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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.

Categories
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.

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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.

Categories
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.

Categories
Genomics

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.

Categories
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:

Categories
Genomics News Oak Research

PhD studentship: Genomics of oak trees and their microbiota

I have just advertised a new PhD studentship opportunity on FindAPhD.com. I am really excited about this project, and we have a huge amount on data already in hand for the new student to analyse. Here is the project description:

Categories
Bottlenecks Genomics

Responding to Felsenstein, Schaffner and Harshman at The Skeptical Zone

Here is the text of a comment I posted at The Skeptical Zone in response to comments by Joe Felsenstein, Steve Schaffner and John Harshman on my Nature Ecology and Evolution blog on human bottlenecks:

Thank you all for interacting with my Nature Ecology and Evolution Community blog, and thanks to Vincent Torley for posting here. Vincent kindly sent me a personal email pointing out this thread to me and asking me to specifically interact with comments made by Steve Schaffner and Joe Felsenstein. I will also comment on John Harshman’s comments as he is making the strongest case against a bottleneck of two, which was not mentioned explicitly by Dennis Venema in his book chapter.

Categories
Bottlenecks Genomics

Adam and Eve: a tested hypothesis?

This blog was written for the Nature Ecology and Evolution Community where it is posted here.

Comments on a recent book chapter

Does genomic evidence make it scientifically impossible that the human lineage could have ever passed through a population bottleneck of just two individuals? This is a question I am asked semi-frequently by religious friends. With my current understanding of the genetic evidence, I can’t state categorically that it’s impossible. In this view, I find I differ from a recent book chapter on the topic. I’m writing this blog to run my thoughts past other biologists, and check I am not missing something.

Categories
Genomics Research

“Abundant bioactivity” of random DNA sequences?

This blog was written for the Nature Ecology and Evolution Community where it is posted here.

Probing the claims of a recent study

Readers of this blog will be aware of the recent Nature Ecology and Evolution paper entitled “Random sequences are an abundant source of bioactive RNAs or peptides”. Rafik Neme, the first author, posted an engaging Behind the Paper blog here.

On a quick look, I thought the study might be the beginnings of the solution to the mystery of orphan genes. (I posted about orphan genes here a few months ago.) The paper appears to demonstrate that an unexpectedly high percentage of random 150 base-pair DNA sequences are functional when expressed in E. coli. If true, this would suggest that de novo gene evolution could occur easily from junk DNA.