Category Archives: Stuff In General.

Things that don’t fit into any other category.

Intro to Schizo

A while ago, I saw an Indian movie in which the female protagonist was afflicted with visual and auditory hallucinations, bizarre paranoia and delusions. Of course, there was a song and dance sequence to accompany it. This movie spurred me to go online and look for more information regarding this ‘madness’. I learnt about Schizophrenia and later about Autism spectrum disorder. There is a TED talk by Jill Bolt Taylor who talked about the most fascinating things in a very interesting manner. You can find that here.

Ever since, I have made an effort to know more about this interesting disorder and today, I wish to introduce this topic to you. Before we do, I believe it is important to understand the structure of the brain. You can find some information here which has a fun, interactive way of learning about the basics of brain and its function.

It is important to know that Disassociative identity disorder (Usually referred to as split personality or multiple personality disorder) is different from Schizophrenia. People afflicted with this disorder, as described above, suffer from hallucinations, delusions, behavioural problems etc. which makes it difficult for them to be accepted in the society.

Most medications prescribed for patients with this disorder belongs to the class of molecules which have a capacity to suppress the activity of dopamine (sometimes serotonin as well) receptors. Clinical studies relating schizophrenia to brain dopamine metabolism have ranged from controversial to negative, with HVA levels in the CSF the same for schizophrenics and controls. There is a dopamine hypothesis theory on the internet, have a look.

Dopamine receptors (D1-D5) are G-protein coupled receptors meaning they work through secondary messenger system (like Adrenalin). Serotonin receptor aka 5-HT receptors are ion gated channels. I remember writing a post about ion channels. Check it out!

Let us see where dopamine is present in high quantity and what it does to the system. The ventral tegmental area (VTA, situated in mid brain) contains the largest group of dopamine neurons in the human brain. The main function of dopamine is to set a threshold for executing behaviors. Meaning, if a certain high level of dopamine activity occurs, a lower impetus is enough to evoke a given behavior. As a consequence, high levels of dopamine lead to high levels of motor activity and “impulsive” behavior; conversely, low levels of dopamine lead to torpor and slowed reactions. Another function of dopamine is to ‘teach’. If an action is followed by an acitivty, it alters the brain in such a way that same action becomes easier to execute if performed at a later time. There are several theories surrounding how this occurs. Most of them involve basal ganglia modifications.

In my next post, I shall talk about the controversy surrounding usage of anti – psychotic drugs for treatment of Schizophrenia.

Till then,
Ciao
Avi

In which I admire stunning glass sculptures – part un.

OK, this is a bit of a tangent compared to the usual serious business that is characteristic of this blog. However, it is still extremely science related, and focuses on the aesthetics of what science may reveal to us.

I am not really talking about Charlie Murphy’s glass casts of naughty bits on display at the Wellcome Collection in London, either, fascinating as they are… Instead, I am talking of Luke Jerram’s Glass Sculptures.

Luke Jerram is an artist from Bristol who produces installation art and glass sculptures, and it is his glass sculptures that I am going to be focusing on. He has basically created some rather stunning glass sculptures of viruses and bacteria and I intend to present some photographs for your edification below.

I went to the Wellcome Collection a few weeks ago and I found this sculpture of the Swine Flu Virus that he’d concocted.

Swine Flu Virus Sculpture by Luke Jerram, top view. Photo taken at the Wellcome Collection by Exploreable.

Same sculpture as above, side view.

That isn’t all there is to it, though, he’s produced a whole set of sculptures under the aegis of the “Glass Microbiology” collection (unfortunately, all of those aren’t at the Wellcome Collection) and as a result I will have to use the good old internet to supply thee with the eye candy thou crave…

The following are from the Glass Microbiology website at http://www.lukejerram.com/glass/gallery

E.coli sculpture

E.coli again.

Those two are of E.coli.

Swine-Flu (Oval) - Close-up.

Swine Flu (Oval) Full unit

Those two are of the Swine Flu Virus.

HPV closeup

HPV from a distance

Those two are of the Human Papilloma Virus

Malaria Sculpture

That one is of Plasmodium vivax, the organism that causes malaria.

What follows is a collection of videos featuring those sculptures

Here’s a BBC interview clipwhere Luke speaks about what motivated him to produce the collection. I think it is excellent, except for the gaffe where E.coli has been labelled as a virus.

Finally, here’s a clip that shows some of the making of Jerram’s HIV sculpture.

