Thursday, 11 August 2011

Interview in: food

Here is the link to my interview I did for food on aquaculture and sustainability, it's essentially a Q & A about the practice of farming fish and shellfish from a scientific perspective. Check it out, I even mention aquaponics and that's just a cool word:

Tuesday, 2 August 2011

Happy feet, the mussel

I just recently reread my articles concerning bad sea food choices and they seemed a little bit too much about doom and gloom and not enough about the amazing amount of healthy alternative and cheap choices out there. This has prompted me to write a few short posts about fish and shellfish which are more positive, extolling the virtues of the fish that you can eat. The first oceanic hero that jumped to mind was the mighty mussel (having just recently been treated to some myself).

Mussels are small filter feeding bivalves that anchor themselves to rocks with a muscular foot, they are hardy and reproduce easily and in great numbers. Given the chance, mussel spat (the word for their sounds so dirty) will land and colonise pretty much any surface that gets a whiff of salt water. This makes them ideal candidates for food farming, based squarely upon their biology.

The great thing about mussel farming, from the grower's point of view, is that it takes care of itself. The mussels grow for two or three years, filter-feeding on plankton and other microscopic sea creatures which are free-floating in seawater, after which time they are ready to be harvested.

The blue mussel...a table favourite

The blue mussel (Mytilus edulis) is both farmed and wild-caught in the UK. In 2009, while 3,400 tonnes were wild-caught, using mussel dredges (which is not as bad as it seems, much less damaging than a trawl), nearly 32,000 tonnes, worth £30m, were farmed, making mussels the most heavily cultivated shellfish in the U.K.

Mussels are also good for you. In terms of healthy fish oils such as omega threes (the ones that pushy mums are intent to drown their children in), they are up their with the oily fish big boys like sardines and mackerel (1000mg per 100g if you are crunching the numbers).

Mussel farming usually has two main forms; bottom culture, or suspended culture. The Marine Conservation Society ranks bottom cultivated mussels as 2 (on their 1-5 scale; 1 being most sustainable) and suspended cultivation as number 1. So good marks all around.

Bottom cultivation of mussels on the seabed occurs in in sheltered bays with good water quality. One such area is the Menai Strait in North Wales which produces over half of the total UK output of mussels and has Marine Stewardship Council certification (this area is one of our better managed fisheries and I might come back to it as an example of good policy decisions). Mussel production here relies on collected spat from the Irish Sea, which is re-laid in plots in the Strait where the mussels can grow to market (or munchable) size.

Mussel spat are collected when they are roughly one year old using mussel dredges. These dredges skim the spat off and leave the seabed relatively undisturbed (when compared to bottom trawling). This does not reduce the natural stocks of mussels because the unstable beds where the spat are collected are often destroyed by winter storms anyway; known as ephemeral beds. The seasonal nature of spat collection also allows gaps in collecting of up to a year, which gives time for the ecosystem to recover.

Suspended mussel culture...yum

Suspended culture is even better, and is where the mussels are cultivated on suspended ropes or poles driven into the seabed. With these methods the collection of the spat does not involve dredging and the ropes are simply pulled in after they mussels have grown large enough. Mussel farming of this kind has actually been shown to improve habitat structure and boost both crustacean numbers and those of small fish, helping to repair the structure of our damaged marine ecosystems (praise the mighty muscle).

All in all the mussel is an excellent choice, both in terms of health and sustainability. They also go great with a white wine sauce and french fries....

Tuesday, 26 July 2011

Cool critter of the month; Wolbachia, not one for the boys (plus why all men are doomed!)

Wolbachia is a type of bacteria that infects insects and mites, and it’s one of those weird little creatures that you couldn’t make up if you tried. (Wolbachia is the little bright dots within the egg cell)

Wolbachia is an intracellular parasite; it lives inside the main body cells (somatic) of both males and females but only the germ line cells of females (the female’s eggs). Being only found in female eggs, not male sperm, it has a vested interest in ensuring that the insects give birth to more girls than boys. As such the tiny bacterium goes about its absolute best messing about in a range very nasty ways with male insects.

