Teaching @ University

Last week I was on a few workshops about teaching strategies @ University. I have rich experience in mentoring students at all levels starting from freshmen and finishing pre-doctoral-thesis graduate students who spent all of the time writing their PhD thesis but I was never teaching before. Boy, I wish I would stay where I was…

It seems to me that the main idea of teaching @ University level (undergrads at least) is engagement. ‘Engagement’ is a key word for everything. Like panacea for terminally ill patient, engagement is the ray of hope for modern higher education system and, I believe, not only higher education. Even thinking about it makes me nauseous…

First of all, why should I treat students like toddlers and seek their attention through this ‘engagement’? I was honestly thinking I am at University, we are all adults. I am ready to treat students with respect they deserved, provide information, insight, answers they might seek, but why would I engage them into artificial relationships with science? Why would I force them to learn something they do not want to learn or not ready to learn, or not interested in learning?

Second, this ‘engagement’ itself substitute active learning which usually based on vivid interest in subject by passive learning through activation of some sort of brain activity and long-term memory. This is, basically, the main goal of ‘engagement’ – to make the passive learners from the students, to trick them into learning, to lure them into knowing something through ‘flash-cards, round tables’ and other bull-shit.
 I am sorry, but it does not fit into my personal values!

My question is – why nobody is talking about real issues in education? Why everybody is focused on teaching excellence, schools supplies and other non-directly related things while the real staff is out of discussion?

Terrarium with three mushrooms

This is very temporary terrarium. It has three small mushrooms. I do not think they will live long, maybe other couple days. I plan to put something different as substitution, more permanent :]

Terrarium – 3 Small Mushrooms :]

vacations are over…

… back to work

My terrariums

Books: “The Jungle Book” and “The Second Jungle Book”

Well, because of some changing in my life situation right now I have to sell some of the books from my collection which is breaking my hart, sniiiffff… I decided to keep everything concerning botany, history of science (oh, well, more or less everything), and majority of botanical prints, but all other books should go.

I think the first one will be: the bundle of “The Jungle Book” and “The Second Jungle Book” by Rudyard Kipling, early edition, published in London by Macmillan & Co, 1898 & 1899. Each volume is an identical reprint from a first UK edition, (1854 & 1855). I LOVE these books: tiny engravings and full-page pictures with superb details. Blue boards with gold embossed vignette on front and spine and gold page edging. As of old books survived so long, spine ends show some wear and corners bumped. Some foxing on the inner pages (especially extensive in The Jungle Book); The Second Jungle Book is signed and have ex-libris. Inner hinges just starting in both books but holding firmly.

My favorite story is from The Jungle Book, and, I think, it is the most famous of the other stories – “Rikki-Tikki-Tavi”, the story of a heroic mongoose.

“The Jungle Book” and “The Second Jungle Book”

More photos below.

BTW, a few words about mongoose. There over 30 known species in the family. Length of the body can be 7 to 25 inches (18 to 64 cm). Imagine 7 inches long mongoose! Tail – 6 to 21 inches (15 to 53 cm), weight 340 gm to 5 kg (12 oz to 11 lb). They live up to 20 years (just like dogs!). They are obligate carnivorous meaning they are eating a LOT of meat. Their diet includes insects, crabs, earthworms, lizards, snakes, chickens and even rodents. Usually mongooses are terrestrial, but there are some species semi-aquatic (most or at least half of the time spend in the water) or even arboreal (most of the time spend on the trees) ones. Though mongooses live in burrows, they seldom dig holes for themselves. Rather, they just move into the burrows left by other animals. A mongoose is fast enough to save itself from the strikes of a snake very easily plus a mongoose has a great tolerance towards the poison of a snake. Mongooses are social and use an alarm call to warn others of any bigger carnivores. As soon as the other mongooses hear the call, they rush to the nearest hole.

Rikki-Tikki-Tavi from The Book of Jungle (1898).

The hand colored lithograph of the mongoose. It is from an exceedingly rare set published by The Zoological Society of London in 1848-1849.

The Flora Universalis: Proof-Prints Study

Some of the scans from possible proof-prints of The Flora Universalis to support my point that they are indeed pre-pocessed botanical prints ‘in work’. I wish I could see the finals, but because the work is very rare I could not find any of my prints as final version.

