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Genomicron

What's wrong with these figures?

Those of you who have been reading Genomicron for some time will have seen most of these already, but it seems worthwhile reviewing them here at the new blog. The game is simple: identify what is wrong with these figures which have been published in science magazines or scientific journals.

Bad quotes about evolution and genomics.

I hesitate to single out colleagues for what is attributed to them in the media, because often what one says in an interview is not entirely what appears in print.

Platypus sex chromosomes and basal-equals-primitive.

Evolution

There has been considerable interest in the publication of the platypus genome, which is good. Unfortunately, much of the reporting has been distorted, which is bad. However, rather than picking on the press, I want to focus on an example from the scientific literature where a misconception about evolutionary relationships seems to creep in and generate confusion.

Nonsensical headlines about the platypus genome.

I am swamped at present and have not had time to discuss the recent publications about the platypus genome. I had planned to wait and to talk about some interesting aspects, but the headlines are just too crazy to ignore.

Reflections on my first experience in scientific research

Biology

I often tell undergraduates about the importance of conducting research projects in their senior year if they intend to pursue graduate studies in science. There are two main reasons for this. The first is that the labs that they have experienced up to that point in undergraduate courses, though useful for introducing specific concepts, are a poor reflection of what real science is like. As such, it is important for them to experience original lab work, rather than simply following a pre-defined, "cook book" protocol with an expected result. Novel studies have no pre-defined sequence, no a priori expectation of the outcome, and in many cases no established methods in place for generating data. The second is that there are some important lessons that they need to learn about research, perhaps most importantly that whatever they try to do in the lab will not work the first time. The sooner they hit that wall -- and get around it -- the better. Nature does not give up her secrets easily, I sometimes say.

Grad student motivation cabinet from Fisher

Always on the lookout for new ways to motivate graduate students to get their work finished, I took note of this handy item while flipping through the Fisher catalogue in search of a flammables cabinet for the lab.

 

 

Evolutionary Applications and Evolution: Education and Outreach

In case you have missed them, two issues are now available for each of the new evolution journals:

Evolutionary Applications

GraphJam on website insanity.

I had mentioned GraphJam on the old Genomicron. It's like LOLcats for nerds. Erm, for even bigger nerds. This one seems highly apt, though ALL CAPS alone is usually sufficient.

 

Phylogenetic Fallacies: Branching From a Main Line

Evolution

In Phylogenetic Fallacies: Early Branching Must Mean Primitive I focused on the misconception that an "early branching" lineage was necessarily "primitive" (i.e., very similar to a distant ancestor). This time, I want to discuss something slightly more subtle, but nonetheless important, with regard to interpreting phylogenies. Specifically, I want to note a problem with the very concept of one lineage "branching off from" another lineage. There can be a tendency to consider evolutionary trees as reflecting a main line with a series of "side branches". This is especially true when the tree is "unbalanced" (lineages are depicted with uneven amounts of diversity) and "ladderized" (the more diverse branches are placed on the same side of each node). The following is a general unbalanced, right-ladderized tree.

Whose genome?

Genetics

The term "genome" is oft-heard but seldom defined, and indeed has more than one meaning. Little wonder, then, that discussions about genome sequences and comparisons thereof can leave otherwise interested audiences more frustrated than enlightened. "What is a genome?" and "whose genome was sequenced?" are legitimate questions, and what follows is an attempt at clarification that is, by necessity, as much philosophical as scientific.

Definition #1: In a broad sense, a genome can be considered as the collective set of genes, non-coding DNA sequences, and all their variants that are located within the chromosomes of members of a given species. This definition does not consider variation among individuals within a species, and instead relates to distinctions between species.

Is this a blog or a column? Yes!

Well, the move to the new site has gone ok, though it seems some old readers are a bit unhappy. All I can say is that the site is a work in progress and that some exciting changes are in the works.

RSS woes.

We're working on connecting the feed from this new Genomicron to the Feedburner feed so that everyone gets counted, but obviously there's something funny going on in the meanwhile. Here is how my Feedburner subscriber totals have fared since the move.

Guide to translating scientific papers into plain English

Humor

Believe it or not, scientists do not always take themselves too seriously. We can laugh at ourselves and the sometimes rigid conventions of our profession. Take, for example, this guide to translating the formal language of scientific articles into plain English. (Note: This has circulated on email among scientists a number of times over at least a 10 year period; I remember taping it on the door when I was a grad student.  An astute reader pointed out that it is originally from Graham, CD. 1957. A glossary for research reports.  Metal Progress 71: 75, though it has mutated somewhat in the interim).

ERV finally makes the big move.

There was a disturbance in the force of the blogosphere earlier when it appeared that ERV was no longer accessible . But you know what they say, if you strike her down she will become more powerful than you can possibly imagine. It certainly took long enough for Seed to call her up to the big show.

The best of Genomicron.

I have promised to move some "classic Genomicron" posts to this new page, but in the meantime here is a list of what I consider the most significant posts from the last year.

Hand versus brick.

This is interesting. You know, in a "I kinda wish I hadn't seen that" sort of way...

Genomicron is moving -- please update your links *plus* banner design contest.

Some exciting news!

After reflecting on the future of Genomicron, I have decided to move it to the Scientific Blogging network. Please update your links and keep reading!

Welcome to the new Genomicron!

Genomicron has recently moved to its new home here on the Scientific Blogging network from its original location. If you are a regular reader, I hope you will like the new look. If you're just finding the blog now, I hope you enjoy reading it!

Phylogenetic Fallacies: Early Branching Must Mean Primitive

Evolution

Evolutionary trees, or "phylogenies", are a major part of modern evolutionary science. They depict hypotheses regarding the relationships among taxa, and are therefore important in reconstructions of the historical path of evolution (Gregory 2008a,b).

Various approaches can be taken to formulating phylogenetic hypotheses, including analyses based on morphological, fossil, and/or molecular data. These methods often agree well, but sometimes one or another can throw up some surprises and challenge previous hypotheses about the relationships among groups of organisms.

Reconstructing the tree of life is a difficult and complicated process, and one should expect there to be significant refinements and revisions along the way. This is especially true of the deepest branches of the tree, which are often the most difficult to resolve.

Case in point, the Tree of Life Web Project gives the following summary of deep branches among major animal lineages:

Non-functional DNA: Non-functional vs. inconsequential

Genetics

Each copy of the human genome consists of about 3,200,000,000 base pairs, and includes about 500,000 repeats of the LINE-1 transposable element (a LINE) and twice as many copies of Alu (a SINE), as compared to around 20,000 protein-coding genes.

Whereas protein-coding regions represent about 1.5% of the genome, about half is made up LINE-1, Alu, and other transposable element sequences. These begin as parasites, and some continue to behave as detrimental mutagens implicated in disease. However, most of those in the human genome are no longer mobile, and it is possible that many of these persist as commensal freeloaders. Finally, it has long been expected that a significant subset of non-coding elements would be co-opted by the host and take on functional roles at the organism level, and there is increasing evidence to support this.

A notable fraction of the non-genic portion of human DNA is undoubtedly involved in regulation, chromosomal function, and other important processes, but based on what we know about non-coding DNA sequences, it remains a reasonable default assumption -- though one that should continue to be tested empirically -- that much or perhaps most of it is not functional at the organism level. This does not mean that a search for the functional segments is futile or irrelevant -- far from it, as many non-genic regions are critical for normal genomic operation and some have played an important role in many evolutionary transitions. It simply means that one must not extrapolate without warrant from discoveries involving a small fraction of sequences to the genome as a whole.

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