Wolbachia will stoop to any level in its war against the male gender (not in humans...for now), here is short list of the tricks it has up its sleeve (and easy to read pictures to boot!):

It kills males during larval development, basically meaning that more females will be born each generation and hence there will be more wolbachia.

It turns males into females, the process of feminisation, resulting in either full blown females or the even less appealing infertile pseudo female.

It manages to let females get pregnant and have female babies without any men involved! This process has the awe inspiring name of parthenogensis. In the Trichogramma wasp, this has been so successful that males aren’t needed at all, the wasps population is now made up nearly all females, the males are redundant and only a few are born each generation.

Using a trick known as cytoplasmic incompatibility, uninfected male bugs are unable to breed with infected females. This cunning trick means that uninfected males have a lower fitness than infected ones, and hence more infected offspring are produced each generation and again wolbachia wins out by spreading its evil man hating ways through the population.

Some strains can prevent reproduction entirely if it is not present. The insects have become so reliant on the wolbachia parasite that they simply cannot live without it. Some species of wasps are now obliged to have this nasty critter in their systems; if you experimentally remove wolbachia from these wasps with antibiotics then they can’t have anymore offspring.

Wolbachia illustrates a general trend across much of evolutionary history, the trend towards feminisation and eventually asexuality. Wolbachia is a super charged version of this principle that is crushing populations of male insects around the world as we speak, but other animals are far from free of similar effects. Humans are also showing a trend towards feminisation.

Basically having different sexes is hard work, it takes a great deal of time and energy. If you need to have lots of gene shuffling (what all the kids are calling it these days) it is a good idea as it produces lots of variation, but it’s not nearly as efficient as good old fashioned asexual reproduction (but substantially more fun!). Over time species that have become established in a particular environment tend to move towards asexuality (as they don’t need all the variation). This is where we come in, we are doing well and released from large areas of natural selection (due to our good diets, modern medicine and lack of man eating tigers), and so we don’t need as much variation. So it seems that males are a waste of valuable resources, all we do is generate variation, we are not needed for producing new offspring. Selection has kicked in and has begun to whittle away at the Y chromosome (which is tiny by comparison to the X anyway). Y chromosome size has declined dramatically over the last few million years. The data is staggering today 7% of males are infertile and ¼ of these cases are new and not traceable to their fathers. This is getting worse, one by one the 27 remaining active Y chromosome genes will disappear, reduced by the relentless onslaught of mutation, and then men will become extinct!

Indeed there is the distinct possibility of humans becoming parthneogentic in the future, with females capable of producing cloned or slightly genetically reshuffled offspring. In addition it would only take a few choice mutations to get females to reproduce sexually with other females. There are incompatibility issues at present, but it is entirely possible for the nuclei of two female eggs to fuse to produce female only offspring. With some clever artificial insemination this trick could be closer than we think.

To put it bluntly males may well be doomed, fortunately for us guys this is a long term problem (some people predicting 125,000 years for total elimination of human males), but spare a thought for our insectiod man friends, who may well be on the out much sooner.

Wednesday, 6 July 2011

The big fish review: part three, the open ocean

The slightly overdue third and penultimate part of my sweeping survey of all things fishy. There are two remaining ecological disaster zones that are as yet unmolested by my withering gaze, the open ocean fisheries (us fishy types call them pelagic) that hold our swordfish, tuna and marlin as well as the silty mangrove swamps in which baby fish and coastal prawns grow up before commuting out to the big sea. Both are critical ecosystems in slightly different ways, and both are being decimated by two very different types of fishing practice. Todays focus is on the open ocean so here's the scoop (or should I say trawl...oh dear):

1) Blue and yellowfin tuna...not so dolphin friendly

A rare shot of a bluefin tuna that isnt rushing past at 20 knots

These are the big guys of the fish world, the top predators in a similar way to wolves in Europe and lions in Africa. Sleek fast, hydrodynamic, with fast metabolisms to keep them active when hunting. Indeed tuna have warm blood and control their temperature in similar ways to land mammals. Being at the top of many open ocean food chains, these rapid hunters act as keystone predators. They influence the numbers and diversity of nearly all other smaller fish in the ecosystem.

