Author Archives: Dr Molecule

About Dr Molecule

My real name is John Runions and I am a cell biologist. BBC Radio's Malcolm Boyden called me Dr Molecule the first time that I met him and, hey... I've been called worse. My research utilizes many kinds of microscopes to study the workings of living cells. Science is the way ahead and I am facinated by everything in science!

Chaser – a dog of many words wins the ‘Dr Doolittle stamp of approval’


This piece was guest-authored by Jess Upson who is studying Biology at Oxford Brookes University

Listen to my BBC radio chat with Malcolm. We discuss Chaser the Border collie and animal languages starting 50 seconds of ridiculous intro chat in this clip:


Do animals communicate more than we think?

Do animals communicate more than we think?

It has long been thought that we humans are ‘top-dog’ with regards to intelligence and communication, but it has recently been discovered that animals may not be as dim-witted as we sometimes give them credit for.

It turns out that if I call you ‘bird-brained’ this may not be so offensive…  Recent studies have shown that crows are one of the most intelligent animals on the planet, demonstrating extraordinary abilities of creative problem solving. These breakthroughs are beginning to shed light on how the brains of many animals work and, as much as we feel so superior, they work not unlike our own.

One of the best ways to understand the mind of an animal is observe how they behave with others of their kind. From a bee’s waggledance which tells others where the best flowers are, to the pops and whistles of dolphins whilst playing, there are a variety of mechanisms used by animals for communication. Perhaps one of the most exciting ideas is the idea that animals having a language of their own.

Studies now demonstrate that animals may communicate in what could be considered a language. A mother and infant dolphin talked over the telephone when placed in different enclosures. Elephants have also been known to demonstrate a sophisticated way of communicating, with each individual producing a unique noise, often in the sub-sonic range that humans can’t hear, and it can travel for miles. The matriarchal female can recognize hundreds of calls from elephants she knows and from huge distances away – that is the equivalent of being able to stand blindfolded in the middle of 1000’s of screaming people – like outside of One Direction’s hotel – and still being able to distinguish the ones you know!

I'll tell you a secret if you promise not to tell anyone else...

I’ll tell you a secret if you promise not to tell anyone else…

But it is not just the larger mammals that can demonstrate this. Work carried out on prairie dogs has shown their ability to produce effective warning calls, with all the details included. It was discovered that each predator had a unique call associated with it, including humans. The call could tell other individuals what the threat was as well as information like its colour and size. When a new object was placed within sight of different groups of prairie dogs, each came up with the same new warning call, showing that there may be something within their culture, a language perhaps, which allows them to convey this sort of information.

Chaser the Border collie sitting with some of her 1000+ toys

Chaser the Border collie sitting with some of her 1000+ toys

So,it is not just humans who have shown the ability to understand different forms of communication. Famously, Panzee the chimpanzee can distinguish more than 130 human words. But it looks like there is a new champion at understanding human-speak, Chaser the Border collie.Tell your dog a simple command and it may respond, but no dog has yet quite matched the ability of Chaser when it comes to understanding our language. Chaser knows the name of every single one of her toys – all 1022 of them! She also understands verbs and conjugate sentences. That’s better than I can do some mornings…

Chaser goes beyond remembering words. She can correctly respond to phrases with three parts (a noun, a verb, and another noun) 75% of the time. This sort of ability is learnt at about the age of three in humans.

It is a baffling question that if we are so ‘intelligent’, why can’t we understand animals when many appear to be able to understand us? But the mechanisms used by different animals to relay information are vast and often very complex. A dolphin clapping its fins could mean multiple things depending on the situation. For example, if you put a hand in the air it could mean you were greeting someone, or waving goodbye, or even indicating the number five, all depending on the situation.

Many animal species have vocal cords that are used for making sounds. During evolution of human speech, we have developed the ability to modulate those sounds using out tongues, lips and larynx. Many scholars are actively engaged in trying to determine how and when in our evolutionary history we developed this extrorinary ability that sets us apart from other animals, including those like the great apes who possess vocal cords.

Talk to the animals

Talk to the animals

Some still argue that the idea of species other than humans communicating through a language is far-fetched. But we are only just beginning to understand the subtlties and intricacies of animal communications. So is animal language really as fictional as Dr Doolittle’s Pushmi-pullyu?

Can animals evolve to survive climate change?


Many who might be skeptical that climate change is a problem that results from Human activities will say, as a last refrain:

“Oh, anyway… animals can just evolve to survive rising temperature.”