If you get a chance to go to one of his exhibitions, then please do!

In the future, I may try to do a post on Annie Cattrell’s work, which is also quite exquisite.

Cheers,
Exploreable.

Ion Channels – a brief overview

I have been reading a book called “Principles of Neural Science” by Eric Kandel. I thought it would be a good idea to write a summary of a chapter that I read recently and tell you all about one the most important structures present in the cytoplasmic layer – Ion Channel. Ion channels allow the movement of ions across cell membranes, and therefore fundamental physiological processes such as muscle contraction.

Ion channels are membrane protein complexes. They are embedded in the lipid bilayer which is made up mostly of phospholipids, which have a hydrophilic head and two hydrophobic tails. The lipid bilayer is the barrier that keeps ions, proteins and other molecules where they are needed and prevents them from diffusing into areas where they should not be. They make good barriers because they are only a few nanometres thick, they are impermeable to most water-soluble (hydrophilic) molecules and are particularly impermeable to ions.

Definition: Ion channels are pore-forming proteins that help establish and control the small voltage gradient across the plasma membrane by allowing the flow of ions down their electrochemical gradient.

Concept of Open/Close

Ion channels provide a high conducting, hydrophilic pathway across the hydrophobic interior of the membrane. The channel, or pore structure, is said to catalyze the ‘reaction’ of transporting charged molecules across a low dielectric medium. The ‘catalytic site’, the central channel, is either open or closed. The conformational change between closed and open state is called gating. Channel gating is controlled by external factors like enzymes are controlled by modulators and effectors.

Types of Ion channels

There are over 300 types of ion channels in a living cell. Ion channels may be classified by the nature of their gating, the species of ions passing through those gates, the number of gates (pores) and localization of proteins.

  • Ligand gated channels
  • Voltage gated channels transmembrane potential
  • Second messenger gated channels
  • Mechanosensitive channels
  • Gap junctions

Structure of a channel

Channels differ with respect to the ion they let pass (for example, Na+, K+, Cl), the ways in which they may be regulated, the number of subunits of which they are composed and other aspects of structure. All ion channels are complexes of transmembrane proteins, sometimes they contain cytoplasmic subunits, often they are glycosylated. The 3-D structure of most ion channels is not known, with two notable exceptions, porins and a K-channel, both of bacterial origin. There exists, however, a multitude of biochemical and functional data, combined with mutagenesis experiments that give information about the transmembrane topology of these proteins, dividing it into transmembrane segments and extramembraneous loops/domains. Often size and location of loops on one side or the other of the membrane can be determined by chemically modifying the protein and analyzing which amino acids have been modified.

For example: Nicotinic Acetylcholine Receptor – nAChR

The structure of nicotinic acetylcholine receptor, has been determined to 0.9nm resolution by cryo-electron microscopy. The nAChR is a heteromeric glycoprotein complex composed of five integral membrane proteins in a stoichiometry of α2βγδ.

The five subunits are arranged in a circular fashion around a central hole that provides an ion pathway across the post-synaptic cell membrane. The pentameric complex has a fivefold pseudo-symmetry because its subunits are not identical. Acetylcholine binding induces the opening of the channel.

Fig: Pentameric arrangement of nAChR subunits

Problems associated with Ion channels

There are a number of chemicals and genetic disorders which disrupt normal functioning of ion channels and have disastrous consequences for the organism. Genetic disorders of ion channels and their modifiers are known as Channelopathies.

For example:

  1. Human hyperkalaemic periodic paralysis (HyperPP) is caused by a defect in voltage dependent sodium channels.
  2. Dendrotoxin is produced by mamba snakes, and blocks potassium channels.

That is it for now. I hope you liked what you read. If you are interested, I could always find more references and papers to support the above data.

Cheers

Avinash

Deadly Organism of the Fortnight: Phoneutria nigriventer.

This fortnight’s post has been a bit late in coming since I’ve been caught up in some academic work, nonetheless, here is a selection that will fuel the fears of arachnophobes. Phoneutria nigriventer is a species of Brazilian wandering spider, and while it is not as venomous as another species in the same genus, P.fera, I’ve chosen it for examination because it is well documented.

Phoneutria nigriventer; threat display.

As with the other candidates I’ve posted about in this series, it is venom that makes it deadly.

