Monthly Archives: September 2012

Hadn’t been for a Portuguese PhD student, Fleming would never have discovered penicillin!

I am a bit tired of hearing about Fleming’s wonderful insight  in the discovery of penicillin. So I decided to tell the real story, so it can remain for posterity and for historians to rectify  the story.

“ Well,  I was a young PhD student at the  Hospital of Madrid” and Fleming was visiting.  I had a bad week since my bacterial colony would not grow. So I went the office of the Director which was my supervisor  to complain about the fact that there were moulds in the lab and they were growing on my plates inhibiting the bacterial growth. There was this English man sitting in the director’s office to whom I was introduced  as a Portuguese PhD student. I learnt that his name was Fleming.

The director asked me to show the Petri dishes and quickly decided that I should  drop  it in the rubbish and start again.  I asked for permission to  change my  PhD line of enquiry and  research why  that blue  mould  which I identified as Penicilium would not let the bacteria grow. The director just said NO and was adamant that I should throw it in the bin.

Then Fleming came to me and asked if he could have a look. I showed him the plates. He asked me if I wouldn’t mind if he kept the plates and took them to England.  Who was I to deny? After all I was just a mere PhD student! So he took the Petri dishes to England and the rest of the story is well known. Hadn’t it been for the stubbornness of my supervisor I would have been to one to have discovered penicillin and get that Nobel Prize. “

Then his face eyes became vacant as if he was  ruminating in that injustice.

I wondered for a bit  if this event could explain the quasi permanent darkness and numbness of his personality. But then I thought that it might be just because he was old and lonely.

Some months later Professor Manuel  Pinheiro  Nunes died. As far as I can remember he might have been as much as eighty something years old (maybe 82) and the year of his death might have been 1979 because this was the last year I was at the Faculty of Pharmacy having changed to the Faculty of Sciences to do Biology.

The night before he died we paid him a visit to check on his heath. He had caught a cold and the  maid was worried. He was in bed, looking very weak and pale. Then he said something like he had the visit of an angel the night before telling him he was going to die. He even commented about the experience saying that since he was an atheist, this angel might have been a creation of his mind.

I wanted to tell this story before I  forgot it. I think this should be included in the history of Fleming’s discovery of penicillin.

As the case of Pinheiro Nunes, I wonder how many more PhD and Graduate students go through similar cases, sparking research ideas on established scientists that end up taking all the credit.

I think that justice must be made to those who are creative and feed the ideas and works of others who later become famous, for without these ideas, they might never have thought about it.,_Manuel_Pinheiro

NOTE: This story was told by an 82 year old man. He  said this happened  in Madrid, but actually he was in Paris at age 32 doing his PhD but  when Fleming did visit Paris during that period.  It is likely that he made a mistake of memory when he mentioned Spain.

At this age memories may get confused in relation to places and times. But I think that the fact the he met Fleming might have remained strongly in his memory and doubting its veracity  it may be out of the question.


Every University Should Offer a Compulsory Course in Critical Thinking

Believing is a natural process of the human mind. Without beliefs we would not make sense of the world. They provide a framework to understand what we see and how do we make sense of it.  It has been argued by some philosophers and shown by studies in animal behaviour that animals- at least higher vertebrates- can also hold beliefs.

Beliefs have been traditionally addressed by philosophy and were defined as follows:  “A belief  is a mental state that predisposes the believer to accept some propositions as being true.” The problem with this definition is that it restricts the concept of belief acquisition to the transfer of information through sentences, as defined by the word “proposition”.  But if we understand proposition as any sort of information acquired by several sensorial means, then the definition can be applied to other animals beside humans.

However for the issue of critical thinking, the definition of belief as presented above is sufficient.

We all form beliefs because people told us things, or in an attempt to understand things we create theories that may explain what we see, hear or sense. Then, we may ascertain that these theories are true and live happy ever after. But what is “TRUTH”?

This is a question that is important to clarify in all areas of human understanding, for differences in what we perceive as being true are the main reason for social aggression. We all assume that what we believe in is true weather it is about common daily life events, or political, religious, social and scientific theories. We fight for what we believe in and in extreme cases, people kill for it.