But is this true?

funny-hot-dog-melting-picsCharled Darwin had a dreadful time trying to convince his Victorian peers that evolution by natural selection was a real process in nature. This is because he could not demonstrate unequivocally that is was happening. And the reason that he could not demonstrate that it was happening is that it happens slowly.

I mean, part of the process of evolution results when organisms adapt to new and changing environments. This adaptation takes place over hundreds or thousands of generations. The snow leopard will not just simply decide that it’s too warm and shed its fur so that all is hunky-dory.

Thinking about Human generation times – arguably 20 years – hundreds of generations means that it takes 5000-10000 years to notice even very small changes that result from mutation of genes that might confer an evolutionary advantage in a given situation. Most organisms have shorter generation times but even the smallest adaptations gotten through evolution will realistically take 1000s of years.

I saw a calculation recently that showed that animals can ‘evolve’ at a rate that would make them able to adapt to temperature change of 1 degree celsius per million years. Present calculations show that our average temperature on earth will likely rise by 4 degrees celsius by the end of this century. Evolution needs to work, uh, let’s see… (4 degrees in 87 years = 1 degree in 21.75 years, and 1,000,000 / 21.75 = 45977), 46,000 times faster than it does now. That isn’t going to happen.

The funny thing is that an average temperature rise of 4 degrees doesn’t seem like that much to us. It will have devestating consequences for our planet, however. Ice sheets will melt and the water cycle will be thrown completely out of kilter with consequences like worsening weather, flooding, and drought like we are starting to experience now.

familyAnimals and plants that have evolved to survive in their special environment (and that’s generally what evolution has done) might survive the onslaught of climate change for a while by moving to adjacent environments where it is (choose one – wetter / drier / warmer / colder) but that is a short-term fix.Plants and animals that are adapted to survive in desert environments are separated by hundreds of millions of years of evolution from those that are adapted to survive in very wet conditions.

Our snow leopard really won’t find the prey items that it needs to survive if its habitat warms, and it can’t simply pick up and find a new home like the Bevely Hillbillies did (Kin folks said, Jed, move away from there…)

Forests using less water because of climate change


This article was originally published in Conversation logoThe Conversation

and in Ars Technicaars-technica-logo

Forests using less water because of climate change – a good thing?

Global warming is primarily driven by increasing emissions of greenhouse gases from human activities. Chief among these gases is carbon dioxide (CO2), which warms the planet by trapping heat that would otherwise radiate into space.

9kvm83bg-1374505630But carbon dioxide has effects on things other than the climate. In the journal Nature, Trevor Keenan of Macquarie University and his colleagues report that trees in some forests are using less water to maintain growth than they did only 20 years ago. This puzzling finding has been attributed to the increased levels of CO2, which trees utilise as their carbon source.

Instruments placed in various US forests have been measuring CO2 and water concentrations in the air for many years. These measurements have been correlated with the amount of CO2 locked up by trees over the same period to show that forests have become more efficient at storing carbon. What is more important is that the measurements suggest that the increase in efficiency of storing carbon is six times greater than would be expected if it was just proportional to the increase in atmospheric CO2 concentration during the same period.

Increased CO2 availability means that trees have to restrict the opening of their breathing pores (stomata) so that CO2 levels inside their leaves remain constant. But this has additional consequences for the trees. Smaller pores means less water evaporates from their leaf surfaces through these stomatal openings. This effect has been called the “CO2 fertilisation effect”, which means plants can utilise more CO2 to make more carbohydrates, like cellulose and sugars, while using smaller volumes of water overall than previously required.

The fine balance between CO2 uptake and water loss is critical for plant survival. Early predictions by climate scientists were that increasing temperatures would devastate forests. That is because elevated temperatures increase the rate of evaporation and transpiration at leaf surfaces, potentially causing trees to suffer from “water-stress”. Instead, this paper suggests that increased efficiency of water-use by forests might mean that water does not become a limiting factor in productivity as temperatures rise.

This new finding seems like unadulterated good news, therefore, until you factor in the effect that water usage by forests has on components of the ecosystem. Trees move an incredible volume of water from the ground into the atmosphere. That water then forms rain, which helps the connected ecosystem thrive. Large forested areas play a very important role in the water balance and ecology of most agricultural land on Earth.

Keenan and his colleagues examined 21 forest sites going back as much as 20 years, with their data limited to the temperate and boreal forests of the Northern Hemisphere. Although this is still a relatively small sample size, this work will probably result in a flurry of research activity to establish what will happen to plant primary productivity in other areas in response to elevated CO2. Keenan said: “We’ve examined the trend upside down and inside out as much as we can, and it is wholly robust.”

