Molecular Biology
pharyngula | July 20, 2006Books from Nobel laureates in molecular biology have a tradition of being surprising. James Watson(amzn/b&n/abe/pwll) was catty, gossipy, and amusingly egotistical; Francis Crick(amzn/b&n/abe/pwll) went haring off in all kinds of interesting directions, like a true polymath; and Kary Mullis(amzn/b&n/abe/pwll) was just plain nuts. When I heard that Christiane Nüsslein-Volhard was coming out with a book, my interest and curiousity were definitely piqued. The work by Nüsslein-Volhard and Wieschaus has shaped my entire discipline, so I was eagerly anticipating what her new book,…
pharyngula | July 19, 2006How do you make a limb? Vertebrate limbs are classic models in organogenesis, and we know a fair bit about the molecular events involved. Limbs are induced at particular boundaries of axial Hox gene expression, and the first recognizable sign of their formation is the appearance of a thickened epithelial bump, the apical ectodermal ridge (AER). The AER is a signaling center that produces, in particular, a set of growth factors such as Fgf4 and Fgf8 that trigger the growth of the underlying tissue, causing the growing limb to protrude. In addition, there's another signaling center that forms…
pharyngula | July 18, 2006
Carl Zimmer wrote on evolution in jellyfish, with the fascinating conclusion that they bear greater molecular complexity than was previously thought. He cited a recent challenging review by Seipel and Schmid that discusses the evolution of triploblasty in the metazoa—it made me rethink some of my assumptions about germ layer phylogeny, anyway, so I thought I'd try to summarize it here. The story is clear, but I realized as I started to put it together that jeez, but we developmental biologists use a lot of jargon. If this is going to make any sense to anyone else, I'm going to have to step…
pharyngula | July 17, 2006
Do vertebrate embryos exhibit significant variation in their early development? Yes, they do—in particular, the earliest stages show distinct differences that mainly reflect differences in maternal investment and that cause significant distortions of early morphology during gastrulation. However, these earliest patterns represent workarounds, strategies to accommodate one variable (the amount of yolk in the egg), and the animals subsequently reorganize to put tissues into a canonical arrangement. Observations of gene expression during gastrulation are revealing deeper similarities that are…
evolgen | July 16, 2006Via Genetics and Health comes this cartoon movie of DNA replication. If you've never taken a molecular genetics course, this may be new to you.
pharyngula | July 12, 2006
Neck anatomy has long terrified me. Way back when I was a grad student, my lab studied the organization and development of the hindbrain, which was relatively tidy and segmental; my research was studying the organization and development of the spinal cord, which was also tidy and segmental. The cervical region, though, was complicated territory. It's a kind of transitional zone between two simple patterns, and all kinds of elaborate nuclei and new cell types and structural organizations flowered there. I drew a line at the fifth spinal segment and said I'm not even going to look further…
evolgen | July 10, 2006I've missed the last two Ask A ScienceBlogger questions. My lack of answers were due to a combination of being busy and apathy toward the questions -- more busy with the science education question and apathy for the science policy question. But this week's question is on cloning, so I kind of feel obligate to post a response (being a genetics blog and all) despite not really being interested in the topic. So, they're asking us:
On July 5, 1996, Dolly the sheep became the first successfully cloned mammal. Ten years on, has cloning developed the way you expected it to?
Ten years ago, I was in…
pharyngula | July 10, 2006
I've written about this fascinating Drosophila gene, bicoid, several times before. It's a maternal effect gene, a gene that is produced by the mother and packaged into her eggs to drive important early events in development, in this case, establishing polarity, or which end of the egg is anterior (bicoid specifies which end of the egg will form the fly's head). Bicoid is also a transcription factor, or gene that regulates the activity of other genes. We also see evidence that it is a relatively new gene, one that is taking over a morphogenetic function that may have been carried out by…
pharyngula | July 9, 2006
Intelligent Design creationists are extremely fond of diagrams like those on the left. Textbook illustrators like them because they simplify and make the general organization of the components clear—reducing proteins to smooth ovoids removes distractions from the main points—but creationists like them for the wrong reasons. "Look at that—it's engineered! It's as if God uses a CAD program to design complex biological systems!" They like the implication that everything is done with laser-guided precision, and most importantly, that every piece was designed with intent, to fill a specific role…
pharyngula | July 9, 2006
Last week, I wrote a bit about maternal genes, specifically bicoid, and described how this gene was expressed in a gradient in the egg. Bicoid is both a transcription factor and a morphogen. The gene product regulates the activity of other genes, controlling their pattern of expression in the embryo. Today I thought I'd get more specific about the downstream targets of bicoid, the gap genes.