Critical Thinking is a methodological approach that helps us to decide whether to accept or reject a claim. This method is applicable to mundane issues as well as to academic discussions. It also helps us to clarify the points we want to make and to build consistent arguments. Therefore all academic education should be accompanied by training in critical thinking. For example in scientific discussions, to know how to think critically is the foundation to many other disciplines which span from discourse analysis to statistics. Sooner or later every academic will be arguing for or against a theory of their like or dislike and in these disputes learning how to think critically is an essential part of putting forward an argument. If your argument is badly constructed and riddle with fallacies, it will  easily fall under the  weight of reasons and justifications that make more logical sense.

In my experience lecturing in several countries I have noticed that the not only undergraduate and graduate students, but many lecturers as well, are not trained in critical thinking. This is an anomaly that has been perpetuated by educational systems limited to a transfer of information from the books to the lecturer and from the lecturer to the students which assimilate the information uncritically just to repeat it in assignments and exams.

Universities in the UK insist that lecturers should assess the critical skills of the student and yet few lectures know how to assess it and even fewer students know how to be analytical.  As a way to go around this problem, lectures simply write their questions with the words “critically“in the question. For example, “Present a critical analysis of the argument offered by author of this paper”. Unless you had done a degree a philosophy, few students would be prepared to address the question. Students understand the word “critically” as bashing, attacking or abusing t what the author said, or the author itself.

We do not know what we are missing until we learn about it. For example, I was always very concerned about animals but having been born in a country riddled by ignorance perpetuated by the weight of the Catholic Church, I never knew that there have been philosophers, scientists and laws that shared the same concerns. I felt that I was awkward by the pressure of the beliefs embraced by the society I was raised in. It wasn’t until I left my country that I opened up my horizon and learnt that there was actually a science called animal welfare and many important and intelligent people did share the same type of concerns as me. I did not feel like an oddity anymore, I felt empowered.  As I studied more and more about animal welfare, I became aware of the immensity of the ignorance that surrounded me before.  I made my plea to teach people all over the world, people who cared but felt awkward among their peers, that there are many good arguments that they can use to support their beliefs, that animals and nature should be treated with respect.

We may feel that we are in the right but we may not know how to argue our case. Nobody is born a motivational speaker and much less knowing how to build convincing arguments. Critical thinking helps us to pinpoint the flaws of the arguments we don’t like or even our own claims. But this is acquired skill. We need to learn how to do it. There are analysis techniques that help us to improve our communication skills.

One day, by mere coincidence I picked up a book with the title “Critical Thinking”. I browsed through its pages and I was amazed by the content. It made me realise that there were things that I needed to know about how I interpreted what I read, how I decided what to accept or what to reject and how to pick up an argument that made sense from the range in offer whether they were about politics, ideologies, religion or science.

Critical thinking is a skill that needs to be trained. If we don’t, our intuition takes over rational thought and intuition is not necessarily right. It cheats us to believe in things that seem obvious but are no more than constructs of our own brains. Illusory correlations that suit what we are predisposed to believe in. For these reasons, critical think should be a compulsory discipline in all university courses, enabling the students to learn to think independently and creatively, to assess the good and the bad from other people’s ideas a theories and to make them able to argue for or against those theories.

I have taught some intensive Post Graduate courses at several universities in the UK and abroad. The courses were not compulsory, but the students who attended came out of the course asking for more.  So I decided to create an online  course in critical thinking that  discusses in detail the issues that we only have to time  address superficially in the  intensive courses and workshops. This online course will be available from January 2013. More information can be seen here:










What do I want from a beginners course in Statistics

Sometimes I am led to think that statistics was invented by some ugly sadist who feels a secrete pleasure in making us –normal mortals-feel inadequate.

First let us understand where do I come from. I am a biologist who managed to avoid Statistics courses as much as possible. I ran away from numbers as the devil from the cross! But when I decided to do a PhD I realised I couldn’t avoid it anymore and Stats was something that I had to learn very, very quickly.

Well… I bought a series of books and started reading them, just to reach the end of the chapters on descriptive statistics and put it aside. It was a hopeless battle. I went to some post-graduate statistics courses and again, they could as well be teaching me Chinese!…
I developed a aversion against stats, and an inferiority complex only to learn that I was not alone. Then I started wondering why so many people would feel the same as me in relation to stats. In my carrier I have met many people who completed PhDs in science and still claim they haven’t a clue about statistics.

