Not about everything

July 20, 2012

Collective mapping of species on the web, current state of affairs

Call it spottings, sightings or observations. Many of us go out in nature and notice birds, flowers, butterflies. We take photos and ID it ourselves or have it ID’d from the photo by others. We can put up the photo for admiration on many sites.

But it can be better. We could put the observations on a map. If many do so, we could together create a species distribution map. And even see how the distribution of species changes over the years.

I love this idea, and I do participate myself. I like the result of our common effort. What I do is go looking for dragonflies. Mainly around where I live, but also in other places where I happen to come and can spare some time. Yes, I have specialized myself. There is always so much to see that one has to be selective. Of course occasionally I record a butterfly, a bird or a plant. But my focus is on dragonflies.

Banded Demoiselle example
Banded Demoiselle, distribution map NetherlandsAn example of our common effort would be the fine grained distribution map of the Banded Demoiselle in the Netherlands. This map is the result of over 12,000 observations from the start of this century till now (July 2012) and shows observations in just over 3,000 square kilometer blocks. It is taken from waarneming.nl (a Dutch project where people can record their observations for the Netherlands).

But the Netherlands is only a small country and it would be nice to see a map of Europe. That is harder to get by. The Dutch site from the previous map has a sister site in Belgium and an international site which is mainly used by Dutch and Belgian participants on holiday. But also some people from other countries contribute (it is available in about 20 languages).
Banded Demoiselle, distribution map on orbervado.org
That international site (observado.org)also produces a map for the Banded Demoiselle: It is clear that the Netherlands and Belgium are much better mapped (the rest of Europe has a total of about 750 observations of the Banded Demoiselle).

For some other countries I know where to get similar maps (with another focus). For the UK on http://data.nbn.org.uk, Germany has a similar project with European pretensions. For Denmark there is Naturbasen.

Maybe there are more maps to find. If you know one, please let me know.

Banded Demoiselle, distribution map on data.nbn.org.uk

Banded Demoiselle, distribution map on Libellen Europas (GER)

Banded Demoiselle, distribution map on Naturbasen (dk)

A global view
There is only one (public) place I am aware of which offers a global view of species observations. That is the Global Biodiversity Information Facility (GBIF) where all kinds of datasets end up. The GBIF distribution map of Calopteryx splendens is below (from http://data.gbif.org/species/1427067). One obvious problem is many empty spaces. Nothing from France and Russia for example. And another big problem: On this map it looks like the Banded Demoiselle is present in Spain. That is however a mistake. Not sure how wrong data ended up in GBIF, but it certainly spoils the fun.

It is not the first time I see clearly erroneous data in GBIF: I have seen recording of the Dwarf Damselfly (Nehelennia speciosa) in the Netherlands on GBIF while that species has been extinct in the Netherlands for 100 years or so. I have traced the errors to a source where damselfly larvae have been ID’d by an institution which clearly lacked the experience (then – the recordings are from the 90’s) to see how extraordinairy such a claim is.

Banded Demoiselle, distribution map on GBIF

More projects
There is Project Noah, which does quite some advertizing now and then. The big problem is that is produces no species distribution maps, it is unclear where the
data go (if they go anywhere) and there is no systematic verification on the recordings. A fixed species list is missing, so searching for “Calopteryx splendens” will return different results then searching for “Banded Demoiselle”. It just depends on what the user entered.

Another project is iNaturalist, which is heavily connected with flickr. I could not find any information about where data go. But it can generate a species distribution map. Although, the map for Calopteryx splendens only showed four locations when I checked. This project at least works with a fixed species list and generates maps.

Some conclusions
There is a lot more to say about such projects, and there are many such projects. But I have tried to keep it short. Some conclusions at the end.

* On a local scale it can work quite well, although that shows only in a few countries in NW Europe (and maybe in the USA). That means that there are enough participants to create a sensible species distribution map.

