Book Review: Bad Science

Ah, yes. Ben Goldacre. I am not quite sure where to start from, so I guess I’ll go from the very beginning of the book which first introduced me to him.

BEN GOLDACRE is a doctor, academic, broadcaster, and science writer who has made his name unpicking the evidence behind dodgy claims from journalists, drug companies, politicians and quacks. His hugely influential  ‘Bad Science’ column ran in the Guardian from 2003 to 2011. His first book, Bad Science, reached Number One in the bestseller charts, selling over half a million copies, and has been translated into twenty-five languages. His second, Bad Pharma, triggered two parliamentary committees and  a global campaign to stop drug trails results being withheld from doctors and patients.

That is the first thing you will read as you open up ‘Bad Science’ or at least that is what I found in my edition which was first published in 2009.

I would give a summary of this book like I have done with the others but I simply cannot. It is an indescribable book, both in the sense that it will not do it justice but also the fact that I simply have no words, but it is a book that I am surprised to catch myself referencing often.

And surprised I shouldn’t be. Having a keen interest in science, Ben Goldacre rips apart the fantasy from the evidence and that is something any scientist aims to do, including myself. What he writes should be relevant and it certainly is as I now look at trails from a new perspective, even if they are only Biology exam questions, and am grateful for the knowledge he bestowed on me as I look to embark on completing an EPQ. So I shall correct myself: it surprises me that this book made such an impression on me.

Let’s start at the heart of the book: the voice, the author. I feel that this needs to be established before I mention any parts of this book that have made a lasting impression on me.

Once you hear Goldacre’s voice, you cannot un-hear it. A few pages in and you feel as if he is telling you directly what he is writing and whenever you think back to anything related, his voice never leaves. I found this to be particularly true when I forgot the p value below which a value had to be to be significant in a test. It was very minor thing and although it was never directly taught in lesson, p values were something I came across frequently when looking over scientific studies and my mind was putting a blank over where the number was supposed to be. As I was trying to shift the mists of haziness in my brain, I had a funny feeling to connecting with ‘Bad Science’-just Goldacre’s voice trying to prompt me. Unfortunately for me, the number remained unclear and although I wasn’t far off (0.01 rather than 0.05), it altered whether I thought the value was significant or not.

The thing that gets me most is that I constantly sway about how I feel about this book and Goldacre. It’s a vicious cycle: you are annoyed because you are embarrassed that what Goldacre writes is true, so you are angry with Goldacre but you know you shouldn’t be and Goldacre knows he is right so he is smug which annoys you more…

I’ll stop waffling now and try to concentrate on some more concrete points. Every chapter deserves a mention because of the content but that would make the post too long and you might as well read the whole book.

One of this first things Goldacre does is to outline the features of a trail which make it a fair test, such as blinding, randomisation and meta-analysis. These points are not only helpful when you look at trails outside of this book but also give you a good foundation to be able to think for yourself as Goldacre takes apart whatever he sets out to destroy in each chapter. For me personally this is one of the main things that I take away from ‘Bad Science’, especially as I look forward to the EPQ.

However, I think it is important to understand that-as always-there are limitations. Of course there is nothing right in only releasing trail evidence that supports your claim and stuffing the other evidence in a drawer, however there may be some practical limitations when designing trails-especially when real patients are involved. Before a drug actually makes it to a human trail there are a whole load of other tests it needs to pass, but we’ll just concentrate on the human stage. We all know a large sample is important but in the real world it is hard to come by. You may have twenty patients of which six do not complete the full trail so you are left with 14 subjects, a far cry from the thousands you may have been imagining. In addition, if a patient requires treatment, you cannot give them a placebo: that is unethical as in effect you know that you are denying them treatment. And more often than not the patients may also be on a variety of other medication which could affect the drug you are testing so the results may be nothing like the ones obtained from a lab workbench with controlled conditions. What I also believe to be happening is that to make it in the scientific world you not only need to publish articles, you need to publish them frequently. As a result, many scientists could be inclined to hold back some data to publish in a different article to have another publication under their belt, and although mostly harmless, you never know how this could end up…