Now sadly for these fish they taste great (although that can be said for most animals depending on who you ask) and we have been fishing them for as long as we had boats capable of getting out to their mid ocean hunting grounds (and for as long as we have had nets and lines capable of catching them). The issue here is similar to that discussed with sharks, these are large slow growing top predators, as such it takes time for them to recover from population losses caused by fishing. Now tuna due produce millions of eggs (as opposed to the handful of shark pups) , but as they are released into the open ocean, only a tiny fraction don't become a whale snack.

As such we have seen dramatic declines in these species. I would also like to point out the folly of buying dolphin friendly tuna, which is a sad story showing that having your heart in the right place doesn't always mean that you get the intended results.

People like dolphins, especially environmentalist types. The traditional method of catching tuna was with a purse siene net, it looks like a big coin purse, and is pulled around a shoal of tuna before being zipped up by another boat, just as you would pull the cord on such a purse. The best way to target the shoal of tuna was actually to follow the pods of dolphins that ate the same small fish as the tuna. The sad fact that a few dolphins were being caught prompted Greenpeace and a few other charities to campaign to get people only to eat dolphin friendly tuna. Purse siening was a very selective method of fishing, apart from the fact it caught a few dolphins, the replacement method long lining was much worse.

Long lines are similar to regular pole and line fishing, the idea is the same, put out a baited hook and wait for the fish to take the bait.
The difference is in scale, long lines are kilometres long and hang millions of baited hooks in the water. These are towed slowly or simply left to wait in the sea, they subsequently catch anything and everything (except dolphins, who don't really go in for baited hooks), this includes critically endangered turtles, regular old endangered sharks, hordes of non target species that are thrown back as bycatch and oceanic birds such as the albatross. Long lining bycatch rates range from 30-60%, much less selective and ultimately much more damaging than the original method! So while dolphins were saved (a collection of species that were not threatened in most of their ranges ) everything else in the sea suffers.

Fortunately we have started to realise the error of our ways and sustainable pole and line caught tuna is making a comeback. If you can't live without it go for skipjack, albacore or blackfin (American south east asian readers should also avoid pacific bigeye) and try to make sure it is pole and line caught. Do this and fish everywhere will thank you, furthermore, you will no longer be an accessory to turtle murder!

2) Swordfish, king mackerel and marlin...heavy death metal

Beautiful animals these guys...and shown with spiffingly brillinat British accents in finding nemo

These charismatic chaps follow very much the same rules as tuna, indeed they are top predators and have been decimated by the practices of long lining. Yet there is an extra piece to fit in this puzzle box, poisonous mercury.

Mercury is a rather nasty heavy metal, in liquid form it looks cool, but inside your body even in relatively small amounts it does some serious harm. Hair loss, seizures, trembling, loss of liver function and kidney shutdown, in extreme doses brain damage and death heads up a symptom list aggressive cancer would be proud of.

Top predators such as swordfish naturally build up mercury in their systems, each tiny fish eaten has a small amount, and as it takes a very long time to get out of their (and our) bodies it builds up. When We eat swordfish steak we get a big dose of this mercury. Indeed swordfish is so loaded with the stuff, one portion puts a regular man up to his weekly safe mercury threshold and is considered a risk to an unborn child. The food and agriculture organisation for the UN recommends that pregnant and breast feeding mothers consume absolutely no swordfish, marlin or king mackerel, as even one portion is loaded with this poison.

Now this problem has been around for a while, but it is getting worse. Incidents of mercury poisoning are increasing year on year in Japan (eat lots of fish) and there have been cases reported of new York lawyers losing their hair and having seizures due to a steady diet of high grade sashimi. The problem stems from our increased industrial activity. Mining for gold and platinum produces mercury waste that ends up being dumped into rivers and then slowly makes its way to the sea. Mercury pollution is also driven by sales of batteries, so if you want to help out the swordfish (and maybe one day eat one that's not loaded with a deadly poison) switch to rechargeable batteries.