The venom’s main component is a peptide called PhTx3 , which is capable of blocking calcium channels that maintain the ion gradients needed by muscles to be able to contract properly following neural activity by motor neurons at the neuromuscular junction. This means that it can inhibit acetylcholine signalling and therefore trigger paralysis. If you wish to delve into the literature here, please see
this paper which details the evidence for the venom being a calcium channel blocker.

There is also a rather unsavoury aspect to P.nigriventer envenomation; it can induce priapism in humans, which is a condition where an erect reproductive appendage doesn’t return to a flaccid state for an abnormally long time; in this case, symptoms can apparently last for hours and may lead to impotence as an aftereffect.

This however also makes it a suitable research candidate for treatments of erectile dysfunction, go figure.
If you need help with that, here is the research paper that describes the confirmation of the activity of one of the components as a potentiator of erectile function in mice http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3019117/?tool=pmcentrez

If you’re interested in going through the amino acid sequences of the proteins in the venom, you may find the following database retrieval results sheet useful http://www.ncbi.nlm.nih.gov/protein?term=Phoneutria%20nigriventer

So guess that is it for this fortnight’s deadly organism of the week.

One of us has just completed another orbit of the Earth round the Sun…

Here is one more general article that is very different in focus from the general trend of articles on the blog; the reason is this, it is Julietooo’s (who is one of the authors on the blog) birthday and I (on behalf of myself and the other authors on the blog) would like to express my thanks to her for her contributions to the blog, all of which have been lucid exhibitions of skeptical analysis pertaining to very relevant social issues and also wish her a happy birthday while doing so.

Her articles have been read more than the articles of any other author, and they have achieved highlights such as being featured on a BBC Buzz page and being linked to blog posts by PZ Myers on Pharyngula, as well as being tweeted to his followers by James Randi, which I think is impressive list for articles on a blog that is still very much in its infancy.

Have a good ‘un, Juliet.

Cake

PS – Please keep those articles coming in the future too, that’ll be ideal 😛

PPS – Now I’ve done this orbit round the sun thing too, you may now thank me now for the information in my posts, or alternatively, for curing your insomnia/sleeping difficulties.

– Exploreable.

Will Indian Society Finally Wake Up?

Hello there,

It isn’t often I blog about social issues but the one we have at the moment is one I deem important enough to the extent that overlooking it would be impossible. We are talking about a further, alarming, skewing of the child sex ratio in India, as reported by in a research paper in the Lancet. The paper in question is “Trends in selective abortions of girls in India: analysis of nationally representative birth histories from 1990 to 2005 and census data from 1991 to 2011, Jha et al, The Lancet, doi:10.1016/S0140-6736(11)60649-1″ which you may access for free upon registering on The Lancet website here

The abstract of the study reads thus

Background

India’s 2011 census revealed a growing imbalance between the numbers of girls and boys aged 0—6 years, which we postulate is due to increased prenatal sex determination with subsequent selective abortion of female fetuses. We aimed to establish the trends in sex ratio by birth order from 1990 to 2005 with three nationally representative surveys and to quantify the totals of selective abortions of girls with census cohort data.


Methods

We assessed sex ratios by birth order in 0•25 million births in three rounds of the nationally representative National Family Health Survey covering the period from 1990 to 2005. We estimated totals of selective abortion of girls by assessing the birth cohorts of children aged 0—6 years in the 1991, 2001, and 2011 censuses. Our main statistic was the conditional sex ratio of second-order births after a firstborn girl and we used 3-year rolling weighted averages to test for trends, with differences between trends compared by linear regression.

Findings
The conditional sex ratio for second-order births when the firstborn was a girl fell from 906 per 1000 boys (99% CI 798—1013) in 1990 to 836 (733—939) in 2005; an annual decline of 0•52% (p for trend=0•002). Declines were much greater in mothers with 10 or more years of education than in mothers with no education, and in wealthier households compared with poorer households. By contrast, we did not detect any significant declines in the sex ratio for second-order births if the firstborn was a boy, or for firstborns. Between the 2001 and 2011 censuses, more than twice the number of Indian districts (local administrative areas) showed declines in the child sex ratio as districts with no change or increases. After adjusting for excess mortality rates in girls, our estimates of number of selective abortions of girls rose from 0—2•0 million in the 1980s, to 1•2—4•1 million in the 1990s, and to 3•1—6•0 million in the 2000s. Each 1% decline in child sex ratio at ages 0—6 years implied 1•2—3•6 million more selective abortions of girls. Selective abortions of girls totalled about 4•2—12•1 million from 1980—2010, with a greater rate of increase in the 1990s than in the 2000s.

