Thirty years of the barrier method and other science stories

Thirty years ago this month I wrote my first professional article. It was a short feature about the biggest organism having the biggest orgasm and was entitled ‘The Barrier Method’. It explained some of the chemistry, biology, and geography of the sex life of Australia’s Great Barrier Reef and appeared in the April 1990 issue of the Royal Society of Chemistry’s young chemists’ newsletter Gas Jar.

Incidentally, I  later renamed the magazine and helped relaunch it in full colour as New Elements with Editor Dr Mandy Mackenzie, which carried my Elemental Discoveries news round-up for several years from 1995 onwards.

I also used to publish Elemental Discoveries online on what was perhaps the first chemistry news website. It was to become a model for several news site launches over the following years that I instigated or was involved with for various organisations, including Reactive Reports for ACD/Labs, PSIGate Spotlight, which became Intute, Spectral Lines (for Wiley, now SpectroscopyNOW.com), Distillates for the RSC magazine Education in Chemistry, and a couple of others. Elemental Discoveries itself was hosted by ChemDraw creators Cambridge Soft for a couple of years before I relaunched it as Sciencebase.com in July 1999.

The article ‘The Barrier Method’ was chosen as runner-up in the 1990 Young Science Writer Awards hosted by The Daily Telegraph and the British Association for the Advancement of Science. A later article entitled “Not every sperm is sacred” won in 1991 and led to my writing about science for The Telegraph for several years after that. I got a merit award after the sperm and eggs with an article about xenon and anaesthesia, but sex science has remained a focus of much of my writing over the years, hah!

You can see a hopefully complete list of all my clients from the last thirty years as a freelance science writer here.

The photo accompanying the article was by Mrs Sciencebase long before she was Mrs Sciencebase. I can’t find the original magazine, hence the monochrome copy.

The Stormy Petrels – a song

In splendid isolation or otherwise, I try to find time to write a song every once in a while. The title of this one – The Stormy Petrels – refers to the desperate fishermen of my home village of Cullercoats who used to brave the North Sea in their cobles regardless of the weather and sometimes taking pride in riding the storms to bring home the catch. Unfortunately, not all were lucky, there were many tragedies.

The Stormy Petrels – a song

The painting I’ve used for the artwork for this song is “Daughter of the Coast Guard” (1881) by Winslow Homer, she’s brandishing a voice horn mentioned in the song. Homer is often known as the American Turner, one of my favourite artists. Spent time in Cullercoats in the 1880s when it had a strong reputation for craggy cliffs and characters (it still does!). It was something of an artists’ enclave, their being drawn by the light, the sea, the craggy characters, back then and to some extent it still is in the modern day. I’ve written about Winslow Homer before and used another of his paintings for an earlier song – The Spate Gatherers – about the village’s fishwives.

The Stormy Petrels

The seas were fair as far as the eye could see
The waters still and bare
The wind laid low, there was time to spare
There’d be no storm to keep us here

The nets were all tied and the fishwives were ready
The cobles would leave on the tide
We’d sail  to the north and head for the shoals
Their shawls held tight, home on the breeze we would ride

The hours went by and the swell it grew heavy
The men would e’er swallow their pride
The rises and falls of the fish life a penny
The true, tried, and tested on-side

The nets were all tied and the fishwives were ready
The cobles they sailed on the tide
We’ll head for the north and race for the shoals
Their shawls they’d hold tight, till home on the breeze we will ride

We rowed a fair clip with a glint in our eye
The tide would carry us wide
The sun it shone through as the land disappeared
The spindrift blew through, but no siren could draw us aside

The net’s been aside and the fishwives were ready
Our cobles they sailed with the tide
We’ll head for the north and race for the shoals
Their shawls they’d hold tight, till home on the breeze we will ride

It was bright and white horses there were none to see
And the wind couldn’t blow owt our oils to deceive
But the pressure will fall we’ll not bear a hasty retreat

Whistle and you will be damned
A hastier judgement to hand
A voice horn calls out
“No survivors will e’er see the land”

The nets were all tied and the fishwives were ready
The cobles would leave on the tide
We’d sail to the north and head for the shoals
Their shawls they’d hold tight, till home on the breeze we would ride

Fen Edge Un-Events

We live on the Fen Edge patch, the south side of the Cambridgeshire Fens. Pre-corona I ran an events page on Facebook, FEE – Fen Edge Events. Sharing gigs, shows, fairs, events, and other stuff of interest to the locals.

In the midst of corona, I have repurposed the page for quarantine times, social distancing, and self-isolation as the Fen Edge Un-Events page and am sharing virtual cinema clubs, isolation gigs, online quizzes, Zoom pub crawls etc.

Museums and galleries, zoos, cathedrals, and other places of interest, even local gardening enthusiasts, offering virtual tours and access to webcams for free.