Ficinia contexta whole [almost] print with drawings and legends. [The size of the prints is not standard, they are larger than A4 and Letter – that is why the bottom is cut off]

Hand writing with pencil and small additional drawings appear on quite a few of the prints. Another example:

Fragment from Fuirena coerulescens print. The picture drawn with pencil and hand colored plus hand writing are very remarkable on this piece.

Many of the prints are only partially colored which most probably indicates color study.

Passiflora print only half colored – probably color study.

Detective story: The Flora Universalis

Awhile ago I bought botanical prints at flea market. The prints were in a bad shape: marked, stained, cut, ripped, with handwriting on the other side, etc. They cost not so much and I planned to use them in my art [to make frames for other botanical prints in my collection]. After some time I looked at them again, this time more carefully and realized – I have got something interesting in my hands…

First of all, some of the prints have the small  additional hand drawings with legends. Second, the colors do not looked finalized but rather resemble washed colors for study. Third, many prints have OTHER prints on the other side, not related to the subject, in some cases it is animal print, plant print, some other things [the final book prints were always one-sided].

Forth, and the most exiting!, the hand writing from the other side and marks and stains are appeared to be the marks from post! There is the address, stamp, signature, the hole from the seal…

I decided to dig into it.

Corydalis botanical hand colored print [fragment].

Even though the colors do not look finalized they are still gorgeous on this print of Corydalis physocarpa!

Backside with name [Herr Ernst Lobe] and address [Weimar], year 1854.

The first clue was a style of the prints and address of course: the style is typical German – no free space, everything is cluttered, multiple species per page. This kind of style appeared with Bertuch’s “Bilderbuch für Kinder” [Picturebook for Children] and existed for some time only in Germany. Friedrich Bertuch used to put at one print more than one plant species and in some [many] cases even mix animal and plants. The whole Picturebook for Children can be found here [check it! it is very interesting].

Zuckerahorn und Kartoffel, Bertuch 1796. Example of the print from Bertuch’s Picturebook for Children.

Unfortunately, knowing year, country and probably publisher was not enough to figure out where these prints came from. Why not? The reason was very simple. The prints came from very obscure work. The prints themselves are NOT final prints but proofs sent from author to artists/publisher/editor [?? unclear]. Anyway, after a few months digging in internet and library I figured it out! :] The prints in my lap are from The Flora Universalis which is fundamental work of Dr. David Dietrich. The Flora Universalis was printed primarily in 1830th, but some parts of it were printed much later during 50th and even 60th. This is obscure and scarce work, consisted of over 4500 prints and 476 booklets. Some of the prints can be seen here and here.

Iris from The Flora Universalis, David Dietrich, 1833-35. From here.

Deceptive butterflies

Many butterflies we used to see as children at the meadows hide a [dirty] secret. One of the most beautiful and well known butterflies in Europe Large Blue or Arion Blue, scientific name Maculinea arion, is one of them.

The truth is all Maculinea butterflies (4 or 5 species according modern taxonomy) are deceptive creatures. It is hard not to notice the beautiful imago butterflies with navy blue or sky blue wings covered with tender black spots. Plus, Maculinea arion is fairly large species, the wing span of this species can rich 16-20 mm. Not surprising, Maculinea arion was in every naturalist collection of Victorian England. However, until late 70th little was known about their unique and fascinating life cycle. Their struggle for survival and the ways they took in their evolutionary history to turn the world around.

In  60th-70th scientist of Great Britain realized that Maculiena arion population is declining with deteriorating speed. At first collectors were to blame. In 1979 no Maculinea arion could be found on the Islands. By that time scientist already figured out that the main reason for extinction of this species is its exceptional sensitivity to the changing environment due to double specificity: the host plant which is very important for survival of the larvae during first three stages of the development and the ant host which ensures further development of the larvae in the ant nest. If either of these factors affected (plants due to early mowing before larvae left the plant; ants due to destruction of their habitat), the butterflies can not finish their cycle and population unavoidably will decline.

To be more specific, the adult Maculinea arion females lay their eggs only on specific plant, thyme, in the summer. The larvae stays on the flowers only three stages and while still very small eventually falls to the ground. The Maculinea larvae produce special chemicals and sounds to lure red ants and fool them into thinking the larvae is ant grub. The fooled ant following its instincts then carries the tiny larvae into its nest. The important point here is that Maculinea larvae can mimic only chemicals and sounds of certain red ant species, all other species will not be so easily fooled by these disguise, which means that only certain number of larvae has the chance for survival to adulthood – only those who ended up in the right nest of the right species. Ideally, the ants never discover that they have been fooled, and instead continue to protect the butterfly larvae for several months and feed them [or, in majority of cases, let the larvae to eat their own brood].

