Recently in Development Category

How to make a snake

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First, you start with a lizard.

Really, I’m not joking. Snakes didn’t just appear out of nowhere, nor was there simply some massive cosmic zot of a mutation in some primordial legged ancestor that turned their progeny into slithery limbless serpents. One of the tougher lessons to get across to people is that evolution is not about abrupt transmutations of one form into another, but the gradual accumulation of many changes at the genetic level which are typically buffered and have minimal effects on the phenotype, only rarely expanding into a lineage with a marked difference in morphology.

What this means in a practical sense is that if you take a distinct form of a modern clade, such as the snakes, and you look at a distinctly different form in a related clade, such as the lizards, what you may find is that the differences are resting atop a common suite of genetic changes; that snakes, for instance, are extremes in a range of genetic possibilities that are defined by novel attributes shared by all squamates (squamates being the lizards and snakes together). Lizards are not snakes, but they will have inherited some of the shared genetic differences that enabled snakes to arise from the squamate last common ancestor.

Sean Carroll live web talk

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As part of a year-long Darwin Lecture Series, evo-devo guy Sean Carroll will be giving a webcast talk based around his Making of the Fittest. The talk is on Wednesday, November 4, and you can sign up for the live webcast here.

I was just catching up on a few blogs, and noticed all this stuff I missed about Jonathan Wells' visit to Oklahoma. And then I read Wells' version of the event, and just about choked on my sweet mint tea.

The next person--apparently a professor of developmental biology--objected that the film ignored facts showing the unity of life, especially the universality of the genetic code, the remarkable similarity of about 500 housekeeping genes in all living things, the role of HOX genes in building animal body plans, and the similarity of HOX genes in all animal phyla, including sponges. 1Steve began by pointing out that the genetic code is not universal, but the questioner loudly complained that 2he was not answering her questions. I stepped up and pointed out that housekeeping genes are similar in all living things because without them life is not possible. I acknowledged that HOX gene mutations can be quite dramatic (causing a fly to sprout legs from its head in place of antennae, for example), but 3HOX genes become active midway through development, 4long after the body plan is already established. 5They are also remarkably non-specific; for example, if a fly lacks a particular HOX gene and a comparable mouse HOX gene is inserted in its place, the fly develops normal fly parts, not mouse parts. Furthermore, 6the similarity of HOX genes in so many animal phyla is actually a problem for neo-Darwinism: 7If evolutionary changes in body plans are due to changes in genes, and flies have HOX genes similar to those in a horse, why is a fly not a horse? Finally, 8the presence of HOX genes in sponges (which, everyone agrees, appeared in the pre-Cambrian) still leaves unanswered the question of how such complex specified genes evolved in the first place.

The questioner became agitated and shouted out something to the effect that HOX gene duplication explained the increase in information needed for the diversification of animal body plans. 9I replied that duplicating a gene doesn't increase information content any more than photocopying a paper increases its information content. She obviously wanted to continue the argument, but the moderator took the microphone to someone else.

It blows my mind, man, it blows my freakin' mind. How can this guy really be this stupid? He has a Ph.D. from UC Berkeley in developmental biology, and he either really doesn't understand basic ideas in the field, or he's maliciously misrepresenting them…he's lying to the audience. He's describing how he so adroitly fielded questions from the audience, including this one from a professor of developmental biology, who was no doubt agitated by the fact that Wells was feeding the audience steaming balls of rancid horsepuckey. I can't blame her. That was an awesomely dishonest/ignorant performance, and Wells is proud of himself. People should be angry at that fraud.

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It's yet another transitional fossil! Are you tired of them yet?

Darwinopterus modularis is a very pretty fossil of a Jurassic pterosaur, which also reveals some interesting modes of evolution; modes that I daresay are indicative of significant processes in development, although this work is not a developmental study (I wish…having some pterosaur embryos would be exciting). Here it is, one gorgeous animal.

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(Click for larger image)

Figure 2. Holotype ZMNH M8782 (a,b,e) and referred specimen YH-2000 ( f ) of D. modularis gen. et sp. nov.: (a) cranium and mandibles in the right lateral view, cervicals 1-4 in the dorsal view, scale bar 5cm; (b) details of the dentition in the anterior tip of the rostrum, scale bar 2cm; (c) restoration of the skull, scale bar 5cm; (d) restoration of the right pes in the anterior view, scale bar 2 cm; (e) details of the seventh to ninth caudal vertebrae and bony rods that enclose them, scale bar 0.5 cm; ( f ) complete skeleton seen in the ventral aspect, except for skull which is in the right lateral view, scale bar 5 cm. Abbreviations: a, articular; cr, cranial crest; d, dentary; f, frontal; j, jugal; l, lacrimal; ldt, lateral distal tarsal; m, maxilla; mdt, medial distal tarsal; met, metatarsal; n, nasal; naof, nasoantorbital fenestra; p, parietal; pd, pedal digit; pf, prefrontal; pm, premaxilla; po, postorbital; q, quadrate; qj, quadratojugal; sq, squamosal; ti, tibia.