Interpretation
Selective abortion of girls, especially for pregnancies after a firstborn girl, has increased substantially in India. Most of India’s population now live in states where selective abortion of girls is common.

They basically carried out analysis of statistics from a survey they organized, the Indian National Health Survey, and Census data from 2011 and 2001, they used a rolling three year average of chid sex ratios for evaluation and they subjected the values from it to linear regression analysis, which is used to identify trends. You may read more about the use of rolling averages here and Linear Regression Analysis here
They accounted for factors such as female infant mortality due to non-abortion reasons et cetera to arrive at a standard that we should expect to see if sex selective abortions were absent, and this is what renders their analysis rigorous.

Some of the findings that have emerged from the study are downright shocking.

Firstly, it would appear that the number of sex-selective abortions as far as girl children were concerned, based on an estimate which they derived using a conditional measure based only on second-born female chidren seems to have shot up drastically, of course, while it appears that the rate of increase is not as rapid in the past decade as opposed to the ‘nineties, the increase in number is rather worrisome.

Secondly, perhaps even more shockingly, the prevalence of sex-selective abortions based on their estimates seems to be more in cases where i) Mothers were educated ii)Households were richer, which is especially alarming. It would also appear that the number of districts in India from which further skewing of the Child sex ratio has been reported has also increased, the conclusion from this being that the practise is on its way up and is spreading nationally. The authors of the paper suspect this may be to do with the ability to afford ultrasound (which is used for sex determination)

The implication of this is that we’ll start to end up with more men than women in Indian society in the next generation (since the current cohort being studied and subjected to evaluation will grow up to be the men and women who define it) and if the problem isn’t dealt with quickly, we will, on a national level, end up with a severe disparity in the number of men and women, and with all the responsibilities women currently hold in the Indian setup and all they do, it could have major social repercussions.

One of the most striking trends that emerges from the published data is the spread of the phenomenon, using data from three decades to see what proportion of the population had a skewed child sex ratios, the authors found that 56% of the population of India lives in states where the child sex ratio (CSR) is skewed, as opposed to 10% in 1991 and 27% in 2001, which would indicate that the spread of Sex-selective abortion has been spreading to more and more places in the country.

I have cited a graph from the original paper under fair use conditions for purposes of scholarship and education that illustrates this.

Distribution of the total population living in states with varying child sex ratios (girls per 1000 boys at ages 0—6 years), 1991, 2001, and 2011 Mean national values for each of the censuses are shown. The vertical grey bar represents a natural sex ratio at birth of 950—975 girls per 1000 boys, where the distribution of child sex ratios at ages 0—6 years would be centred in the hypothetical absence of selective abortion of girls and equal girl and boy child mortality rates.

Please right-click the graph and use the menu to bring up a larger image, I hope you can see how the practice has been taking hold in India and how it is increasingly skewing child sex ratios.

Here is a map illustrating geographical changes in child sex ratio, again from the same paper and cited under fair use provisions.

Child sex ratio of girls to boys at ages 0–6 years in 2001 and 2011, by district Of the 623 districts, data were available for 596 in the 2001 census and 588 in the 2011 census. The blue highlighted states are Gujarat, Haryana, Himachal Pradesh, and Punjab, which have shown consistently lower child sex ratios at ages 0–6 years in the last three censuses. State names are Andhra Pradesh (AP); Assam (AS); Bihar (BR); Chattisgarh (CG); Gujarat (GJ); Haryana (HR); Himachal Pradesh (HP); Jammu and Kashmir (JK); Jharkhand (JH); Karnataka (KA); Kerala (KL); Maharashtra (MH); Orissa (OR); Punjab (PB); Rajasthan (RJ); Tamil Nadu (TN); Uttarakhand (UK); Uttar Pradesh (UP); West Bengal (WB); and Arunachal Pradesh, Manipur, Meghalaya, Mizoram, Nagaland, Sikkim, and Tripura (collectively NE).

Again, right-click the map and use the pop-up menu for a larger image.

Further Information and Links

You can also read an article by Kalpana Sharma of The Guardian here , read the BBC’s coverage of the reaction to the data that has emerged in Bihar (which is a very bad offender)
here and in Kashmir here. You can also read a case report on female foeticide and infanticide from Gendercide.org here


Spread the word, share these articles, talk about the issues at hand, pretending there isn’t a problem while maintaining a facade of perfection as a country is going to achieve bugger all! Only when people are willing to come to terms with the presence of a problem can efforts be made to look for solutions, only when there is strong consensus will people begin to make that effort. We just cannot put up with abortions being carried out because a foetus happened to be the second one in gestation and lacked a Y chromosome.

