<![CDATA[Dr K Science - DrK_Science Blog]]>Tue, 09 Feb 2016 08:26:36 -0800Weebly<![CDATA[A2 Chemistry - making use of DNA]]>Mon, 10 Nov 2014 20:17:58 GMThttp://drkscience.weebly.com/drk_science-blog/a2-chemistry-making-use-of-dna1Based on what you have read in class and the blog entry on predictive genomics below (click for direct link), comment on the following statements.
1) The DNA profiles of all UK citizens should be taken at birth and stored in a government database.
2) Assuming the technology to rapidly sequence an individual's DNA is available, medical insurance companies should have access to their customers' DNA profiles.
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<![CDATA[Smart Revising]]>Sat, 29 Mar 2014 10:04:17 GMThttp://drkscience.weebly.com/drk_science-blog/smart-revisingHere's something that I have shared with my A-level students recently. I can't claim complete credit for it, since I first saw a student do this sort of thing really properly a couple of years back, but it got me thinking about playing the exam game. Unfortunately, to get top marks in an A-level subject like Chemistry, it takes more than just being a good chemist. You need to be very syllabus savvy.
This is my suggestion. For each module, (e.g. Developing Fuels on the OCR Salters course) take a sheet of A3 paper and, in the centre, stick an A5 version of the syllabus for that topic (depending on the size of the syllabus, this may mean you have to use both sides of the paper). Then do the following:

1) Go through the syllabus point by point, and try to write notes for each syllabus point. Check you've covered the key points by referring to a revision guide or your notes, and amend as appropriate. For syllabus points where you were far less sure, go and learn these properly, using your revision guide, textbook, own notes, etc. and then demonstrate your understanding by adding notes to your revision sheet without any help. Repeat this learning process until you can do this confidently.
2) Then go through your class notes and look for work and tests where you received feedback on things you got wrong or could have done better. Add these points to the relevant syllabus points, perhaps in a different colour.
3) When answering past paper questions and using the mark schemes to check your answers, if there's anything you learn here, add that to the relevant point(s) on the syllabus on your revision sheet. Again, using a different colour might help.

As I see it, there are several advantages to this approach over ploughing through a revision guide or just your class notes from beginning to end.
1) It ensures that you cover everything you need to know and nothing else, since you won't be tested on things not on the syllabus.
2) It allows you to review what you do know and not waste time revising areas of strength.
3) The focus on the syllabus should allow to get into the examiner's head. Remember, the questions that they set directly relate to the syllabus and, in many cases, the syllabus contains the specific answer to a question. For instance, on the Salter's Chemistry specification, there are the steps for determining the concentration of a coloured solution by colorimetry, the similarities and difference between line absorption and emission spectra, and the reasons why clinical trials for drugs are required, to name but a few, which are the direct answers to the typical questions given on the exam papers that relate to these topics. Simply no other answers are required, or, indeed, necessarily accepted. More subtly, there are other cases where a knowledge of the syllabus will help you to appreciate what things a question wants mentioning. An example on the OCR course is in Agriculture and Industry, where the syllabus says that students must recall the physical properties of different types of substances, but in brackets lists solubility in water, melting point and ability to conduct electricity. So if you get a compare and contrast question on the properties of different substances, these would be the properties to go for.
4) It forces you to learn from your mistakes, be that through the course of the year or at the end of revision when doing past papers.
5) You end up summarising a whole unit on one A3 sheet of paper, which is a personalised, paired-down summary that hopefully can be learnt in the time available to you.

Good luck!]]>
<![CDATA[A2 Chemistry - making use of DNA]]>Mon, 14 Nov 2011 19:59:13 GMThttp://drkscience.weebly.com/drk_science-blog/a2-chemistry-making-use-of-dnaBased on what you have read in class and the blog entry on predictive genomics below (click for direct link), comment on the following statements and vote in a poll by clicking this link and entering the code that represents your opinion (submit entries for each statement separately).
1) The DNA profiles of all UK citizens should be taken at birth and stored in a government database (Poll codes: 357442 - I agree; 357443 - I disagree; 357444 - I'm not sure)
2) Assuming the technology to rapidly sequence an individual's DNA is available, medical insurance companies should have access to their customers' DNA profiles (Poll codes: 357919 - I agree; 357920 - I disagree; 357921 - I'm unsure).
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<![CDATA[Not the breast tweet]]>Wed, 20 Jul 2011 09:40:38 GMThttp://drkscience.weebly.com/drk_science-blog/not-the-breast-exampleIf you have been following DrK_SCInews, you may have noticed that I have received some pretty vociferous feedback over the following tweet:

‘Staring at breasts for just a few min/day can improve a man's health + add up to 5 years to his life. Source: Closer magazine (v.reliable!)’

