Kick-sampling

Kick-sampling is a technique for assessing water quality in the wild. I've done some kick-sampling myself. Heck, I've taught kick-sampling. Almost the only time I ever used the Lidl middle-aisle fisherman's waders were for kick-sampling up to my knees in a stream.

This year, for the first time, we're doing something different with our traditional hay-meadow: harvesting the seed to [potentially, hopefully] propagate wild-flowers away from our nursery. We were requested-and-required to remove and Ragwort Senecio jacobaea from the meadow before harvest. Insects and pollinators like the bright yellow flowers but the whole plant is generally poisonous to live-stock, especially horses. It is a prolific of seed which are wind-dispersed, but the plant is a biennial, so a rigorous regime of uprooting [traditionally by small farm-children] will eventually get the scourge down to manageable proportions. Every year, if we look, ragwort will be found; but only a few scattered plants which are a distinctive green at a moderate distance and have unmistakable leaves close-up. Ragwort is thus a 101 task but it takes a little time to course systematically over the estate.

We were also instructed to remove "thistles". As I found last year, there are two closely related thistles common in Irish fields one of which Cirsium dissectum is a desirable indicator species and the other Cirsium arvensis a terrible creeping thing altogether.  But in the priorities of seed-collection it is Caedite eos kill them all - or at least stop t'buggers propagating.

Accordingly, over a couple of days, whenever the spirit was upon us (and it was not drizzling - for who wants wet socks?) one or other of us would sally forth with clippers and a feed-sack to heap cut thistles into sheafs and dump them at the field margin. 

Gotta say that it's the best sort of work: necessary, a bit physical, a bit mindless, in the fresh air <hello trees, hello sky>, WFH. I clocked off several hours of my then current ear-book The Education of an Idealist [2019] by Samantha Power: one time Dubliner [Hartigan's], one time war reporter [Bosnia]; one time US Ambassador to the United Nations [Obama]. It is readable and gives good insight about how firm beliefs and election manifestos turn squidgy under the pressures of Realpolitik. Despite pre-election promising to close up Guantanamo Bay, Obama was still its commander in chief at the end of his 8 year presidency.

I show-and-told the results of seed-stripping 10 hay-rattle plants. One collateral benefit of coursing over the meadow, stalking and killing thistles was to fill my loosely tied boots with misc wildflower seeds. It was striking a) how much of the kick-sampling was hay-rattle seed b) the huge discrepancy for seed-size among different species [from much smaller than a poppy-seed to big-as-tomato-seed] c) the wild variety of seed shape and seed-appendage and d) how each adaptation might help a seed get somewhere else and then get a grip on the earth and still have some oomph to get something green above ground to start photosynthesis. Chekkittout:

 

Street-light biology

There it is [the Mountain River] running under the (locally) famous viaduct of the long defunct railway that went from Bagenalstown to Wexford between 1858 and 1947. For the last 15 years of its existence the railway operated solely for hauling sugar beet from Ballynowhere to the Sugar Factory in Carlow. The town of Borris, which runs up from the river valley, abstracts its drinking water from the Mountain River, fouls it, treats it and discharges the effluent a little further downstream. It is just as well that, like time's arrow, water flows in one direction. The Public Meeting was called, for 1930hrs 13 Feb 2019 in the boutique wee hotel at the top of the town, to encourage dialogue between ordinary people on the ground OPOGs and All Agency Experts AAEs who occasionally parachuted in to make some desultory, irregular, duplicated, uncoordinated measurements of the river before flitting off to the next project.

• The OPOGs include 
• anyone [N=800 incl. 80 Polish-originally] who has to drink the water in Borris; 
• The town's main's water supply installed in the 19thC was replaced in 2017: Causing transitory transit-jams but great reducing the leakage of treated drinking water
• farmers with bank-side fields [that would include us as owners of The Field Over The River Aughnabrisky] anywhere up the catchment area; 
• anglers; 
• hill-walkers; 
• fly-tippers.
• The AAEs include
• The County Council CWCoCo
• Irish Water [the lads who can't / won't stop discharging raw sewage into Irish Water]
• The EPA
• Inland Fisheries Ireland IFI

The Public Meeting was for Consultation on the local River Basin Management Plan RBMP [we are not nearly finished on the acronyms!]. They were hopelessly optimistic about the amount of interest in their work: the hotel's ballroom was rented and 50 wedding-reception seats were laid out in an arc; 15 OPOGs turned up only just exceeding the functionaries who had to be there to answer questions and explain what they had been doing with their time, and our money, since the Local Authority Waters Programme LAWP kicked off two years ago. The OPOGs were not exactly hostile but were certainly critical of how their tax-payers money had been, and would be, spent. The LWAB, for example, just for the Sunny SE of Ireland employs seven people to carry out audits of water quality.

