Tag Archives: Genetics

Evolutionary enamel loss linked to molecular decay of enamel-specific gene

The evolutionary history of mammals can be reviewed as the evolutionary history of tooth loss. The early mammals had many teeth, and every now and then in evolutionary time, a tooth is lost wiht subsequent species arriving from that n-1 toothed form having that smaller number of teeth. With ver few exceptions, no mammals have added a tooth during the history of mammals. (Excepting maybe the very very earliest period, but probably not.)

ResearchBlogging.orgWell, the loss of enamel itself is also an evolutionary trend in mammal history, and recent research published in PLoS Genetic associates genetic changes over time with what is known of the morphological evolution of mammals.

Continue reading Evolutionary enamel loss linked to molecular decay of enamel-specific gene

The Three Necessary and Sufficient Conditions of Natural Selection

Natural Selection is the key creative force in evolution. Natural selection, together with specific histories of populations (species) and adaptations, is responsible for the design of organisms. Most people have some idea of what Natural Selection is. However, it is easy to make conceptual errors when thinking about this important force of nature. One way to improve how we think about a concept like this is to carefully exam its formal definition.

In this post, we will do the following:

  • Discuss historical and contextual aspects of the term “Natural Selection” in order to make clear exactly what it might mean (and not mean).
  • Provide what I feel is the best exact set of terms to use for these “three conditions,” because the words one uses are very important (there are probably some wrong ways to do it one would like to avoid).
  • Discuss why the terms should be put in a certain order (for pedagogical reasons, mainly) and how they relate and don’t related to each other.

When you are done reading this post you should be able to:

  • Make erudite and opaque comments to creationists that will get you points with your web friends.
  • Write really tricky Multiple Choice Exam Questions if you are a teacher.
  • Evolve more efficiently towards your ultimate goal because you will be more in control of the Random Evolutionary Process (only kidding on this third one…)

Continue reading The Three Necessary and Sufficient Conditions of Natural Selection

BBC: DNA mutations followed by selection does not lead to new species!?!?

In an BBC article describing a Royal Society paper on the rate of mutation in warm vs. cooler climates, the BBC made this statement:

DNA can mutate and change imperceptibly every time a cell divides and makes a copy of itself.

But when one of these mutations causes a change that is advantageous for the animal – for example, rendering it resistant to a particular disease – it is often “selected for”, or passed down to the next few generations of that same species.

Such changes, which create differences within a population but do not give rise to new species, are known as “microevolution”.

I suppose the BBC is into the Hopeful Monster theory or something.

Read it here, come back, and fight it out.

An important role for junk DNA????

Junk DNA is like bigfoot. If a zoologist says something like “Hmmm… it would be cool to find bigfoot” all the other zoologists jump on him or her, drag the poor sap into the alleyway, toss on a blanket, and beat the scientist with rubber hoses until the movement stops. Same with junk DNA. If you mention that junk DNA may have a use or a role or something …. INTO THE ALLY WITH YOU!!!

The difference is, there is no bigfoot, but there may be some interesting stuff happening in the so called junk DNA.

Part of the problem is in what we call “junk.” If it does something, it isn’t junk. So, for instance, there are genes where a string of codons code for a string of amino acids. But in order for that to happen, other parts of the DNA have to be involved … parts that are not the codons coding for the amino acids that will become part of the protein. That is obiovusly not “junk” but back a few years before these bits of DNA were understood, that was “junk.” You cans see the problem.

All of which is a long run-up to a press report from Princeton talking about a possible role for junk DNA. I’ll let the Princeton press report team speak for themselves, and then I’ll enjoy reading your comments:

To comment on this post, please visit this open thread on my old blogs. The commenting system on this blog is currently broken. Sorry for the inconvenience.
Continue reading An important role for junk DNA????

The Identification of the Two “Missing” Romanov Children Using DNA Analysis

I first became acquainted with the Romanovs (as historical figures, not the actual Romanovs) reading in middle school about Russian History. Later, someone turned me on to Massie’s Nicholas and Alexandra, which is quite a well known popular historical account of the last Czar of Russia and his family. Everyone knows the story of the end. The core of Czar’s family — the Czar Nicholas, his wife Alexandra, and his children — had been arrested and all of them were transported to a remote location in the Urals. A complex series of events had begun involving Czarist and Revolutionary forces. At one point, it occurred to the local revolutionary officials who were responsible for the incarceration of the Czar and his family that their execution would be a good idea, to avoid their recapture by Czarists forces in the area, and to break the loyalty of Czarist supporters still resisting the Revolution. So, on July 17th, 1918, the Czar and his family, their doctor and a nurse were escorted to an empty room in the compound in which they were being held and shot. The details are rather ghastly, as summarized by an eye witness to the event.
Continue reading The Identification of the Two “Missing” Romanov Children Using DNA Analysis

A dead gene comes back to life in humans

ResearchBlogging.orgWhy is there “junk DNA”? What is Junk DNA? What is a Pseudogene? What is Gene Duplication?

Goodness, you certainly do have a lot of questions. And some of them can be answered, or at least addressed, on examination of a very interesting new paper recently published about a gene that became a useless “pseudogene” a very long time ago and has recently been revived by evolution to serve once again as an active member of the community we know of as the genome. In humans.
Continue reading A dead gene comes back to life in humans

Evolution of the Lexicon

I recently posted about the work by Pagel and colleagues regarding ancient lexicons. That work, recently revived in the press for whatever reasons such things happen, is the same project reported a while back in Nature. And, as I recall, I read that paper and promised to blog about it but did not get to it. Yet.

So here we go.
Continue reading Evolution of the Lexicon

Why didn’t Darwin discover Mendel’s laws?

