Reading Old Books with your Nose

On this week's Naked Scientists NewsFlash, how the smell of old books can help to preserve them, deleting old memories to make room for new ones and the frightening rate of...
16 November 2009
Presented by Ben Valsler


On this week's Naked Scientists NewsFlash, how the smell of old books can help to preserve them, deleting old memories to make room for new ones and the frightening rate of Greenland ice loss. Plus, we look back to this week in Science history and the life of Nobel Laureate Daniel Nathans.

In this episode

A multi-volume Latin dictionary (Egidio Forcellini: Totius Latinitatis Lexicon, 1858-87) in a table in the main reading room of the University Library of Graz. Definitely an old book!

01:35 - Smell Test for Old Books

Don't judge a book by its cover - judge it by the smell instead!

Smell Test for Old Books

There's the old saying, 'never judge a book by its cover' and indeed you shouldn't - now chemists are saying you should judge them by their smell, instead. Publishing in the Journal Analytical Chemistry the authors have come up with a test that can measure how fast an old book is degrading, according to its odour. And this new sniff test could be really valuable to museums and document libraries because it has the potential to be completely non-invasive.

Latin Dictionary from 1858And we actually did a question of the week on this about a year and a half ago, with one of the authors on the paper. Jana Kolar, together with colleagues from University College London and Slovenia have isolated the 15 main VO Cs - volatile organic compounds - which the paper releases. Each of these volatile organic compounds are emitted from the paper as a result of: the original make-up of the paper in the document, the glues used to bind it and the ink used for the print.

The researchers looked at 72 papers from 19th and 20th centuries to find out which contained the most fragile components. They already knew these included rosin (pine tar) and wood fibre which are related to increased levels of acids, like acetic acid, in the paper as it ages. And these acids can eat away at the paper itself. So they collected and analysed the volatile organic compounds using a combination of gas chromatography and mass spectrometry.  And then to 'test their own test' or find out which of these compounds were the ones libraries should be looking out for, they took a few small samples of the paper itself to look at its composition.

Combining the results gave them 15VOCs which give an indication as to the condition of the paper and how much acid or even peroxide/ie. bleach it's producing as it decays. They've dubbed the smell test 'material degradomics.' And now that they know the smell test works on these 72 samples they can develop this method to be completely non-invasive. And that's useful to any old documents library because currently, you have to actually cut a small sample from a document in order to test how it's faring.

And I'm sure many of you will have experienced these smells. They hit you like a slightly spongy wall when you walk into a well-established library like the ones you find here in Cambridge. The authors describe some of these smells as , "A combination of grassy notes with a tang of acids and a hint of vanilla over an underlying mustiness ."

Merope star

04:50 - Lithium shows scientists where to find far-off planets

A European team of scientists may have discovered a shortcut to finding distant planets orbiting far-off stars - you look for lithium, or rather a lack of it...

Lithium shows scientists where to find far-off planets

A European team of scientists may have discovered a shortcut to finding distant planets orbiting far-off stars - you look for lithium, or rather a lack of it...

Lithium is the third lightest element in the Universe and small amounts were produced, alongside hydrogen and helium, by the Big Bang. Consequently it turns up together with these two other elements in stars and ought to be present in roughly the same amounts everywhere.

But a long-standing mystery scientists haven't been able to explain is why some stars appear to have plenty of the stuff, the presence of which is apparent within the spectrum of light given off by a star, whilst others - our own Sun included - contain less than 1% of this amount.

To get to the bottom of the problem, Garik Israelian and his colleagues, writing in Nature, surveyed more than 500 similar stars, including 70 known to have planets orbiting them.

When the data from these stars were compared, and factors such as age were taken into account, a surprising trend emerged. Stars like our own Sun, with planets, lacked lithium, whilst their more lonely counterparts were more likely to be lithium replete.

The researchers think that the presence of planets somehow stirs up the substance of the star, pulling the lithium from the star's surface to the much hotter interior where it is consumed.

The team say it's now up to the theoriticians to figure out exactly how this happens, but the key point is that looking for a lack of lithium in the spectral signature coming from a star could provide space scientists with a shortcut way to find new planets much more quickly.

Drawing of a cast to illustrate the relations of the brain to the skull. (Superior temporal gyrus labeled at center, in green section.)

Deleting old memories to make room for new ones...

I'm sure most of you out there will have run out of disk space on a computer and had to overwrite a few files. And it looks like the short-term memory of animals isn't all that far-removed...

Publishing in the journal Cell, neuroscientists reported that, in mice and rats, newly formed neurons seem to be deleting older connections. Kayoru Inokuchi and colleagues from the University of Toyama think that short term memory is updated by new neurons emerging in the hippocampus area of the brain, which is sort of in the bottom middle bit, and these new neurons essentially overwrite connections between the old ones.