• One of our OPOGs had been asked by ALL the AAEs for permission to walk through his fields to access the river. "Do you share your data with the Fisheries people?" he asked but what he meant was, the fellow from Fisheries was knocking on my door three weeks before you came. In a free and transparent society these data should be put up in the public domain; as well as the intended schedule of sampling so that IFI and EPA could, say, share the petrol costs. The subtext here was that maybe either the EPA effective or the IFI effective could be laid off and we-the-people could save €80K salary+costs+mileage+PRSI a year. That would go a long way to making the Water Treatment Plant in Borris functional.
• Another farmer worried that the River Barrow was running dry . . . because so many entities were abstracting water. That's a worry because there will be less water to dilute any accidental (or deliberate) discharge. We wouldn't need water treatment if we banned flush toilets.
• None of the OPOGs at the Wednesday meeting admitted to fly-tipping their trash over a convenient bridge across the Mountain River, but many asserted that it was a regular occurrence under named bridges in their neighbourhood. 
• If a hoodlum fires a used soda bottle out of the window, I will clean it up during the annual An Taisce Spring clean.
• If a hoodlum dumps a load of car-batteries or paint-pots into a river someone has to clean it up ASAP (I'm too busy with the bottles). Leaving them there leaching toxins will make a disaster out of a problem. This is not the sort of things that the County Council prioritises: the crud is out of sight from the road and will cost a lot of billable hours to clean up. 

How do assess the quality of river water? The quick-and-dirty way is to jump in the river and do some kick-sampling. This is what LAWPers do: they kick-sample a bucket of aquatic invertebrates out of the river and count the numbers for different key species of creepy-crawlies. If you find caddis-fly (Trichoptera spp.) [example L] and mayfly larvae, (Rhithrogena semicolorata or Ecdyonurus venosus), the water is safe to drink. If they are absent you may not know exactly what's gone wrong with the ecosystem but you know it is poor quality. You could be much more expensive and "scientific": quantify the metals with AAS or FES; measure the nitrates; the Biological Oxygen Demand BOD; TriHaloMethane THM . . . but that would take time, kit and money. otoh, you're not better off by checking for key mammals like otters Lutra lutra: because that species is rare there is not enough granularity in the data. After the talk Ipulled on the lapel of the head LAWPer to suggest that kick-sampling and counting caddis-fly larvae is sooooo 19thC and salary-time-consuming. Why not, I suggested, take a sample of water + river-bottom and run it through a DNA sequencer. It is so cheap to sequence DNA now  and that will give you an estimate, not only of the countable invertebrates but also, of the microbial community . . . and probably the fish species as well from the fish-shit. Concentrating on the countable is a classic example of street-light science: it gives you a handle on what's easily available which may be almost irrelevant to a true measure of biological diversity or water-quality.

It was clear that DNA analysis hasn't arrived in LAWP-land yet - if it ever will. I therefore switched tack and asked what they were doing about [measuring, legislating for, informing the County Council] light-pollution. Here I must confess that I was channelling my pal Rene from St Mullins who, before he left the Netherlands 25+ years ago, was fattened on eels Anguilla anguilla. When he arrived in St Mullins on the River Barrow in the early 1990s, eels were plentiful. When they came back from the Wild Sargasso Sea as hatchlings, some of them turned right and swam up up the Mill Stream in search of a new home. Then the County Council installed a street-light on the narrow road bridge that crosses the stream as it met the Barrow. That was end of eels up the Mill Stream - they travel at night, avoiding light, which exposes them to predators. Same thing happens where the Mountain River goes under Main Street in Borris. Light and Dark are natural! they happen every 24 hours many / most / all animals have adapted to the change. Now, for the trifling convenience of people walking to the pub at night, we have daylight all night with utterly unconsidered consequences for the natural world.

In the wet

Maude Delap was a real water ecobiologist who embraced a life in the wet.  Yesterday, I went off-site pretending to be a freshwater ecologist with ο συνάδελφός with whom I share my office and the Yr4 Environmental Chemists. We motored North in convoy to the picturesque village of  Castledermot which, given the Irish name Diseart Diarmad, could have been translated less war-like as Dermot's Hermitage.  The River Lerr skirts the East fringe of the village and is conveniently accessible if you wish to sample a fresh-water ecosystem.  My EnvChems have measured water quality in the lab (nitrate, pH, turbidity).  But these measures, although sciencey, are only surrogates for the actual quality of the water as measured by the type and number of invertebrates that are prepared to live in it.  Ecologists divvy up the species into several bands according to their tolerance of lower oxygen levels, pH and concentration of miscellaneous toxins.  They then identify these sentinel species and count them. For example, red Chironomus (a dipteran midge) indicate poorer water quality while green Chironomus are only found in well oxygenated water.  We know this already because it's the red ones that you find in your stagnant water-butt.

