Organising a herbarium

Today was day one of curation experience. We effectively became volunteers, helping out with tasks to get an idea of what the job is like. I was in the flowering and seed plant division of botany today. After a brief tour, I spent the morning sorting out herbarium sheets a bit like these:

Source: https://commons.wikimedia.org/wiki/File:Joseph_Banks%E2%80%99_herbarium_sheet,_Treasures_Exhibition,_Natural_History_Museum_08.jpg

Each specimen should be representative of the plant. Very small plants can be pressed whole, but for anything bigger than a miniature daffodil it's usual practice to just sample a twig or branch, incorporating a leaf, stem section and reproductive parts. Often, any flowers are pressed on the sheet and fruits and seeds are stored loose, either in a little envelope stuck to the sheet or in a separate box for the big ones. One of the biggest seeds in their collection is the scandalous Lodoicea maldivica (worthy of an image search); that clearly wouldn't dry flat. The NHM has certainly hundreds of thousands of the sheets, probably more, with some dating back to about 1700. But these aren't the oldest: those sheets are stored in another part of the building, in the historical collection, and they date from more like 1550. Fortunately, the sheets I was manhandling were only on the order of decades old(!).

The herbarium had been housed in the Waterhouse building until 2008, the building you probably think of when you imagine the NHM, then moved to the Darwin Centre. Rather than just move the collection across, the curators decided it would be a good opportunity to update their classification system. It's primarily based on taxonomy, which for many organisms underwent massive changes when molecular phylogenetics came on the scene. Flowering plants were no exception. There are still specimens that have yet to be put away in the correct cupboards, though whether most of them are left over from the move or just new specimens coming in I'm not sure. So, our job was to look up the family and genus of these lost souls in the museum's shiny mostly-taxonomically-correct-for-the-time-being index and write, in very careful handwriting, an index number on each that designated which cupboard it belonged in. Handwriting really was crucial: just reading the information labels is a skill in itself, especially with elaborate old-timey cursive.

After lunch, we did another curator a big favour by sticking hand-sized blocks of foam in the backs of cupboards. Unfortunately, these (many many many) cupboards were the wrong size. As you removed stacks of herbarium sheets in their paper folders from the cupboard shelves, the corners could very easily catch on the metal rim of the door, causing a surprising amount of damage. After much deliberation, they decided that the most reasonable solution was to stick these foam blocks behind where the folders sit, shoving them forwards by a centimetre or so, so they don't slip behind the metal rim. But this wouldn't work for the top, bottom or very middle shelves because the sticking-out folders would then stop the door from closing. To make matters worse, the cupboards are stacked, so each line contains two rows. The top row needs a stepladder to get to. Because the folders require very careful handling, a lone curator would need to climb the ladder, take out one shelf's worth of folders (with ten shelves per cupboard), climb down the ladder, put down the folders, climb back up the ladder with the foam, stick the foam in the back, climb back down the ladder, pick up the folders, then climb back up, put the folders away and start again. Because there were six of us we could do this in pairs, the extra hands making a real difference. It was actually great fun.

Finally, we watched a demonstration of the exciting upside-down herbarium scanner, used in their massive digitising project. The NHM is home to a huge number of type specimens, the individual organisms that represent their species. Researchers from all over the world can ask to see the type specimens, usually to help with identifying their own specimens and seeing whether things might be new species. Digitising makes high-quality images of specimens available over the Internet, so researchers don't need to fly across the world to see them. There's been an ongoing project to digitise all of the botanical type specimens for several years.

You can get high-quality scanners easily. The problem with herbarium sheets is that the plants often aren't attached to the paper very well, so turning them upside down is the stuff of botanical nightmares. Someone at Kew solved this problem by building a rig where the sheet sits on a foam platform that can be raised up towards an inverted scanner. They patented it, sold it at very high prices and are apparently now very rich indeed. Unfortunately, to be contrary, the NHM uses a slightly bigger sized herbarium sheet than Kew (and indeed, the rest of the world), so sometimes you need to scan the same specimen twice to get both the top and bottom. At the time of writing, 136,775 NHM specimens have been digitised and uploaded to the JSTOR library (http://plants.jstor.org).

Tomorrow I'll be in palaeontology. They have recommended we wear clothes that can get dirty. Should be fun!

Spotted

My normal routine is to catch a very early off-peak train and spend the first part of the morning in the university library, before lectures start at the museum. The library is currently undergoing some building work. I assumed that a student was behind this nice addition:

...but since the university suffered a rather scathing report into equality and discrimination recently, I'd like to think it was a senior manager turning over a new leaf.

Meanwhile, in a dusty corner of a museum courtyard, I found these:

I imagine some poor grad student spending hours and hours scraping all of the fungus off the world's largest arachnid.

Back to the museum

I'm very happy to be back at the NHM this week. My commute is an hour each way instead of two, and there's no hanging round for the best part of another hour waiting for transport. I was last here in December, and there have been some changes since then.