Tips and tricks for homeschooling, drawing and sketching techniques, maths tutorials, quizzes for adults and children, free books (electronic and audio), magazines (many free online if you have a library card).

Virtual cinema, book clubs, shared music, DJing, live streaming gigs (classic, rock, pop etc) and shows (comedy, theatrical, musical, opera, ballet).

Recordings of local shows and gigs, including CTW pantos.

Home workouts.

Music lessons and tutorials.

Science stuff, such as astronomy and observing info, birdwatching, and more. Also, citizen science projects you can join from home.

Suggestions for sharing images such as beaches, silent cities, teddy bears, rainbows, jokes.

Live (pub) quiz nights.

There will also be occasional public service announcements (PSAs), about the disease, about resources and utilities, grants for the vulnerable, wellness and mental health advice.

STAY HOME, STAY EDUTAINED, STAY WELL – We will get through this together, apart!

Join here https://www.facebook.com/groups/cottenham

New ways to detect emergent viruses

In a recently published review dedicated to the diagnostics of viral infections, a Russian research team featuring MIPT (Moscow Institute of Physics and Technology) researchers is the first to systematically describe and summarize the cutting-edge technologies available. A number of new effective methods of virus detection have been developed over the past few years, including those targeted at unknown pathogens. The authors described the so-called high-throughput next-generation sequencing as a potent new approach. The method promises to revolutionize the detection and analysis of new pathogenic viruses, but it will be at least several years until it is introduced into mainstream clinical practice.

“There are, by various statistical estimations, over 320,000 viruses that can infect mammals,’ explains MIPT’s Kamil Khafizov. “To date, less than 1% of this vast multitude has been studied.”

Most viruses, including those that cause respiratory, digestive, and other diseases in humans, remain unresearched and thus almost undetectable. The reason behind this is the narrow spectrum of viruses that the modern testing systems are designed to target.

‘Metaphorically, we are attempting to look at a vast sea of threats through the eye of a needle,’ the authors write in the review. Among other things, they explore the shortcomings of the polymerase chain reaction method. This essential technique for microorganism molecular testing fails to identify poorly explored viruses, and this constitutes one of the key problems in modern virology. There are, however, new methods that may potentially solve the issues of detecting and identifying new microorganisms. The authors describe next-generation sequencing as the most promising. Also known as high-throughput sequencing, it enables the analysis of multiple DNA molecules in parallel, be it a set of samples, different regions of the same genome, or both.

“Efficient mathematical algorithms are a key part of the method,” explains says MIPT grad student Alina Matsvay. “They allow researchers to compare the genome of an unknown virus against all available references of viral genomes, and predict all of its possible characteristics, including its pathogenic potential.”

Khafizov noted that the coronavirus pandemic has demonstrated the importance of next-generation sequencing methods for identifying new pathogens in clinical samples and studying the molecular mechanisms of virus transmission from animals to humans.

https://doi.org/10.3390/v12020211

Smart phone test device for Covid-19

Scientists in the UK are developing a new smart testing device for the coronavirus and now need backers to get the device manaufactured quickly and in large quantities.

The team from Brunel University London, Lancaster University and the University of Surrey reckon the can test for Covid-19 infection in half an hour. The device has already been successfully tested in The Philippines to check chickens for viral infection and the team has now adapted it to detect Covid-19 in people. The system is quick and easy to use, requires little training and could be used by healthcare workers and even lay people.

“Now we have access to multiple genomes (blueprint) of SARS-CoV-2 virus, we can develop reliable molecular assay in a week and have them up and running on the device in three or four weeks,’ explains Brunel’s Wamadeva Balachandran. “We are confident it will respond well, and we rapidly need industrial partners to come on board. It will have a huge impact on the population at large,” he adds.

The operator takes an oral or nasal swab, puts it into the device and connects to the smart phone app. Samples do not need to go to a laboratory and the same device can be used to test six samples simultaneously. The addition of telemedicine functionality will make the device even more useful. The idea is to try and make it cheaper than other tests so it can be used worldwide at home, in doctor’s surgeries, hospitals, and workplaces. Once the infection is identified, the intelligent system will track down all people who had close contact with the newly identified patient in the previous two weeks and alert them to the threat.

Source: https://www.lancaster.ac.uk/news/uk-scientists-develop-new-rapid-smart-testing-device-for-coronavirus

Covid-19 chain-letters and friend of a friend BS

I am receiving an inordinate number of personal messages on social media and emails asking about different aspects of Covid-19 and the coronavirus. Often the question will be about some email that has purportedly arrived from a friend of a friend in China or Italy or wherever and claiming all sorts of conspiratorial nonsense, proclaiming the end of civilisation, or pointing out how some miracle cure might be a miracle cure (it won’t be). Often recipients are told to urgently share the message with all their contacts.