Climate scientists use data from studies such as this one to build long-term computer simulations that help them examine potential effects of alterations in variables like temperature, ocean currents and rainfall. Decreased volumes of water being moved by transpiration into the atmosphere will now be added as an input in these simulations in an attempt to predict what the medium and long-term effects of the new observations might be.

On the one hand, more consumption of CO2 by forests will help stem global warming. But on the other hand, less water circulated through more efficient use by trees will mean that non-forest ecosystems may get into trouble.

Tweaking plant biology to solve the food crisis


This article was originally published at The ConversaConversation logotion.

Hacking plant ‘blood vessels’ could avert food crisis

Today’s wars are not about food, but not too far in the future they could be. The number of people dying of starvation has been falling for decades, but the decline in the numbers of hungry people is slowing down. More than 800 million people remain undernourished. With nine billion mouths to feed by 2050, the task of feeding us all is only going to get harder.

There is a solution, though, according to a recent paper in the journal Nature written by some of the world’s leading plant biologists. They show that, by hacking how  plants transport key nutrients into plant cells, we could solve the impending food crisis.

Each plant is made of billions of cells. All these cells are surrounded by membranes. The pores in these membranes are lined with special chemicals called membrane transporters. They do the job of ferrying nutrients that plants capture from soils with the help of roots.

What scientists have learnt is that if such membrane transporters are tweaked, they can enhance plant productivity. When these tweaks are applied to crops, they can produce plants that are high in calories, rich in certain nutrients or fight pests better. All these methods increase food production while using fewer resources.

Currently, world agriculture faces the problem of shrinking arable land, which is the area that is fit for food production. This is why the world’s leading plant biologists argue in the Nature paper that we must embrace genetically modified (GM) plants, many of which have better membrane transporters making them more productive without increasing land use.

Good modification

ngtpvbfh-1368974463Over two billion people suffer from iron or zinc deficiency in their diets. Biofortification involves increasing concentration of such essential minerals. Simple genetic modification increases the amount of membrane transporters that ferry these minerals. Such plants when ready for harvest can have as much as four times the concentration of iron, compared to that of common crop variety.

A little known fact (pdf) is that making fertilisers consumes about 2% of world’s energy. This makes the process a significant contributor to emission of greenhouse gases. Modifying membrane transporters can help cut those emissions, because it can make a plant more effective at using plant fertilisers.

For instance, only 20-30% of phosphorus added to soil as fertilisers is used by crop plants. Tweaking transporters such as PHT1  can increase the uptake of phosphorus. Similar results can be obtained when NRT genes are modified, which increase uptake of nitrogen from fertilisers.

Better resistance

About a third of the Earth’s ice-free land is acidic. The problem is that in highly acidic conditions aluminium in soil exists in a form that is toxic to plants. Such land cannot be used to grow food, but if crops were able to counteract the effects of acidity on growth that land would become available.

Scientists have found some varieties of wheat that have a trick to enable them to grow in acidic conditions. One of its membrane transporter called ALMT1 pumps out malate anion from its roots into the soil which traps the toxic form of aluminium.

Varieties of wheat without this natural transporter can be improved by breeding with varieties that do. But, crops such as barley, which have no comparable system of transporter in its membrane, need to be genetically modified to express the ALMT1 transporter protein. This allows for greatly increased yields even in acidic soils.

When salt is bad

Much of the world’s arable lands are becoming salty as a result of current irrigation practices. This happens when, on evaporation, salts in irrigation water are left behind inthe soil. Salts are toxic to plants and are severely limiting yields in over 30% of irrigated crops.

But there are membrane transporters which can stem the flow of salts into plants. These transporters, from the HKT family, rid the water of sodium before it is taken up by the plants. One example is that of durham wheat, which was modified to possess the HKT5 gene. The modification helped increase its yield in salty soils by 25%.

Fighting from the inside

gmbp69dh-1369048466Disease-causing micro-organisms, pathogens, manipulate a plant’s functioning and consume the fruit of its labour. Most crops have membrane transporters called SWEETs that move sucrose made by leaves from photosynthesis to other regions where it may be stored. Plant pathogens have evolved to manipulate SWEET genes so that sugars are moved to cells where they can feed on the goods.

Now scientists have found a way of disrupting this pathogen-induced manipulation by a method called RNA-silencing. These reduce, or sometimes eliminate, the pathogens’ ability to feed on the plants’ hard work, and in turn they help increase plant productivity.

