I just committed to a big project that overlaps with my blogging activities (yes, I’m dropping a big hint as to what this big project might be). So until that project is near completion, I will not be posting any new entries.
How Assembly Theory can help us understand the Metabolism-First Theory of the origin of life
So a few weeks ago, I wrote a semi-critical post of Assembly Theory. There have been other criticisms leveled at Assembly Theory, some valid and some a little overblown. Despite all this, I do believe that there may be some use for Assembly Theory in further understanding and developing the Metabolism-First Theory of the origin of life. This post is dedicated to exploring these ideas.
Read moreAssembly Theory and “Selection”: A Failure in Interdisciplinary Science Communication
This past week a very provocative paper was published in Nature on Assembly Theory. What was provocative, was not just the main idea that was advanced, but also how this idea was presented by the authors. What jumps out of the page of their manuscript, for anyone who is even casually acquainted with concepts in evolutionary theory, is the use of the word “selection”. I discuss how selection is defined in standard evolutionary theory and how this differs from how this word is used by the authors of Assembly Theory.
Read moreDeterminants of genome size
A few weeks ago, I wrote about a thoughtful review of Larry’s book, “What’s in your genome” by Gert Kertof. One of the most interesting aspects what Gert wrote was his confusion about the determinants of genome size. Interestingly, he has all the pieces of the puzzle, but somehow doesn’t see the big picture. I’ll try to put together the facts in this post.
Read moreThe importance of charity in making forceful arguments
I really enjoy reading pieces written by smart, intelligent, thoughtful individuals, even if I do not agree with their conclusions. They make valid points and provide some useful perspectives on complicated issues. One case in point is this review of Larry Moran’s book “What’s in your genome?” by Gert Korthof.
What I would like to highlight today, is that his review brings up a valuable lesson: the importance of charity when advancing viewpoints that critique prevailing modes of thought.
Read moreAbbreviations are your enemy!
One of the aspects of the scientific literature that I despise is the ubiquitous use of abbreviations, acronyms, and invented terms. Please stop.
So why do scientists write like this? It all has to do with chunking. And if you understand that, maybe you can do something about it.
Read moreWhere I convince ChatGPT that junk DNA exists
ChatGPT is clearly confused about junk DNA. If it is able to access the vast amount of information on the web and has the capability to “evolve” over the course of a conversation, maybe I could get it to re-examine the issue.
Here’s my conversation:
Read moreThe most important number in human biology
There is one number that encapsulates our evolutionary history. It dictates the degree to which natural selection has shaped us. It has impacted how our bodies are put together, how our genome works, how we interact with parasites, and how susceptible we are to disease. It is instrumental to understanding what is, and isn’t functional in the genome. It is the most important number in human biology.
Read moreRobin Reed
In the past week I learned that Robin Reed had passed away. Although we had a rocky relationship, I owe my own personal scientific journey to her.
Read moreDoes the EES chalenge the Modern Synthesis? Or is it a tempest in a teapot?
There has been a lot that has been said about the recent Guardian Article on the group of evolutionary biologists who claim that the Modern Synthesis needs an update and should be replaced by the so called Extended Evolutionary Synthesis (EES). Interestingly, the reaction of most evolutionary biologists is not a rejection of these new ideas, but rather “meh”. Hardly the response you would expect from a direct attack on the core guiding principle of the biological sciences.
Read moreThe Blank Slate and the Swiss Watch: two widely held but incompatible views
Some thinkers believe that differences between human cognitive function, such as intelligence, are due solely to environmental differences. Other thinkers believe that the genome is filled to the brim with functional units that are exclusively shaped by natural selection. Although I do not know this for a fact, I believe that many thinkers, including many life sciences researchers, hold both of these beliefs. What these individuals fail to recognize is that these two views are mutually incompatible.
Read moreNeutral theory, genotypes and phenotypes
At the molecular level, much of our evolution is dictated by the random drift of nearly neutral genetic changes. How this applies to phenotypes has remained controversial. New data from GWASs (Genome Wide Association Studies) clearly show that slightly deleterious mutations undergo random drift in a way predicted by neutral theory. So neutral theory is really a thing, even at the level of traits and phenotypes.
Read moreArguing with Junk DNA deniers. Part 1: The Onion Test
Too often reviews on lncRNAs begin with the same old tired trope: “junk DNA was long dismissed as useless, but now we know better”. Do you? And more importantly, do you really understand where the idea of junk DNA came from? If you want to engage in this debate you really have to understand key concepts that support the idea of junk DNA. If you do not, and simply sidestep all of these issues, then you are not really engaging in debate. You are just ignorant. In this post we look at the first concept that junk DNA deniers must contend with: The Onion Test.
Read moreThe doorstop fallacy
Once upon a time a researcher walked into the office of one of his colleagues. He was amazed to see that his colleague’s door was propped open by a stone. He then exclaimed “I finally figured out the function of all these darn stones. They are all doorstops!” This parable mirrors the logic that can be found in a great number of reviews on lncRNAs. But why? I suspect that there are a few reasons …
Read moreWhy extracurricular activities can make a difference
I am often in a position to give advice to young scientists who want to know, how did I become a professor. In these discussions it is always important to remember one key aspect of life: luck. But you can always build your luck. And often this can be accomplished through extra curricular activities.
Read moreThe frustrated gene, the frustrated writer
Recently, my grad student and I published an article that articulates a number of ideas that have been bouncing around my brain for quite some time, “Non-Darwinian Molecular Biology”. While writing this piece, I wanted to bring up some great conceptual ideas that I had read in a perspective on the relationship between the evolution of elaborate gene expression machinery in eukaryotes and selfish DNA. The problem was, I could not remember who wrote this perspective or where it was published …
Read moreScience and trust: why most sci comm gets it wrong
New social media platforms have encouraged the proliferation of science communicators who practice “Sci comm”. Many of them are great. But most are mundane. Worse of all, there is this belief that Sci comm should simply take in scientific findings, process these into easily digestible forms and wrap them up in a nice sugary coating so that they can be easily digested by the masses. This is what I like to call the “golly-gee-wiz” presentation of science. A less charitable description would be the infantilization of science. Ultimately, the scientific endeavor is never really discussed in a serious manner in the public sphere. How can we change this …
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