The Hintze hall (the main bit) is mostly closed off for the dismantling of Dippy and, erm, mantling of the blue whale:

Note the blatant disregard for rules that a staff badge brings

The tunnel isn't huge, so staff are strongly encouraged to take alternative routes across the site. This means I've been exploring the basement between lectures. There are maps on most junctions. It's not unlike Ikea.

Someone was about to come through those doors. I took this, shoved the camera into my pocket and tried to act natural, not like a weirdo who takes photos of basements.

Plus, one of the many many cafes has been re-done as "The T. rex Grill". I was pleasantly surprised to see the correct name format, at least on the web page, though not the banners. A palaeontologist said last term that there was a debate going on among the staff over whether the decoration should have a feathery T. rex or not. It doesn't. But I suppose that's still open to discussion.

 

Staff member anonymised by a generic basal ornithopod, who is far too boring to ever have a grill named after it.

In other news, this week's topic is palaeontology. There's still some difficult computing but the lectures have been good. Last year's class went on a field trip, but this year there are over forty of us including visiting students from the other campus (their turn to take a bus) instead of seven, so that's out. I'm not disappointed. It would probably be more than a day and I have a strong history of hating fieldwork.

Instead, I've been in contact with a palaeontologist friend who runs fossil walks at the very same site. I'm hoping that the dozen or so of us interested can get down there for an unofficial field day with no write-up. Organisation will be a challenge, but the course hasn't been perfectly organised so far so I like to think we have low standards.

Finally, a strange biological phenomenon: a collection of fresh insect bites up my leg. In January. It's either global warming or fleas.

Birdwatching

The buildings where the statistics classes are held are out in the countryside. After a really productive morning it looked like we'd finish early, so me and a friend went for a walk around a local lake. I've done a lot of garden birdwatching over the years, but water birds are mostly a mystery, so I hoped to see something new and exciting.

There was a lot of ice about. We got excited when we heard movement in the trees down a bank, but it turned out to be an ice sheet moving underneath, catching low-hanging twigs. We then found some mallards, but, y'know, mallards.

Eventually, the ice gave way to open water, and we came upon half a dozen great crested grebes and a big flock of tufted duck. I'd only seen grebes from a distance before, so that was exciting, and tufted duck were completely new. The males are black with bold white wings, and both sexes have the eponymous tuft off the backs of their heads. Fabulous!

My friend is a keen photographer. Here are a couple to set the scene:

 

A beautiful close-up of two of the grebes:

And a lovely shot of the two of us:

Here at Organising Life, we respect privacy.

Modelling and statistics

This week we've been back in the wonderful world of statistics. I quite like this stuff. One particularly important concept that's really been driven in is that anything beyond the most basic of statistics is actually a type of modelling. But modelling involves models, which by definition aren't real, so how does they help to analyse real data?

The most basic: descriptive statistics
First, a quick reminder of the sorts of statistics most people are familiar with. These are called descriptive because they simply look at the data and tell you exactly what's there.

These describe the centrality (average):

• Mean ('average')
• Median (middle value if you listed them all in order)
• Mode (most common value)

These describe the variance (spread):

• Range (difference between the largest and smallest)
• Variance
• Standard deviation

These might be simple, but they can be very helpful. I'm always finding the means and standard deviations of things. Their limitation is that they do just describe the data, whereas in biology we usually want to be able to take our data and make predictions from it. You might have studied the amount of cabbage eaten by caterpillars reared at 10°, 15° and 20°, but what about temperatures in between? It's sensible to use your data to predict that, but descriptive statistics won't help you do it.

The ones that use models: parametric statistics
Here's some fake data about a particularly difficult video game:

16 people each played one level of eight, and the number of times their character died before they managed to finish the level was recorded. It seems that, in general, the higher levels were more difficult.

Unfortunately, the researcher had left her glasses at home and didn't realise that only every other level was tested. What about the missing levels?

The statistically knowledgeable reader might suggest drawing a line of best fit:

Now we aren't limited to reading up from existing x values. We can read from anywhere, because the line of best fit should represent the general pattern of the data. These in-between values aren't real, but from what we already know we can make a reasonable guess of what they are. For example, it looks like someone playing level three can expect to die seven or eight times.

This is exactly what a model does: the line of best fit is a model of the data. I've been learning to use linear models, which are lines drawn to fit the data as accurately as possible. The better the model fits the data, the more faithful its predictions will be, so the more we can trust them. Parametric statistics are named so because they are described by parameters of the data, like the mean and the variance.


A line fits this data pretty well, but what about data that follows different shapes, like arcs? Mathematically, you describe an arc in a similar way to a straight line, but with an extra parameter that makes it a bit more complicated. To make a line with multiple bends you add more parameters, and so on. The video game data isn't a perfect straight line, so you might extend its model to end up with something like this:

 Or even this:

The last one might describe the data perfectly. However, it's going to be extremely complicated and difficult to make predictions from. This model is as impenetrable as real life. That's not the point.