Two of the content highlights for me were the classy way Goldacre cut through homeopathy without even batting an eyelid as well as his focus on the placebo. I thought he explained this phenomenon very well considering the mystery of it all. The colour of pills, administration and the ceremony are all part of the effect. For example, one of the experiments he mentions is that students sitting in a boring lecture were told they would receive either a stimulant or sedative. In fact both pills were sugar pills but of different colours and found that the “pink sugar tablets were better at maintaining concentration than the blue ones”. He carries on to say that “since colours in themselves have no intrinsic pharmacological properties, the difference in effect could only be due to the cultural meanings of pink and blue: pink is altering, blue is cool.” Another study suggested that Oxazepam was better at treating anxiety when green and depression when yellow. To have a general picture, a survey of coloured pills currently on the market showed that stimulant medication is usually in red, orange or yellow tablets while antidepressants and tranquillisers are mainly blue, green or purple, as seen in Prozac which comes in white and blue. Capsule’s also seem to come across as more effective than pills, as portrayed by a study using chlordiazepoxide. The ceremony is also vital as in three different experiments an injection of salt-water had a greater effect than sugar pills for blood pressure, headaches and postoperative pain. There are no benefits of salt-water but an injection appears a “much more dramatic intervention than just taking a pill.” Packaging also plays its part and although there are no pharmacological differences in brand-name painkillers and just your standard painkillers, a study done by Branthwaite and Cooper showed that brand-name painkillers are in fact more effective. Although they used aspirin versus sugar pills, both were administered in either “blank, bland neutral boxes” or ” full, flashy, brand-name packaging”. Clearly the aspirin had more effect, but they also found that the flashy packaging increased the effect of both pills. The placebo is a fascinating effect and I have only picked a few examples here. More can be found in the placebo chapter of the book but also one of my friends wrote an article about the placebo on our collective biology blog if you want to have a look: https://wgsbiology.wordpress.com/2017/01/31/mind-over-matter/

‘Bad Stats’ is also a chapter that I would highly recommend to have a greater general understanding of statistics (it’s also that chapter that actually mentions those p values!!). One of the stand out examples for me was on the risk of having a heart attack which looked at the use of something called ‘ relative risk increase’. I’ll use the same example as Goldacre did. Out of hundred men with normal cholesterol, four will be expected to have a heart attack while out of one hundred men with high cholesterol, six will be expected to have a heart attack. This means there are two extra heart attacks per one hundred and this is known as ‘natural frequencies’. This is relatively simple because you do not do anything to a number (unlike with percentages or probabilities) but you just count, like when teachers count the student in their class. For this example you could also have a 50% increase in risk (pretty worrying, right?) which is known as the ‘relative risk increase’ or even a 2% increase, known as the ‘absolute risk increase’, which seems less fearful. Here the take home message is that natural frequencies are not only much easier to comprehend and compare, but also figures, especially statistics about increases, can be portrayed in a number (see what I did there!) of ways, which, while not untrue or intentional, may be misleading.

As intense, and emotionally draining, as ‘Bad Science’ is I would recommend it to anyone, which may be why I have two more of his books on my shelf waiting to be read. What Ben Goldacre says, whether you agree with it or not, is relevant to anyone working or looking into a scientific field. Goldacre went out to tear apart the frills and pretty bows surrounding the actual evidence and that is what he accomplished, and whether you like it or not, someone had to go and it and so you may as well read the accounts from his point of view. And you might, just possibly, even enjoy it...

Key definition:

  • Cherry-picking: “Selectively choose from what is available” (definition taken from Google)

“Pick out the trails that give them the answer that they want to hear, and ignore the rest.” Ben Goldacre on Homeopathy in ‘Bad Science’

Figure 1. Bad Science by Ben Goldacre

Enlightening the World of Electrons

“Curiously, electrons fill orbitals like patrons find seats on a bus: each electron sits by itself in an orbital until another electron is absolutely forced to double up. When electrons do condescend to double up, they are picky. They always sit next to somebody with the opposite ‘spin’, a property related to an electron’s magnetic field.” Sam Kean in ‘The Disappearing Spoon’ on the Pauli Exclusion Principal. 