Thanks for reading,now go spread the word.
– Ankur “Exploreable” Chakravarthy.

White people believe that they face the worst racism

…according to a study in the journal Perspectives on Psychological Science.

The study, called ‘Whites see racism as a zero-sum game that they are now losing‘, by Michael Norton and Samuel Sommers, suggests that white Americans surveyed think that they are now more widely discriminated against than black people, and that this supposed ‘anti-white bias’ is a bigger societal problem than the real anti-black bias. (This is an American-based study, and I think the problem is probably more prominent there, but since I only know the UK, and I see a similar trend happening over here, I will be using UK-based examples.)

After all of the wrongdoings of the past, governments are now at least trying to make society more equal for everyone, but the damage that has been done has penetrated society too deeply to disappear overnight. Ideas that black people and indeed people of other ethnicities are in some way inferior are ingrained in the collective consciousness, to the extent that when their position in society begins to improve, white people have started to cry ‘racism!’ Are we really selfish and shortsighted enough to convince ourselves that all along, all they were complaining about was the fact that white people had a more privileged position in society? Is history no longer taught in schools?

Many of my black friends have talked to me about the racism they experience in daily life, whether it’s a remark they have overheard from someone in the street, or discrimination by the authorities. A large proportion of my black friends have been subject to at least one stop and search by the police. As far as I know, none of my white friends have. Figures published in 2010 indicated that black people were seven times more likely to be stopped than white people.

These stops and searches under Section 44 were last January ruled illegal by the European Court of Human Rights for their arbitrary and widespread usage, as well as their disproportionate targeting of blacks and Asians. Now are we going to label this as racism against white people? Of course not, because it is utterly transparent that this was a case of inequality. So how can the same principle of removing inequality apply in other situations and be called ‘anti-white bias’?

This is how I see it. Most white people don’t even know they are white until they are in a room full of black people. They don’t have to; society holds them in a more privileged position by default, and in the past it was a rare occasion that a white person would find themselves in such a situation. Now, however, it is becoming more common.

Having used this example already, I will continue with it. The stop and search issue can be held at arms length and viewed relatively objectively by white people as inequality that needs to be extinguished. Why? Because it just doesn’t happen to white people. But when the situation for non-Caucasians starts to improve in other, less subtle ways, why is the reaction turned on its head?

I have seen this time and time again in previous jobs; the anecdote of the poor white person who lost out on a job opportunity to the black person who ‘wasn’t even as good at the job’. ‘Political correctness gone mad’, they say. Whenever I hear this it makes me cringe. Yes, there are guidelines to say that workforces (dependent on who applies) need to be representative of the general population, but why do I find it hard to believe that a less skilled person would be favoured over a more skilled person? From a productivity point of view, it doesn’t make sense for a company to employ an inferior applicant. Surely it’s more likely to be the case that the two people are equally skilled, but the white person doesn’t know how to react because it’s an unfamiliar situation they find themselves in, but in the name of improving standards of equality it has to happen. I suspect that if the job was given to another white person, then sure, the other candidate would be annoyed, and would probably make some digs about capability, but as soon as preference is given to a black person, the problem becomes about skin colour. It’s an easy target.

To cite another article:

a co-author of the study called the results “surprising.” That’s putting it mildly. But maybe we’ve missed the way white Americans have been systemically deprived of access and opportunities. Maybe we’ve overlooked all the times whites have been targeted by implicit and explicit race-baiting attacks, whether they’re playing professional sports or seeking elected office. Maybe we didn’t get the memo on the way the legacy of discrimination against white Americans continues to manifest itself in worse outcomes in income, home ownership, health and employment for them, the way white people are told they’re “objectively” ugly, and the disgust so many Americans felt the last time a white person ran for president.

Now imagine all this actually happening to a white person. Quite simply; it would not happen. The privileged position we hold is so blinkered to reality that it’s only when someone uses analogy like that displayed above that we realise it’s really not so bad after all. Yet some people will continue to complain. Please open your eyes. Try shutting up, listening and learning something. Racism is still a part of the daily life of non-white people, manifesting itself in all aspects of their lives.

So if you are a white person and you have read all this and disagree: Think you know racism? Think again.