The technique we used was a form of stream-dipping called kick-sampling (see left) which requires you to plant your feet and a collecting net on the stream-bed and shuffle your boots about to dislodge the livestock, which will get swept down current into the net.  We brought four broad 60 x 50 x 10cm white plastic trays to empty the catch into and were able to carry out a preliminary (!positive!) assessment of the water quality by finding caddis-fly (Trichoptera) and mayfly larvae, (often Rhithrogena semicolorata or Ecdyonurus venosus).  The common names for Mayflies - there are 33 different species native to Ireland - sound, for obvious reasons, like the things fly-fishermen make out of silk and wire: Large Green Dun, Angler's Curse, Pond Olive, Dusky Yellowstreak etc. In many European languages Mayflies are named for their ephemeral nature, (they often become adult, mate and die in a single 24hrs period):  German Eintagsfliege, Dutch eendagsvlieg, Slovenian enodnevnica, Swedish dagslända, Danish and Norwegian døgnflue, Polish jętka jednodniówka, Latvian viendienītes, Finnish päivänkorento, Hebrew בַּריוֹם, Turkish birgün sineği, Russian подёнка, Ukrainian поденка, Bulgarian еднодневка, and Greek εφήμερος. The Greek name, transliterated ephḗmeros (Modern Greek: [eˈfimeɾos]), is the origin of the names in Romance languages: French éphémère, Italian effimera, Portuguese efêmera, Spanish efímera, and Romanian efemeride. The EnvChems spend part of the afternoon identifying the small creatures they had caught using a dichotomous key.

met.ie rainfall radar 07/04/14

If the cartoon chappy above looks like he's just about to fill his boots it's because he is just about to fill his boots!  As happened to one of the three people who brought regular length wellingtons. On instruction, I had brought my father's old waders and a spare pair of wellington boots, which was just as well because half the students came in their trainers, and only one of them was half-willing to get into the stream bare-foot.  But when I stepped into the water to help with the sampling I had an ominous sensation of wet-sock and didn't hang about in there waiting for the perished rubber to fail - those waders must be at least 50 years old. It's a Good Thing to get out in the fresh-air and we were lucky with the weather - getting an hour beside and in the water between showers:

Shackleton Base, Leinster

A few years ago I was chatting over the fence with my neighbour. He confessed that his wife had forbidden him to go shopping anymore. She'd send him into town to buy milk and flour at LIDL, and he'd come back with flour and a set of 48 drill-bits - which he figured wouldn't go off and would be handy sometime in the future. Before I stopped shopping altogether, I was in LIDL during their Polish week and bought a set of €9.99 to-the-armpit fishing waders! MY reasoning was that, once a year, I took my 4th year water chemistry students to do kick-sampling in a local river. Next year I was time-tabled off that course and so the waders have been on a bottom-shelf in my tool-shed ever since.

The waders came out this morning!  Storm Emma started cutting up at tea-time yesterday: bringing a lot of low-pressure moisture to add to the Baltic jet-stream we've had coming from the East for the past week. It's been snowing modestly since Tuesday evening with whistling Easterly wind which stripped the snow off the open fields and left it is heaps on the lee of hedges and at the gates between fields [must be the vortex]. I was a little concerned because there were drifts in the sunken lane that runs up to our house, particularly above us where open fields come right up to the lane; below the trees we have planted tend to drive the snow up and over the dip. At the top of our garden, I measured a drift at 65cm.  Woke up this morning to find that modest and elegant sweep of white had grown to 2m! It's still precipitating [L, red dot marks Shackleton Base]

How did I get up there to find out? I slipped into my Polish waders to shovel a few paths:

• From the back-door to the front-door which was almost snow free anyway; with a spur to the tool-shed (to get to my waders).
• Up the steps behind the house to our N=29 sheep which spent the night in the **** Polytunnel Hotel. The Beloved TB had bought a week's worth of #3 Sheep Muesli and insisted on bringing the sheep into shelter from the storm. They and the feed-troughs got covered in snow anyway but it was only a dusting.

Prepper TB had also bought a snow-shovel and a nice robust yard-brush: shovelling need not be a penance if you have the correct kit. I was chatting to another rural pal two days ago and said that, if I lived in suburbia, I'd be doing more shovelling because the sidewalk and drive-way would be a finite do-able task; I can't shovel all 300m of lane, so I won't do any of it. We have flour so bread can be made. We also have oats, for flapjacks.  I'm keeping back one sack of sheep muesli for me in case this lasts a week. I think there are 29 snow-ploughs in the whole country, so we'll be dependent on the rain which may come up from the South over the weekend. With 2m drifts in the lane that handy access route is probably fritzed by Monday.  But with electricity still hanging on by a copper thread, we're better off than some thousands of people N and E of here - still bloggin' as you see.