ResearchBlogging.orgPerhaps we are all subject to falling into the trap of what I call the Hydraulic Theory of Everything. If you eat more you will be bigger, if you eat less you will be smaller. Emotional states are the continuously varying outcome of different levels of a set of hormones, forming “happy” or “stressy” or “angry” cocktails. Your brain is a vessel into which life pours various elixirs. Too much of one thing, and there will not be enough room for something else. Even political arguments are hydraulic. The ‘balanced’ middle view between two arguments is like the mixture of contrasting primary colors on a pallet.
Continue reading Why didn’t Darwin discover Mendel’s laws?

Mutation Patterns in the Human Genome are More Variable Than Expected

I want to bring your attention to a somewhat dense and possibly inconclusive (but important) paper accompanied by a very informative overview in PLoS Biology, concerning mutations in the human genome.

ResearchBlogging.orgMutation rates and patterns of mutation are important for a number of reasons. For one thing, the genome itself is a data set that is both broad and deep. There is a lot of information in a given individual genome (a haploid set of genes from a person, for instance) but there is a wide range of variation in that information. So, inferences or assertions regarding the nature and distribution of genes or their variants cannot really refer to a single version of the genome, but must also take into account the variation in DNA sequences.

A very obvious area where variation is important is in reconstructing phylogenies. “Family trees” of populations or species can be reconstructed by estimating the genetic difference between pairs of samples, and from this, estimating the amount of time that has passed between a Last Common Ancestor and each of two later populations. These dyads (or triads, depending on how you count them) can then be pieced together to get a phylogeny … a graph representing the historical divergence of populations or species … that tells us a particular version of history. Obviously, the rate of mutation must be known or assumed to make this work. Variation in mutation across the genome, or across a population, or across the structure of the family tree itself will cause incorrect inferences.

The research paper is “Cryptic Variation in the Human Mutation Rate” by Hodgkinson et al. Here’s the key finding:

Continue reading Mutation Patterns in the Human Genome are More Variable Than Expected

The Perfect Bird Family Tree…

… is certainly still in the future. But we have seen a step in that direction in a new paper, coming out this week in Science. This research applies intensive and extensive genomic analysis to the avian phylogenetic tree. The results are interesting.ResearchBlogging.orgThis paper is summarized in a number of locations, most notably here on Living the Scientific Life. Here, I will summarize it only very briefly. However, there are two observations I would like to make about this paper and its apparent meaning. One has to do with the nature of science, and the other has to do with the nature of evolution in particular. I’ll argue that we can quantify (almost non-trivially) the number of times science is wrong. I’ll also argue that Stephen Jay Gould was wrong (not totally, but not trivially) about one of his most important assertions (other than his musings about the myth of vaginal orgasms … we’ll talk about that another time). Continue reading The Perfect Bird Family Tree…

Genome Size and Flight in Bats

i-68efa548cdb44e33126c5936c96fe3ed-evolution_2008.jpgContinuing with our discussion of the Evolution 2008 conference, I was hoping to meet T. Ryan Gregory yesterday. He is listed on the Evolution 2008 program as an author of a talk on genome size. Goodnews/badnews: Gregory did not show, but the talk, given by his coauthor working in his lab, was excellent, so we didn’t need him.The research was done, and the paper delivered, by Jillian Smith. The title of the paper was “Genome size evolution in mammals” but it was more focused on specific results Jillian had come up with regarding bats.i-3117c0a3e6ded7c6ab8d12c4393c42c2-bat.jpg

source
The bottom line is this: Genome size does not have a lot of function or interest other than simply knowing the size of the genome you are about to delve into on a research project (so it’s like knowing how far away your field site is so you can budget travel, or how big your grocery store run is so you can decide if you can walk to the store or drive, etc.). But there are a couple of ways in which genome size might be interesting in a way that relates to adaptation and/or evolution. Continue reading Genome Size and Flight in Bats

Biology Will Never Be the Same Again: Scott Lanyon

i-68efa548cdb44e33126c5936c96fe3ed-evolution_2008.jpgThe Evolution 2008 conference started out today with a special program for K-12 teachers (mainly life science teachers) organized by the Minnesota Citizens for Science Education (MNCSE). The opening speaker was Scott Lanyon, director of the Bell Museum of Natural History. (The Bell hosted this event.)i-360cbb04fb3ca5b4766c7598e92870d3-Scott_Lanyon.jpgScott’s objective was to outline several areas of evolutionary biology where fundamental changes had occurred over recent years. This was to provide perspective and food for thought for the Life Sciences teachers attending the event, and Scott was very successful in this effort.In each case, Scott described a similar trope … “Not so many years ago, understanding [this or that thing] was thought nearly impossible…. but today, look what we have….”Specifically, Scott, a bird phylogeny expert, outlined four areas of research corresponding to four major areas of evolutionary biology: Continue reading Biology Will Never Be the Same Again: Scott Lanyon

“US government gene guru to resign”

i-77a4808a182ec3600f39515d54605f2b-Francis_Collins.jpg

Photograph of Francis S. Collins
Just passing along the details from Associated Press:

WASHINGTON (AP) — The government is losing its gene guru: Dr. Francis Collins, who helped lead the breakthrough unraveling of the human genetic code — and found common ground between the belief in God and science — is resigning.Collins, arguably the nation’s most influential geneticist, announced Wednesday that he will leave the National Institutes of Health this summer, to write a book and explore other opportunities.The folksy geneticist helped translate the complexities of DNA into everyday vernacular. Collins led the Human Genome Project that, along with a competing private company, mapped the genetic code — or “the book of human life,” as he famously called it…..

Read the rest here.Here is part of an email from Collins: Continue reading “US government gene guru to resign”