A opened a statistics book again when I was asked to teach a course on methods in animal behaviour. There were other courses I was happy to lecture, but they came in a package and refusing to teach methods in behaviour would imply that I would not be able to lecture the other issues that I liked so much. So I went back to my search for the perfect book in statistics.

I goggled Statistics for dummies, Statistics with and without  tears,  but nothing!  Attempting to learn statistics alone usually ends up with tears! I couldn’t find a book that answered my questions about statistics. But on day I stumbled on the book by Dytham, C. (2003) Choosing and Using Statistics: A Biologist’s Guide. Blackwell Publishing. This was an great day. The book skips  all the unnecessary mathematical complications on how do we end up in the formulas for standard deviation, Person’s coefficient and so on and instead it focuses  on explaining when and why should we use a particular statistical test .

In fact, this is what I was looking for. I don’t care about how  the formula for a Pearson correlation or the sum of squares look like. I need to know about the sum of squares as much as I need to know the screws and bolts propelling my car. I need a car to go from A to B and eventually I just need to know when to change the oil and fill it up with petrol. I don’t need to know the chemical composition of the oil and where does it go in the engine.

The same way I don’t need a mechanical engineer to teach me how to drive a car I also don’t need a statistician to teach me how do we arrive at the formulae to calculate standard deviations and all other statistical opacities. The only think I need to know is what is the meaning of those statistics. What does it tell me about my data? Do I need to know if my data is normally distributed? Yes… but once I know the answer I just use this information to determine what type of tests should I use to test my hypothesis. I care as much about the formulae that enables me to calculate normality as I care about how to calculate the square root of 456 by hand. This is what calculators and stats programmes are for. We just have to insert our data on a spread-sheet and then click on an off the shelf statistics test included with the package.

To me the goal of learning statistics is not about learning how the test works, but what the results mean. What do these tests tell me about my data? I think this is where people that teach statistics get it wrong. They start by giving us all sorts of unnecessary information that does not provide  much help on how to interpret our data and results. Especially, what we need to know is the meaning of the tables displayed at the end of an analysis provided by the package.

I have questions such as “why are degrees of freedom always presented as n-1?

“Why not n-2 or n-35 for that matter?” .What are degrees of freedom any way? What are they for?

The other problem with  statistics courses is that  they start  without providing an overview of probabilities. And her we are we looking at  something like P<0.05 without having a clue what the P stands for.

Many people just memorised a rule of thumb; if they get something like P<0.05 that is a good thing ! It  confirms what they wanted to prove. This is not good enough!

It wasn’t until I started teaching critical thinking in science, and issues about causal reasoning and bias that I finally understood the philosophy behind the need for statistics.
It felt as if I had been living in a hazy landscape where the statistical formulae where nothing more than the grey contours of trees in the horizon. And now, the sun is starting to shine through the clouds and I realise that those trees actually have green and interesting leaves.

I think that statistics is hated because there are few people who can explain it properly. Statisticians may well know a lot about statistics, but in my experience they have great difficulty in conveying that information to beginners.

My suggestion to teachers of statistics is to start by explaining the principles of the scientific method. Teach first how to generate hypothesis and how and why attempt to refute them.

Many of people I have talked to about statistics, have difficulty understanding that they are trying to  refute a hypothesis. They start their research by wanting to prove that what they believe is true rather than attempting to disprove it.

Actually what we attempt to do with statistics is not to prove that the alternative hypothesis is true, but that the zero hypothesis is likely to be false.

Usually when people start doing research their first instinct is to seek confirmation of their theories and this is the wrong approach. These concepts are necessary to understand even before we start calculating means, medians and modes. They are the framework that holds the whole picture. Otherwise statistics becomes nothing more than some incomplete blots on an impressionist aquarelle.

When I was teaching methods in behaviour a created a power point from the Dytham, C. (2003) book which I gave away to many graduate students struggling with the very same conceptual problems that I had when I stared doing science. I got a positive feedback. Many said that this PowerPoint helped them to put all the tests they read about in papers, in perspective. The slides also provided some complementary help to the book.

The problem with books is that they are static. Especially when they present a load or numbers and graphs. All those numbers feel like visual pollution or like a pneumatic driller in the street  when you are trying to listen to Beethoven. But when we see the numbers and explanations appearing progressively in animated slides and the graphs start taking shape before our eyes then things start making some sense.