So, when you make a model to pull out the gist of data, there's a trade-off between making it realistic enough for trustworthy predictions and simple enough to be useful. Statistics involves using numbers at exactly the right level of pretendness.

Lactose tolerance: how humans evolved to drink milk

A big part of my course is working with DNA, but you don't just use DNA to identify things. An interesting topic that I've been revising lately is how you can see which genes in a population have been evolving recently by comparing DNA between individuals. Genomes (the entire DNA sequence of an individual) collected in the present can say quite a lot about the past. One particularly nice story is how some humans recently evolved to digest milk as adults, something which only matters to people who herd animals. These people adapted to a new environment, through natural selection, and that new environment was a step away from hunter-gathering and towards agriculture.

What's important about digesting milk?
All mammals start life getting all of their nutrition from milk. The main source of carbohydrate in milk is the molecule lactose, which is built from two simple sugars (galactose and glucose) stuck together. Inside the baby animal, the enzyme lactase breaks lactose molecules to release the simple sugars, which can then be broken down by other enzymes and absorbed. Once the animal can feed itself and stops drinking milk, it no longer needs to produce lactase because lactose isn't found in other foods, so lactase production stops.

The same is true of most humans. Give a typical adult a drink of milk, and the lactase will travel through the digestive system untouched. They won't be able to absorb the sugars, so won't get as much energy from the milk as a baby would. Too much unabsorbed lactose can also cause problems1:

• It increases the water potential of the gut contents, so more water is drawn into the gut by osmosis. This can cause diarrhoea.
• It can be broken down by certain gut bacteria, which release hydrogen and carbon dioxide as by-products, causing pain and bloating.

These are symptoms of lactose intolerance, and they're not pleasant. But because adult humans have spent almost all of our evolutionary history not consuming lactose, it wasn't an issue until recently.

Why did lack of lactase become an issue?
The difference came when some people began herding animals and recognised milk as source of food for everyone rather than just infants. Pastoralism (animal husbandry) developed independently in the Middle East about 10,000 years ago and Africa about 8,000 years ago, and has flourished since.

Just because your culture keeps cattle doesn't mean you need to drink milk to survive, but an opinion I read somewhere too long ago to source argued that milk would have been an important hardship food. Even when staple plant foods are hard to find, livestock can keep producing milk (to an extent). In times of hardship, people who could get by on milk and not much else would have had a significant advantage over those who got ill by doing so, even if they performed equally when there were plenty of alternative foods. Milk could also have been a necessary long-term supplement to a poor diet.

In any case, lactase persistence evolved independently about five times in humans, so digesting milk must have been important. We say that there was a selection pressure: that natural selection favoured those who, by some genetic quirk, produced lactase for longer. Those people were more likely to have more children (because they weren't ill or dead), so their genetic quirk for lactase persistence also persisted.

How do we know this happened?
Because some people today aren't lactose intolerant.

Yes, but what's the science?
I'm glad you asked. A key feature of a gene that's been under recent natural selection is that it's very similar across the population. Imagine a population where individuals come in many different colours. Their hypothetical 'colour gene' would be very varied, because across the population there would be some blue copies, some red copies, some green copies, and so on. Now imagine a terrible disease arrives that wipes out every individual apart from the yellow ones. The survivors might be quite a mixed bunch, but they would all have one thing in common: the yellow variant of the colour gene. The colour gene now has no variation at all, because all of its copies are the same.

A similar thing happens in real populations. One study2 compared the genomes of people from Kenya and Tanzania. Kenyan people generally have high lactase persistence, and Tanzanians virtually none. The amount of variation in the lactase gene was much lower in the persistent genome, showing that they had had selection on that gene recently. There hadn't been any clear selection there in the non-persistent population because they haven't been under pressure to produce lactase differently. The researchers could even use the amount of variation to date the time when most people in the Kenyan population became lactose-persistent: 5-8,000 years ago. This matches really well with the date of pastoralism on the continent.

Conclusion
Lactose-persistent populations are better adapted than non-persistent populations to drinking milk, so they're better adapted to an environment where drinking milk is important. Natural selection was still driving evolution in humans even in the first stages of agriculture, which was just a very very short time ago in the grand scheme of things.

References

1. Lomer, Parkes & Sanderson (2007) "Review article: lactose intolerance in clinical practice – myths and realities" http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2036.2007.03557.x/full
2. Tishkoff et al. (2006) "Convergent adaptation of human lactase persistence in Africa and Europe" http://www.nature.com/ng/journal/v39/n1/full/ng1946.html

Mystery plant thing II

After three weeks, has anything grown from that enigmatic lump of compost?

Yes, but probably not what the manufacturer intended. There are about half a dozen little seedlings, all sprouting from the compost shell rather than the little mesh bag. But often seeds take longer than this, so there's a chance the main player might still be alive. I'm considering digging it out before I go back to London to see if I can identify it, and maybe give it more appropriate conditions. This windowsill is not known for keeping plants alive!