Now, I am not medically trained, I cannot give medical advice. But, what I do know is that random notes of unknown original source about scientific and medical matters from non-scientist, non-medical friends are invariably BS, they were long before Covid-19 and will remain so long after it’s over and we’ve moved on to the next crisis.

Often the BS is sprinkled with truth glitter as a kind of camouflage, but the stinking turd beneath the shiny, thin veneer of sparkles is still unpolished, fake news, scam fodder, or somehow maliciously biased ordure. It may also just be common or garden bovine waste of the kind you might use to condition allotment soil to make your rhubarb grow thicker if there were not sufficient equine output available.

If you receive such a message, just delete it. It takes a simple swipe, tap or click and you can then forget about it. Please don’t share it. Please don’t email it to people you imagine might be able to remove the glitter and reveal some hidden truth.

If you have real concerns and questions about Covid-19 and the coronavirus that causes it, visit the websites of the NHS or the WHO and take note of their advice and guidance.

Stay well friends :-)

Learning a little birdsong

Back in the pre-covid good old days, when you could take a countryside or woodland walk and chat to others on the highways and byways, the conversation would almost always turn to birds, especially if one of you were carrying a set of bins or a camera with a big lens.

blackbird firethorn 4
Blackbird

If you reveal any sort of knowledge about which bird is which, people are even more surprised if you know which call or song you can here. I’ve not counted how many birds I recognise from their songs and calls but a few of the ones I know for definite would be: Blackbird, Robin, Dunnock, Wren, Song and Mistle Thrush, Magpie, Jay, Rook, Raven, Carrion Crow, Jackdaw, Blue, Great, and Long-tailed Tit, Buzzard, Goldcrest, Treecreeper, Yellowhammer, White Throat, Black Cap, Chiff Chaff, Reed Warbler, Reed Bunting, Bearded Reedling, Green and Great Spotted Woodpecker…I’ll stop now…

Goldcrest
Goldcrest

Anyway, there’s a crowdsourced website called Xeno-Canto where you can hear recordings of the calls and songs of birds from around the world.

chaffinch 768
Male Chaffinch

But, as we’re all at home now, here’s a selection you might hear from an open window in your self-isolation.

Chaffinch – song, call

Blackbird – song, alarm call

Song Thrush – song

Robin – song, call

Dunnock – song, call

Wren – song

Great Tit – song

Chiffchaff – song

You can find the complete tick list for our garden birding here.

More funking songs

Just in case you’d had enough of the doom and despair, here’s a short playlist of some of my funkier tunes from recent years, all free to stream and download right now.

Funktastic!

When the beat hits your heart

Gravity’s Rainbow

Latin Class

Running out of favours

Lift me up

Dawn Chorus

All words and music written, performed, and recorded by yours truly. Except where stated regarding drums, synths etc.

The coronavirus crisis – Covid-19

There is a lot of disinformation about Covid-19 (FAQ here) out there and it can be very disheartening to read the nonsense and conspiracy theories especially when they come from moronic world leaders.

Indeed, when the US president tweets that there is no problem and then a week later claims he knew it was a pandemic before anyone else it becomes very depressing watching this play out. His daily “fake news” tweets about what drugs might work are completely inappropriate from a pharmacological point of view. He mentioned one drug that would have no effect on a virus and then a drug combination that can actually cause heart failure and so is never used.

Additionally, some countries (the UK) are misguidedly opting for their own version of the WHO recommendations. This seems just as ludicrous especially when we were still seeing people huddled together in pubs until last Friday and teens on the street even today acting as if nothing has changed in the world.

It makes one wonder how we are ever going to get through this. I have pointed out elsewhere, with my purportedly scientific head-on, that as far as I understand it there are many significant obstacles to overcome yet. It is not yet known whether post-infection immunity for those who recover from the disease persists. Also, we have not found a way to make vaccines for other coronaviruses, so what are the chances with this one.

There is a glimmer of hope. Scientists have known about the possibility of an emergent pandemic for decades. I reviewed a book – Virus – for New Scientist back in the day (1997) that predicted the emergence of such a disease. We have seen some hints of such an outbreak that would engulf the world with SARS and MERS and others and we managed to overcome those. We have known about coronaviruses for decades and studied them in detail. We have known that some coronaviruses that infect bats could make the leap from bat to human without chicken or pig as an intermediary. One potentially lethal coronavirus was found in the Brazilian vampire bat in 2008, for instance. As such, we have been analysing them in detail and accumulating fundamental scientific knowledge.

That knowledge was never going to stop the emergence of a pandemic virus, but we can build on what we have learned in the last 20 to 30 years and ultimately find a way to overcome this disease.

Within minutes of writing this blog post, an update arrived on how the WHO is about to push fast-track megatrials of four contenders for drug combinations to beat the disease.

