Genomics News Research

A genetic basis for COVID susceptibility

A paper published yesterday supports a hypothesis that Richard Nichols and I made in March 2020. We published an article in The Conversation arguing that we need to know if someone’s chances of severe COVID symptoms are affected by their genes.

We suggested:

“It may be that just one or two genes are involved. Perhaps broken genes involved in the immune system or lung cell surfaces…It may be that there are thousands of genes involved. Perhaps a complex mix of genes involved in lung physiology, upper respiratory tract shape, and many other things we have never even thought of.”

Yesterday, the journal Science published a paper that begins to confirm this. It reports the discovery of broken immune system genes in some patients that have severe COVID symptoms.

The paper, titled “Inborn errors of type I IFN immunity in patients with life-threatening COVID-19” gives evidence that thirteen genes involved in the immune system have loss-of-function variants in a subset of patients with severe COVID symptoms.

An accompanying paper, titled “Auto-antibodies against type I IFNs in patients with life-threatening COVID-19” gives additional evidence that type I IFNs are critical to the body’s immune response to COVID. Impairment of their functioning leads to more severe symptoms in the patients they studied.

These studies are based on relatively small numbers of patients, and only studied a handful of genes that seemed likely from the outset to be involve in COVID immunity. If genome-wide association studies were conducted on large numbers of patients, as Richard Nichols and I suggested in March, we may discover that the 13 genes reported yesterday are just the tip of the iceberg.

Genomics News Research

Could we predict personal coronavirus risk from our DNA?

This article, co-authored with my colleague Prof. Richard Nichols, was published at The Conversation on 17th March 2020. Since then, Science has published a news article about efforts to do the type of studies that we advocated. NB. This is not about testing to see if we have coronavirus – this is about testing how badly affected we would be if we got it.

Coronavirus: sequencing the DNA of patients screened for coronavirus might save lives

Scientists should start sequencing the genomes of coronavirus patients. We should look for DNA differences between patients who are severely affected and those with mild symptoms. This could allow us to predict who else would be vulnerable and advise them to take precautions. We may be able to use this knowledge against the coronavirus epidemic before a vaccine is widely available.

Evolution Faith

Did Darwin make atheism credible?

Imagine that my wife and I walk into our living room one morning to find that our son’s toy box has fallen over, and pieces of BRIO train set track lie jumbled on the floor. But eight of the pieces are joined together in a perfect circle, lying on the floor, with a train on top of the tracks. My wife asks me: “Did you make that railway?” I say “No – it must have been you”. She says it wasn’t her. We look at each other for a moment, thinking and then we come to two different conclusions.

My wife is worried and says: “Someone must have come into the flat last night. Railways don’t just spontaneously appear from a jumble of fallen pieces. We need to check my jewellery is still there.”

I shake my head and say “This is evidence that there are billions more BRIO sets in the world than anyone has realised. I am going to call a stockbroker and buy some shares in BRIO PLC.”

“Are you crazy?” my wife asks.

Bottlenecks Faith Genomics

Adam and Eve our ghostly ancestors?

This blog was first posted at Nature Ecology & Evolution Community on 4 March 2020

That a single couple could be the ancestors of all living humans is widely seen as an area of conflict between genetics and the Abrahamic religions. Though little detailed attention has been paid to this idea in the scientific literature (see ‘Adam and Eve: a tested hypothesis?’), current models of the history of genomic variation in African populations tend to forbid a bottleneck of two in the human lineage within the last five hundred thousand years (see ‘Adam and Eve: lessons learned’). Thus, belief in a literal pair of ancestors for all humans would entail an older date for Adam and Eve than believers had expected, or a revised understanding of human molecular evolution.

In a recent book, The Genealogical Adam and Eve, S. Joshua Swamidass, an Associate Professor at Washington University in St Louis, Missouri, seeks to resolve the dilemma faced by believers. He makes a major contribution to the debate, taking both sides seriously. Swamidass is a Christian himself, and a well-established scientist in chemical bioinformatics and drug metabolism. He has clearly read widely and deeply in evolutionary genetics. He outlines his ideas with caution and many references to the literature. He deserves a hearing by anyone who is interested in a better relationship between science and religion.

