This is my abortion

We’ve all seen the protesters; the banners, placards and pictures of all too often, still born babies or fetuses with severe birth defects deeming them not compatible with life. They do of course have the odd fetus too.

The lengths of term can often be so off, they can only be intentional lies.I’ve seen an anti-abortion poster of a near fully formed fetus with the caption stating it was 6 weeks.

These are to convince us of the messy, disgusting, disturbing and murderous action of abortions. Enter Jane.

“Recently, I had an abortion.

Lining the street in front of the clinic were a dozen or so protesters. They held up large banners with anti-abortion slogans, religious iconography, and images of dead babies.

Just past the bulletproof security doors, the graphic nature of that imagery haunted me in the waiting room. What would my abortion look like? I decided to secretly document my abortion with my cell phone.

At 6 weeks of pregnancy, my abortion looked very different than the images I saw when I entered the clinic that day.”

You should go to the site and check out the comments, too.

 

 

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Channel 4s Documentary on GMOs, Animal Farm

“SHEEP WITH HUMAN ORGANS, GOATS THAT PRODUCE SPIDER WEB IN THEIR MILK, RABBITS WITH FLUORESCENT EYES AND AN ALLOTMENT OF GROWING HUMAN NOSES: WELCOME TO CHANNEL 4’S ANIMAL FARM”

and blogger with a foaming mouth, with advertising like this of course I was excited to watch Animal Farm.

The three part series covers the state for genetic modification and engineering today, from selective breeding to transgenic species.

Presented by Dr Olivia Judson a biologist and a food critic, Giles Coren the documentary seems greatly bias against GM products for the out set. The two presenters make their views clear at the start – Doc is pro, critic is, well, a critic. To me, the narration also seemed skewed against GMOs.

The brand of documentary requires serious objectivity, which granted is not as sexy or easy to sell as Frankenstein scientists scaremongering. However, GMOs are the future and will be required more and more as the population continues to grow and that’s that this documentary lacked. Serious refection as to why scientists are creating these animals and crops.

Increase crop yield, reduce land requirements. Simple, right?

Wrong, the lack of refutation towards Giles comments was annoying and the biggest issue with this documentary, if someone makes a derogatory comment on either side it should be, specially in a documentary, be rebutted.

Regardless, I did enjoy the documentary but more due to the fact that it does show some pretty amazing creations. From glow in the dark pigs to a herd of cloned cattle to mega muscular cows the show is filled with curious things that are pretty amazing. Watch it!

It’s available of 4OD for viewers in Ireland and the UK here. If you’re outside IRL and the UK you might find it somewhere else.

Asking questions about animal behaviour

There are many approaches to asking questions about animal behaviour. Firstly we should have an idea in mind defining what behaviour is.

Behaviour can be defined as;

All observable processes an animal responds to in the external world or in the internal state of its body & Any action that can be observed and described, and must be observable and describable.

The latter is a relatively broad definition, ranging from slight muscle twitches to sophisticated displays.

Methods in asking questions about behaviour

Repeatable measures

There is an inherent consistency to many behaviour patterns displayed by animals. Repeatable measures allow for reliable repeatable observations of individuals, of a species. This is because members of a species share behaviours that are general and recurring. These patterns are identifiable activities, recognisable and distinguishable from other identifiable patterns preformed by the species.

Functions of behaviours

Animals appear to do things in order to achieve something, i.e. carry out particular behavioural patterns or sequences of behaviours that have a functional response, and this is reflected in how we describe behaviour:

  • Searching for food

Hiding from predators

Attracting a mate

Displaying to a competitor

The means to an end

We can interpret apparent purposefulness as indicating some kind of internal representation of what has to be achieved, this could be a mental image; a squirrel sets out with an image of food in its head or a bird weaves twigs to its internal mental notion of a nest.

Goal directedness (Goal directed behaviour) describes this purposefulness based on internal representations. An example: The goal directed digging wasp digs burrows and stocks them with provisions for their larvae, when the burrow is finished and the larvae and rations are in place, the wasp moves on to dig another burrow. But how does the wasp know when a burrow is finished? Perhaps she works to an internal representation of what a burrow should be, expressing goal directed behaviour or she may simple be digging down for X number of minutes and laterally for Y number of minutes.

A manipulative experiment was carried out, artificially extending and filling in burrows digging wasps were working on.

The experiment showed; wasps would extend burrows which were filled in, and fill in burrows which were artificially extended. This indicates the digging wasp exhibits goal directed behaviour and have an internal representation, some criterion for deciding when a burrow is finished.