The researchers looked at this by irradiating rat's brains, which considerably slows down the formation of new neurons in the hippocampus. And they placed the rats in a chamber which would give their feet an electrical shock! Once the rats had this experience in their short-term memories the researchers applied a bit of x-ray radiation and afterwards the rats continued to use their hippocampus to recall that fear memory. But in those rats without x-ray treatment the fear memories were eventually displaced to elsewhere in the brain.

The researchers knew this memory displacement was occurring because they also looked at mice which were born without the ability to make new hippocampal neurons and mice who received an infusion to block any neuron activity in the hippocampus. That way they could tell which animal was depending on its hippocampus for memory and which wasn't.

Again, mice which couldn't produce new hippocampal neurons seemed to rely on their old short-term memories when placed in the shock chamber. And the researchers said this is because there were no new neurons to displace the old ones and essentially push them into long-term storage, somewhere else in the brain.

They've known for a while that exercise can improve short term memory so they put some of these mice onto an exercise wheel and lo and behold, they did not use the same area of the brain for their fear memories. And the scientists think this is because the exercise made them generate new neurons in their hippocampi.

So the conclusion is that if you can't make new neurons then you could have problems because the brain's short-term memory is literally full. So perhaps this could lead to a better understanding of memory-related diseases such as dementia and Alzheimer's.

Greenland Ice Sheet changes

11:12 - Monitoring the Greenland Ice Sheets

The melting of the Greenland Ice Sheets is accelerating and Jonathan Bamber discusses the evidence...

Monitoring the Greenland Ice Sheets
Jonathan Bamber, Bristol University

Chris - Well also in the news this week.  We've got some worrying news emerging from Greenland because scientists have shown that the ice there is melting, and the time that it's doing that at, the rate which it is melting at is increasing. So the melt rate is accelerating.  But how do we actually quantify how fast ice is melting from a land mass with any accuracy?  Well, there's a paper in the journal Science this week, it's by Bristol University scientist, Professor Jonathan Bamber and his colleagues, and it might be able to help us.  And Jonathan's with us now to tell us a bit more.  Hi, Jonathan.

Jonathan -   Hi.

Chris -   Welcome to the Naked Scientists.  So tell us, first of all, what the issue is with Greenland.

Jonathan -   So Greenland is the biggest ice mass in the northern hemisphere.  It's got enough ice in it to - if it melted, if you took away a whole ice sheet.  It would raise global sea level by about seven meters.

Chris -   To put that into perspective then we would be looking at, the Pennines would be about the only bit of Britain left above water, wouldn't they?

Jonathan -   No, no.  It's not quite that bad, but you can say bye-bye to the Houses of Parlaiment which might be a good thing but, you know, I couldn't comment on that.  But seven meters, that's what - about 25 feet, so I'm not suggesting that that's going to happen tomorrow or anything like that, but there is a huge potential for sea level rise in the Greenland ice sheet.  I think the other thing about big ice masses like Greenland and Antarctica is that once you set them on a certain course, they're like the super tankers of the climate world.  Once you've pointed them in a certain direction, it's very, very difficult to turn them another way.

Chris -   How do you quantify how much weight ice, water, is going from Greenland?

Jonathan -   Well, there's a variety of techniques.  But what a lot of scientists have been very excited about in about the last five, six years is a satellite mission called GRACE, which stands for Gravity Recovery and Climate Experiment.  It doesn't matter what the acronym is, but it's an absolutely amazing mission.  It's actually two satellites and it's able to measure very, very accurately, small changes in the gravity field of the Earth.  And so, if an ice sheet like Greenland loses mass or gains mass for that matter, it can actually measure those variations, and it does it on a, roughly, monthly timescale.

Chris -   And what has this told you?

Jonathan -   So a number of scientists have looked at this problem with GRACE and with other satellite data as well.  And the problem is being with all the previously published results is that there's been a lot of variability in the numbers.  In fact, the numbers have differed from each other by about a factor of  two, you know, some have been double others.  But what we've done is actually compared two different approaches using GRACE and an entirely independent approach for measuring the mass loss of the ice sheet, and they tie up pretty well.  So it gives us a lot of confidence on our results, and we think that we've sorted out a lot of the issues that existed with earlier observations.  And yeah, I guess it's a pretty disturbing picture.  In the early '90s, the ice sheet looked like it was relatively close to balance, maybe losing 50 gigatons of ice.  A gigaton is one billion tons.  And in the last few years, that rate has increased to something like 273 gigatons a year and that's a lot of ice.

Chris -   That's - well, 273 gigatons, that's a cubic kilometre per gigaton.  So that's 273 cubic kilometres.

Jonathan -   So, I mean, just kind of try and, it's pretty hard with numbers that big to really know what you're talking about here, but one gigaton is about the volume of Lake Windermere.  So we're talking about 273 Lake Windermeres.

Chris -   Per year?

Jonathan -   Per year.  But I think the other interesting statistic I like is that 4 gigatons is enough water to supply the entire domestic water supply of the UK.  So 273 is pretty much the water supply of the whole planet.