Not all bad

Researchers have been quietly chugging away in labs working on making such radical improvements to crops. Breeding of plants, a form of untailored genetic modification that bestowed most of the benefits to agriculture a generation ago, is not able to keep up with the pace of change required for an ever-increasing demand for food. That is why it is important that we understand the science behind the process of tinkering with specific genes, before jumping on the “GM is bad” wagon.

Scientists are aware of the moral, ethical and environmental discussions surrounding production of GM food, and have been working carefully to address those issues. It is important that they continue to do so, while exploring the full potential of GM research to tackle the issue of hunger that looms large over the future of our species.

How does Santa get to all the boys and girls in one night?


Malcolm and I discuss Santas science secrets starting at 1 minute and 8 seconds into this audio clip:

[audio – Fun ‘facts’ about Santa.mp3]

Once, when Dr. Molecule was younger, he went on holiday in the North and while collecting ice samples from glaciers (which is, oddly, what he does on holiday), he chanced upon a man who he identifies in his notes only as Joe – Joe was collecting ice too, but apparently he only needed ice cubes for his drink. Anyway, below is a small bit (an excerpt) taken from the 3 volume Story of Santa written by Dr. M of which only one copy exists in Joe’s library… (the three dots mean that I could go on but let’s get to the excerpt…)

Excerpt from the 3 volume work – Some interesting mathematical equations explaining how Santa does it.

How does Santa get to all of the boys and girls in a single night?  b_1321273447415

That’s a poser.

Using all of my great powers of scientific reasoning, I have been unable to understand all of the technical issues that Santa must overcome to accomplish this enormous task.  When faced with a situation that I don’t understand, I consult with the experts and that is exactly what I have done in this situation. For a number of years now, Santa has been working with the people at Really Extra-Incredible North-Pole Dynamics, Ltd. who supply Efficient Expediting with RedNose™ Systems. if you find this is a bit of a mouthful, the company is generally referred to by the acronym REINDEERS.

Doris Elfman (what she lacks in tallness she makes up in brains, I can tell you) is the Chief Scientific Officer of REINDEERS and she was able to help me with some of my questions such as the 5 Hows: How fast does Santa go? How does he fit down chimneys? How does he read all of the letters? How does the sleigh hold so many presents? and How many children get presents?

The most important of the Christmastime technologies is RedNose™ which is like BlueTooth™ except that it’s a different colour. Rednose™ sends out a signal that pinpoints the location of houses with children who are getting Christmas presents. These signals are then mapped to a grid that Santa reads using the SatNav feature of his sleigh. The fantastic thing about RedNose™ is that it also detects cookies and other sweeties that Santa needs to keep him going during the long night of delivering presents – he is a big man, you know!

North Pole scientists have been trying to perfect sleigh guidance tech for a number of years. When BlueTooth™ first came out the lead reindeer was William (Billie) the Blue-toothed reindeer. All of the other reindeer used to laugh and say he looked ridiculous with his tiny-little headset. And that wasn’t the worst thing. Billie was addicted to sugar cubes which are bad for your teeth and caused all sorts of problems with navigation. That is why RedNose™ has now taken over and, these days, the new lead reindeer is Rudy who looks smashing with the RedNose™ receiver unit on his nose.

Santa’s sleigh is a marvel of old-time craftwork, not like modern sleighs with all of the cheap plastic dials. It is necessarily quite large but it still doesn’t look big enough to hold all of the presents. That’s because it is like a Tardis – the adult reading this to you will know what a Tardis is but, basically, it’s bigger inside than outside (ask the adult who else has a Tardis. When they answer, say ‘Who?’ and keep saying that… it makes for endless hours of fun).

There are some interesting sleigh accessories that help Santa. Access to the top of the cargo hold is made easier by ladders provided by the Rose Suchic Ladder Company, and reindeer assist thruster technology is similar to the oscillator caboobillator system used by the car in that old film that you’re probably too young to remember. The SatNav is an advanced version of the one that makes adults use bad language. In early days Santa used to get misdirected… to the South pole once because the wires got crossed. Hover technology is simply a reindeer-assistance accessory that allows the sleigh to take off straight upwards meaning that the reindeer don’t need a long runway. It has voice-activation and Santa used to say ‘hover, hover, hover’ when he wanted the reindeer to take off. As he is a film buff, Santa has shortened the activation command to ‘HoHoHo’ because it reminds him of the ‘Go, Go, Go’ command that one often hears in movies.