I am not sure whether you have read my previous post (found here: Book: The Disappearing Spoon) but I was talking about a book which I have read: “The Disappearing” Spoon by Sam Kean. The book scorches the history of the Periodic Table and its many, many elements. I was about to explain one of the stories which caught my eye as I was reading the book, however I soon realised that it would need some background chemistry-chemistry that I found very, very interesting as I was reading it.

I am by no means a Physics student-I only took Physics at GCSE, however the great world of electrons always fascinated me because I felt it was a key to the door of having a deeper understanding of Chemistry.

The story which is the basis for this post is how europium is used as a anti-counterfeit in euro notes. However, to understand how the element works in its important job, we need to have a basic understanding of how electrons emit light . (In case you were wondering, the quote above doesn’t have that much to do with we will be talking about shortly, but I really like that analogy for how electrons occupy orbitals in an atom, so I thought I would share it.)

Before we get to the nitty-gritty, we must first think of a different analogy: the one where electrons orbiting around the nucleus are compared to planets circling around a sun. Kean himself states that it’s not bad analogy, however “it has a flaw if taken literally”. Electrons do not orbit randomly around the nucleus, they live in orbitals and move within shells at different energy levels which are distinct: there is no energy level between levels one and two, two and three, etc… and so they can only orbit around their ‘sun’ at certain distances (and they also happen to orbit in oblong shapes at funny angles). More important is the fact that if excited by heat or light energy, electrons can jump from it’s low-energy shell home to an empty higher-energy shell. However, the electrons cannot outstay their welcome in the high-energy state, and soon they crash back down. During this crashing, the electrons “jettison(s) energy by emitting light”.

The interesting thing is that the colour of the emitted light depends on the relative heights of the levels that the electron jumped. For example, a crash between only closely spaced levels releases low-energy reddish light while a crash between widely spaced levels releases high-energy purple light. Since electrons are limited to jumping between whole-number levels, the emitted light is also constrained-it is a very specific, very pure colour, which is unlike white light emitted by a lightbulb. We must also note that since each element’s shells are at different heights, each element therefore releases characteristic bands of colour.

Moving back to europium. Europium is a lanthanide, meaning it cannot absorb incoming light or heat efficiently but is able to emit light in a way other than simple absorption. This feature is called fluorescence (important side not here-please see at the bottom of the post) and in general terms while normal emissions of light involve only electrons, fluorescence involves whole molecules. Another difference is that while electrons absorb and emit light of the same colour, fluorescent molecules absorb high-energy light (UV) but emit lower-energy visible light. In europium’s case, depending on what molecule it is attached to, it can emit red, green or blue light.

Now we can explain how the EU uses it in the ink on its banknotes. To prepare the ink, chemists lace fluorescing dye with europium ions. The dye consists of two parts. The first is the receiver, the antenna, which forms the majority of the molecule and its role is to capture incoming light energy (which the europium, as mentioned earlier, cannot absorb), and transform it into vibrational energy (which the europium can now absorb) which is moved down to the tip of the molecule.  The europium electrons become excited and leap to higher energy levels, but before they jump, crash and emit, a small part of the incoming wave of energy ‘bounces’ back to the antenna. Normally, this wouldn’t happen with just isolated europium atoms, but in this case “the bulky part of the molecule dampens the energy and dissipates it”.

This shift is more than just accidental. The dyes are selected so that the europium appears dull under normal visible light (which may lead a counterfeiter to think he’s got a good replica) but once the note is put beneath a special laser, the paper goes blank and “small, randomly oriented fibres laced with europium pop out like parti-coloured constellations”. Europe glows green, a pastel wreath of stars becomes yellow or red and other monuments, signatures and hidden seals become royal blue.

Euro banknotes under UV light
Fig 1. Image of euro banknotes under UV light (taken from Google).

And so: violà. The hidden euro will catch out any counterfeit.

Side note: I’m going to take a moment to clarify some terms which Kean also took the time to clarify in his “Notes and Errata”.

Luminescence- general term for a substance absorbing and emitting light. 

Fluorescence- as described above.