Expression domains of the gap genes. The pink bars chart the strength of gene expression as a function of position along the lengths of the embryo for hunchback (hb), huckebein (hkb), tailless (tll),…
pharyngula | July 9, 2006
In my previous comments about maternal effect genes, I was talking specifically about one Drosophila gene, bicoid, which we happen to understand fairly well. We know its sequence, we know how it is controlled, and we know what it does; we know where it falls in the upstream and downstream flow of developmental information in the cell. So today I'm going to babble a bit more about what bicoid is and does, and how it works.
Bicoid is a transcription factor.
The diagram above illustrates what a transcription factor (in this case, called "gene X") is. Gene X is transcribed to form a strand of…
pharyngula | July 9, 2006
In developmental biology, and increasingly in evolutionary biology, one of the most important fields of study is deciphering the nature of regulatory networks of genes. Most people are familiar with the idea of a gene as stretch of DNA that encodes a protein in a sequence of As, Ts, Gs, and Cs, and that's still an important part of the story. Most people may also be comfortable with the idea that mutations are events that change the sequence of As, Ts, Gs, and Cs, which can lead to changes in the encoded protein, which then causes changes in the function of the protein. These are essential…
pharyngula | July 5, 2006
Last week, I received some delusional e-mail from Phil Skell, who claims that modern biology has no use for evolutionary theory.
This will raise hysterical screeches from its true-believers. But, instead they should take a deep breath and tell us how the theory is relevant to the modern biology. For examples let them tell the relevance of the theory to learning…the discovery and function of hormones…[long list of scientific disciplines truncated]
Dr Skell is a sad case. He apparently repeats his mantra that biology has no need of evolution everywhere he goes, and has never bothered to…
pharyngula | July 2, 2006The science blogosphere must be getting big if it can support biology subspecialty carnivals: now you can read collections of posts about just bioinformatics or genetics. And here I thought a general science carnival might be too narrow to draw in a wide readership, way back in the dark ages!
pharyngula | June 27, 2006
One of many open questions in evolution is the nature of bilaterian origins—when the first bilaterally symmetrical common ancestor (the Last Common Bilaterian, or LCB) to all of us mammals and insects and molluscs and polychaetes and so forth arose, and what it looked like. We know it had to have been small, soft, and wormlike, and that it lived over 600 million years ago, but unfortunately, it wasn't the kind of beast likely to be preserved in fossil deposits.
We do have a tool to help us get a glimpse of it, though: the analysis of extant organisms, searching for those common features that…
pharyngula | June 23, 2006Two short articles in this week's Science link the orb-weaving spiders back to a common ancestor in the Early Cretaceous, with both physical and molecular evidence. What we have is a 110-million-year-old piece of amber that preserves a piece of an orb web and some captured prey, and a new comparative study of spider silk proteins that ties together the two orb-weaving lineages, the Araneoidea and the Deinopoidea, and dates their last common ancestor to 136 million years ago.
Araneoids and Deinopoids build similar looking webs—a radial frame supporting a sticky spiral—but they differ in how…
pharyngula | June 21, 2006
PvM at the Panda's Thumb has already written a bit about this issue in the article "Human Gland Probably Evolved From Gills", but I'm not going to let the fact that I'm late to the party stop me from having fun with it. This is just such a darned pretty story that reveals how deeply vertebrate similarities run, using multiple lines of evidence.
Here's the start of the situation: fish have a problem. Like most animals, they need to maintain a specific internal salt concentration, but they are immersed in a solution that is much more dilute they they are (for freshwater fish) or much more…
evolgen | June 19, 2006Humans have been genetically engineering agricultural crops ever since plants were domesticated. Notice the difference between maize and teosinte. Or how about what we have done to create modern
wheat. By either imposing an artificial selection pressure on a few important loci (in the case of maize) or encouraging larger, polyploid individuals (wheat), we have been manipulating the genome of plants for a long, long time. More genetic manipulation of agriculture below the fold.
The difference between the genetic engineers of yore and those of today are the tools at their disposal. The…
pharyngula | June 16, 2006
Maternal effect genes are a special class of genes that have their effect in the reproductive organs of the mutant; they are interesting because the mutant organism may appear phenotypically normal, and it is the progeny that express detectable differences, and they do so whether the progeny have inherited the mutant gene or not. That sounds a little confusing, but it really isn't that complex. I'll explain it using one canonical example of a maternal effect gene, bicoid.
Bicoid is a gene that is essential for normal axis formation in the fly, Drosophila. It is this gene product that…
pharyngula | June 8, 2006
The fugu is a famous fish, at least as a Japanese sushi dish containing a potentially lethal neurotoxin that was featured on an episode of The Simpsons. Fugu is a member of the pufferfish group, which have another claim to fame: an extremely small genome, roughly a tenth the size of that of other vertebrates. The genome of several species of pufferfish is being sequenced, and the latest issue of Nature announces the completion of a draft sequence for the green spotted pufferfish, Tetraodon nigroviridis, a small freshwater species.
Tetraodon has about the same number of genes as we do, 20,…