I tweeted this claim (from my wife’s magazine) because I found the notion of a scientist performing such a study hilarious. For a start, scientists have to apply to research councils for funding and the grant application – with the justification for the research – would have been priceless.

@Saaoirse correctly pointed out that ‘Scientists have been trying to justify misogyny through statistics for so long.’ However, I would like to firmly state that this was in no way an attempt to support such a justification. On my cursory, prima facie, inspection, the result of the study was not wholly implausible, possibly explained in terms of motivated changes to lifestyle resulting from the regular observations. However, when I started to think about it after @Saaoirse’s reply, it did occur to me that no study could ever justify the claim of adding 5 years to people’s lives (since the only way to make this claim would be to follow the people until they died), so whatever the results, they had been over-pitched. Also, any effect would probably have been too insignificant to pick up.  So I decided to go and read the source article. A quick Google search led me to the name of Dr Karen Weatherby, a German researcher (just as Closer had said) who published the research in the New England Journal of Medicine. All good so far - I had heard of that journal. Only problem was, when I checked the New England Journal of Medicine on-line, I found no record of the paper. Nor could I find it on Pubmed (a search facility for scientific papers), or, as a last resort, Google Scholar.Conclusion: the research is fictitious and I had been duped. Not quite a Murdoch-scale ‘most humble day of my life’ but I do feel like a bit of a fool. Sorry @Saaoirse!

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<![CDATA[Curiosity and immortality]]>Mon, 18 Jul 2011 18:05:46 GMThttp://drkscience.weebly.com/drk_science-blog/curiosity-and-immortalityI have just been looking on the website of a Discovery Science show beginning in August, called Curiosity. The show promises to 'ask and answers the most fundamental questions facing the world today ... [looking at] enduring questions in science, technology, and society'. One such issue is that of immortality - living forever. A blog post on the website concludes that it is unlikely that humans could live forever, and, indeed, mentions a possible upper limit of 125 year. Immortality has actually worried me for a number of years and a few years ago I wrote an article in Pi Squared, a UCL newspaper, where I discussed some research on extending life through eating less (caloric restriction) and then pondered whether an ability to live forever would be a good thing.

The immortal MRS GREN

The teaching of the biological sciences begins with a consideration of the characteristics of life. In the memorable form of MRS GREN, the National Curriculum suggests an acronym that can be drilled into fresh-faced secondary school students to enable them to recite these characteristics on request (i.e. in a GCSE examination). My rather over-zealous biology teacher, however, had formed his own longer and less memorable acronym, DOCMERRING (1). In a rather macabre way to start thinking about life, the ‘D’ (not present in MRS GREN) stood for death - all things of flesh and blood perish.

Why do we grow old and die? Jared Diamond, in The Rise and Fall of the Third Chimpanzee, summarises:

We constantly invest resources in the repair of our bodies, just as we do with our cars. Unfortunately for us and for all other animals, there is a limit to the resources that natural selection found it worthwhile to programme into our self-repair [whilst maximising our reproductive output]. As a result, we eventually grow old and die, but at least we age more slowly than our ape relatives. (2)

Yet humans have never been satisfied with their three score and ten years, and tales of great feats of longevity have been celebrated throughout history - like that of Methuselah, who is quoted in the Hebrew bible as being 969 years old when he died in the year of the Great Flood (Genesis 5:27). Moreover, according to Kant, ‘God, freedom, and immortality are the three great objects of speculative thought,’ although his ‘immortality’ is an ethereal one.

Caloric restriction, ageing and pha-4
As far back as the 1930’s, a link between caloric restriction and longevity has been known: mice subsisting on a calorie-restricted diet (reduced food intake but still healthy) have been shown to live longer than those on a normal diet by up to 40%. Only now though, 70 years later, does a new study from the Salk Institute in California provide the link between caloric restriction and longevity (3). Using the nematode worm, C.elegans, a workhorse of modern cell biology, researchers have found that a gene called pha-4 plays a key role. Loss of this gene resulted in worms that showed no enhanced longevity while on the calorie-restricted diet; conversely, over-expression of the gene (putting in more copies) led to a significant increase in lifespan. Dr. Dillin, the principal investigator, explained that, “Pha-4 may be the primordial gene to help an animal … live a long time through dietary restriction conditions.”

The pha-4 gene has orthologues (relatives) in humans and the identification of this link between caloric restriction and ageing may allow the development of drugs that mimic the effects of a calorie-restricted diet without having to forgo your double cheeseburger with fries.

