-Methylbutyl butanoate
  • 3-Methylbutyl nonanoate
  • Pent-3-enyl butanoate
  • Methyl decanoate
  • Hexyl butanoate
  • Ethyl decanoate
  • trans-Hex-2-enyl butanoate
  • Isopropyl decanoate
  • cis-Hex-3-enyl butanoate
  • Hexyl decanoate
  • 1-Methylhexyl butanoate
  • Methyl dodecanoate
  • Octyl butanoate
  • Ethyl dodecanoate
  • 1-Methyloctyl butanoate
  • Methyl hexadecanoate
  • Decyl butanoate
  • Methyl octadecanoate
  • Ethyl but-2-enoate
  • Methyl octadec-9-enoate
  • Methyl 2-methylbutanoate
  • Methyl octadeca-9,12,15-trienoate

Lactones

  • γ-Hexalactone
  • δ-Octalactone
  • δ-Hexalactone
  • γ-Decalactone
  • δ-Heptalactone
  • δ-Decalactone
  • γ-Octalactone
  • γ-Dodecalactone

Acetals

  • Dimethoxymethane
  • 1-Butoxy-1-ethoxyethane
  • Diethoxymethane
  • 1-Ethoxy-1-pentoxyethane
  • 1,1-Dimethoxyethane
  • 1-Ethoxy-1-hexoxyethane
  • 1-Ethoxy-1-methoxyethane
  • 1-Ethoxy-1-hex-3-enoxyethane
  • 1-Butoxy-1-methoxyethane
  • 1,1-Dihexoxyethane 17, 18
  • 1-Methoxy-1-pentoxyethane
  • 1,1-Diethoxypentane
  • 1,1-Diethoxyethane
  • 1,1-Diethoxyoctane
  • 1-Ethoxy-1-propoxyethane

Furans

  • 2-Furfural
  • 2,5-Dimethyl-4-hydroxy-2H-furan-3-one
  • 2-Furancarboxylic acid
  • 2,5-Dimethyl-4-methoxy-2H-furan-3-one

Aromatic compounds

  • Benzyl alcohol
  • Benzyl acetate
  • 2-Phenylethanol
  • 2-Phenethyl acetate
  • 2-(4-Hydroxyphenyl)ethanol
  • Methyl salicylate
  • trans-Cinnamyl alcohol
  • Ethyl salicylate
  • Benzaldehyde
  • Methyl cinnamate
  • Acetophenone
  • Ethyl cinnamate
  • Benzoic acid
  • 4-Vinylphenol
  • 4-Methylbenzoic acid
  • 2-Methoxy-4-vinylphenol
  • 2-Hydroxybenzoic acid
  • Eugenol
  • Phenylacetic acid
  • 1-Methylnaphthalene
  • 3-Phenylpropanoic acid
  • 2-Methylnaphthalene
  • trans-Cinnamic acid

Sulphur compounds

  • Methanethiol
  • Methylthiol acetate
  • Ethylthioethane
  • Methylthiol butanoate
  • Ethyldithioethane
  • Dimethyl disulphide

T erpenes

  • Limonene
  • Borneol
  • a-Pinene
  • Isofenchyl alcohol
  • b-Pinene
  • Linalool oxides
  • Linalool
  • a-Ionone
  • Nerolidol
  • b-Ionone
  • a-Terpineol

b-D-Glucopyranosides

  • Benzyl b-D-glucopyranoside
  • 2,5-Dimethyl-4-hydroxy-2H-furan-3-one
  • b-D-glucopyranoside
  • 2-(4-Hydroxyphenyl)-ethyl b-D-glucopyranoside
  • 2,5-Dimethyl-4-hydroxy-2H-furan-3-one
  • 6@O-malonyl-b-D-glucopyranoside

From Zabetakis I., Holden M.A.,, (1997), Strawberry Flavour: Analysis and Biosynthesis, J Sci Food Agric Vol.74, pp421-434

Published in: on October 18, 2010 at 8:46 pm  Comments (66)  
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