Goal achieving behaviour is where an animal has no internal representation of its goal. The goal is only recognised when it has been encountered, woodlice express goal achieving behaviour.

Woodlice are found in dark moist environments, but do not set out to find them. If an individual finds itself in a bright and dry environment, it starts walking. The louse moving somewhat randomly does not know where it’s going, just where it prefers not to be. The brighter and drier the conditions of this unsavoury environment the quicker the woodlouse will move. When the louse finds itself in a sufficiently dark and moist environment it will recognise this as where it wants to be. The goal is recognised once it is encountered.

Locomotory responses are taxes and kineses: Taxes are orientated responses – Phototaxis is a direct response to light. Kineses are non-orientated responses – Hydrokinesis is a somewhat random response to moisture.

There are different levels at which you can study animal behaviour:

Tinbergen is one of the founders of the modern study of animal behaviour for which he won a noble prize in 1973. Tinbergen split the study into four questions:

1)      Mechanism: how is a particular behaviour achieved? How does an animal use its sensory and motor abilities to achieve/modify its behaviour? It’s the mechanism within the animal of the body itself.

2)      Development: How does behaviour develop? How does an animal’s behaviour change during growth in response to experience (a = gene, b = environment: it could be a or b, or an interaction between a + b) e.g. pollutants in the environment can change an animal’s behaviour.

  • Mechanism and Development approaches are proximate approaches looking at proximate measures in the animal to discover how behaviour is achieved and developed.

3)      Function: What is the behaviour for? How does it promote survival and reproduction? How is it selected for over time?

4)      Evolution: Where has the behaviour come from? We can compare the behaviour of closely and distantly related species, what does this tell us about the origins of the behaviour? In birds, simple pecking can evolve into complex displays, for example.

  • Function and Evolution are ultimate approaches relating to the survival, reproduction and evolution of the animal.

There are several techniques used to answer Tinbergen’s questions:

1)      Experiments: Manipulating variables of interest and controlling or remove confounding factors. Manipulative experiments are the most powerful way to distinguish between rival explanatory hypotheses.

2)      Observations: Useful when manipulation is not possible or unethical. You can record unwanted variables and control in subsequent analysis’. Analysis must be driven by a priori predictions e.g. you should always test specific hypotheses.

3)      Comparison: You can compare across different species and environments. Different selection pressures are expected to mould behaviour in predictable ways.

4)      Theoretical modeling: Mathematical equations or computer programs can take essential elements of a system and can; make precise predictions, simulate outcomes and compare these to the real world.

The road to the modern study of animal behaviour.

Ethology led to behavioural ecology using hypotheses driven investigation, it is the biological study of behaviour. Ethology is an all encompassing European approach to how and why animals achieve things, covering the four different aspects. A wide range of species were studied in their natural context. It gave detailed descriptions of behaviour but declined due to lack of experimental support.

Comparative psychology is the American approach looking for general laws of behaviour applicable to all species, focusing on mechanisms and development. Contrasted with Ethology, by studying adaptive specialisation, with an emphasis on fixed behaviour patterns.

Behavioural ecology is the dominant field in the study of animal behaviour. It is a mixture of Ethology, Ecology and Evolutionary Biology focusing on questions of evolution and function. It’s a very successful predictive science e.g. Evolutionary Stable Strategies (ESSs), where adaptive decision making is often frequency dependent. Criticism include: Has a reduced focus on mechanism and development and it views many aspect if an organism as a perfect adaptation to something.

Evolutionary psychology is a relatively new discipline and primarily focuses on human cognition. In the past psychologists talented to focus on mechanisms of learning but ignored it adaptive value, how it evolved over time but have since recognised the importance of natural selection.

Is the study of animal behaviour what you thought it would be?

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  • Barnard, C (2004). Animal Behaviour: Mechanism,  Development, Function and Evolution. Pearson Education  Limited, Essex.
  • Salonen, A. & Peuhkuri, N (2006). The effect of captive  breeding on aggressive behaviour of European grayling,  Thymallus thymallus, in different contexts. Animal  Behaviour 72: 819-825

Could Recent Genetic Findings Completely Alter The Way We Classify Life?

1837 Darwin wrote "I think" above the first evolutionary tree.

That’s a bit of a stretch, but geneticists believe they may have found evidence that could alter the foundations of the tree of love…

The first tree of life was sketched by Charles Darwin in 1837. Its purpose was to represent the how all species are related, but still connected. Darwin regarded evolution as a branching process, where populations alter over time and may speciate into separate branches or terminate by extinction. Darwin thought the most appropriate way to represent this was a large branching tree. He was right; and we still do use a tree of life,   phylogenetics is the study of how different species are related, using DNA sequencing, the subsequent relationships are represented in a phylogenetic tree.