Chris -   And that's just melting every year.  Has that changed though because one of the points you make in your paper is that there appears to be an acceleration going on?  This, one would presume, would be secondary to global climate change.  So what's the pattern of that acceleration?

Jonathan -   We've seen - GRACE only went up in 2002 and the reliable measurements are only about six years of observations.  So we don't have a very long record from GRACE, but just in that time, we have seen the rate of increase, increase by about 2.5 times.  So I think the mean for the period for 2003 to 2008 is about 180.  But the last two years, it's gone up to something like 270 gigatons a year.  So that's a big acceleration in mass loss.

Chris -   So it's almost like Greenland is sort of a barometer of what's happening potentially in other bits of the world, isn't it?

Jonathan -   Well, that's one of the interesting things because I think until we started making some of these observations, most glaciologists and climate scientists felt that the ice sheets responded very, very slowly, and not very dramatically to climate change.  What we're seeing in Greenland is completely the converse, and I think it's surprised a lot of scientists.

Structure of the homodimeric restriction enzyme EcoRI (cyan and green cartoon diagram) bound to double stranded DNA (brown tubes)

17:05 - TWiSH - The death of Daniel Nathans

This week in science history saw, in 1999, the death of Daniel Nathans, microbiologist and co-winner of the 1978 Nobel Prize for Medicine or Physiology for his work on restriction enzymes, essential tools in the world of genetics...

TWiSH - The death of Daniel Nathans
TWiSH -Daniel Nathans

This week in science history saw, in 1999, the death of Daniel Nathans, microbiologist and co-winner of the 1978 Nobel Prize for Medicine or Physiology for his work on restriction enzymes, essential tools in the world of genetics.

Born in Wilmington, Delaware in 1928 to Jewish immigrant parents, Nathans grew up in a supportive household, and followed his sisters and brothers to the University of Delaware, where he studied chemistry, philosophy and literature. Coming to the end of his degree, he chose to study medicine, and gained his MD degree in 1954. After a time spent working in clinical medicine, Nathans knew his heart lay in medical research, rather than in treating patients.

Structure of the homodimeric restriction enzyme EcoRI (cyan and green cartoon diagram) bound to double stranded DNA (brown tubes)The two other winners of the Nobel Prize, Werner Arber and Hamilton Smith, discovered restriction enzymes in the 1960s, but it was

Nathans who realised their potential for use in genetics. The enzymes, also known as restriction endonucleases, were first isolated

from bacteria, where they helped to protect the bacteria from infection with viruses called phages. They did this by chopping up the

virus' DNA, while another enzyme protected the bacteria's own DNA.

So how do restriction enzymes work? Well, they scan along a DNA molecule until they reach a particular sequence of the bases A, T, G and C. For example, the enzyme EcoRI recognises GAATTC, and TaqI recognises TCGA. When it finds this sequence, the enzyme cuts the chemical bonds in the backbone of each strand of the double helix. They either cut or 'cleave' the DNA strands straight across,

known as a 'blunt end' or in places a few bases apart on each strand, leaving overhanging bases on each strand, known as 'sticky ends'. The enzymes useful to genetics are the sticky ends types, but more on that in a bit.

Nathans was working at Johns Hopkins University in Baltimore in 1969 when he received a letter from Hamilton Smith detailing his discovery of the restriction enzyme in the bacterium Hemophilus influenzae. Nathans used this enzyme to cleave the DNA of the simian virus SV40 into 11 specific fragments. This and later work, where the virus' DNA was cleaved in different places using different enzymes, showed that the base sequence of a whole genome could be determined using restriction enzymes.

Cutting DNA using restriction enzymes, known as a restriction digest is the first step in many genetic techniques DNA fingerprinting in crime and paternity cases, RFLP analysis to detect genetic diseases such as cystic fibrosis and for genetic recombination. This last technique may not ring any bells, but it will have saved your life if you suffer from diabetes, it's how scientists can produce human insulin by inserting the gene into bacteria and making them produce it in bulk.

Nathans showed that the 'Sticky ends' of the DNA left by some of the enzymes were sticky for any corresponding sticky end, whether it had come from the original DNA or not making joining human and bacterial DNA together possible. As long as the bacterial DNA was cut with the same enzyme used to cut out the human gene, the sticky ends would match and the gene could be inserted.

Nathans continued to work at Johns Hopkins until his death, becoming President of the University in 1994. He was awarded the National Medal of Science by President Clinton in 1993, and Johns Hopkins named its Institute of Genetic Medicine after him and Victor McKusick in 1999 after his death. In his autobiography on acceptance of the Nobel Prize, Nathans paid tribute to his interesting and cordial colleagues and his family, saying he felt 'struck by the good fortune that came [his] way' in his life.

Many genetic techniques that we now take for granted would not have been possible without the work of the three Nobel winners, but it was Daniel Nathans' vision that helped him realise the full and far reaching potential of restriction enzymes.


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