Food Fight! My Battle With Strawberry Pests.

My last post spoke of my battle with the shade. One of the survivors was my strawberries - apparently thriving and producing flowers and even fruit. I planted 22 plants one year ago, and I now have 140 (and I've given away a bunch). After one year, the time has arrived to finally start harvesting my produce. Having neglected my plants for about three days, with promising white to pink strawberries festooning the ground, I returned with great hope that I would find a bunch intact. I had even taken the precaution of placing the best of the strawberries on lids within bigger lids such that they were surrounded by a moat of water.

I leave you to judge the result!

Todays strawberry harvest. Yum!The 

Of my 21 ripe strawberries (I cast two into the road with snails attached), not one has survived intact. Every strawberry is either small, malformed (water or nutrient deficiency?), or rotten, or eaten by a combination of birds, snails, slugs, weevils, wood louse and millipedes. Until I started my own veggie garden, I did not even realize that wood louse and millipedes could be considered a pest. I thought they hung around mainly underground! Even my Solar Strawbs - an elevated pipe bearing strawberry plants, had one fruit that was not sufficiently hanging off the side entirely devoured by birds, and another with a millipede still chomping on it. Several entire plants have been ripped up by our friendly foraging dogs. Well, they have just been demoted to my second-best friend!

Woodlouse on a fresh organic home-grown strawberry

What is to be done about it, if The Naked Botanist cannot even grow his own strawberries in a wonderful organic setting which has never seen a pesticide in its life? I am certainly starting to have sympathy for non-organic farmers who utilize pesticide. Fortunately I am not surviving off my produce, nor making a living off them... but if I were?? Any recommendations?

Garden encounters of the Pulmatophageous kind

Giving my once promising garden the displeased eye, I decided to start rebuilding it. A long winter combined with a toxic cocktail of shade, neglect and a veritable menagerie of herbivorous pests have left my organic vegie garden a grassy and weed infested knoll. The survivors: a pitiful assortment of spindly carrots, a flowering broccoli, three snail-eaten spinach plants, and  a lone embittered beetroot. In fact the only chlorophyllous life that is thriving turns out to be strawberries and mustard. The latter which unlike the snails, I find akin to aloe juice and goose faeces on the unpalatability scale.

I attempted to beat into the soil a plank that served as a boundary to my former vegetabilian paradise. Unsuccessful, I hauled it out, revealing a small snake snoozing beneath the wood. How it survived my attempt to reseat the plank seemingly undamaged, I do not know. I scurried inside to grab my camera, and was just in time to witness a tail disappearing between the grass. Not having had time to identify the snake yet as poisonous or otherwise, I made a grab for the tale, and came up with an innocuous and unthreatening head dangling from my digitarial grip.

Having taken some photographs, I placed it on the scanner which resulted in these images showcasing its beautiful undercarriage. It turns out to be the common slug-eater, Duberria lutrix.

I've been told recently that its safe to hold a snake by the tail. Clearly this snake didn't get the message, as it quite happily lifted its head towards my hand, and as if trying out for a position at the circus - eased its way through the gap formed between my thumb and forefinger.

Oh, and in case you were wondering about the title - slugs are from the orders of Pulmonata, and phagy is latin "to eat".

The advantages of living at the foot of a forest - Cicada scanned

Living within an ancient forest certainly has its advantages. Five minutes ago I flicked a cicada from my finger back into the nocturnal sodium twilight of the city. After flying around frantically in the room, I was surprised how calmly it sat while I scanned it. There were a few surprises in store for me when I examined the scan, and also when I read about them on Wikipedia.

My first attempt to scan - immediately after catching the cicada.

Please excuse the dust and scratches. Think of the cicada as an astronaut cicada with a giant finger holding it in place in space, and the twinkling dust of the stars in the background. From a quick search it seems like it could be Platypleura capensis.

Here you're starting to see the "pupils" of the eye that follow one around, and two bright dots.

Those three white dots turn out to be Ocelli

A view from the side

Did you notice curious things? What are those mirror-like things between the eyes? They are ocelli, very simple eyes that pretty much detect light vs. dark. It is theorized that it used in navigation and orientation, as the eyes are typically more sensitive than the primary eyes.

I also learned that they don't rub their legs against their bodies creating a rasping sound like many other insects, but they use tymbals, drum like organs with muscles that click each time they move in or out. Read loads more about Cicadas at http://www.cicadamania.com.