This PowerPoint is not yet complete, but I am just giving you access to part of what I have done so far and I would like to ask you if this helps.

Statistical Tests

Clarifying SASHAR

Secularism, Atheism, Scepticism, Humanism, Agnosticism, Rationalism

SASHAR is a made-up word for the six concepts expressed above

When I started to get an interest on issues about religion, I noticed that different concepts were used as equivalent. For example in the atheist literature, it is common to find the SASHAR concepts as interchangeable or equivalent.But things are more complex that that. Here are some definitions that may help to understand the differences and similarities between these concepts:


It is common to hear people referring to secularists as an equivalent of atheism. This is wrong!
Secularism is the concept that government or other entities should exist separately from religion and/or religious beliefs. In one sense, secularism may assert the right to be free from religious rule and teachings, and the right to freedom from governmental imposition of religion upon the people within a state that is neutral on matters of belief. So the concept of a secular society involves the image of a religion free political and social system. Some ideas of modern secularism were developed by deists.

Deism holds that reason and observation of the natural world can determine that a supreme being created the universe but it does not intervene in human affairs nor suspends the natural laws of the universe. Deists typically reject supernatural events such as prophecy and miracles, tending to assert that God (or “The Supreme Architect”) has a plan for the universe that is not to be altered by intervention in the affairs of human life. Deists believe in the existence of God without any reliance on religious authority or holy book or the need for organized religion.

Secularism is not a modern phenomenon. Its intellectual roots are believed to go back to Greek and Roman philosophers such as Epicurus (341 – 270 BC) and Marcus Aurelius (121-180 AD). During the Dark Ages, secularism was embraced by some medieval Muslim thinkers. For example Averroes (1126-1198) a Muslim polymath born in Córdoba (Spain). He is also known as one of the founder of medical principles. But it is during the Enlightenment (18th century) that secularism becomes a widespread ideology promoting the separation of church and state. Many Christians support a secular state.
So to claim that you are a secularist because you are an atheist is a non sequitur, since many believers can also be secularists. However, if you are an atheist you are necessarily a secularist.


Scepticism refers to an attitude in relation to accepting information without subjecting it the scrutiny of reason, rejecting magical thinking, superstition and other irrational beliefs. Experience is often a poor guide to reality. Scepticism helps us to question our experience and to avoid being too readily led to believe what is not so.

There is indeed a philosophical school of thought known as Philosophical Scepticism. Sceptics critically examine the meaning systems of their times, and this examination often results in a position of ambiguity or doubt.

The earliest sceptics can be traced back to Pyrrho of Elis ( about 360 BC) a Greek philosopher who felt uneasy by the disputes between all philosophical schools of his day. According to a later account of his life, he became overwhelmed by his inability to determine rationally which school was correct. Zen Buddhism has also been described as a form of ancient eastern scepticism since it is not concerned with whether a thing exist or not.

Modern scepticism is associated with critical thinking and is one of the ground stones of the scientific method.

Some people, such as scientists for example, can reconcile their belief in a divinity or some sort of magical thinking about the power of crystals and the stars and some dose of scepticism about the events that punctuate their daily lives and the surrounding world. It is like if they compartmentalized their thought process. When they are in the lab they use the principles of scepticism and apply them with minutia to their scientific research, but once their hang their white coat behind the door and go home, leaving their scientific credentials together with heir scepticism in the drawer of their office desk.

Other people apply scepticism to all areas of their lives, making it difficult to accept the existence of entities with magical powers that could have an effect on their decisions and daily activities.

So, one could describe himself as being sceptical, but still accept the probability of the existence of some divinity. This brings us to the definition of agnosticism.


Agnostics are sceptical about the veracity of claims that ascertain the existence of any deity. In consequence, they are also doubtful about the truth of religious and metaphysical claims.
According to agnosticism it is impossible to make any sort of judgments about things that are unknown.