If unsure about the levels of mercury in fish you can consult this handy chart, if you are pregant or breast feeding (or thinking about it), this list if quite important.

Friday, 17 June 2011

Cool critter of the month: The orb web spiders

Many people don’t like spiders, 8 legs, lots of eyes, fangs and the potential to lay eggs in your ear while you sleep (slightly exaggerated perhaps...), but I think this group gets too much bad press. So I will offer some defence for the spiders, showing lots of pictures of spiders to people who hate them is unlikely to change their minds, so I have chosen a group that not only have beautiful colouration but also build some of the most fantastic webs of all our eight legged allies (against flies, who let’s face it are annoying).

Orb web spiders are common; some of the first webs that you ever saw as a child were most likely orb webs. I remember going out into my misty, dew covered back garden and coming face to face with one of these for the first time:

Simple elegant and beautiful the work of Metellina segmentata the common orb weaver.

Even building these (relatively) simple webs is pretty hard work:

Yet there are many more ticks that the orb weavers have up their sleeves, and the less common varieties make webs of all kinds of brilliant shapes and forms. The wasp spider is an EU and U.K. resident that are not content with a standard orb web; they like to mix it up with some flare. Zigzag decorative silk patterns are built into their webs. They also have the ability to take on bombardier beetles (who defend themselves with a spray of noxious boiling acid), by shooting silk countermeasures at them before the beetle comes into range for its own acid attack (Pokémon like battles can be imagined at this point).

Argiope bruennichi the wasp spider has stylish taste, and its attacks against bombardier beetles are super effective!

Not to be outdone, there are a range of other orb weavers of the family Argiope that also produce awesome web enhancements called stabilimentum. Here is a choice selection of their brilliant webs:

The aptly named St Andrews cross spider (Argiope keyserlingi) has a thing for Scotland, too bad it lives in Australia...

I couldn’t find an ID for this guy, short of being an Argiope. This issue is fairly common in spiders (not being an expert!) as many are virtually impossible to tell apart to species level without years of training. Nevertheless, very cool web decoration.

Again another unknown Arigope, but so pretty I couldn’t resist!

Argiope aurantia the writing spider goes nuts with its own central decoration

The orb weavers have more tricks up their sleeves than just fancy decorations in the middle of a web. They are also the masters of size and scale in web design as well as raw web power. The golden orb web spider, Nephila maculata builds webs that are stronger than Kevlar. Most people know the fact that spider web is stronger than steel gram for gram, that is nothing to the golden orb weaver. Their webs are large (2m or so) and strong enough to catch birds.

Raw web power at its best...

Indigenous people of the Solomon Islands used the nets for just this purpose, along with fishing lines and even bandages. The slightly golden covered webs have been looked at by scientists hoping to grow replacement artificial human ligaments and tendons to be used to treat chronic injuries. In addition, since it is stronger than Kevlar, military type chaps are also figuring out how to make spider web bullet proof vests (sign me up for a suit of golden spider armour!).

Another species of Nephila, N. Komaci holds the title of the largest orb weaving spider known to man. These guys were just discovered in South Africa in a local park after two scientists were kicking around on their lunch break. It builds giant webs over 6m in diameter, and like many spiders the female has the nasty habit of eating the male either after or during sex. Of course who could blame her, she has so many eggs to make and the male is less than 1/10 of her size (no more than a light snack).

This is just the webs of one group of spiders; there are whole hosts of other fancy webs out there. Many don’t have the elegance of the orb weavers, but I’m sure I can come back to them at some point in the future. Maybe some of these beautiful webs can even convince you to foster a bit of spider love...

One step at a time perhaps!

Thursday, 9 June 2011

My horoscope for today?