Where's That Hi-Res, USB 3.0 Colour Flatbed Scanner??

A quick rant about my Braun Slide Scanner 4000.
A few years ago I purchased a dedicated $1 600 Braun Slide scanner, which I used for several thousand slides before it broke. It was doing excellent work where I spent many hours scanning in precious images of biodiversity for free. I loved that I could rack up 100 slides at a time in a carousel, and leave it to run. I thought the software that came with it was somewhat lacking though. One day though, a slide caused it to jam, and try as I might I couldn't free it. I had to take it to a local photographic repair company for repairs where I was charged four times what the local repair man charged them, to have it taken to him. After repairs the scan feeder would only move backwards through the slides - inconsistently. Its been nearly a year since I personally took it through to Holland from South Africa via France and Israel, where I met a wonderful person on the train who promised to post it to Germany. A year later it is still at the Braun Factory for repairs. We're at a bit of a stand-off, because I missioned to get my scanner to them, and yet they are still insisting on payment. I would have hoped for better from what I believed to be a credible German company.

Erica cygnea - one of 1100 slides scanned in by my Braun Slidescan 4000 from Keith Kirsten's Erica collection

A fun picture of an old school geezer with Erica daphniflora

Flatbed scanning: The Canoscan 8800F, A robust workhorse!
This article however is focused on flatbed scanning, particularly for scanning 3-D objects, particularly plants. My mainstay has been my Canoscan 8800F. This has been an incredible workhorse with which I have scanned in hundreds of squashed plant specimens, carted it around the country on dusty rugged dirt roads in the Crazy Daisy on field trips, and dropped it at least once off the table where I had precariously balanced it - and yet still she lives!

I've been scanning in live specimens, dissecting them, and arranging the pieces. The results have been close to spectacular (Fig. 1). At full resolution, or 4800 DPI, It is possible to see nearly every hair and gland on a leaf or flower (Fig. 2). I have come up with the workflow that allows me to remove the background and put together a plate in about an hour. However, it's been three years since Canon brought out the affordable Canoscan 9000F flatbed scanner. One would have thought that by now technology would have improved somewhat. What would that wish list include?

Fig. 1. A composite of Hermannia concinnifolia

Fig. 2. A close-up of a petal showing the hairs on the claw

More Speed!
On the top of the priority list would surely be USB 3.0 connectivity, available since 2008! Scanners are notoriously slow at high resolution, churning out hundreds of megabytes. The data needs to be acquired by the scanning device, processed locally, then pumped through to the computer for storage. An inch of scanning at 4800 DPI probably takes one minute. It takes 22 seconds to initialize and calibrate the scanner at this resolution, finishing the task in 1 min 25 seconds. They all tout the warm-up time being zero for LED lamps, but what about this not insignificant initialization time?? For a several inch long object, this becomes very significant.

I feared I was alone in ranting about this, but I see that this photoreview website states that:" Although the CanoScan 9000F boasts an 'instant' warm-up time, it actually takes roughly five seconds before it starts working after one of the direct buttons is pressed. This is because each scan involves capturing a preview which includes preliminary adjustments". 

The warmup time at a lowly 300DPI is still six seconds for the initial calibration. Thereafter it is 3 seconds. A 300 DPI scan is four seconds. I notice on the Canon 9000F it touts a blistering 7 second speed to scan in a full A4 colour page at 300DPI. In other words exactly the same blistering speed as the 8800F on the shelves in 2007 already. Five years later still the same unimproved blistering speed!

Higher resolution
Although 4800DPI scans are great, they just can't quite resolve the smaller hairs and details of plants. 9600 DPI is only double this. We should be pushing for greater scan resolutions, though arguably if one wants that much detail - get a microscope!

Maximum scan size
Additionally, there is a maximum size of 21000 x 30 000 pixels which equates to 4.3 inches x 6.25 inches. I'm sure there is a perfectly good reason for this limit, but I would love to know what it is. Fortunately a quick Google search reveals that the Canon 9000F mark II increases this maximum resolution to 50 000 x 50 000. A welcome change in size.

3-D scanning.
It is said that for 3-D scanning, equivalent to using the scanner as a camera, a good depth of focus is needed.
David Walker reveals in his post that there are two kinds of consumer scanner sensors: CIS (Contact Image Sensor) and the CCD (Charge Coupled Device) designs. CIS, a relatively recent innovation is more compact and energy efficient with the sensor lying very close to the glass. Additionally they are relatively cheap as they dispense with the lens, mirror, lamp, and the A/D chip. The CCD on the other hand, as Carl McMillan shows, gives far superior depth of field however, about one inch of useable DOF. For 3-D scanning we clearly need a maximum depth of field, so CCD is the route we need to take. This means that for 3-D scanning, a thin scanner like the LIDE series is NOT what you want.

