This is the blog of Neil Ingram and reflects a variety of my interests over the years. As a biology teacher, university academic, examiner and author.
I have been deeply interested in the use of IT in schools when Windows 3.0 came out in May 1990.
About ten years ago, I was invited to be part of the Hewlett Packard Catalyst initiative and I developed a model about how school pedagogy could work in the Web 3.0 world. Some of this has been published, but quite a lot has not.
The development of Artificial Intelligence systems is generating the same levels of excitement as Windows 3.0. As the CEO of Microsoft said, “It feels like the 1990s again!“.
I have developed an introduction to the thinking:
Pedagogy AI is a roadmap for the pedagogy of a lesson using AI with students.
This is based on the ideas in a series of ten linked posts, called Teaching and learning with AI.Part one is here.
To show you round the rest of the site:
Stories from Nowhere was a lockdown project, trying to use stories to bring important ideas into middle years biology lessons. It is built on observations in a wood and work we were doing on a 16-19 curriculum framework for the Royal Society of Biology
Exploring the epigenetic landscape is a microsite about how genes interact with the environment and uses the ideas of Conrad (Hall) Waddington.
The home page contains a mixture of posts relating a university course I ran on genetics, society and education.
There are also posts on Evolution relate to a book I co-authored for Oxford University Press.
The title “tools for clear thinking” is based on a book by Conrad (Hal) Waddington, whose ideas run through every article on this site. The cover image was designed by Dall-E3, and the prompt included Waddington’s term “epigenetic landscape. I was delighted that its rendering resembled the original conception by the painter John Piper.
The Oxford Biology primer contains a number of case studies on the evolution of familiar and unusual organisms, from finches to giraffes, peppered moths to wood rats!
Here are some pages that give a feel for the book.
Darwin’s finches have captured people’s imaginations ever since he first described them. In the 1970s they hooked Peter and Rosemary Grant, evolutionary biologists who were interested in the forces that drive evolution. They thought Daphne Major, one of the smallest islands of the Galapagos, would be a perfect place to study selective forces because it is uninhabited, and so small they would be able to become familiar with every single bird on the island. Like Darwin, they went for two years: their research there lasted 40!
They began their studies on Daphne Major in 1973. Every bird was captured, a numbered ring placed on its leg, and they recorded other features such as beak size. The birds were called medium ground finches, Geospiza fortis. Their diet was mainly seeds, and they showed considerable variation of beak sizes, from relatively small to relatively large.
In 1977, there was a prolonged drought and many of the plants on the island died. Those that were left had very large, hard seeds. Heartbroken, the Grants could only watch as natural selection took place before their eyes and dozens of birds died of starvation. By the end of the drought they were amazed to see that the distribution of beak sizes in those medium ground finch adults which had bred the previous season had changed completely.
Look at Figure A. Can you see what happened during the drought? Only the birds with the bigger beak sizes survived. Furthermore, the distribution of beak sizes in the offspring was completely different to what it had been before the drought: the modal group had moved from 8.8mm to 9.8mm! Why do you think this happened?
In 2003, a drought similar in severity to the 1977 drought occurred on the island. However, late in 1982 a breeding population of large ground finches (Geospiza magnirostris) had become established on the island. This species has a diet overlap with the medium ground finch (G. fortis) and were competing for the larger seeds. Following the drought, the medium ground finch population had a decline in average beak size, in contrast to the increase in size found following the 1977 drought (see Figure B).
The Grants hypothesized that the smaller-beaked individuals of the medium ground finch may have been able to survive better this time by being able to eat smaller seeds, avoiding competition for large seeds with the larger ground finches G. magnirostris. The 2003 drought and resulting decrease in seed supply may have increased competition between G. fortis and G. magnirostris, particularly for the larger seeds which had enabled survival of the medium ground finches 25 years earlier. As they had larger beaks, the population of G. magnirostris had a competitive advantage when it came to eating the larger seeds. This led to the decrease in average beak size among G. fortis despite the drought conditions being very similar.