Some people claim to be able to predict minute details of our lives based on the positions of the planets at the times of our births; this is the practice of astrology. Every so often a piece of pseudo scientific bunk comes and gets right under my nostrils and wafts itself just long enough to cause my eyes to water. This results in me ranting to Bob (who sits next to me in the office) until he tells me that I should actually write something about such foolishness...this is the result.

I went online and downloaded 15 horoscopes for me (a Cancer if you must know) that makes some predictions about my emotional or physical state today (June 09, 2011). Now 15 isn’t a massive sample size, but more than enough for the tests that I am planning to do on the data. If I really wanted to prove this I would collect a few more horoscopes (to the critics out there).

Now from these datasets individuals were asked to rate how positive the predictions or assessments were. A score of 1 meant it was a bad day, hopelessness and despair reign; apparently I would be best just staying at home hiding from the world. A score of 5 meant that I have a brilliant day to look forward to; bunnies, rainbows (with pots of gold), romantic success and work brilliance. So now we have an index of how well each horoscope felt I would do on this one particular day. All horoscopes were constructed using the same system of Western Sun sign astrology (no Chinese zodiacs creeping in here, although it didn’t stop one from mentioning Ganeesha who is not responsible for any zodiac system) so should as such make similar predictions for my day. Well here are the results:

Not many 1’s but a pretty even mix of all of the other values. Is it different to a random selection of scores? I simulated 100 datasets of 15 values 1:5 using a uniform distribution, i.e. any one of the values were equally likely. I then compared these simulated (and totally random between 1:5) values with our list from a horoscope. The result was, no significant difference in the mean scores between these samples (p-value = 0.6, mean of the horoscopes= 3.4, mean of the randoms= 3.51). So there is basically no difference between making up a score for the horoscopes and the relative predictions they make.

At this point someone could jump in and say, ‘Well Mark! Horoscopes may well differ in how they present the information, but the core message is conserved.’ This could indeed lead to different emotional scores and yet have the same key message underneath it all. I also did a keyword analysis to debunk this. Keywords (such as fear, hate, success, opportunity, love, magnetism etc) were only repeated in two of the horoscopes. With fuzzy matching (happiness is the same as joy, hate the same as anger etc) this number only rose to 4. Indeed results ranged from predicting a monetary windfall from an aging relative to romantic success, accelerated mental processes (awesome!), oozing charm and all the way to serious emotional disturbances.

Four of the entries were directly contradictory, noisy and disturbed thoughts and difficulty concentrating was the exact opposite to sudden insights and enhanced mental processes. Equally brilliance at work was predicted by one website followed by patience and persistence required with a project going nowhere by another.

I say, go out and check for yourself, consistent records between individual horoscopes have shown time and time again that they are not consistent. If there was a genuine casual mechanism responsible for changes here on earth relating to planetary position, it would be measurable and testable. There could well be a mechanism by which gravity of foreign bodies affects our behaviour; it’s not beyond the realm of logic. The sun and moon do have measureable effects on human happiness, with suicide being directly related to day length (sorry Sweden). I am simply showing that current astrology does not hold to a meaningful method (it is not consistent) and fails to make testable predictions.

Tuesday, 24 May 2011

I am not alone!

As my 10,000th page view close approaches (very that I may well be alone!), I thought I would just put up a short prompt to all of the other scientists who also have philosophical or spiritual trends that they may be keeping in the closet!

A recent paper by Elaine Howard Ecklund and Elizabeth Long in the Sociology of Religion (2011) called Scientist and Spirituality interviewed nearly 300 natural and social scientists at 21 top US universities in order to determine details of their religious and spiritual beliefs. Over half were atheists, which is to be expected from a scientific group (if anything being in the US made this a little lower than we might expect over in the U.K.). Yet nearly 1/3 of the participants identified themselves as spiritual atheists.

Common trends included; personal and consistent spirituality, ethics and philosophy of science forming a spiritual base, opposition of organised religion, disconnection with theism in particular, a close connection with nature (especially us natural scientists), connection with Eastern philosophical traditions, and spirituality likely to promote public engagement and positive action.