Light fall-off
Light fall-off is the best term I can find for the rate of reduction in light from the light source to the object, and back to the sensor. Now although light dissipates at a known rate from a point source, this is not the case for a focused source like a torch. This is something that LED's natively do. So why do my objects fade into black so quickly. This has a number of negative impacts. I lose a significant amount of the plant into the background. Furthermore it becomes increasingly difficult to demarcate the black background from the object, leading to the most horrible artefacts where the magic one has decided to include the object in the background, and thus remove it. Is this necessary? Can a future model of scanner provider greater depth of field and a greater penetration of light?

A demonstration of the artifacts of light fall-off on Hertia alata.
Note the distant foliage that could not be seperated from the background
so was effectively cut out.

Shadows

The shadows thrown by the plant onto the background screen are the absolute bain of my existance. I spend maybe half an hour instead  of 3 minutes isolating a plant from the background when there are significant shadows. Putting the sensor closer to the lightsource may help reduce the shadows. Otherwise is there some clever software or hardware solution??

So one squashes the plant and provides a white background to avoid light fall-off,
only to encounter the dreaded shadows that take an ETERNITY to isolate from the plant.

Passive scanning
Why does no scanner thus far allow for passive scanning, or at least a customisable light source brightness? The rationale is that for artistic and 3-D scanning, it would be nice to use natural or other light sources. Now although LEDs are arguably not dimmable, using rapid switching technology should allow one to customise the effective brightness of the LEDs. Combined with a customisable passive scanning option, this would allow the scanner to do a quick scan without lights, perhaps a second active scan, and then using that information provided user tunable options to light the 3-D object optimally.

Automatic compositing
Say you have a document or object that doesn't fit on the scanner. Simply scan one part of it, click on the "scan next portion" button. Move it, leaving an overlapping section. And scan again. The scanner automatically stitches them together based on overlapping pixels. Theoretically! Why does no scanner include this as a standard feature?! Grrr.

Black Background Technique
A user recommends using a black cloth to remove the background. I experimented with numerous cloths trying to find The most matt one, including velvet, but found that invariably dust or reflections would wreak havoc with my black background. Finally I settled on a box which I place on the scanner. My current box has a depth of about 40 cm, and even the dark red colour of the box does not show in my scans. This has the added advantage of not disturbing carefully placed arrangements on the page, like a cloth would do., including velvet.

JPEG XR Format
Oh how I lament the fact that no cameras save as JPEG XR -but that is a topic for another blog. The JPEG XR codecs have been out since 2009 and it is supported by most good image software such as Irfanview and Photoshop. There are a whole bunch of advantages to saving images using  JPEG XR as it offers numerous advantages over JPEG including: better compression; lossless compression (with, tiled structure support (so that only a portion of the image needs to be decoded); greater colour accuracy including 24-Bit RGB (true colour) and even 48-Bit integer RGB (deep colour); greater HDR support; greyscale and multi-channel colour codings (so one should be able to store the infra-red information); and transparency support through an alpha channel. In a nutshell, JPEG XR provides better image quality at less than half the file size with a bunch of useful image options, and lossless compression at 2.5x smaller file sizes than the original data.

So come on Scanner companies. Its been 5 years since we've had any major strides in the consumer scanner field, and no, upgrading the software on the 9000F and calling it mark II does not count! Here are a bunch of obvious milestones that could (read should) be implemented in a nearby future model. USB 3.0, easy. JPEG XR, just a codec implementation. Passive scanning - switch off the LED's for a start. And surely you can be more honest about the start-up time, and find ways to reduce that, like not calibrating it every time you scan at the same resolution!

That list again:
1) More speed including quicker start times, quicker scan speed, and quicker transfer speed (USB 3.0).
2) Greater depth of field (probably not so easy to implement).
3) Automatic stitching option for large objects.
4) Passive or even better, adjustable light acquisition.
5) Dealing with shadows cast by 3-D objects
6) Better compression - implementation of JPEG XR.
7) Higher resolution - have we really maxed out at 9600DPI native resolution?