In the meantime, keep your distance and be vigilant of symptons.

Most of us will get through this together…apart.

Stay well

Bird Report 11 – Out and about – or not!

UPDATE: 20:45, same day – The National Trust has issued a new statement just hours after I posted this, no longer allowing access to their land other than the public places they manage.

UPDATE: March 2020. Oh, the irony. I wrote this article for our village newsletter long before the Covid-19 pandemic had arisen. Since then, so much has changed and so many places are shut down. The countryside is still open, of course.

So, if you’re not self-isolating, you’re not in a vulnerable group, and you’re practicing social distancing, there are still plenty of places to visit to see the wildlife. The very wildlife that is entirely unaware of humanity’s woes and may benefit in some way from falling pollution levels through lower numbers of flights and other activities.

Anyway, on with the original newsletter report:

I occasionally mention sightings of interesting bird species from places other than in and around Cottenham itself. It is possible, nay probable, that some readers might not know about other patches they might visit that are just a short hop from the village. Most, I’d admit are not within a short walk, but some are accessible by bicycle and certainly by car. I’ll leave readers to plot their own route and decide on their means of transport if they fancy visiting.

Among the more well-known spots is the National Trust’s Wicken Fen, which is always worth a visit, although it can get busy, which means less chance of seeing birds closeup. They usually have a noticeboard listing sightings, but I think that’s their overall tick-list and chances of seeing a range of species will depend on time of day, time of year, and the weather. There are commonly marsh harriers quartering over the parts farthest from the visitor centre, as well as some hen harriers. But, your mileage will vary.

You will be almost certain to see a buzzard or a kestrel, but they’re quite common over much of our local countryside. In the summer months you might catch sight of a hobby catching and eating dragonflies on the wing. Hobbies are a falcon that resembles the peregrine and the kestrel but sits, in size between the two, it’s a summer visitor. There are lots of Reed Buntings at the Fen and in the summer, you’ll likely see and hear various warblers, including reed warbler, sedge warbler, white throat, and others.

Head out beyond Wicken itself to Adventurer’s Fen and Burwell and Tubney Fens. If you want to see the short-eared owls that have taken to Burwell Fen and mentioned in my previous report, you will probably have to wait until next winter when they come back from their far-north breeding grounds. But, you will see barn owls anywhere around these fens at dusk on a good day. Oh, and on your way back don’t forget Kingfisher Bridge Nature Reserve, which has some interesting species as well as a couple of constructed nesting sites to attract sand martins.

There are plenty of fens around and plenty of lakes, commonly ex-gravel pits that play host to quite a range of species, with the odd rarity turning up every now and then. Check the lakes and land of RSPB Ouse Fen (coming from either the Needingworth or Over entrances) and if you’re keen-eyed you will almost undoubtedly see any of the above depending, again, depending on conditions and time of year. There are often snipe and green sandpipers to be spotted at the Reedbed Trail side of the reserve (Over) and a couple of pockets of bearded reedlings (formerly known as bearded tits). That species is quite shy and does not like the wind much, but if you hear a pinging type call from the reeds watch out for this unique species darting about, the males sporting their black sideburns on a grey face.

Great white egret, little egret, and grey heron frequent this area too and you might hear booming bitterns in the mating season or if you’re lucky spot one taking a short flight between nestling areas of the reedbeds. As mentioned in an earlier report, occasionally cranes will fly high over this, and other reserves, and in the summer months on a hot day replete with lots of dragonflies you might see half a dozen, if not more, hobbies.

On the Needingworth side and other areas waders, gulls, terns (in the summer, including black terns) are all keen on the feeding here. At the time of writing there were numerous smew on one lake as well as a plethora of more common waterfowl such as tufted duck and wigeon. Cormorants are frequent flyers here too and you will often see them on the water’s edge perched and drying off their wet wings in the classic pose of this sooty species.

So, where else might you visit for a bit of bird watching? RSPB Fen Drayton (which we used to known as Swavesey Lakes) has a similar profile to Ouse Fen but often has good-sized starling murmurations on winter dusks. NT Anglesey Abbey and Wimpole Hall are perhaps less for bird watching than tree and flower watching, but there are woodpeckers, treecreepers, hawfinches (sometimes at Wimpole), nuthatches, and the usual range of what we might call “garden birds” to see there, but in a more natural habitat than the garden. Milton Country Park at quiet times is also as good a place as any for a quick avian detour It has plenty of different types of gull and several kingfishers, which you might see darting back and forth across a lake to a central island. Rarities do turn up, such dunlins, goosander, some of the more obscure warblers, and others.

As I’ve hopefully helped you note in previous reports you don’t have to go far from your home in Cottenham to see any of dozens of species of bird. Check the back issues for more info on local warblers, owls, cranes, raptors, garden birds, and more.