Immortality: not what Nature intended
Steve Connor, reporting in The Independent, has hailed pha-4 as “the gene that decides how long we live”. That’s a little simplistic, though. This discovery, by itself, is also not going to allow the human race to realise immortality any time soon, but perhaps, with stem cell therapy developments and the like, one day we might.

But would immortality be such a good thing? It may be because I am an atheist but I have nightmares over living forever in Heaven; living forever on an imperfect Earth is positively terrifying!

A solemn appreciation of death brings meaning to one’s life. Mortality is a humbling condition and the knowledge of our future death allows us to put our lives into perspective and plan to give them meaning and substance. A life with no end would surely be a wretched one.

However, we have to put life extension in perspective. If a man on his death-bed were offered the opportunity to live for another 20 years, he may well say yes. If a man were asked at the beginning of his life whether he wished never to die, he may well have doubts. What is certain is that an ability to considerably enhance our lifespan above what is naturally possible, or in the extreme, become immortal, would leave us with a difficult decision of when to end it.

In a way, though, Nature, and its mechanism of evolution, has already provided us with an ability to achieve (impersonal) immortality through reproduction in our mortal lives. As Diotima explains to Socrates in the Symposium, “The mortal nature is seeking as far as possible to be everlasting and immortal. [Men hope that offspring] will preserve their memory and give them the blessedness and immortality which they desire in the future.”

1. DOCMERRING: Death, Osmo-regulation, Cells, Movement, Excretion, Reproduction, Respiration, Irritability (sensitivity), Nutrition and Growth.

2. Opening to chapter 7.

3. PHA-4/Foxa mediates diet-restriction-induced longevity of C. elegans Siler H. Panowski, Suzanne Wolff, Hugo Aguilaniu, Jenni Durieux & Andrew Dillin (2007) Nature Advanced Online Publication, doi:10.1038/nature05837

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<![CDATA[Scandium - the vindication of Mendeleev's table]]>Fri, 15 Jul 2011 09:05:22 GMThttp://drkscience.weebly.com/drk_science-blog/scandium-the-vindication-of-mendeleevs-tableNice piece from @GrrlScientist in the Guardian today (http://www.guardian.co.uk/science/punctuated-equilibrium/2011/jul/15/1?CMP=twt_fd), on one of the lesser-known elements, Scandium. She links to the @PeriodicVideos video on the element, where Martyn Poliakoff (who's worth watching for his hair, if nothing else) explains how Mendeleev predicted that an element with the properties of what is now known as scandium (Mendeleev called the undiscovered element eka-boron) would exist, based on the structure of his Periodic Table. The history of the makings of Mendeleev's table (published in 1869) is a wonderful statement of the need for creativity in science. Prior to Mendeleev's work, some chemists thought that the answer to ordering the elements lay with grouping by chemical properties, having observed similar reactions with certain triads of elements, such as the three known alkali metals (lithium, sodium, potassium). But this only worked with some of the elements, as lots were yet to be discovered. Dalton made an attempt to impose order on the unruly world of the elements based on mass and Berzelius set about measuring the relative atomic masses of all the known elements. However, other chemists disagreed with his values and it was not until Cannizzarro invented a new way of measuring atomic masses based on the new gas laws that chemists were really able to progress with ordering the elements. Despite this advancement, arranging the elements in order of relative atomic mass gave no discernable pattern in properties. However, in 1863, John Newlands noticed that the elements arranged by atomic mass showed repeating properties in octaves (8 elements). Newlands’ ideas were not well received and it took the work of Mendeleev to finally piece together an order for the elements. Critically - and here comes the genius of the man - Mendeleev’s approach was different from other scientists. Previous orderings were based either on atomic mass or properties - Mendeleev used both. The problem was that not all the elements had been discovered (only 63 by that time), but here came Mendeleev's second piece of genius: (apparently) he had a dream where he saw his completed table and from this, he realised that to make the table work, he had to leave spaces for elements that were unknown. This was an incredibly bold move and showed his trust in the predictive power of his Periodic Table. He was ultimately vindicated, through the discovery of elements such as scandium and gallium. Now his table hangs in nearly every science classroom in the world. Why? Well, for precisely the same reason as it became accepted by other chemists initially: its predictive power. You don't need to know the properties of every element, you simply find its place in the Periodic Table and you can work them out by knowing only a few basic trends in reactivity for Groups (columns) and Periods (rows). Thanks Mendeleev, for making chemistry easy!
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<![CDATA[Predictive genomics - still early days]]>Thu, 14 Jul 2011 21:23:41 GMThttp://drkscience.weebly.com/drk_science-blog/predictive-genomics-still-too-early-to-get-testedWatching the excellent Science on Science show on Discovery Science reminded me of a university essay that I wrote 7 years ago (PDF). The subject was predictive genomics: scanning a person's genome to determine the likelihood that they'll develop this or that disease. Very simply, you give, say, a saliva sample, and then your DNA is screened for certain mutations that are known indicators of disease. This is great on two conditions: the first is that the presence of a marker is a reliable predictor of whether you will develop a certain disease, and the second is that, armed with this information, you could change your life to mitigate the effects of the impending doom that awaits you. What I found interesting in this programme was that we have progressed very little since I wrote my essay on the prediction side. The interplay between different (faulty) genes in bringing about disease states is still far too complex for us to be able to reliably predict disease from our genes. Of course, the situation is also greatly complicated by most diseases resulting from a combination of faulty genetics and environmental (lifestyle) factors. So, genetic testing is currently very limited and may cause unecessary worry for those getting tested.
However, this doesn't mean that we can't consider a situation where reliable predictive genomics does exist - a Gattaca-type society, for those who have seen the film - and the consequent possibility for discrimination based on your genes. This was the actual subject of my essay, which concluded:

"Even if in the future the ability to predict the more common, multifactorial diseases does become a reality, we all posses dozens of glitches in our genomes that probably predispose us to a great number of diseases and it will again be difficult to discriminate between different people. Furthermore, if we do reach a stage where common diseases are easily predictable, surely the level of understanding that we would then hold would lead to the development of effective treatments, such as gene therapy, and the abolition of any genetic underclass."

So if condition one is met, condition two should follow and, hopefully, lead to genetic equality. We'll see how the future pans out.

Read the essay here.

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<![CDATA[Youngest ever dinosuar fossil doesn't prove the asteroid theory.]]>Wed, 13 Jul 2011 09:34:34 GMThttp://drkscience.weebly.com/drk_science-blog/youngest-ever-dinosuar-fossil-doesnt-necessarily-prove-the-asteroid-theoryAs covered at GCSE, there are several theories put forward to explain the extinction of the dinosaurs. The most widely accepted theory is that an asteroid crashing into the Yucatan Peninsula in Mexico around 65 million years ago was responsible (the impact may have thrown dust up into the atmosphere resulting in a nuclear winter, for example). However, other paleontologists have suggested that the dinosaurs were already in decline due to other reasons like climate change and that the asteroid impact may have had little impact or just finished them off. This theory is supported by a paucity of dinosaur fossils found in a 3 m zone below what is known as the Cretaceous-Tertiary boundary (confusingly referred to as the K-T boundary). This visible line in the rock strata containing high levels of iridium marks the asteroid impact and the end of the Cretaceous Period. Now, a fossil fragment of a Triceratops has been found, only 13 cm from the K-T boundary (don’t ask me how close in years this makes it but the experts say pretty close) suggesting that at least this species was alive and kicking quite close to the asteroid impact, thus lending support to the argument that the impact killed them off (Guardian science piece expounds this argument - http://www.guardian.co.uk/science/2011/jul/13/last-dinosaur-fossil-asteroid-theory?CMP=twt_fd). The fact still remains, though, that the 3 m fossil-poor zone in the Upper Cretaceous still exists, and one fossil fragment does not change this. The debate continues...

This is a lovely example of how current scientific theory is based on the balance of evidence and how scientific theory is constantly evolving.

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<![CDATA[Freerice - A morally virtuous Sporcle?]]>Mon, 11 Jul 2011 17:36:11 GMThttp://drkscience.weebly.com/drk_science-blog/freerice-a-morally-virtuous-sporcleOne of the slightly more odd postings from the Royal Society of Chemistry this week is a mention for Free Rice, an initiative sponsored by the World Food Programme. It has a very simple concept: you answer multiple choice questions on a variety of topics and for each correct answer, they donate 10 grains of rice to 'hungry people'. Who exactly these hungry people are and who delivers the rice, I haven't quite figured out. Nor have I figured out whether I can really be justified in thinking that I have done my part to help alleviate third world hunger by answering a couple of quiz questions instead of putting my hand in my pocket. However, like Sporcle, it is surprisingly addictive - perhaps because the questions are quite straightforward - and you'll feel compelled to sample all of the categories (science students may be particularly interested in the element symbols quiz). It also has league tables to allow you to compete against your friends and so, I suppose, in its goal to raise awareness, it does actually succeed quite well. ]]><![CDATA[DrK_SCInews blog is live!]]>Thu, 07 Jul 2011 20:23:32 GMThttp://drkscience.weebly.com/drk_science-blog/drk_scinews-blog-is-live