Darwin had hypothesized that the changes leading to speciation happen very slowly. Looking at the wildlife around us we get the impression that species stay the same from year to year, and this is probably why most people in the time of Darwin, including Darwin himself until after he’d returned from the Galapagos, did not believe in the transmutation (changing from one kind to another) of species. However, the Grants have demonstrated that perhaps we are simply not observant enough. Close observation of a species in the wild can show significant fluctuation in appearance, caused by the selection pressure of a mix of biotic and abiotic factors, over a relatively short period of time.
As Jonathan Losos, a Harvard evolutionary biologist, has observed, ‘Perhaps the biggest contribution of the Grants’ work is simply the realization not only that evolution can be studied in real-time, but that evolution doesn’t read the textbooks.’
The average PhD research project lasts only three years. What are the implications of this for studying long-term processes such as ecological change and evolution?
It is February 1908 and Reginald Punnett has just finished giving a lecture to the Royal Society of Medicine in London, when the unthinkable happens. He is ambushed by a question he cannot answer, posed by his enemies.
By 1908, Mendel’s ‘lost’ paper had been re-discovered for eight years. Punnett’s boss and mentor William Bateson, one of its re-discoverers, was making Cambridge the centre of the new “Mendelian genetics”. This annoyed a rival school of human geneticists based in London, centred around Karl Pearson. They called themselves the “Biometricians”.
The Biometricians were having an ongoing row with the Mendelians that was bitter and nasty. The row slowed down the acceptance of Darwin’s theory of evolution for many years.
There is a lot more about this fascinating argument and how it was resolved in chapter four of our book on Evolution published by Oxford University Press. You can find out more about the book here and on this website.
So, what was this killer question? Udney Yule hated Bateson and any idea of Mendelism, and he set Punnett a trap concerning brachydactyly. This is a medical condition where the fingers and toes are shorter than usual. It is caused by single gene and is a dominant characteristic.
Why, wondered Yule, innocently, if the condition was dominant, would we not expect to find three times more people with brachydactyly than normal length fingers, assuming random mating for this condition?
Punnett was stuck for an answer and burbled something about two Aa heterozygotes mating to produce more heterozygotes. This is true, but does not answer the question.
As luck would have it, the next day Punnett was playing cricket in Cambridge with the mathematician G.H. Hardy. Whilst they were waiting to bat, Punnett grumbled to Hardy about the question. Hardy is said to have scribbled a solution on a postcard, giving it to Punnett, with the comment, “I would have expected you and your colleagues to have known this already.” Hardy eventually published his solution in the journal Science in 1908.
So, what did Hardy write? Essentially, it was a new way of thinking about genetics. Mendelians studied the inheritance of characteristics in families produced by parents with known genotypes. The Biometricians did much the same with their human family trees. But populations are different: we cannot determine which individuals will breed to form the next generation.
The approach is to stop thinking about individuals and think about alleles instead. (In 1908, the terms ‘gene’ and ‘allele’ were not used, and Hardy did not use them, but it is easier, here, to use the modern terms.)
For a single gene, with two alleles, A and a, allele A is dominant to allele a. The frequencies of these alleles in a population are not known, so we can call:
the frequency of A = p
the frequency of a =q
(p+q)=1
Hardy pointed out that:
(p+q)2=12
(This is the binomial theory that is today taught in Year 12 mathematics.)
Expanding the equation:
p2+2pq+q2=1
This gives us the frequency of the genotypes:
AA = p2
Aa= 2pq
Aa= q2
So far, so good. But what about the next generation? Assuming random mating, each A allele is equally likely to combine with allele A or a. So, using Mendel’s method:
Allele
A (p)
a (q)
A (p)
p2 AA
pq Aa
a (q)
pq Aa
q2 aa
The genotype frequencies in the next generation are the same as the previous generation.
AA = p2
Aa= 2pq
Aa= q2
Because the allele (and their genotype) frequencies stay the same, they are said to be in equilibrium.