Phosphorescence- similar to fluorescence in that molecules absorb high-frequency light and emit low-frequency light but phosphorescing molecules continue to long long after the light source is removed. 

Author’s note:

This post is based entirely on what Kean wrote in his chapter “Elements as Money” in “The Disappearing Spoon”. He deserves the credit and I would recommend you read the full book as well. If you want a further idea of what the book is about, please see my previous post and the link to it is posted at the start. 🙂

Book: The Disappearing Spoon

“The Disappearing Spoon” is a great read for any Chemistry enthusiast which includes myself.  Although I had to read this in small chunks, Sam Kean managed to make every moment enjoyable and seemed to bring to life a common-place concept which is part of every Chemist.

The book goes through most of the elements in the Periodic Table, unravelling secrets about their discoveries or any related feuds and demonstrates the powerful depth and history of the poster that hangs in every Chemistry teacher’s classroom.

The disappearing spoon

For me, I think the book highlighted the fact that the scientific world is not all nice and friendly. To a certain extent, scientists are in competition with each other: who discoveries this first or who invents that. This crops up in numerous points throughout the book, as for example, having discovered elements 97 and 98, the scientists at the University of California at Berkeley named them berkelium and californium respectively. One is left to wonder whether the names give any hint at the place of discovery of the elements…

However, the fact that chemistry and the table of elements affects everyday life also becomes evident. One aspect features prominently in history and also today: money. Although a whole chapter is devoted to this topic, I’ll pick out just two little sub-stories.

The first is about the myth of Midas, a myth which I first heard of in an English reading practice for SATs at the end of my primary school years and a myth that now appears to have a plausible origin. Most people have heard of the story surrounding king Midas-he wished for whatever he touched to turn to gold. I’m not saying that that happened to the real king Midas, but there may be a reason as to why he is associated with the metal. The story starts during the Bronze Age which began in Phrygia (Midas’ kingdom which is now in Turkey) around 3000 BC. Casting bronze, which is an alloy of tin and cooper, was the thing to be done during those days and the skeleton of the king who was popularly called Midas (but was later found to be his father, Gordias) was found in his tomb in Phrygia surrounded by bronze bowls and bronze cauldrons and wearing a bronze belt. However, a number of different alloys with different ratios of metals are classified as bronze and the colour depends on the ratios of tin, copper and other elements. Coming back to Phrygia, the unique feature of metallic deposits in the area was that there was an abundance of zinc ores. Zinc and tin ores commonly commingle and can be easily mistaken for each other. The little twist here is that zinc mixed with copper forms brass…not bronze. Furthermore, the earliest known brass foundries existed in the part of Asia Minor where Midas reigned once upon a time and this little fact leads us to the heart of the tale.

Bronze
Fig. 1 Image of bronze (taken from Google).
Brass
Fig 2. Image of brass (taken from Google).

If you compare bronze and brass (shown by figures 1 and 2), bronze is shiny with ‘overtones of copper’, whereas ‘the shine of brass is more alluring, more subtle, a little more…golden.’ And so Midas’ touch a is touch of zinc in the soil of his part of Asia Minor.

The second story is more concerned with modern-day currency. Counterfeiting is an age long problem-even Newton himself encountered it during his years at the Royal Mint of England. Nowadays, the EU uses europium as a anti-counterfeiting tool in the ink it uses on its paper notes, however I am going to explain the mechanics of this in another follow-up post because this is getting rather lengthy and I want to focus a little on light emitting and electrons in general, something which this book first introduced me to.

As a fountain pen user, the iridium story was fascinating as was the cadmium story with its links to the itai-itai disease and Godzilla. This may also be a story that I shall look into a little more.

As you can probably see from my post, this book is quite intense and cannot be read in one sitting. I found reading it in small pieces helped to try to get my head around the new concepts but it is definitely a book I would recommend to anyone interested in Chemistry to have a better understanding of the elements and collecting curious nuggets of information along the way.

 

Book: Emergency Doctor

After reading the first chapter, ‘Emergency Doctor’ was not really a book I thought I would enjoy. For me personally, it felt a little slow, too laden with details and didn’t really have the spark that I tend to look for in books.