Agnosticism is much more than an attitude towards religion. The very word agnostic means without knowledge (a= without gnosis= knowledge). The word was coined by the English biologist Thomas Henry Huxley –also known as Darwin’s bulldog- in 1869. However the points of view sustained by agnosticism were promoted as early as the 500 years BC. Protagoras (490-420 BC) a pre-Socratic Greek philosopher is usually referred as one of the earliest known agonistics. “He is also believed to have created a major controversy during ancient times through his statement that “man is the measure of all things”. This idea was revolutionary for the time and contrasted with other philosophical doctrines that claimed the universe was based on something objective, outside the human influence” (see Wikipedia).
Agnosticism is the most rational standing when we cannot prove the existence or non-existence of things.
Logically it is impossible to prove a negative, therefore it does not make sense to see proof of the non-existence of something. However we can never be sure that this particular “something” does not exist. For example, until the discovery of New Zealand, Europeans believed that ALL swans were white. If someone suggested the existence of black swans, an agnostic response would sound like this: “ I cannot prove that black swans exist, but I cannot prove that they don’t exist either” . Then they found black swans in New Zealand!

Thus it mean that I could also believe in the existence of rainbow coloured swans? What would be the most reasonable answer?

Religious agnosticism applies the same line of reasoning to the existence (or non-existence) of a deity. Agnostics simply assume that it is impossible to know if God exists or not.

Some people would describe several categories and degrees of agnosticism which would ultimately lead to atheism.

Increasing levels of conviction about the non-existence of a deity.


The difference between agnosticism and atheism is that while the first claims that they do not know about the existence of a deity, the latter are sure that such a deity does not exist.
Nowadays atheism is often associated with the New Atheist movement (which I’ll discuss in detail in later blogs), but atheism is not a recent phenomenon. It was present in Classical Greece when the first philosophers attempted to explain the world in terms of the processes of nature instead of by mythological accounts. The 5th and 4th centuries BC were prolific in generating thinkers with atheistic views.

There are also a number of atheistic religions. They are considered atheistic because they have no God or deities. For example Paganism, Animism and Pantheism are atheistic religions in that sense that there is no personified Gods.
Some religions of the Far East focus on a contemplative life not revolving around the idea of gods. For example, Jainism, a religion believed to have raised about 3,000 BC does not have the concept of God. Other religions such as Buddhism, Taoism and certain sects of Hinduism also offer alternative life paths not cantered on the worshiping of a deity.


The term “humanism” can be confusing because it has expressed and different intellectual movements have been identified with it over time.
Humanism is philosophical school that focuses on human values and concerns focusing on moral virtues such as humanity.

The roots of modern humanism go as far back as to the 6th century BC expressed in an Indian school of thought known as the Carvaka system which was atheist in nature, It did not merely question whether there was a deity, it asserted that there was not!

In Ancient Greece, Protagoras was perhaps one of the philosophers closest associated with the ideals of humanism. During the Renascence and the Enlightenment humanism focused on reforming education promoting rationalism and emphasising scientific studies.
Humanists sought to create a citizenry (frequently including women) able to speak and write with eloquence and clarity and thus capable of engaging the civic life of their communities and persuading others to virtuous and prudent actions (see Wikipedia).
The term humanism can mean several things, but in the modern context of religious debate it is usually perceived as a secular ideology which advocates reason, ethics, and justice, whilst specifically rejecting supernatural and religious dogma as a basis of morality and decision-making. This type of humanism is known as Secular Humanism which congregates people that seek to explain the events of the world through a rational approach.

In recent years there has been a raise in humanist societies and action groups which attract secularists, atheists, agnostics and sceptics leading the lay man to assume that the modern humanistic movement is an umbrella for the expression of atheist ideals.

The International Humanist and Ethical Union (IHEU) is an organisation that represents humanist societies spread around the world. The member organisations must abide by the following statement:

Humanism is a democratic and ethical life stance, which affirms that human beings have the right and responsibility to give meaning and shape to their own lives. It stands for the building of a more humane society through an ethic based on human and other natural values in the spirit of reason and free inquiry through human capabilities. It is not theistic, and it does not accept supernatural views of reality.”


In its modern sense, rationalism is a view that appealing to reason as a source of knowledge or justification for all claims. According to rationalism, knowledge and truth are acquired through the deductive method. The reliance of this method varies which promotes different degrees of rationalism. For example some philosophers defended that morality was a pure rational exercise, while others accepted the role of emotions in determining what humans may find morally repugnant. So while moderate rationalism assumes that “reason has precedence over other ways of acquiring knowledge”, extreme rationalism claims that “reason is the only path to acquire knowledge”.