All of the battery power in all of the electronic toys provides the vital boost of energy needed to propel the sleigh at such high speeds. That’s why batteries in your toys are often flat on Christmas morning. The effect of emptying the sleigh is that it loses power and has to be shipped home on a specially modified hovercraft which is also activated by saying HoHoHo. Captain of the hovercraft Dave Donnerundblitzen comments, ‘have you ever tried delivering something to somewhere that has a top secret location – that’s why Christmas only happens once a year!’

Banbury-SantaSome random musings on Santa himself. Santa looks larger but it’s not the bad kind of overweight – it’s like the water-weight that some adults claim to have. 8 months of the year, Santa basically sits around eating and watching telly. He is awoken from this reverie in about early November when it is time to do the pre-Christmas meet and greet junkets – Santa finds these tiring but acknowledges that it is important to meet kids and talk with them – Mrs. Claus calls this ‘keeping it real’ but I don’t know what she means by that.

Throughout December, Santa slims down by eating Brussels sprouts so that by December 24th he is fighting fit. A little known fact is that chimneys in Brussels are more narrow than normal so it is a good thing they have the spouts. A side effect of eating these is used to heat the sleigh – Santa blames the smell on the reindeer – don’t believe him.

Santa’s red suit uses the old Flannel Red Over-Suit That’s Invisible (FROSTI) technology from the North-Pole Men’s Haberdashery Shoppe (No, I don’t know why ‘Shoppe’ is spelled like that but I suspect it’s because people at the North Pole leave school to work at REINDEERS and never really learn to spell very well). The suit reflects light in a strange way that makes Santa particularly hard to see. What would you do if you could get your hands on a suit like that? Newer versions of these suits use the Camouflage Russet Under-Suit That’s Invisible (CRUSTI) technology but Santa only uses these for underwear.

As well as the hard-to-see red suit, Santa has the big beard. This is surprising in this day and age when men are always shaving with razors that have anything up to 20 blades for a close shave. The reason Santa still has his big beard is simple, duh… it’s so that you don’t recognize him!

How can Santa possibly read all of those Christmas letters? In olden times, letters were delivered to the North Pole by the Post Office. This system is now called snail mail because in some countries they use snails to make the stamps stick. The problem with letters is that people do go on. By the start of December, the North Pole sorting office would be bursting at the seams with great long lists of wishes. It turns out, surprise, surprise, that Santa and his helpers were completely incapable of reading all of the letters. Just ask your adult reader if they ever got something that wasn’t on their list to Santa. I once got a toothbrush (but I digress). To combat the increasing trend towards more and more wishes, the North Pole have recently been moving to an online Christmas letter system in which children are limited to 140 characters when asking for presents. You need to be very succinct! ‘Lalaloopsy Harmony B Sharp’ uses up 26 characters right there – and that’s without saying ‘please’ or ‘thank you’.

santa-sleigh_1780995cAs to who’s been naughty and who’s been nice, all children are basically good (ask the adult who is reading this to you to ‘please keep the eye-rolling to a minimum’. Remember to say ‘please’ because it is important to be polite – and you are, after all, basically good).

For Santa to get into your home, a chimney is good but there is a small detail. Most modern homes don’t have big chimneys like they did in the old days. Chimneys these days are either small like in Brussels or non-existent. I know you’re worried about this but Santa uses lots of fancy-schmancy science to get around this problem. One neat little device is made by the Managing Access and Getting In Quickly company based in Northern Norway (This company still doesn’t have an acronym – can you think of one?). The device is called iSanta and is no bigger than a smartphone app. Santa gets that familiar twinkle in his eye when he talks about it. It is well known that if you stick an ‘i’ in front of a normal word then the word becomes turbocharged. Well, when you put an  ‘i’ in front of Santa, all sorts of crazy things happen. The device produces a ‘virtual’ version of Santa which is indistinguishable from the real thing and which can project into your home to leave presents (and eat cookies). The only place iSanta can’t project into would be a home completely lined with diamonds (because, obviously, the tight carbon lattice interferes with the signal). Let’s face it though, if your home is completely lined with diamonds, you should be buying the Christmas presents for everyone else! And, no, I don’t know how iSanta works. It’s a heavily guarded technology. If it fell into the wrong hands, anybody could go around leaving presents.

How far and fast does Santa travel? Of course there is a mathematical equation to describe how Santa can possibly visit all of the children’s homes in one night. It looks complicated but I can assure you that it is quite simple really:

Santa equation v2

I don’t know what the sideways 8 at the end means but I suspect that Santa ‘ate’ and then needed to have a lie down. Otherwise, if you’ll be patient, I think I can explain the rest of this gobbledeegook…

dt means ‘change in time’ and refers to the way Santa can alter time so that the presents all get delivered in one night. A very clever man called Albert once said that if you travel very, very fast – then time slows down for you. Santa uses this principle in reverse – he travels very, very slowly which causes time to speed up for him. Albert isn’t sure why this works but he is content that the world is a weird place. dt equals all of the stuff to the right of the equals sign added up.