The point where the three domains join on the tree signify the first major evolutionary divergence of very early life forms on earth, the three domains are; Archaea, Bacteria and our domain Eukarya.

Woese's three-domain system, 1990

A team of geneticists lead by Jonathan Eisen at the University of California, Davis Genome Centre along with Craig Venter of the J. Craig Venter Institute, Rockville have recently made a brave claim, they believe they may have identified genes so exceptionally unique; they are only minimally related to early cellular life, which may potentially define a new, fourth biological domain of life. The last time the domains were shifted around was only in 1990, by Carl Woses. Woses reclassified the Kingdoms Eubacteria and Archaebacteria to Bacteria and Archaea respectively, he also grouped Protista, Plantae, Fungi and Animalia into the domain Eukarya.

The majority of species on earth are very small and do not contain the quantity of DNA required for genetic analysis. So to make an accurate phylogenetic tree, the species need to be  cultured, in a lab where the colonies contain enough DNA to accurately analyse a species genome . But there’s another road block, the vast majority of these microscopic species simply will not grow in a lab.

Eisen and Venter, unable to culture the species turned to a relatively new technology, metagenomics, which provided a way to gathering genetic data by sampling directly from the environment. The technology was impressive, Eisen said, it can “sequence the crap out of any DNA samples”.

Venter's Yacht

Venter voyaged across the globe obtaining samples, using this metagenomics technology. The Global Ocean Sampling Expedition provided some very interesting results, genes called small subunits rRNA; recA, and rpoB were discovered and are almost completely dissimilar to all other known genes.

Metagenomics is a messy process; the organisms are completely destroyed while the genes were being retrived from the samples. So, we have the genes but we don’t know which organism they came from.

The team narrowed down the potential mechanisms that may have lead to the existence of these evolutionarily novel gene sequences; to be either:

1) the possible genetic sequences from novel viruses

2) the sequences may indeed be from a fourth major branch on the tree of life.

Eisen said “we do not have a conclusive explanation for the origin of these sequences. But as far as we can tell, they truly could be from a fourth major branch of cellular organisms”.

However, 4th place at the Domain table may not be Eisens for the taking.

(L to R) Archaea, Bacteria, Eukaryotes, and Giant viruses

A team of scientists in France have been studying viruses called Nucleocytoplasmic Large DNA Viruses (NCLDV). The virus is very unusual. It has >1000 genes, a huge genome for a virus, 100 times the genes of your general, every day flu virus, which has maybe 10 genes. NCLDV are indeed viruses though, they hijack host cells as all viruses do. Didier Raoult et al. compared one set of genes in giant viruses to their counterparts in other families. The genes are very different, so much so that some scientists are arguing, that the giant viruses, Mimivirus, should represent the fourth domain of life.

Perhaps the fourth domain name will go to another taxa entirely, I’m going to stick with Occam’s Razor on this one, but you never know maybe Thomas Cavalier-Smiths recent 2004 organismal classification will catch on after all, he rejects the three-domain system entirely, I wonder where that would leave us?

 

 

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The project lasted six years and the paper was published in the free online science journal research PLoS One (Reference: DOI: 10.1371/journal.pone.0018011) (Direct Link: http://tiny.cc/gx79d)

Also lead author Jonathan Eisen instead of doing a press release, blogged it: http://phylogenomics.blogspot.com/2011/03/story-behind-story-of-my-new-plosone.html

What’s this SuperMoon tat?

I dislike the word Supermoon very much, it’s in no way descriptive and somewhat childish.

The tides are the rise and fall of the oceans, caused by the combined forces of the moon and sun along with the rotation of the earth.

The earth and moon are both substantially large objects in space and have a gravitational pull that is significant enough to keep the moon in orbit around our planet. The gravitational force of the moon also attracts the surface of the ocean, forming a bulge.

The moons gravity pulling on the oceans

As both the earth and moon are rotating in space, the centrifugal force generated causes another ocean bulge to form on the far side of the earth.

The centrifugal force causing the second bulge on the ocean.

Therefore, the oceans of the earth are not uniform but form two bulges on the earth (See image below).

The size of the tides depends on where the moon and sun are in relation to the earth.

Aside from simply ebbing and flowing, the height of the tide is changeable depending on the position of the moon. When the earth, moon (full and new moon phases) and sun line up (called syzygy) the gravitational forces combine and cause high tides to be higher and low tides to be lower, these are Spring Tides.