Limusaurus inextricabilis

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My previous repost was made to give the background on a recent discovery of Jurassic ceratosaur, Limusaurus inextricabilis, and what it tells us about digit evolution. Here's Limusaurus—beautiful little beastie, isn't it?

limusarus.jpeg
(Click for larger image)

Photograph (a) and line drawing (b) of IVPP V 15923. Arrows in a point to a nearly complete and fully articulated basal crocodyliform skeleton preserved next to IVPP V 15923 (scale bar, 5 cm). c, Histological section from the fibular shaft of Limusaurus inextricabilis (IVPP V 15924) under polarized light. Arrows denote growth lines used to age the specimen; HC refers to round haversian canals and EB to layers of endosteal bone. The specimen is inferred to represent a five-year-old individual and to be at a young adult ontogenetic stage, based on a combination of histological features including narrower outermost zones, dense haversian bone, extensive and multiple endosteal bone depositional events and absence of an external fundamental system. d, Close up of the gastroliths (scale bar, 2 cm). Abbreviations: cav, caudal vertebrae; cv, cervical vertebrae; dr, dorsal ribs; ga, gastroliths; lf, left femur; lfl, left forelimb; li, left ilium; lis, left ischium; lp, left pes; lpu, left pubis; lsc, left scapulocoracoid; lt, left tibiotarsus; md, mandible; rfl, right forelimb; ri, right ilium; rp, right pes; sk, skull.

What's especially interesting about it is that it catches an evolutionary hypothesis in the act, and is another genuine transitional fossil. The hypothesis is about how fingers were modified over time to produce the patterns we see in dinosaurs and birds.

Snails have nodal!

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My first column in the Guardian science blog will be coming out soon, and it’s about a recent discovery that I found very exciting…but that some people may find strange and uninteresting. It’s all about the identification of nodal in snails.

nodal_guts.jpg

Why should we care? Well, nodal is a rather important — it’s a gene involved in the specification of left/right asymmetry in us chordates. You’re internally asymmetric in some important ways, with, for instance, a heart that is larger on the left than on the right. This is essential for robust physiological function — you’d be dead if you were internally symmetrical. It’s also consistent, with a few rare exceptions, that everyone has a stronger left ventricle than right. The way this is set up is by the activation of the cell signaling gene nodal on one side, the left. Nodal then activates other genes (like Pitx2) farther downstream, that leads to a bias in how development proceeds on the left vs. the right.

In us mammals, the way this asymmetry in gene expression seems to hinge on the way cilia rotate to set up a net leftward flow of extraembryonic fluids. This flow activates sensors on the left rather than the right, that upregulate nodal expression. So nodal is central to differential gene expression on left vs. right sides.

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How can I respond to a story about zebrafish, development, and new imaging and visualization techniques? Total incoherent nerdgasm is how.

Keller et al. are using a technique called digital scanned laser light sheet fluorescence microscopy (DSLM) to do fast, high-resolution, 3-D scans through developing embryos over time; using a GFP-histone fusion protein marker, they localize the nucleus of every single cell in the embryo. Some of the geeky specs:

  • 1500x1500 pixel 2-D resolution

  • 12 bits per pixel dynamic range

  • Imaging speed of 10 million voxels per second

  • Complete scan of a 1 cubic millimeter volume in 3µm steps in 90 seconds

  • Efficient excitation (5600 times less energy than a confocal, one million times less than a two-photon scope) to minimize bleaching and photodamage

Evolving snake fangs

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fang_embryo.jpg
Ontogenetic allometry in the fang in the front-fanged Causus rhombeatus (Viperidae) displaces the fang along the upper jaw. Scale bars, 1 mm. We note the change in relative size of the upper jaw subregions: i, anterior; ii, fang; iii, posterior. d.a.o., days after oviposition.

I keep saying this to everyone: if you want to understand the origin of novel morphological features in multicellular organisms, you have to look at their development. "Everything is the way it is because of how it got that way," as D'Arcy Thompson said, so comprehending the ontogeny of form is absolutely critical to understanding what processes were sculpted by evolution. Now here's a lovely piece of work that uses snake embryology to come to some interesting conclusions about how venomous fangs evolved.