Yule’s hypothesis was shown to be false, the frequency of brachydactyly in the population will stay the same, given certain assumptions. The frequency will change only if the assumptions are not true. These assumptions are:
random mating
no mutation
no immigration or emigration from the population,
large population size (N>10)
no selection of phenotypes.
By a cruel twist of fate, one month earlier, in January 1908, Wilheim Weinberg read a paper to a meeting in Stuttgart in Germany, in which he proposed the same equilibrium model. It was obviously an idea waiting to be discovered. History credits both people in the name ‘Hardy-Weinberg equilibrium’.
Punnett has been criticised for not thinking of the idea for himself, but this is rather unfair. Neither Yule, Bateson or Pearson saw it either, even though it develops directly from Mendel’s paper. At least Punnett recognised the problem and discussed it with Hardy, who was probably the best mathematician in the world. This is what excellent scientists do, they share questions and collaborate on answers.
Punnett became a professor of genetics and did important work testing the limits of Mendel’s ideas. In doing so, he and his colleagues discovered linkage and the effects of two genes on the same characteristic (epistasis). He was also able to improve the breeding of poultry. He was the author of the world’s best selling genetics textbook and introduced the Punnett square method of displaying crosses to the world. His students remember him as a caring and thoughtful teacher.
The world’s first Punnett Square from 1907
It just shows how useful cricket can be!
I am grateful to A.W. F. Edwards for his 2008 paper (Genetics 179: 1143-1150) for the inspiration for this story.
There are a number of case studies in the Oxford Biology primer on Evolution that are revisited several times in the first four chapters. This post illustrates this for the story of the evolution of the peppered moth. This is an iconic example, which is taught all over the world as an example of natural selection in action.
The book is beautifully illustrated and engaging. It is are aimed at 16 to 19 year olds who want to learn more and who may be contemplating a biological career. However, we also have several non-biologist and non-scientific adult friends who have bought and enjoyed Evolution.
The first two chapters explore natural selection and how it leads to evolution, as well as giving insights into those who played key roles in the story of the theory of evolution. For instance, did you know that there were two ‘parties’ in the early 20th Century who were at loggerheads with each other – the Mendelians and Darwinists?
The next two chapters focus more on types of evidence for evolution, as well as how the theory of evolution is itself evolving. Learn the latest on the story of how the giraffe got its long neck and how genomics is putting the cat among the pigeons of established consensus.
The final two chapters look at human evolution. After explaining what palaeontologists look for when they classify hominim fossils, the chapters go on to show how ancient humanity became a patchwork of small, very genetically diverse, groups interbreeding to eventually create Homo sapiens.
The book contains case studies, with opportunities to see the ‘bigger picture’ and regular stops to ‘pause for thought’. Each chapter ends with a summary, recommendations for further reading as well as broader discussion questions, suitable for individuals or use with classes. There is a useful glossary of technical terms.
You can purchase the book at the following online stores:
A recent review of the book on Amazon. A recent review of the book on Amazon
A 5* review from Kathy Freeston (@KJF239):
The Evolution edition of the new Oxford Biology Primers series was written with the intention to stimulate the curiosity and interest of A level students who may be considering studying life sciences at university. I found this book has met its objectives well and would recommend it to any student keen to further their knowledge beyond that covered at A level as well as any teacher looking to deepen their own understanding.
The book has six sections covering the birth & death of species, the evidence behind the theories, the changing views on the topic and human evolution. Alongside the main text each section includes well laid out diagrams and figures, discussion questions and suggestions for further reading. The discussion questions are designed to make the reader think about the section in more depth rather than the questions found in textbooks which tend to solely test knowledge.
The main text of the book tells a story rather than being a dry regurgitation of facts, and uses a more demanding level of literacy than the average A level textbook. It allows the reader to take their own knowledge and expand on it by putting ideas into the context of the time in which individual discoveries were made. The book uses many interesting examples to illustrate the complicated theory of evolution including modern research such as the mosquitoes of the London Underground and the beaks of Great Tits in the UK and The Netherlands.
Having an accessible, high level modern book on Evolution can only be a good thing to encourage young people into further study of this area of Biology.