Π – This symbol is called pi and means the number 3.14159265359 (memorize that and wow your friends at parties!). It is used in math when circles like the Earth need to be measured. This would come in handy if you were trying to, for example, calculate how far Santa has to travel to deliver all of the presents. In reality though, pi is just in the equation accidentally. It turns out that Santa likes pies (eskimo) and the elf writing the equation misinterpreted what he was saying.

J – This symbol stands for Joule and it means energy – the amount of energy needed to propel Santa’s sleigh at such high speeds. Unfortunately, that same elf writing down the equation wrote J for Joule when Santa actually said ‘jewel’ while finalizing the Christmas present list for Roger Stevens (no, I don’t know what kind of jewel Roger was getting).

Θ is a symbol called theta and a professor would use it to calculate an angle like, for instance, the angles needed for reindeer to speed off at after HoHoHovering.

∑ is a symbol that teachers use to confuse you. It really just means ‘sum’ like when you add things up. Santa was just saying that he would have ‘some’ of Mrs. Clause’s fabulous pie and the elf… well you know what the elf did.

People that know a lot more about math than you and me do have observed that if you squint at the end of the equation you see JΘ∑ – which looks like JOS – and which has historically been the reason that Santa is known as a Jolly Old Soul (I personally think it looks more like JOE and think that Joe is what we should call Santa from now on).

I hope this excerpt helps with some of your questions about Santa and his technology. May you have a jolly holly Christmas and may your house not be lined with diamonds! Hover, Hover, Hover…

Girls’ world record attempt to measure gravity


Malcolm and I discuss the giant physics experiment starting at 7 minutes and 37 seconds in this clip.

[audio – Science in UK and GSDT giant physics experiment.mp3]

At 11:30 this morning, more than 2,300 schoolgirls between the ages of 10-15 attempted to set a new world record. They set out to measure the force of gravity… The good thing about this attempt at classical physics experiments was that it was going on simultaneousley in 26 different academy schools of the Girls’ Day School Trust in the UK. If successful, the girls will have set the record for the largest (most participants), multi-location physics lesson/experiment ever conducted.

A couple of things that I would like to address:

i) How does one measure the force of gravity?

ii) Why is it significant that the Girls’ Day School Trust is carrying out this experiment?

(I’ll finish this blogpost later but wanted to get the clip up so that the GDST students could listen if they want)

#organellewars – a fun school project in cell biology


Malcolm and I discuss #organellewars starting at 6 minutes and 15 seconds in this clip.

[audio – Star Trek tech and organellewars.mp3]

Lysosomes for the win

I don’t need write very much more about #organellewars because my colleague Dr. Anne Osterrieder has explained it on her blog at Anne describes this innovative approach to teaching as ‘The organelle presidential campaign 2012‘.

Mighty Mitochondria

Briefly, high-school science teacher Brad Graba, who teaches AP Biology at William Fremd High School in Palatine, IL., has conceived a biology learning project that involves social media in an innovative way. His instructions to his students (#organellewars – Cell Organelle Campaign) are straightforward. Each group is to assume the identity of a cellular organelle (nucleus, mitochondrian, chloroplast, whathaveyou…), and to wage a campaign about that organelle. The campaign is intended to teach about that organelle and here’s the fun part. Among tasks that the students are expected to carry out is a mudslinging smear campaign against the other organelles! This aspect of the project has been largely carried out on twitter and I am absolutely amazed by the sheer volume of tweets that this has generated (See some of these storified).

Go Go Golgi

Not only has the twitter-based discussion and mudslinging fest been popular with the Grade 10 students, but scientists worldwide have jumped into the fray. Go onto twitter and search #organellewars for just a small fraction of the tweets that make up this campaign.

Whether the kids realize it or not, to smear another organelle, you’ve got to know what you’re talking about. In other words, they are learning about cells and organelles and having a lot of fun while doing so.

What’s my favorite organelle today… let me see, perhaps the pre-vacuolar compartment or the early endosome…

What’s yours? I’ll write later to let you know the final outcome of the campaign.

Your DNA doesn’t contain as much junk as your teacher says it does!