(Less of this)

Scientists seem to have a much greater chance of seeking out their own philosophical and religious convictions and are rarely carried along with family or local trends when compared to the general population (of course as a good scientist I would also point out that this data has not been corrected for IQ or wealth). We also have a philosophical framework to fall back onto, not many other professions can claim this (although I am now inspired to write philosophical tracts for accountants, bricklayers and insurance salesmen). The philosophy of science has been shown to be associated with certain ethical paradigms such as open mindedness, collaboration and consideration. Here we have one of the interviewed chemists discussing the conflict of science and religion:

‘Interviewer: Some might say that there is a conflict between religion and science, an irreconcilable conflict. How would you respond to that kind of statement?

Chemist: [sigh] [ pause 9 seconds] There is surely not any irreconcilable conflict between spirituality and science. You know, I would adopt the views of Einstein on this, who always
claimed to be an extremely spiritual person, but he had no use for religion. He was always in
awe and wonder at the universe.’

As a group we don’t respond well to organised religion, even the theists were poor church goers and largely found their own connection to God. The idea of a personal deity didn’t receive much love either, even amongst religious scientists. Mathematicians and physicists in particular were more likely to identify with a life force or non personal deity than any other group (used to working with abstract concepts perhaps?).

To my great joy large numbers of the group including theists identified a close connection to nature a source of spiritual beliefs. Natural scientists were particularly strong here with 100% of them using the word nature directly after being asked about sources of spirituality. Intimate knowledge of the natural world was almost universally seen as eminently positive and informative to other aspects of life amongst us natural scientists. Here is a biologists thoughts on the topic:

‘You know that feeling you get standing by the seashore looking out over the endless expanse of water—or standing in the rainforest listening to the insects and the birds and their huge diversity and incomprehensibility. Or the feeling you get considering the age of all things in existence and how long it could go on. Sort of awe at the totality of things. If that’s what spirituality is, then I get it. But I have the feeling I am missing the point when I say things like that because my Christian friends don’t talk that way.’

Buddhism came up on a number of different occasions, as did Eastern and Hindu (Taosim remaining the stalking ninja of the eastern philosophical traditions). While the number of direct adherents to Eastern religions was small, just under ¼ of the group mentioned at least one of these three words. Two different psychologists when interviewed came up with the following:

‘I consider myself in one sense a spiritual person, wondering about the complexity and the majesty of existence as I understand it. And I happen to be very influenced by Buddhism as a system of ethics and thought, but I don’t consider Buddhism a religion. It’s really a philosophy, but it’s a philosophy imbued with a lot of spirituality. So that plays a role in my personal life, but not the belief in God or the angels’

‘My own spirituality might be closer to almost an eastern kind of tradition than a western tradition, even though I was raised a Catholic. I feel a little more comfortable with certain eastern ideas about individuality as an illusion. . . . And so these kinds of ideas give me comfort when I think about mortality, but they’re not really ideas about a god or anything. But they are ideas about before and after and meaning of life as it is being lived now.’

Best of all scientists were more likely to actually do something external about their spiritual belief than the general public (very surprising, but it turns out the general public is more likely to feel shame and resentment over their spiritual beliefs). Spiritual beliefs were strongly identified with positive action, environmental and social activism and leading or teaching future generations.

So it turns out I’m not really alone! Large numbers of scientists have arrived at what the author called spiritual atheism (next stop 100,000 page views). So I end this post with a question asked to an economist:

'Interviewer: How about spirituality? Is that important to you or different than religion
for you?

Economist: I’m going to sound like some flipping New Ager here. . . . I have a very strong commitment toward the outdoors and the environment and I think that can kind of be a spiritual commitment. I’ve made provisions to give a substantial amount of money in my will to the Nature Conservancy, for example.'

If you are a spiritual scientist in hiding out there, its O.K. you won’t be labelled a New Ager, 1/3 of your colleagues most likely think the same way!

(That's more like it!)