Maculine arion life cycle, from MacMan project.

Macodes petola

Even though I planned [and promised] to write about Maculinea butterflies, let me put this post first. I just got Macodes petola or Jewel Orchid in my mail box. The plant is beautiful with all these tender gold veins on the leaves… It was damaged – the top leaf [the very new one] was pinched and dried off. Now I worry if the plant will survive. The bottom leaves are seemed rigid, but those on the top are slightly drooped.

Macodes petola from Curtis’s Botanical Magazine, 1889, vol. 115 (Ser. 3 no. 45) pl. 7037


Mission accomplished

The good news! One of my papers was accepted for publication in Molecular Biology and Evolution. This is one of the best journals publishing evolutionary biology research. To be honest, this paper suck too much blood from me that I do not want even celebrate the positive final of the [never-ending] struggle.

The paper entitled: Vertical evolution and horizontal transfer of CR1 non- LTR retrotransposons and Tc1/mariner DNA transposons in Lepidoptera species.

In a few words, there are two forms of inheritance  – vertical, from parents to children, and horizontal – between non-related organisms.  The vertical inheritance is somewhat familiar to everybody, we all have features we got either from paternal or maternal lineages. The most obvious could be the color of hair and eyes, inherited disorders, etc. The horizontal inheritance is very common among bacteria. For example, the resistance to the certain antibiotics can be acquired from non-related bacterial cells or even from different bacterial species co-existing in habitat. The horizontal inheritance among bacteria is possible thanks to the existence of the special circular DNA ‘chromosomes’ [called mobile elements; mobile  plasmids; etc.] which can travel from one cell to another. These mobile plasmids carry special genes which make bacteria-recipient resistant to the particular antibiotic. BTW, these features are very widely utilized in modern molecular biology, [bio]medical engineering, and biotechnology. The horizontal inheritance was unknown for eukaryotes (non-bacterial species, including human) till about 25 years ago. However only in post-genomic era of biology, when we gain the access to the enormous amount of genetic information, we were able to detect numerous cases of horizontal transfer of genes between various eukaryotic  species/groups.

In my research I tried to address one of the key problems in ‘horizontal inheritance among eukaryotes’ – possible mechanisms involved in the process. The  major problem is that we and other eukaryotes do not have any special highly-tuned systems for horizontal transfer of genes, which means – all reported cases of horizontal transfer were spontaneous and, most probably, did not utilize any universal ‘schemes’. One of the possible mechanisms could involve package of the random DNA into virus particle and subsequent transfer between species. In this paper we explore a little bit more complicated potential pathway for the horizontal transfer between butterflies from the genus Maculinea and moths from the genus Bombyx.

I think my next post will be about Large Blue Maculinea butterflies…

Maculinea arion or Large Blue butterfly completely extinct in the UK in 1979. After 25-year effort to restore this amazing butterfly in UK, researches finally announced triumph in 2009. Meticulous research showed that the extinction was caused by a subtle change in habitat that disrupted the unusual life cycle of this spectacular butterfly. Previously, the extinction had been attributed to the work of overzealous collectors.

Not quite mosses

… or! To be more accurate, not mosses anymore, but not ferns yet. Who are they?

The are Lycopodiophyta: Club Mosses, Spikemosses and Quillworts.

They might look like mosses and still use spores for propagation but they already posses some features of the higher or vascular plants such as true roots and vascular system. It is not surprising, that the modern evolutionary systems put Club Mosses (and others) between mosses and ferns.

Figure 1. The image (on the left) belongs to BioLib. The evolutionary tree (on the right) is represented according to Bowman et al., 2007 [1] and Berbee and Taylor, 2001 [2] with minor modifications. Divergence times (Mya – million years ago) are indicated according to Hedges, 2002 [3].