New scientific evidence, released this week as the ENCODE project, tells us that our DNA has a lot more information in it than we had previously expected

Listen to my BBC radio chat with Malcolm. We discuss the ENCODE project starting at 47 seconds into this clip:

[audio – ENCODE and a gene for trotting.mp3]

Follow this link for a good GuestBlogged essay on the information contained in DNA.

Whales committing suicide en masse… why?


On a recent weekend, whales stranded themselves on 4 different beaches around the world. Why do they do this?

Listen to my BBC radio chat with Malcolm (actually, with Nick Piercey this time. We discuss whale strandings starting at 25 seconds into this clip:

[audio – Beached whales and tree diseases.mp3]

Whales and dolphins stranded on a beach

Stories about animals committing mass suicide are just not true – whether the animals in question be lemmings or whales. On of the central tenets of evolutionary biology is that the gene is selfish. Mass suicide is not a biological imperative – animals seek to reproduce and raise their young in all cases. While it is true that evolutionary theory talks of a ‘struggle for survival’ and ‘survival of the fittest’, there is no indication that whales that strand themselves are at less than peak fitness. So, although the reasons for whale strandings are unclear, the thing that you can be sure of is that whales are not ‘committing suicide.’

An engraving depicting three beached sperm whales that dates from 1577

Why then do these terrible tragedies occur? It is easy to point the finger and say that man is to blame. That might be partially true, and I will explain why in a bit, but there have been documented whale strandings since well before we filled the ocean with human technology that might confuse whales.

What is usually true is that it is the ‘toothed’ whales like pilot and sperm whales that beach themselves. These are the whales who hunt and eat meat like fish and seals. Larger whales such as Blue whales who filter zooplankton (the baleen whales) much less commonly beach themselves. The suggestion here is that it is the act of hunting in packs for animals that shelter in shallower waters that contributes to whale strandings. I hear you say, ‘But whales aren’t stupid!.’  Far from it, I think I made the point already that they wouldn’t have survived this long if something as common as a bit of shallow water was going to confuse them so much that they died.

Humans rescuing beached whales

My contention is that shallow waters have probably resulted in confused and stranded whales throughout evolutionary history but that it is exactly this that should have selected for whales that are exquisitely able to survive in these environments. Orcas have been observed to beach themselves as a hunting strategy. They catch seals on the beach and wait for the next wave to re-float them. This is a learned / evolved behaviour that not all whale species have acquired. Evolution is a slow process – especially for large, long-lived organisms that take years to produce successive generations. That’s why deer haven’t ‘evolved’ the ability to avoid cars. No predators with which they have evolved move as fast as a car, and cars have only been around for a few decades. I can imagine that if we kept driving cars at deer for many thousands of years that the ability to avoid them would evolve in deer.

OK, so whales have evolved to survive in shallow water environments and should be able to avoid being beached. It still happens – and it happens much more commonly on some beaches than on others. Scientists postulate that when pods of hunting whales stray into unfamiliar territory, they can become confused. This confusion is most prevalent in areas where the angle between beach and sea bottom is very shallow – it does not, therefore, reflect the sound that whales make as a navigation aid back to them and they remain unaware that they are dangerously close to the beach. This situation combined with strong current or tides is why whales end up high on beaches.

A Long-finned Pilot whale being rescued by crane

Whale rescue agencies have been set up around the world and are staffed, generally by volunteers, so that they can be mobilized quickly when whales beach or, even better, when a pod of whales gets close to a stranding site. Whales have not evolved to support their own weight for very long (I even find it a bit uncomfortable when I lay on the couch for more than a few hours watching TV!) and they quickly become very ill when beached. Even when rescued, they commonly remain confused and often re-beach themselves.

I mentioned at the top that human human activity might play a role in the increasing number of whale strandings that are being observed. In early September this year (2012), pilot whales beached themselves at 4 different locations around the world. That just seems like too much of a coincidence. One factor that seems to cause a great deal of confusion in whales is noise. And man do we fill the oceans with noise. Not only the din caused by ships engines but, increasingly, SONAR from military exercises. These sounds can be louder (240 decibels) than any sounds on land including jet engines and rock concerts. Think about whales who have evolved to navigate using sound – hear for yourselves the plaintive whale sounds that some species can detect from hundreds of miles away. The incidence of whales beaching increases after military exercises involving SONAR, and scientists have observed that many of the whales involved in these beachings have acoustically-induced hemorrhages around the ears.

We must consider the natural environment of these animals before we deploy things like load SONAR for military purposes – is it worth it?