Environment Faith

Unselfish gardeners? Christianity and the environment

Human degradation of the natural environment is a great tragedy of our time. One of its major drivers is selfishness leading to over-consumption and waste. Despite growing concern about the environment, the majority of us struggle to forgo convenience and consumption for the long-term good of the planet.

Genomics Research

Lost elms of Kent

Mature elm trees in the English landscape are something I and many other have never seen. Dutch Elm Disease killed them all in the 1960s. Only the older generation can remember what we have lost. Browsing through some local photos from the 1930s this weekend, my eyes were opened to the size and grace of the elms that once existed. Here are some of those photos, from Capel, Kent. Beneath each one I show a picture of what the scenes look like today.


How to lead a journal club

Getting together to discuss a published paper is a classic way of keeping on top of the literature and training students how to read it.

During my postgraduate studies I went to a journal club every week organised by my PhD supervisor. It was here that I learned how to read a scientific paper, and gained confidence in critiquing published studies. Now I run a journal club for my MSc students, and sometimes (but not often enough!) for my PhD students. Here are some tips I give my students before they lead a journal club meeting.


How similar are human and chimpanzee genomes?

I recently participated in a discussion on the Biologos forum on the degree of similarity between the human and chimpanzee genomes. I was asked for my current view on this issue by Dennis Venema, who had found a old quote online from a newspaper article that I had written in 2008 on this issue. In 2008, in a couple of newspaper articles, I did some simple calculations based on the 2005 Chimpanzee genome paper. On the basis of these, I had come to the surprising conclusion that these data suggested that the human and chimpanzee genomes in their entirety could be only 70% identical. Dennis Venema asked me if this was still my view. You can read the whole discussion here. It is rather long, with lots of tangential contributions. If you want a quick summary of my perspective,  here is my final closing statement (which I originally posted here):

“How similar are the human and chimpanzee genomes?” is a relatively straightforward scientific question. We are hindered by the still somewhat incomplete nature of both the human and the chimpanzee reference genome assemblies, but we can make this clear in our assessments and allow for the uncertainties that it raises.

The best way to assess the similarity of two genomes is to take complete genome assemblies of both species, that have been assembled independently, and align them together. The alignment process involves searching the contents of the two genomes against each other.


Local parents should be consulted on the new Mortlake secondary school provider

Were parents properly consulted about the provider for a new state secondary school in Mortlake? As far as I can see, they were not. The Borough Council has prematurely chosen a provider that may not be suitable for the local area. This school is an exciting opportunity to improve local education. For the good of our children, need to get it right.

As a local parent, I am not satisfied with the process that has been followed, and I am not convinced that the chosen provider is the best fit for the area. This will be my family’s closest secondary school, but I am deeply concerned that it will not be the right one for us.

Bottlenecks Genomics

Adam and Eve: lessons learned

This blog was first posted at Nature Ecology & Evolution Community on 14 April 2018

Preliminary conclusions about the possibility of a short, sharp human bottleneck

A few months ago I asked this community if modern genome science had tested an “Adam and Eve” hypothesis that the human lineage has passed through short, sharp bottleneck of two at some point in its history. While this question may sound bizarre to some, it is one that is often asked by those with a background in Abrahamic faiths. My post has therefore been taken up and discussed extensively on the Skeptical Zone and Biologos Forum over the past few months, as well as by various blogs.

The claim that genomic methods have been used to test and reject an “Adam and Eve” hypothesis was central to the recent book Adam and the Genome. My post, which critiqued the arguments made in that book, has received a broad level of explicit or tacit agreement in subsequent online discussions. More adequate ways of testing the hypothesis have been suggested, and preliminary results have been obtained.

Here I will share some of the lessons I have learned from these discussions and from further reading. These are somewhat tentative, and not all are based on published peer reviewed literature. In a short blog I cannot do not do full justice to all the contributions that have been made by various scientists within the online fora, so as far as possible I will try to provide direct links to the contributions of others.

Here are the lessons I have learned so far: