Wednesday, 5 October 2016

Exclusve Guest Blog coming soon: Professor Dennis Burton, The Scripps Institute, California.

Over the next week or so, I will be working with Professor Dennis Burton, the current James and Jessie Minor Chair in Immunology and Chairman of the Department of Immunology and Microbial Science at the Internationally renowned Life Sciences Research Institute in San Diego, Southern California: simply known as "The Scripps". Dennis was born in Cumbria and following degrees in Chemistry and Biophysics at the Universities of Oxford and Lund, Sweden, he has made a series of landmark discoveries in immunology. His list of achievement are summarised here. His current research focuses on the development of a vaccine to combat the global threat of AIDS. I am looking forward to sharing Dennis's story with you this month. If you are interested in earlier Guest Blogs from eminent scientists you can read about Professor John Guest, one of the team that determined the relationship between gene and protein sequences. Or Sir Rich Roberts, who was awarded a share in the Nobel Prize for demonstrating that vertebrate genes contain introns and exons (this one comes in 3 parts!). One early visitor to the UTC, and a local Liverpool lad, was Professor Phil Ingham, who tells his story about discovering a gene that determines how Drosophila (and humans) develop: Hedgehog. Finally, you can see what it is like to be a scientist in Hungary here (this is in 2 parts).

To be continued soon.....

Wednesday, 28 September 2016

Fueling our life and our lifestyle: Molecules for October 2016

It has been argued that chemical engineering has done more to protect the whale, than any environmental group, and, after giving it some thought, I think it may well be true! The cartoon on the left shows sperm whale celebrating the discovery of petroleum and a method for its distillation to kerosene, thereby increasing their collective lifespans! It might be difficult to imagine today, but the oil that we typically extract from the sea bed or the deserts of the Middle East and North Africa, used to be swimming around in the oceans of the world! Let me begin with a few dates and events that will focus your minds:
  • Large scale commercial whaling is in full flow at the turn of the 18th century, peaking in the late 1850s
  • The Industrial Revolution in the UK gathers momentum between 1780 and 1840, by 1850, it is "full steam ahead"
  • In 1849, Abraham Gesner devises a method for distilling kerosene from petroleum (rock oil: petra (Greek) + oleum (Latin))
  • In 1859 New Bedford (near Cape Cod, Massachusetts) is the wealthiest town (per capita) in the USA and in the UK, from time to time in the 19th century, it is Liverpool. Both seafaring towns were at the centre of the whaling industry; on opposite sides of the Atlantic 
  • Just to the East of Massachusetts, in Pennsylvania, in the same year (1859), the first serious oil well yields crude oil, and thus begins the age of gasoline and petroleum
  • In 1972 the sperm whale is declared an endangered species "and the loss of whale oil had a profound impact in the automotive industry, where for example, transmission failures rose from under 1 million in 1972 to over 8 million by 1975"
  • In 1986, the International Whaling Commission banned all commercial whaling: however whaling for scientific research remains legal
These events made me realise something I had not thought of before, how was farm machinery lubricated and what was burned in oil lamps before Edwin Drake struck "gold" in Pennsylvania? The claim in the first paragraph is simply a reflection of the fact that the global growth of industrial nations was oiled and fueled by the dominance of petroleum products over whale oil. As a result, the number of whales killed for oil decreased massively: in 1846, 735 whaling ships are documented, but by 1876, only 39 remained. So what do these "molecules" look like and why are they so useful?

This month's molecule(s) are the molecules that provide the fuel for human endeavour. Let's begin with sperm oil, or spermaceti. The image on the left shows the organ found in the head of the sperm whale from which sperm oil is extracted. It isn't clear what role this organ plays in whale physiology, but buoyancy is one popular theory and echo-location another. The major product of this organ has the structure shown below (which is closely related to jojoba oil.
During the boom years of the whaling industry, sperm whale oil, including spermaceti, was used in lamps since it burned bright and was relatively odourless.
It was also prized since it retained its viscosity over a wide range of temperatures.  The market for sperm oil reached a peak in the 1840s, but it was shortly to be replaced by kerosene (its American name) or paraffin (the UK name). The structure of kerosene, or dodecane is shown above: it is an alkane, isolated from petroleum and with the discovery of oil fields in Pennsylvania the second half of the 19th century, the demand for whale oil crashed; and with it the whaling industry. The related product of the fractional distillation of petroleum is gasoline (USA), or petrol (UK). In its pure form, petrol is the hydrocarbon octane, which, when combusted to water and carbon dioxide, generates sufficient energy, when harnessed by the internal combustion engine, to power motor cars (or automobiles!). The thrust needed to propel a rocket can be provided by the combustion of kerosene (the fuel is usually combined with liquid oxygen in the "classic" rocket engine). So as the 19th century rolled over into the twentieth, virtually all of our fuel came from coal mines and oil wells. And so it remains, as we attempt to grapple with alternatives from nuclear power to modern windmills.

Why have I focused on these molecules for October? Well they illustrate the relationship between organic chemistry, physical chemistry and combustion. I am sure you will appreciate the challenges of harnessing the energy of such fuels: just think of the safety measures surrounding a typical rocket launch or the devastation caused by an exploding petrol tank in a car. Living organisms, such as aerobic mammals, are required to fuel their physiological functions at modest temperatures and pressures. You can read about the discovery of metabolic pathways in one of my earlier posts. See (RHS) what can happen if our own fuel molecules catch fire spontaneously! How much energy is required by a typical human to walk, say 5km, compared with an average car (let's assume we calculate on the basis of per km traveled per kg body (or machine) mass)? Such calculations are complex and require considerations relating to the energy input to develop the human, or to build the car. But the simple calculation for an average person versus and average car is that in petrol terms we can cover around 500km per gallon equivalent, compared with around 80km per gallon for a car. However, the time taken to cover say 5km by the fastest runner is around 13 minutes, considerably slower than a car which can easily cover 5km in 2-3 minutes. For comparison jet planes and a rockets cruise at speeds of 20km and 300km per minute respectively (very approximate figures). (If you are interested in the metrics and economics of fuel consumption and transport, take a look here: it is of fundamental importance for the sustainability of the planet!). What's my point? The fuels that we use to power engines are typically alkanes, but the fuels we make use of are sugars, fats and proteins. Engineers have developed engines and associated fuel tanks in order to make the combustion of alkanes safe and efficient, but unfortunately not sustainable (any more). Can we bridge this Chemistry-Biology gap?

Since the pioneering years of the subject, Biochemists have been fascinated with understanding how food is converted into energy and growth. It is clear that biological energy transformation, whether it is in photosynthesising plants or respiring mammals, is highly sophisticated and can teach us important lessons about efficient conversion of fuel into energy. The important objective is to make any new energy source affordable and clean. At the start I said that Chemical Engineers have done more to save the whale than environmentalists, and today Chemical Engineers are increasingly turning to Biology in order to develop the fuels and engines of the future. One of the aims of Synthetic Biology (a hybrid field in which Molecular Biologists and Engineers are collaborating extensively) is the replacement of the inefficient Biofuels found in Nature, with those more familiar to engineers. This is being approached by engineering organisms to produce the kinds of molecules that we have come to rely on for domestic transport and for heating our homes.Examples of organisations that are investing in this area include the JCV Institute, articles are regularly appearing in the News, and such issues are high on our own government's agenda.