A breaching humpback whale

While I’m on the topic of what we do to the whales environment, watch this amazing video of a humpback whale being rescued from a fishing net. I just about didn’t watch it because I was concentrating on whale strandings when I found it. It leaves me with mixed emotions. On the one hand, the majesty of the animal and it’s apparent cooperation with the humans. On the other, what if they hadn’t encountered the whale. It would just be a statistic on its way to extinction.

Google… how did the internet work before?


Co-founders are multi-billionaire mathematicians and computer scientists.

Listen to my BBC radio chat with Malcolm. We discuss Google after 1 minute 30 seconds of ridiculous intro chat about Kenny Rogers in this clip:

[audio – Google and artificial hearts.mp3]

How do you get to be one of the biggest companies on the planet when your website looks like this?

Google grew out of the vision of Larry Page and Sergey Brin who met as PhD students at Stanford University in the early 1990s. Since its inception, it has grown to become one of the world’s biggest tech companies. You know you have achieved a milestone when your company name becomes a verb – this has happened with Hoover (must irritate Dyson), Xerox and Skidoo among others. When we refer to searching for something on the web, we almost invariably say that we ‘googled’ something – even if we used a competitors search engine!

How a search engine works

For 5 or 6 years before Google came along, the internet worked differently. If you found a webpage about a subject you were interested in, you bookmarked it immediately. Webpages were only discoverable by entering their exact html address and it became very tedious listening to people read out all of the words and slashes (is it a backslash or a forward slash?). Gradually, early search engines like Yahoo and Alta Vista started to group links by interest category and this is when the internet took off – companies recognized the need to have their names grouped with competitors. I recall hearing a pundit in 1995 saying ‘any company that isn’t on the web won’t survive.’ I was shocked at the time about the prophecy of the importance of the world-wide web but I very quickly came to see the truth in what was said.

As a student looking for a PhD project, Sergey Brin was interested in data mining. At the same time, Larry Page was studying the idea that the importance of publications was linked to the number of times they were cited… These two interest sets mesh nicely and, in retrospect, I can see how the two came up with the idea of Google. Personally, I’m too thick to have even appreciated what they had done when I saw it in action — even when I started using it habitually. Gradually I stopped using the bookmarks feature in web browsers. It was actually easier just to type in the keyword or a company name and the website would magically appear.

Brin and Page’s idea was that web searchers needed a prioritized list of websites that match search terms entered by the user, i.e. if I search for Hoover, I probably am more interested in the actual Hoover website than just a randomly ordered list of all websites that mention the word ‘hoover’ (noun or verb – for any North Americans that might have accidentally strayed into this blog, we in the UK ‘hoover’ rather than ‘vacuum’). But how do you prioritize the results of a web search? Simple, you could list web pages that mention a search term based on how many other web pages refer to them. The more a page is refered to, the more important it must be – right? Of course, nowadays, the algorithms (methods) that search engines like Google use are much more ‘intelligent’ than that in my simplified example but that was the genesis of an elegant idea.

A web-crawler. These guys do the work so that a search engine can make your life easier

All the search engine company needs to do is to read every webpage on the internet, catalogue every word that’s written into a giant index, and be able to instantaneously deliver your web search results. Sounds daunting but computers are fast and getting faster all of the time. Companies like Google employ spiders – well software that they call web crawlers or web spiders – to systematically search the web for purposes of cataloguing words. That’s why we are told to be sure our web pages have pertinent titles and keywords – so that the spiders find us and display us on Google. This page, for example, has tags like ‘fun science’ and ‘technology’ that the spiders will read. It won’t be catalogued immediately but within a few days it will start to appear in Google searches (how did you get to this page?).

How many computers running crawlers and answering search queries must a company like Google have in order to keep up with the demand? The answer is astounding. Probably more than a million – running 24/7 – and they’re not insignificant computers either. All spread across at least 6 sites around the world.

How does Google make money? Simple, they will prioritize your website to a higher level if you pay them to. Notice the sites that appear at the top of you Google search that are just slightly shaded in color – they’ve paid for the privilege of being at the top of your search return. Many of us just click the first link we see when our search is returned and, chi-ching for that company.

How big can Google get?

Where is the internet going? Not-so-simple. I don’t know, but then again you know that I’m not very good at seeing the need or the promise in new web ideas. I can tell you that I’ve just gotten a new smartphone that runs the Android operating system developed by Google. That purchase was so that I could more easily interface with my email and calendars at work because we’ve switched over to Gmail (what would you guess the ‘G’ stands for?). I am now a member of Google ‘circles’ although I haven’t yet figured that out completely (Twitter takes all of my time!).

So from small things big things come. Will Google get as big as Cyberdyne Systems? Should I get a Google tatoo…?