However, I must admit it did hook me and I do look back fondly on it. So here I am dedicating a post to this book which actually provided a lot of insight into a doctor’s life.

Emergency doctor book

‘Emergency Doctor’ is really just a series of accounts about life in the Emergency Department at the Bellevue Hospital, however very quickly it becomes more than that. You build a relationship with the key characters, both the doctors and patients, and I believe this allows you to feel the atmosphere that is being reported. You are able to see both perspectives: the doctors who have dedicated their life to helping people and of course the patients, who come from a variety of situations. You sympathise with the doctors as they deal with difficult patients, recurring patients who seem to not take advantage of the help or mainly people who are just simply very worried and therefore not at their best.  You empathise with the patients who come in with varying conditions and feel the pain that is at the centre of their world.

Although this may not be clear from my photo, there are many cut up post-it notes sticking up from the pages. These post-its signify places that were of interest to me and I’ll share a few that still remain with me after a while since I’ve finished the book.

(Of course I can’t find anything now because there’s too many post-it notes.)

  1. There is a case where a patient has been diagnosed with having a grand mal seizure who does not want to make a report to his employer. Later it is clarified that he is a pilot. Goldfrank (a doctor at Bellevue with whom Edward Ziegler, the author, cooperated with) was then quoted to have said “this was one of the rare cases where the obligation of the physician to honour the confidentiality in treating a patient runs right up against our responsibilities to society”.  Here, of course, is the classic case of a patient not wanting to reveal his medical condition because of the threat this could impose on his job, especially as he has a family to support. However, it is also the doctor’s duty to inform the airline as the pilot would be endangering the lives of many more people, and, as Goldfrank explains, there is a very thin line between patient confidentiality and the welfare of society, especially in such a responsible job like a pilot.
  2. “On Old Olympia’s Towering Tops/ A Finn And German Viewed Some Hops” is a mnemonic used by many doctors to indicate the succession of questions asked depending on the 12 cranial nerves: Optic, Olfactory, Oculomotor, Trochlear, Trigeminal, Abducens, Facial, Auditory, Glossopharyngeal, Vagus, Spinal accessory and Hypoglossal, to confirm injury to the brain. (Ok, I didn’t remember this but found it when I was flicking through.)
  3. Another mnemonic, but now for the first evaluation of a traumatized patient: “ABCDE”. A for airway-making sure it is open. B for breathing. C for circulation. D for disability, specifically neurological. E for exposure, expose the patient completely to avoid overlooking any hidden injuries.
  4. The five key parts of diagnostic perceptions: blood pressure, pulse, depth and rate of breathing, temperature and level of consciousness. Next comes vital signs: the colour of the patient, whether white (possible shock), blue (not enough oxygen), bright red (too many red blood cells) or yellow (jaundiced). Then motor status: writhing, hunched, immobile or uncoordinated.
  5. There’s plenty of other interesting facts concerning emergency medicine (such as the fact that nylon should be used to close wounds in the Emergency Department and not silk because there is only 2 to 3% infection rate rather than 10 to 15% with silk), but I’ll let you find out the rest of those yourself. Of course this book was first published quite a while ago (in the 80s I believe) so, as always, medicine has evolved but there’s still a lot you can take away.

I found that highlighting relevant pieces of information really helped me to focus on the key points among the pages bursting with information. And so, to conclude, I will leave you with my two stand out quotes:

  • [When talking about working with the homeless] Goldfrank: “you appreciate the most basic aspects of humanity what’s left when all the trimmings of society are removed…We’re fighting to preserve the integrity of the individual and uphold each person’s potential strength. When you understand this…you grasp the human experience in a way that I think equips you to work with all human beings.”
  • And, most importantly: “as care givers our responsibility is to see the worth of each person as a human being and to give them all you’ve got. And you can’t just give them cold and detached attention-even if it meets the technical standards of good care. There has to be some feeling to it, some warmth. Even the down-and-out are very perceptive-of your beliefs, your philosophy, the way you treat them and the way you look at them.”

Chemistry experiment: analysis

In our Chemistry lesson on 26th April we carried out two experiments focusing on analysis.