Posted 23 Oct 2013 by
TNB
Twitter: @TNBLoganist
email: capebio (at) gmail.com

New species found along roadside - promptly destroyed.

An Amazing Finding:
I am a botanist who undertook a ten year PhD on a fascinating group of 250 plant species, the dolls roses. I recently found a new species of dolls rose growing on the roadside - a beautiful creature with an evocative scent, flame-coloured petals, heart-shaped leaves, and star-like hairs. I decided to tie in awareness of this flagship species, with an article on the value of roadside reserves to conservation. The key finding of my research is that the road reserves have a 25% higher diversity than the world’s richest nature reserve, Table Mountain National Park (TMNP). Additionally, these road reserves are more than seven times the area of TMNP. These delicate ecosystems are being systematically degraded by municipalities throughout the country, acting on insensitive, misguided and outdated legislation.

A Grave Shock: 
Two weeks later I drove past the locality, and to my horror found two tractors with brushcutter attachments careening through the remaining natural vegetation, not two kilometres from the new species. Alongside were a team of seven workers wielding weedeaters, all bent upon the same task of pointless destruction. Although I tried stopping them, the massacre continues across the country. I have witnessed the loss of vegetation at the bulb capital of the world - Niewoudtville, the previously beautiful roadsides around Darling. For that reason, and 9600 others, we need to change legislation to conserve rather than destroy these man-made arteries of the world's smallest floral kingdom. Less than 3% of the renosterveld remains, and its diminishing fast. Its time to act before all we have left is weed infested grass.

The Plan:
To change legislation to conserve our flora I need to spread awareness and raise funds - urgently, so that the spring flowers have a chance to set seed, and the woody plants remain. Today I launch an auction of the right to name the new Hermannia, and for this enchanting pendant made by Nic Bladen (http://www.nicbladen.com/) cast from the flower of this new species. Bid at: http://bit.ly/16rmL2N.

Next week I embark on a series of talks, known as my my Springtacular to raise publicity and funds which would be to give evening talks at six venues across Cape Town. This is part of my lecture series in which I showcase the most astonishing plants I have encountered in my 17 years as a botanist. Book here (http://bit.ly/171fYxB), find updated information here at http://www.casabio.blogspot.com, or contact David directly on capebio@gmail.com or (South Africa) 072 368 9244

This is just a start. I also want to enthuse school children to become explorers of our own natural treasures, and thus give schools an opportunity to raise funds towards this objective. This forms part of my Bucks4Biodiversity programme.

So please. Spread the word of the auction (http://bit.ly/16rmL2N), come to the talk, or donate directly to the NGO:
http://www.casabio.org/sponsors.html
-TNB
Twitter: @TNBloganist

Hermannia mysteriosa - lost to science due to road maintenance?

The Plant Collective #5 outing to Piketberg yielded a few gems with various strategies to promote outcrossing - transferring pollen between plants rather than within a plant. All these plants were found along the road reserve - in dire peril of being trashed. The vast majority of the road reserve had been mowed or herbicided, and thus was a combination of weeds and grass. Our target for the trip was Hermannia mysteriosa m.s.. It was first collected by Elsie Esterhuysen without flowers in 1956, and thus never described. I accidentally chanced upon it twelve years ago, also a sterile specimen, and vowed to return to collect it one day. Twelve years later I returned, but the area I collected it in was unrecognisable. The vegetation has been transformed into wheatfields, and the entire stretch  of road that used to house the most delightful assembly of plants had been "maintained" to the detriment of H. mysteriosa. Is it lost to science forever?

Hermannia mysteriosa from between Piketberg and Het Kruis - another casualty of road maintenance

Serruria

Our first entrant in the Mr. &Mrs Road Reserve beauty pageant is Serruria. Serruria (Proteaceae) is a bisexual genus of 65 species endemic to the Cape Floristic Region (CFR). As with many Proteaceae, the pollen is held on the inside of the petals at the top of the flower tube. The stigma is unreceptive at first, and merely presents the pollen that it gathers from the stamens, hence being called a pollen presenter in the Proteaceae. After a few days, it becomes receptive, and ready to receive pollen from other plants. I stand open to correction, but I would say this is a form of dichogamous outcrossing known as protandry.