But I think that going local is the only way it really can work. It is necessary to have experts to check incoming observations, and global experts are almost impossible to find. Even if an ID can be verified, it is hard to know if a location makes sense. Calopteryx splendens is not present in Spain, and if someone claims so in an observation, there should be extraordinary evidence.

* Joining the maps together on a worldwide scale, isn’t working very well. GBIF is disappointing: information from most locations is missing and in some cases existing information is wrong.

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December 28, 2010

My first twitching experience

Filed under: biology,bird,nature — takaita @ 09:13
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Birdwatchers (or twitchers) have it easy. Personally I am more into dragonflies. Of course there is information available about which species can be found where. But then still the area is a lot larger then the dragonfly, which means some searching and luck or experience.

Birdwatchers do it differently. Whenever there is a rare bird, they come from all places to “spot” it. Some even have a deal with their employer that they can leave their job to spot a new species for their list. They get notified on their mobile phone, by email or whatever means there is for instant communication.

This time I read about an invasion of Bohemian Waxwings. A bit of a rarity. Several individuals were spotted in my city, on walking distance from my home. So I walked there. There was only one left, but so easy to find.

People watching a Bohemian Waxwing

Permanently a small group of people was standing and staring. The people can be spotted from far away. And on arrival they kindly pointed to the top of the tree where the bird was. I took a photo as well.

Bohemian Waxwing

October 17, 2010

Damselfly Valentine

Damselflies copulate in the form of a heart. Valentine is about love too. So why not offer some of my photographs of damselfly couples as a very special valentine card?

Here are some. Order them from Redbubble.

Love Dance

Emerald Couple

Hold Me

July 22, 2009

Some pretty damselfly photos

Just to show to the world some of the Damselfly photos I made this year. If you are really impressed: click on the photo and order a print. But it is fine with me if you just enjoy looking at them here.

Red-eyed damselfly
Female Red-eyed Damselfly (Erythromma najas). The rain left some drops on her wings.

Green Emerald Damselfly
Female Green Emerald Damselfly (Lestes viridis). The sunlight shines on the grass from behind.

Emerald Damselfly
Male Emerald Damselfly (Lestes sponsa). Holding on to grass on a very windy day.

Common Winter Damselfly
Female Common Winter Damselfly (Sympecma fusca). A new generation has emerged. Winter Damselflies get through the winter as an adult, reproduce early in spring. The last of them can be seen until half June. Then the new generation emerges halfway July – this is one of them.

March 13, 2009

The Robin is a curious bird

Filed under: biology,bird,nature,things to do — takaita @ 22:30
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The Robin is a curious bird. I only found out since the time I usually carry around a camera on my walks.

European Robin

Currently I am more into dragonflies than into birds. Mainly because dragonflies are easier to photograph, but also because there are fewer species of them which makes them usually easier to identify. But because the dragonfly forum which I frequent, is on the same site as a bird forum, I sometimes read go to read that bird forum. Especially in the winter when there is not much to do at the dragonfly forum.

That bird forum is interesting. When I was young I had some interest in birds and bought a quality bird guide (from my own hard-earned money) in order to identify the species I saw. I still have that guide, but it is totally out of date. It seems that every species in that guide now has been split into several species or subspecies. Of course that is mostly done to satisfy the need of the bird watchers. They love to have a check behind as many species as possible. Did you know that there is a special word for this kind of people? They are called “twitchers” and it is not easy to become a fully accepted twitcher. There is a long trajectory, in which you first see only common species, then find out that there are rare species too – which you apparently start seeing everywhere until you realize that you are just fooling yourself (and others) and return to seeing common species everywhere with only very occasionally a rare species (after which that sometimes gets eaten).