Sorcerer

I don't think  he's a sorcerer but J Craig Venter (Happy Birthday 1946 boy) has been involved in so many shape-shifting projects that normal people might be a little envious. Last night my roomie at The Institute gave me a New Scientist article (How to be a Genius by David Dobbs 18 Sep 2006) which holds with Edison that genius is 99% perspiration. If I haven't seen as far as Craig Venter it's probably because I've been too lazy and/or complacent.  I've been both of those and am reasonably
smug content with myself so my main feeling about Venter is admiration. At least two of his game-changing projects might have won him a Nobel Prize for Medicine and Physiology, if he hadn't pissed off so many people along the way.   I've never met him but I don't get the sense that he's obtusely boorish, he just tends to tell it like it is.  Having served in a front line triage centre in Vietnam as a very young man, he's seen things and done things that the rest of us have not been challenged by.

He certainly annoyed me (so much for "Dr Equanimity") more than 20 years ago when I was just starting to motor in the world of bioinformatics. I was tasked to work out how synonymous codon usage worked for humans.  The database was tiny in those days, although we thought it was huge and gathering a robust dataset that wasn't padded out with duplicates or fragments was a lot of hard work. Book-keeping and keeping track of all the data - just to big to be processed one-a-time - needed coding and attention to detail.  in 1991, there were a little over 1000 human genes (now >130,000) to play with. We were scooped by our rivals in Paris because they were less pedantic, a little more slap-dash and that bit quicker than we were.  Their paper said what ours would have said despite their data being noisier.  This was true because the available data was broad enough that a few errors didn't affect the overall picture. Dang! Very shortly afterwards a paper was published by a team from Venter's lab that reported fragmentary sequences from 600 novel genes expressed in the human brain. In one swoop they had increased the available data by 60%!  Because each of these genes was only partly sequenced, I didn't have the tools or the mindset to incorporate the data into my analyses. I therefore thought the whole submission was an annoying barrage of noise that would just get in everybody's way.  I was completely wrong, locked into past processes and incapable of seeing that this approach was an immensely powerful tool for understanding a) the scope of human genetic diversity and b) the locations where, and activity with which, each gene was 'expressed'. I caught up about 10 years later and published an analysis of these quick-and-dirty "expressed sequence tags" (ESTs). Mobilising ESTs to study human health could have snagged a Nobel, except that Venter tried to patent his newly discovered information to win time to generate gene-based therapeutics for megapharma. Not the sort of thing a gentleman would do.

He could also have secured a prize for geeing up the Human Genome Project from outside, so that it raised its corduroy trousers off the comfy chair in the Senior Common Room, took off its tweed jacket and started to race to deliver under the threat that Venter's team would raise capital and hire bodies and buy equipment and deliver the human genome within 18 months. Venter was gracious enough to suggest that the huge, methodical and slightly unwieldy international consortium could have the mouse genome to play with after his efficient capitalist machine had knocked off The Big One. You can see how that sort of play would annoy The Suits and their tweed-jacket boffins - do you hear a grinding of pipe-stems? It didn't turn out like that though: the Wellcome Trust (whose senior people went to the same school as the genome chappies) freed up a barrel of cash for the 'public' venture and the two projects finished neck and neck in 2003. That was at least 2 years ahead of schedule.  That's a lot of time if you're dying from a genetic disease.

I wrote in May 2013 about Venter's announcement of the creation of "the first bacterial genome whose parent was a computer". That was clever and I got a kick out of solving the puzzle that Venter's chaps had embedded in the genetic code of their artificial life-form.  But that project was a mix of technology and bravado rather than being a game-changer. I'm probably wrong in that assessment also. Sequencing the genome of his poodle Shadow showed a hubris not calculated to please the rank-and-file.

Another insight that deserves enormous credit was Venter's project to sample the microbial flora of the whole ocean. Human genome not big enough? He kitted out his private yacht Sorcerer II as a floating laboratory and sent it off on a round the world cruise sampling the sea-water at intervals and purifying the DNA out of the soup that came up in their nets. The DNA enabled his people to say how many bacteria of what types were present in each different part of the wet globe. That was a Great Leap Forward for microbial ecology and I think it has been widely under-appreciated for both its vision and its achievements. The big surprise was that the ocean is a very poorly stirred soup.  The microbial community in the Caribbean is significantly different from the bugs you find off the coast of Ireland despite the fact that the Gulf Stream (aka North Atlantic Drift) connects them in a warm bath that moves relentlessly East by North-East at nearly 10km/h (it takes about a month to arrive here). The bacteria seemingly don't go with the flow. That's really surprising.

Time for old fashioned joke:
Q. Are you a sorcerer?
A. No, I drink out of a cup like everyone else.
But Craig Venter drinks different harder stuff than me, that's why he has the yacht and I have a duck-in-my-bath