The first experiment involved us coming up with our own method in order to identify five unknown solutions. The first step was to use blue litmus paper to identify which solution was nitric acid as the paper would turn red. Using this solution we then identified the sodium carbonate, as when the nitric acid was added to each solution, the sodium carbonate produced effervescence since carbon dioxide gas was produced. The sodium carbonate solution was then used to  identify the silver nitrate as upon adding, a dirty white precipitate (far right test tube in figure 1) formed while the other solutions showed no reaction. The silver nitrate and nitric acid were then used to identify the two remaining solutions, both of which were halide salts. The formation of a white precipitate indicated the presence of chloride ions and therefore identified sodium chloride (far left test tube in figure 1) while a yellow precipitate showed the presence of iodide ions and so indicated potassium iodide (middle test tube in figure 1).

Fig. 1 Positive analysis tests for experiment 1
Fig. 1 Positive analysis tests for experiment 1

The second experiment focused on identifying two salts consisting of Group 2 cations and which has different solubilities. Figure 2 shows the results, with the far right test tube showing a white precipitate that dissolved in excess ammonia, the second left test tube showing effervescence and the two remaining test tubes showing the formation of white and yellow precipitates.

Fig. 2 Positive analysis results for experiment 2
Fig 2. Positive analysis results for experiment 2

Overall, I think I preferred the first experiment because the fact that you had to come up with your own method meant that you had to think about the experiment more carefully and concentrate on what you were trying to find and what steps you should carry out in which order.

 

 

Biology experiment: Antibiotics

Although we did this experiment a while ago (22nd March ) I’ve finally grabbed a moment to write about it.

The experiment involved producing a pour plate and since microbes are always present in the air, we worked around a lit Bunsen Burner which produced upward air movement to try to minimise the risk of contaminating the plates.

We produced two pour plates to investigate: one with Escherichia coli and the other using Micrococcus luteus. To both we added an antibiotic susceptibility testing ring and left the pour plates for a week.

Fig. 2 Pour plate using E. coli
Fig. 1 Pour plate using E. coli

 

Figure 1 shows the pour plate with E. coli. There are two very clear exclusion zones around the cefoxitin and streptomycin antibiotics which shows that these antibiotics were the most effective in killing the bacteria. Although the photo it is not very clear, you may still see a halo effect around the streptomycin and one reason for this may be antibiotic resistance. For me this was surprising to hear but also very enlightening on the issue of antibiotic resistance. If antibiotic resistant bacteria can be cultured in school on a simple pour plate, how are we going to control the increase of antibiotic resistant bacteria on a greater level, especially in the health industry? Although this has been an ongoing problem for a number of years, I don’t think I have ever realised the impact of this until one of my friends wrote a post about the subject. One of the main take away messages was that if the problem continues to grow, the practice of medicine is going to have to change. How can surgery be performed if the main way of treat bacterial infections is useless?

Fig. 1 Pour plate with M. luteus
Fig. 2 Pour plate using M. luteus

So, coming back to the pour plates. The other pour plate was less successful as M. luteus is very hard to culture and so the effect of the antibiotic is less noticeable. In addition the white ‘splodge’ that can be seen in Fig. 2 shows that the plate has been contaminated. It is most likely to be some form of fungi because on close observation the ‘splodge’ was furry.

Overall it was a very interesting experiment to carry out, not only because I have never produced pour plates before but also because of the results it produced.

Hello

So, here we go!

As you can see this is my first post on here so I’m going to take the opportunity to let you know what I’m planning for this blog to be.

I am an aspiring medical student and have a keen interest in science so I just really wanted a space somewhere to get my thoughts down.

At the moment I’m sure whether this blog will focus on something more specific or remain fairly open, but I’m hoping to be posting about any books I read or articles I find, anything which grabs my attention in class or just general thoughts.

I’ve started this blog before exam season to, in a way, actually make sure I do it because it’s an idea I have been thinking over for a while. However this also means blog posts will not be regular (not sure if they ever will be!) and I am hoping to do an ‘About Me’ type of page if you want to know a little bit more about me, however again I am not sure when this will be complete.

So, I guess all that remains for me to say is thanks for reading and coming along for the ride!