Hemimeris racemosa

Hemimeris racemosa - front view

Hemimeris racemosa - rear view

Hemimeris racemosa (Scrophulariaceae) is the next endemic to the CFR, this time with only four recognised species, although I'm convinced that close scrutiny will reveal more species. Despite being bisexual, with a big bulging father christmas beard and a firemans hat, it has got to be Mr. Roadside Reserve. It has the intriguing and unusual feature of being didynamous (male and female seperate), with a peculiar strategy coined by Anton Pauw (2005) as inversostyly (http://www.ncbi.nlm.nih.gov/pubmed/21646105). To ensure outcrossing, each plant will either have the style in the upright position, or the down side, with the stamen countering it. This means that when a bee collects the nectar, it gets a dab of pollen on its head, and if that is the case, that pollen will only be transferred to a plant with the style in that position. I presume the lower position would dab the pollen under its abdomen.

Even more intriguing is that Anton Pauw (2005), that living legend of nature photography and pollination ecology found that Rediviva bees visit these flowers. Whereas most bees gather pollen or honey, Rediviva bees are solitary bees (they don't live in a hive) that are known for their ability to harvest oils. They have legs with brush-like hairs that mop up nectar - in this case from the pits visible from the back. This energy-rich substance they feed to the young developing bees. Incidentally, Kim Steiner discovered 13 new species of Rediva bee by examining the pollinator of the closely related genus Diascia. Diascia is distinguished from Hemimeris by being pink not yellow, and having spurs not sacs. It appears that each species of Diascia has its own spur length, and thus its own  pollinator. Kim coincidentally also discovered 13 new species of Diascia. Take a look at the amazing pictures on his webpage of bee leg hairs and bee leg-lengths (http://www.calacademy.org/science_now/archive/academy_research/kim_steiner.php).

Two plants of Cytinus sanguineus. Most of the plant is underground

The exposed male bits (left) and female bits (right).

A ring of anthers on the male plant

The two glorious lobes. Zoom in for a close look at the glandular hairs.

The male with enormous nectar wells below.

Aah, the heterosexuals make a grandiose entrance in the form of Cytinus sanguineus (Cytinaceae). On the left we have Mr. Road Reserve with a ring of white anthers, and on the right, his Mrs with giant stigmatic lobes. This species is dioecious from the greek meaning seperate households - the sexes are completely separate. Look closely at the close-up of the female plant and you will notice the wetness. This is nectar that I couldn't resist sticking my tongue into. It was copious and delightfully sweet, the perfect reward for a foraging rodent, and a delight for a team of enthusiasts. Thanks Marion, Boet and Dee.

Stripped! A new spate of bark stripping threatens Newlands Forest.

Last week Newlands Forest came under a fresh wave of attack from bark strippers reaping bark for cash. The targeted species this time is boekenhout (Rapanea melanophloes), a species most prevalent in the younger forest, and easily identifiable by its lenticelled bark and pink flush of young leaves. Patricia Littlewort, "custodian" of Newlands Forest who has been walking and documenting the forest for over sixty years found the trees following a description of the locality by Sean Archer.

Over 25 trees were counted in an initial assessment by Patricia and myself, representing the largest single attack on Newlands Forest to date. Bark stripping has been responsible for some of the largest trees in the forest, including a massive >500 year old cape olive, succumbing to starvation. The phloem in bark carries the nourishment for the plant from the leaves to the roots. By ringbarking the tree this nourishment is effectively cut off, leaving the tree to slowly die from root starvation over several months.

It has been argued that trees regenerate after bark stripping - not so in Newlands Forest. The summer-drought period in the SW Cape means that the plant dessicates and experiences stress during summer. This is the period when growing and regeneration of stripped bark would take place in summer-rainfall regimes. If this stress doesn't kill off the tree, the tree is left defenseless without its bark, so the stripped area becomes a site of both insect and fungal infection.

What is to be done about it? More policing? Fix the holes in the fence? 

I recommend coming up with a technological solution providing electronic eyes and ears for the forest. A similarly technological solution has been implemented in the amazon with cellphones that "listen" for the sound of chainsaws (http://www.care2.com/causes/how-your-old-cell-phone-could-save-the-rainforest.html). 

We could use relatively cheap Arduino chips or something similar (eg. http://mashable.com/2013/05/03/spark-core-add-wifi-to-anything/) linked to mobile phones, cameras and trip beams. These should be placed strategically, and if the switch is triggered, a photo gets sent to headquarters or an internet site for threat assessment. This could be locally developed, and would cost a fraction of the cost of increased policing. 

Contact David on capebio@gmail.com to get involved in funding or developing such a system.

-TNB
Twitter: @TNBloganist