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. Read More
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. Read More
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.
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: Read More
This is Part 1 of my response to Dr Dennis Venema’s second Biologos Blog “Adam, Eve and Population Genetics: A Reply to Dr. Richard Buggs (Part 2)”. Dr Venema was responding to my blog at Nature Ecology and Evolution Community about his book Adam and the Genome. Since Dr Venema’s Part 1 blog responding to me, a vigorous debate has been ongoing on the Biologos Forum here. This debate is now beginning to come to a conclusion, so I have a bit of time to respond to the Part 2 blog by Dennis, which branched out from the Forum debate. Here is Part 1 of my response.
Just before Christmas, I was interviewed by Howie Shannon for The Economist’s “Babbage” podcast. Here it is!
This is my response to Dennis Venema’s Biologos blog that he posted after I published my email and blog at Nature Ecology and Evolution Community about his book Adam and the Genome. This text is also placed as a comment under Dr Venema’s blog post on the Biologos blog page.
I am glad that we are now establishing a dialogue about the scientific credibility of a bottleneck of two at some point in the history of the human lineage. I am hoping that during the course of this discussion we will be able to examine in detail the claims that you make in chapter three of Adam and the Genome, and that you will respond to all the critiques and questions that I have raised in my email to you and my blog at Nature Ecology and Evolution Community.
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. Read More
This blog was first posted at Nature Ecology & Evolution Community on 31 October 2017
Last week in Stockholm the forest geneticist Prof. Ron Sederoff was awarded the Marcus Wallenberg Prize. Informally known as the “Nobel Prize for Forestry”, this two million Swedish Krona award is presented by the King of Sweden each year. It is the first time for a decade that the prize has gone to a biologist.
In the 1980s, Ron Sederoff realised that molecular genetics had the potential to transform research on trees. Read More