An essential part of bird watching is bird listening. I remember reading a story on mentioned forum about someone who though he had seen an extremely rare species (at least for the Netherlands).  Because many bird species migrate between their summer and winter residence, bird listeners spend a small capital on microphones and spend days and nights on locations where these migrating birds fly over and occasionally come to the ground to feed. With these microphones they try to identify migrating birds by their sound. I don’t know how hard that is. I have trained myself to recognize about 10 or 20 bird species by their sound. It always makes me happy to hear the first Chiffchaff again in spring – and it can surprise me sometimes that others don’t notice. But the real twitchers take that to another dimension with their microphones. So this person wrote on the forum about a sound he heard, which was familiar, but then he swa the bird and it did not look like the species it sounded like. Then he remembered that there was this species which sounds like the familiar one, looks a bit like another (also familiar) species, but is very, very rare. Did he see that very very rare species? He could not be sure, because he heard nor saw it again. But he wrote a long story on the forum with remarkable details such as how many meters away he saw the bird (he measured it very precise, something like 84.5 metres), wrote about the sound he heard and what he thought about it at that moment and then what he thought when he saw the bird and if he could be sure if the bird he saw was the same one as the bird that made the sound. I was impressed. True, not everybody on the forum was as impressed as I was.

Anyway, these kind of stories are what keeps me interested in the bird forum. People want so much to see some rare species and at the same time are aware that they are probably mistaken when they think to have seen one. This tension between desire and self-control and an effort to be ‘scientific’ gives many contributions on this forum a great suspense.

The Robin is a curious bird. I only found out since the time I usually carry around a camera on my walks. First time was when I took the photo displayed at the top. Walking in the dunes I noticed a Robin. I prepared my camera in a reflex, but mosty expecting that the bird would have flown far away by the time I had it in focus. To my surprise it did not fly away, but kept sitting there, seemingly watching me.

Last week I must have remembered that moment, when I was in a city park which has some pretentions to be natural, and saw another Robin no too far away. The thought came to me that I should just stay there with my camera ready until the bird would come to watch me from a bit closer. Half to my surprise that was exactly what happened. The bird came to me to have a closer look. And this was the result.

Robin

December 11, 2008

Promiscuity of males and females

Filed under: biology,mystery — takaita @ 20:49
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Sometimes a magazine makes about poll with a question involving the promiscuity of its readers.  Such a poll is of course only meant to write an interesting headline for one of the issues of the magazine. And an interesting headline is of course that there are differences between the promiscuity of the two human sexes.

Differences in promiscuity between males and females are however non-existent, at least when it comes to heterosexual partners. That is because the amount of males and females on this world are about the same. In every heterosexual contact, both a male and a female are involved.  To make the math a bit easier, let’s simply divide humanity in two pools: one of females, and one of males. With every heterosexual contact, each pool gets a point. There is no other way, because a heterosexual contact always involves both a male and a female.

After a certain period of time, the average number of heterosexual contacts per individual can be calculated by dividing the total number of points of a pool by the number of individuals in that pool. The math is easy. Both pools have the same amount of points and both pools have the same amount of individuals. Ergo: the average male has just as many heterosexual contacts (and partners) as the average female.

The really interesting thing is why polls sometimes show otherwise. The first thing that comes to my mind is that for magazines it does not make an interesting headline if males and females are just as promiscuous.  Magazines might “interpret” the poll results  just to make an interesting headline.

Other things might play a role. Maybe some very promiscuous individual are excluded from the polls, for example  prostitutes. If males count their contacts with prostitutes, but the prostitutes do not participate in the poll, then the poll would say that males are more promiscuous than females.  Also other non-representative samples are thinkable. Maybe the readers of the magazine (=respondents to the poll) do not form a representative sample of the population.

Another source of bias can be in the minds of people. Maybe women remember more of their sexual partners. Males don’t count those they have forgotten about, maybe they were not important enough to remember. Such a thing would result in females giving a higher amount of sexual partners than males. Or maybe it is the other way around. Another thing might be that males count something to be sex, which females do not count to be sex. How far do you go before you call it sex?

Anyway: if polls show a difference between the promiscuity of males and females, then the conclusion that males or females (whatever the outcome was) are more promiscuous is false. The really interesting question is why such a difference is reported.

November 29, 2007

Does the Great Tit have a mask in UV-light?

Does the Great Tit have a mask in UV-light?
Does the Great Tit have a mask in ultraviolet light? This photo has been processed to enhance the blue on the head of the bird. It was taken by a regular digital camera (Canon 350D) without UV-filter, while the bird was in full sunlight. The Great Tit is supposed to have a coal black head, and that is also what our eyes see. But even a normal camera can capture UV-light, and will probably show it as blue.I did some searches and found a research paper that mentioned the Great Tit indeed has a crown that reflects UV-light. But I could not find out if there is a visible pattern on the head of the Great Tit in UV-light. If the blue really is caused by UV, then the black parts can be some shadows, or they can be a color pattern that only shows up in UV. It seems that the Great Tit has a black beard and a black mask. I have some more photos of the same individu which display a similar pattern.

July 20, 2007

I said “thank you” to an insect

Filed under: biology,nature,photography — takaita @ 19:49
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It’s true, I am into dragonfly photography. It must have started last summer, when I discovered a population of Banded Demoiselles (Calopteryx splendens) quite close where I live. Amazingly that is in the middle of a city. At least I think it is amazing. Such pretty blue-winged damselflies are supposed to live in far-away countries or areas that can only be accesed with great difficulty. Now I just come home after work, take my camera and after a short walk over paved streets they are there.

That was last summer. This year they were back. The damselflies I mean. Last summer I made hundreds of photos (most of them not worth keeping). This year I found another spot close by with dragonflies, with other species. So I have divided my attention, resulting in a lot less photos of the Banded Demoiselles. I know that the year is not over yet, but the Banded Demoiselles have had their peak, now there are only a few of them, sometimes.

On one of the days that I visited “my” population, I saw a male Banded Demoiselle sitting in the sun on a leaf. As I approached with my camera it tried to hide, but then it probably made up its mind and decided that I was harmless. It just sat there and it let me photograph it.

Banded Demoiselle (Calopteryx splendens)

Banded Demoiselle (Calopteryx splendens)

After I was finished taking photos, I looked at the damselfy still sitting there, and I said aloud “thank you”. Then I realized it was stupid to say that to an insect. But I meant it anyway.

March 10, 2007

The beneficial prion, evolution and the origin of life

Filed under: biology,idea — takaita @ 23:01
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This article is speculating about evolution of species which is not based on changes in DNA.

Horizontal Gene Transfer
Currently, evolution is seen as DNA-based, because DNA is regarded as the only part of organisms that is inherited. DNA is the blueprint for an organism in the next generation. Richard Dawkins, in his book “The Selfish Gene” even shifted the focus of natural selection from complete genomes (species) to single genes. There is recently some unrest about Horizontal Gene Transfer (HTG, also called Lateral Gene Transfer). HTG is troubling, because it impacts our view of the tree of life. If genes are tranfered from one species to another, then the Tree of Life no longer has only branches (where species split of), but also knots (where the genome of different species are mixed to produce a new species).

Horizontal Gene Transfer is however not the only reason that the Tree of Life might have knots. There are researched cases of new species developed from hybridization of two other species, for example in the butterfly genus Heliconius and cichlids in Lake Tanganyika (fishes in East Africa).

The beneficial prion
A prion is an infectious protein. Some diseases are caused by prions, such as the Mad Cow Disease. A protein is a long chain of amino acids. Proteins can carry out their function in a cell because they have a special three-dimensional shape. Some proteins can be folded in different shapes. When such a protein has been folded differently, it will no longer be able to carry out the function it used to do. Prions are proteins that are shaped differently and also have the ability to refold other proteins into their own shape. The latter makes prions infectious. Once a single prion comes into a cell, it folds another protein. After finishing the job, there are two differently shaped proteins which each can fold another protein into their own shape. Then there are four, eight, sixteen etc of them.