Positioning of the earth, sun and moon (full and new phases) causing spring tides.

When the moon is in its first and third quarter phases (image below) the suns gravitational pull is perpendicular to that of the moon, stealing water created by the moons pull and lessening the height of high tides and increasing low tide level.

Positions of the earth, moon (1st and 3rd phases) and sun causing neap tides

Now, these are the celestial forces we’ve all come to know and love which work in cycles over a short period of time. However, the moons orbit around the earth is not circular but elliptical, where sometimes it’s closer to the earth and sometimes farther.  This is the reason the moon sometimes appears larger or smaller in the night sky and can appear a great deal large, 12 – 14%! Today, March 19th 2011 the moon will appear it’s largest in nearly 20 years.

Difference between lunar perigee (near) and apogee (far)

Today, March 19th 2011 the moon will appear it’s largest in nearly 20 years, which some people fear will cause an increase in earthquakes and volcanic activity.

As we’ve seen above this lunar perigee will give us above average high tides and lower lows but by only a few centimetres, not even 3cm! Though the moons gravity does affect us, it’s relatively weak and no match for earth’s internal processes which do cause earthquakes and volcanic discharges.

Today we will experience a high tide higher than average and a low tide lower than average (twice), but don’t cower and hide from the geologic forces the pseudoscientists would have you believe are a’comin.

Forget all that, go look at the moon, it’ll be big and cool!

A small aside: Strictly speaking, perigee and apogee are the terms given to the positions of the earth in it’s orbit in relation to the sun for example, celestial bodies  have their own personal suffixes, the moons being lune. Today the moon will be in perilune.

Of politicians and ditches

Studying an environmental science isn’t easy, we spend years studying to get a grasp of complex systems so to expect anyone to just understand in a 5 minute conversation is quite unfair. This post is a remark upon the irrational manner in which local councilors have reacted to the allowing hedges to grow in summer, allowing among others, birds to nest.

We know when political figures think they can gain a vote or two, logic and reason take flight only to be replaced by ridiculous arguments and to be honest, they are not usually eloquent.

The Anglo-Celt reports that Cavan County Council attacked The National Wildlife Service over the dates which hedgerows may be cut.

Under section 40 of the 1976 Wildlife Act, as amended by Section 46 of the Wildlife Amendment Act, 2000, it is forbidden to cut or remove hedgerows or destroy other vegetation during the bird nesting season, from the 1st of March to the 31st of August each year.

Cllr. Danny Brady (FF) (no relation) has stated that most farmers comply with the rules when it comes to hedge and verge cutting. However, there were some who didn’t comply and should expect a visit for The National Wildlife Service. Though Cllr. Brady doesn’t appear to agree, it would seem from the Anglo-Celts article that Cllr. Brady does not care these people broke the law.  Is anarchy this Finna Fáil members approach to society?

Brady does state the danger of over grown hedges, which of course is very real and being from rural Cavan, I know them only too well. Which was a more sensible argument than Cllr. Shane P. O’Reilly (FF) made it comes down to what’s was more important – the life of a swallow or the life of a human. Which is basically a false dichotomy, humans and swallows can co-exist quite peacefully I think you’ll agree.

The general departure from reason is where I take issue. It appears a pack mentality set in on the councillors over this topic, everyone knew about this problem, it’s a disgrace, it an attack on rural Ireland, it’s this and that but IT’S THE LAW! And has been for some time, amended ten years ago from a 35 year old wildlife act. Why is it only now that this issue is being raised?

This isn’t a recent problem; hedgerows have always grown out in the summer to be cut back in autumn, since I was a child anyway. The problem is the increase in traffic in rural areas, all the houses lining once beautiful countryside need entrances, but the councillors didn’t think of that when they were granting housing permissions left, right and centre, they didn’t think an increase in population will require an increase in spending to upgrade and maintain services. Which isn’t done.

We, living on an island have inherited a quite unique heritage of Flora and Fauna, in recent times more and more species populations have started to decline and of course there have been extinctions, but we now know the importance of small seemingly insignificant habitats, they are vital homes for hundreds of species. If the councillors cannot understand the importance of biodiversity, then should they really be standing for positions of power in a constituency that is heavily reliant on agriculture? And in what field exactly have these councillors been educated? Surely none have a biological or agricultural background. Why did they wait until September to raise this issue? The hedges are all nice and trim now.

Here’s a nice paper on hedgerows in Ireland by Notice Nature, if you fancy reading up. Perhaps some of the councilors will read it?

FYI, if you didn’t know already 2010 is the UN designated year of Biodiversity.