My interest to this particular group of plants emerged from my graduate study of the genomic content of mosses [4]. At some point I realized that if I would like to understand what had really happened and is really happening in mosses genomes evolution I have to take steps back and forward: one step back – towards green algae as the most primitive green plants, and one step forward – towards club mosses and their relatives.  Luckily for me one of the spikemosses, Selaginella moellendorffii, was already in the list of species for whole genome sequencing and even some progress was already made towards decoding its genome [5]. While the genomic sequence is still a first draft, it offers terrific opportunity for comparative analysis and evolutionary studies. After genomic sequence became available to researchers Selaginella moellendorffiiis conquering scientific world. More and more scientific papers published include studies of these fascinating plants.

The Selaginella moellendorffii is not only spikemoss which is getting all the attention. A few years ago the beautiful movie about Selaginella apoda life cycle was published on Vimeo by Ciaran Moloney.

Club mosses and spikemosses are between the most popular plant for terrariums not only because they are truly wet-legs+shade lovers but also for their ‘exotic’ appearance and, for some species, stunning foliage. Selaginella uncinata is called ‘Blue spikemoss’ or ‘Peacock moss’. Blue spikemoss got such name for its metallic blue iridescent foliage. From certain angles the leaves of Selaginella uncinata are unbelievably brilliant blue, changing with the slightest movement of view point. There are two types of color – chemical and structural. Iridescence is a form of structural color where the observer experiences a change in hue according to the angle from the iridescent structure is viewed [for review, 6]. Structural color has been well characterized in animals, but very little studied in plants. Blue spikemoss (as well as Selaginella willdenowii [7]) became one of the model species for plant iridescence studies [8].

Figure 2. Selaginella uncinata. From: Vukusic P, Sambles JR. Photonic structures in biology. Nature. 424:852-855 [8].

[Dr. Heather Whitney is a molecular biologist by training, but now uses ideas from across the scientific spectrum (from optical physics to beekeeping) to study plant-animal interactions. As both a researcher and speaker, she hopes to show that plants are much more sneaky than is usually suspected — they have to do everything that animals do (from finding a mate to coping with predators) but manage it without moving.]

Another beautiful species Selaginella erythropus is highly prized for it’s blood red underside and called ‘Ruby Red’. Its bright red stems accent the upright leaflets and dark green tops. Under cold temperatures, the foliage will turn red on the top but under normal growing conditions it is green on top and stems and underside to be the ruby red color. Thanks to this unusual foliage, like many other common Selaginella species, Selaginella erythropus was introduced in the horticulture. However, beware if [gardening/terrarium] on-line shop page informs that selaginellas are easy to grow. Majority of the selaginellas are very picky. Selaginella erythropus, for example, should be in shade (at least 50%!) and very high humidity [it will enjoy even dripping water!]. Other selaginellas are not SO hydro-lovers but almost all species available on the market need high humidity of their habitat. The soil should be rich and well drained, never allowed to dry. Majority do well in a soil mix consisting of 2 part peat moss to 1 part loam to 1 part small pine bark. The light fertilizer (the regular fertilizer significantly diluted) is recommended weekly during the period of active grows.


1. Bowman JL, Floyd SK, Sakakibara K . Green genes-comparative genomics of the green branch of life. Cell. 2007 129: 229-234.

2. Berbee ML, Taylor JW.  Fungal Molecular Evolution: Gene Trees and Geologic Time. In: McLaughlin DJ, McLaughlin EG, Lemke PA, editors. The Mycota: a comprehensive treatise on fungi as experimental systems for basic and applied research. Volume VII: Systematics and Evolution, Part B. New York: Springer-Verlag. 2001 pp. 229-246.

3. Hedges SB. The origin and evolution of model organisms. Nat Rev Genet. 2002 3: 838-849.

4. Novikova O, Mayorov V, Smyshlyaev G, Fursov M, Adkison L, Pisarenko O, Blinov A. Novel clades of chromodomain-containing Gypsy LTR retrotransposons from mosses (Bryophyta). Plant J. 2008 Nov;56(4):562-74.

5. Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, et al. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science. 2011 332:960-963.

6. Doucet SM, Meadows MG. Iridescence: a functional perspective. J R Soc Interface. 2009 Suppl 2:S115-S132.

7. Thomas KR, Kolle M, Whitney HM, Glover BJ, Steiner U. Function of blue iridescence in tropical understorey plants. J R Soc Interface. 2010 7:1699-1707.

8. Vukusic P, Sambles JR. Photonic structures in biology. Nature. 424:852-855.

BTW, BioLib is very good library of historic and modern biology books. Many antique books are in pdf format.