It is interesting to notice that prions are self replicators. They require a very specific substrate which is only found in certain living cells.

Prions are usually a disease. They disturb the normal functionality of proteins and replace it with another (or no) functionality. That is what they have in common with mutations in the DNA, a change in a gene produces will produce a changed protein and only very rarely this protein has a beneficial effect on the organism. However these rare beneficial mutations in DNA are assumed to drive evolution.

Are there any beneficial prions? It is thinkable, and in fact there is an example of it. In yeast, a prion has been identified which in certain circumstances is beneficial, see for example Prions act as stepping stones in evolution. The remarkable thing is that the effect can be passed on to the offspring.

Inheritance of prions
It is important to notice that reproduction of organisms does not only involve the passing of DNA. Sexual reproduction involves an egg and a sperm cell. A sperm cell is assumed to be just DNA, encapsulated in machinery to transport the DNA into an egg. The egg however contains the complete machinery of a living cell: organels, proteins, ribosomes. That is needed because DNA on its own can not replicate, DNA on its own isn’t alive. DNA needs the machinery of a cell for reproduction.

A female who has acquired a beneficial prion might be able to pass this prion on to her offspring through the egg. And the offspring will then also pass this prion to the next generation. The prion is inherited.

There it is: a non-DNA-based mutation which is inherited.

Co-evolution of self-replicating systems
Continuing to speculate, I would like to consider living organisms not as just a machinery to replicate genes. This latter view, which has been promoted by Richard Dawkins in his book The Selfish Gene, seems too limited. There is more to an organism then just the manifestion of the information stored in the DNA. There is more inherited then just DNA.

There are several theories about the origin of life (I wish to ignore the creationist theories). They all agree on one point: it started with something able to self-replicate. In some theories that first thing is RNA. In other theories it is metabolism-first.

I like to think about the origin of life in terms of co-evolving self-replicating systems. There was RNA, there were bubbles of lipids, there were reaction chains (metabolism) and they all were self-replicating independently. RNA and reaction chains which would get into a bubble of lipids formed a self-replicating system and they co-evolved to living cells. The self-replication of each element became heavily dependent on the self-replication of the other elements. In the safety of the cell, RNA has partly been replaced by DNA.

A beneficial prion is a inheritable mutation in the metabolism-system, but not in the DNA-system. The different self-replicating subsystems of a living cell still have the possibility to evolve. Of course the DNA-based evolution is the most obvious. The blueprint model is the easiest to understand. It is the subsystem which has been subject to research when it comes to evolution.

What to research
I admit that there is a lot of speculation in the above. It needs research. And here are a few ideas for that. The trouble is that all living organisms are supposed to have evolved from a single common ancestor which already had evolved considerably. This Last Universal Common Ancestor (LUCA) must already have been pretty good at self-reproduction, because it outcompeted all rivals at the time. It must have had a well-developed integration of the different subsystems. What we should be looking for is examples of differences between species in the integration of the subsystems. Because we are facing the situation that all living organisms stem from this well-integrated LUCA, it is probably impossible to find a totally different way of integration. Although there is an exception: viruses. Viruses are not considered to be part of the LUCA ancestry. The origin of viruses is speculative.

The proteins of a metabolism-chain are currently seen as the result of DNA-based evolution. If they are the result of co-evolution between DNA and the metabolism-chains, then the metabolism-chains might have adapted to the DNA. As DNA (indirectly) produces proteins, some metabolism-chains might have changed to use available proteins. This opens the possibility that related metabolism-chains in different species rely on totally different genes. Are there any examples of this?

Are there more beneficial prions then the one found in yeast. Are there any proteins that act like prions, but are so beneficial that every member of a species has this prion.

Can viruses be considered as a different result of co-evolution of subsystems?

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