Basal snakes, animals like boas, lack venom and specialized fangs altogether; they have relatively simple rows of small sharp teeth. Elapid snakes, like cobras and mambas and coral snakes, are at the other extreme, with prominent fangs at the front of their jaws that act like injection needles to deliver poisons. Then there are the Viperidae, rattlesnakes and pit vipers and copperheads, that also have front fangs, but phylogenetically belong to a distinct lineage from the elapids. And finally there are other snakes like the grass snake that have enlarged fangs at the back of their jaws. It's a bit confusing: did all of these lineages independently evolve fangs and venom glands, or are there common underpinnings to all of these arrangements?

I happened to read PZ’s write-up Local Boy Gets Obnoxious, in which he mentions how he has been interviewed by the Seattle-PI. If I had known PZ was in town, I would have attended the Pacific Science Center talk. Instead I ended up at a Seattle Skeptics “An Evening with PZ MYERS” event. This well attended meetup included a fascinating lecture about the evolution of the eye and introduced me to several aspects of eye evolution with which I had not been familiar.

On Quintessence of Dust Steve Matheson, a biologist at Calvin College, has back to back posts on the role of gene regulation in the development of ‘novel’ structures. The first, How the bat got its wing, describes the work of Chris Cretekos and colleagues on the regulation of Prx1, a gene influencing bone morphogenetic proteins which are involved in limb elongation. The protein coding regions of Prx1 in bats and mice are virtually identical, but in nearby regions thought to contain elements regulating the local expression of Prx1 there are some substantial sequence differences. Replacing the mouse Prx1 forelimb regulatory region with the bat Prx1 regulatory region resulted in mice with significantly elongated forelimbs. Read Matheson’s post for the rest of the story.

In Finches, bah! What about Darwin’s tomatoes? Matheson describes new genetic research on an old friend, the tomato specimens that Darwin brought back from the Galapagos. Didn’t know Darwin brought tomatoes back from the Galapagos? Again, see Matheson’s post for

… an example of a change in a regulatory region of the DNA, the kind of change that evo-devo theorists have predicted to be fairly common in the evolution of new forms.

Evolution of the Heart

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Hearts come in a variety of shapes and forms all the way from single chambered hearts to multi-chambered hearts with 2, 3 and even 4 separate chambers. How could evolution have achieved such a feat one may wonder, and indeed creationists have held up this minor mystery as something evolutionary theory could and would never be able to explain.

As is so often the case with such gap arguments, science has not failed to disappoint our creationist friends.

Science Daily gives us a hint of what science has uncovered in an article called Hearts Or Tails? Genetics Of Multi-chambered Heart Evolution

The expanded cardiac field in Ets1/2-activated mutants results in a proportion of animals having a functional, two-chambered heart. “The conversion of a simple heart tube into a complex heart was discovered by chance, but has general implications for the evolutionary origins of animal diversity and complexity”, says Mike Levine, a co-author of the paper.

UNSW&Caltech: Embryology

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Cst800.jpg The University of New South Wales has some fascinating resources on embryology, including the full set of Carnegie stages for the Human Embryo
ts25.jpg Caltech µMRI Atlas of Mouse Development an interactive 3D atlas which is part of a collection of Caltech MRI sites which include the Quail and the Lemur brain

Whale evolution: The blowhole

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The evolution of the blowhole in whales, which according to the fossil evidence moved from the tip to the vertex of the head, has caused some concerns amongst our creationist readers who wonder how such a feat could have taken place.

From Milan Klima, Development of the Cetacean Nasal Skull 1999 Springer

The fact that the cetacean nose moved, in the course of evolution, from the tip of the rostrum up to the vertex of the head, is among the most perfect of adaptations to aquatic life. In this and many other special adaptations of their morphology and physiology, cetaceans surpass most primarily aquatic animals even though they themselves have developed from land mammals that breathe with lungs, and have only secondarily conquered the aquatic environment. To a certain extent, cetaceans can be considered to be the most successful group of aquatic animals of all time.

Conclusive paleontological evidence shows the way in which the nasal openings were moved in the course of phylogeny (see Kellogg 1928; Slijper 1962; Gaskin 1976; Oelschlager 1978, 1987, 1990; Moore 1981). That this evolutionary process is repeated in a way during ontogeny became obvious through external observations on embryos and fetuses (Kukenthal 1893). At the earliest embryonic stages the nasal openings are still situated at the rostra tip like those of land mammals; they are gradually shifted more and more towards the vertex of the head at the older stages. At the same time, a long rost rum with narrow jaws develops. Until recently, practically nothing was known about the morphogenetic processes concealed in this metamorphosis, about what cranial structures take part in it, and about the exact way in which the cetacean skull becomes transformed during embryogeny.

Dicyemid mesozoa

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You know how people can be going along, minding their own business, and then they see some cute big-eyed puppy and they go "Awwwww," and their hearts melt, and then it's all a big sloppy mushfest? I felt that way the other day, as I was meandering down some obscure byways of the developmental biology literature, and discovered the dicyemid mesozoa … an obscure phylum which I vaguely recall hearing about before, but had never seriously examined. After reading a few papers, I have to say that these creatures are much more lovable then mere puppy dogs. Look at this and say "Awwwww!"

dicyemid.jpg
Light micrograph of Dicyemid japonicaum rhombogen. AX, axial cell; C, calotte; IN, infusorigen; P, peripheral cell.

O dicyemid mesozoan, how do I love thee? Let me count the ways.

Continue reading "Dicyemid mesozoa" (on Pharyngula)

Evolution Matters

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The University of California, San Diego (UCSD), the alma mater of Discovery Institute’s spokesperson Casey Luskin, explores why “Evolution Matters”. In cooperation with UCSD-TV, they bring us a fascinating lecture series:

For 2007-08, the Division of Biological Sciences is launching Evolution Matters: The Diversity of Development. In this series of 5 lectures, held over the course of the year, leading cell and developmental scientists will explore the evolution of plants, animals and humans and will discuss how their research into this field holds promise for finding solutions to key health and environmental issues facing us today.

Educational Website: Grey Matters

Educational Website: Science Matters

Atoms to Xrays

Neil Shubin’s latest book on evolutionary theory is by all standards a great success. It ranks around 200 in Amazon books and first in Evolution Science Books. When I checked the book’s availability in our library system there were close to 40 pending holds.

A sales rank of 200 means 225-250 books per week are sold. Compare this to a rank of 24,000 for Behe’s boo “Edge of Evolution” sold at a bargain price of $6.99 down from $28.00 or 111,550 for the regular priced version. Those numbers translate to few copies per month being sold.

Neil Shubin is a professor of organismal biology at the University of Chicago. He, as part of a team of scientists, discovered the now infamous Titaalik transitional fossil which causes so much consternation amongst Intelligent Design Creationists. His book Your Inner Fish introduces its readers to an exciting overview of how our evolutionary history links us back to a common ancestor with fish. Of course, that’s not where our common ancestry ends.

Why do we look the way we do? What does the human hand have in common with the wing of a fly? Are breasts, sweat glands, and scales connected in some way? To better understand the inner workings of our bodies and to trace the origins of many of today’s most common diseases, we have to turn to unexpected sources: worms, flies, and even fish.

In Your Inner Fish, Neil Shubin tells the story of evolution by tracing the organs of the human body back millions of years, long before the first creatures walked the earth. By examining fossils and DNA, Shubin shows us that our hands actually resemble fish fins, our head is organized like that of a long-extinct jawless fish, and major parts of our genome look and function like those of worms and bacteria.

The New York Academy of Sciences provides us with access to a talk by Nobel Laureate Christiane Nüsslein-Volhard on how genes drive development, no need for unspecified ‘Intelligent Designers’, no need for miracles, just hard work by scientists who are committed to discovering the details of how, what, when and so on. Compare this with how ID explains the development of the embryo.

Click on the Flash presentation

nusslein15_small.gif

I also suggest that interested readers get their hands on her book “Coming to Life: How Genes Drive Development” by Christiane Nüsslein-Volhard or read an excerpt of the book: Chapter IX — Evolution, Body Plans, and Genomes

One in the eye for intelligent design

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We are all familiar with the creationist argument about the eye, an argument which Darwin already addressed in his original work. And while creationists are still in much of a denial about eye evolution, science keeps on closing gaps.

In the Australian a second paper addressing eye evolution is discussed.

On Quintessence of Dust, associate professor of Biology Stephen Matheson (yes a Steve Steve), treats us to a fascinating trip through morphospace. He discusses a recent paper by Prusinkiewicz et al.titled Evolution and Development of Inflorescence Architectures, published in Science 8 June 2007:

In this paper, the authors not only show how, despite a multitude of possible forms, severe constraints are placed on biological diversity, but also show how the existence of ‘worm holes’ in fitness space link the various architectures. A beautiful story about scientific inquiry.

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