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Continue reading  “Get your beachfront property now...”

Posted by Nick Matzke on September 20, 2006 | Comments (24)

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Continue reading  “Lakes on Titan!”

Posted by Matt Inlay on July 20, 2006 | Comments (12)

In Chapter 6 of Darwin’s Black Box, Michael Behe listed several immune subsystems that he considered irreducibly complex (IC), and therefore (according to him but no one else) unevolvable. One incredibly complex immune subsystem that Behe neglected to mention was the system that genetically modifies antibody genes during the course of an immune response. This system is largely responsible for our ability to generate stronger and faster resistance to subsequent infections, and is integral to why vaccines work. 3 recent papers used concepts in evolution to help characterize one of the most interesting and novel immunological genes discovered since the RAGs in the late 80s, a gene called activation induced deaminase (AID, pronounced as initials), a gene pivotal to antibody modification. Not only did these papers reveal interesting functional insights into AID, but also helped solidify a model for the origin and evolution of this system. Two of the articles come from labs instantly recognizable to most molecular immunolgists, but are totally unknown in ID/evolution circles. The third comes from a lab that most of the regulars here at the Panda’s Thumb would immediately recognize, PT’s own Andrea Bottaro.

Continue reading  “3 recent reports use evolution to study mechanisms of antibody diversification”

Posted by Nick Matzke on May 5, 2006 | Comments (25)

Posted by Dave Thomas on January 27, 2006 | Comments (8)

Continue reading  “The "Ostrich Dinosaur Body Plan" has Evolved ... Twice!”

Posted by RBH on December 25, 2005 | Comments (3)

Posted by Tara Smith on November 15, 2005 | Comments (96)

Continue reading  “Evolution of resistance--bacteria win again”

Posted by Tara Smith on September 16, 2005 | Comments (28)

Continue reading  “Dobzhansky and anthrax”

Posted by jml on June 2, 2005

From EurekaAlert:

A male fly's sexual courtship of a female fly is a complicated business of tapping, singing, wing vibration, and licking, but a single gene is all that is needed to produce this complex behavior, according to new research published in this week's issue of the journal Cell.

The gene encodes the Fruitless protein. Male and female flies carry different versions of the fruitless protein, as a result of sex-specific splicing of the mRNA. The male form of Fruitless is critical for the male courtship ritual and males' preference for mating with females, as previous studies have shown.

Now, Barry J. Dickson and Ebru Demir of the Institute of Molecular Biotechnology of the Austrian Academy of Sciences show just how intimately fruitless is linked to these stereotypically male behaviors. They discovered that female flies with the male version of fruitless behave like males, directing at other females a sexual display nearly identical to their male counterparts.

See also: Ebru Demir and Barry J. Dickson: "fruitless Splicing Specifies Male Courtship Behavior in Drosophila" Cell, Vol. 121, 785–794, June 3, 2005. DOI 10.1016/j.cell.2005.04.027

All animals exhibit innate behaviors that are specified during their development. Drosophila melanogaster males (but not females) perform an elaborate and innate courtship ritual directed toward females (but not males). Male courtship requires products of the fruitless (fru) gene, which is spliced differently in males and females. We have generated alleles of fru that are constitutively spliced in either the male or the female mode. We show that male splicing is essential for male courtship behavior and sexual orientation. More importantly, male splicing is also sufficient to generate male behavior in otherwise normal females. These females direct their courtship toward other females (or males engineered to produce female pheromones). The splicing of a single neuronal gene thus specifies essentially all aspects of a complex innate behavior.

Petra Stockinger, Duda Kvitsiani, Shay Rotkopf, László Tirián, and Barry J. Dickson: "Neural Circuitry that Governs Drosophila Male Courtship Behavior" Cell, Vol. 121, 795–807, June 3, 2005. DOI 10.1016/j.cell.2005.04.026

Male-specific fruitless (fru) products (FruM) are both necessary and sufficient to “hardwire” the potential for male courtship behavior into the Drosophila nervous system. FruM is expressed in ∼2% of neurons in the male nervous system, but not in the female. We have targeted the insertion of GAL4 into the fru locus, allowing us to visualize and manipulate the FruM-expressing neurons in the male as well as their counterparts in the female. We present evidence that these neurons are directly and specifically involved in male courtship behavior and that at least some of them are interconnected in a circuit. This circuit includes olfactory neurons required for the behavioral response to sex pheromones. Anatomical differences in this circuit that might account for the dramatic differences in male and female sexual behavior are not apparent.

Posted by Dave Thomas on April 3, 2005 | Comments (5)

Frodo Baggins (L), Aragorn (R)?

Several of the fossils of the celebrated “hobbit-sized” hominid Homo floresiensis have apparently been irreparably damaged by the researcher who spirited them away from the discovery team for months.  This strange and sad story first appeared in USA Today on March 21st, and was reported in Science on 25 March 2005; (307: 1848)

Usually Carl Zimmer’s The Loom keeps us up to date on the diminutive Homo floresiensis with great posts like this one, but he must be really busy this week.

Anyway, here follows the sad news from USA Today.

Continue reading  “Hobbit Fossils Damaged...”

Posted by Nick Matzke on March 31, 2005 | Comments (6)

I’d like to point you to a new website, EvolNews.org!:

Welcome to EvolNews.org!

EvolNews.org is a site geared toward sharing new and interesting research in Evolutionary Biology with other researchers and with anyone interested. Face it, you’re a busy researcher- and you probably find all fields of Evolutionary Biology interesting, but you barely have time to keep current with the research in your own sub-discipline. Well, this web site is designed to give a brief summary of the latest breaking news in evolutionary research that occurs in peer-reviewed journals, and provide you with handy-dandy links to the articles. There is also the ability to start discussions by posting replies to the articles, but that is for the readership to decide. We are always open to suggestions to improve the website, including adding new topic areas and features, as it’s all fairly uncomplicated with the wonderful software PHP-Nuke. What this site will not support is teologlogical debates, creationism/evolution debates, etc.- although they can be presented as articles and comments if published elsewhere.

I daresay that it is a good thing that they avoid “teologlogical debates,” given the mess they made of the word “teleological”.  Never fear, that is what Panda’s Thumb is for!

Posted by Pim van Meurs on March 17, 2005 | Comments (121)

New Scientist reports on the findings of a study on the impact of genes on religious inclinations

Genes may help determine how religious a person is, suggests a new study of US twins. And the effects of a religious upbringing may fade with time.

Until about 25 years ago, scientists assumed that religious behaviour was simply the product of a person’s socialisation - or “nurture”. But more recent studies, including those on adult twins who were raised apart, suggest genes contribute about 40% of the variability in a person’s religiousness.

But it is not clear how that contribution changes with age. A few studies on children and teenagers - with biological or adoptive parents - show the children tend to mirror the religious beliefs and behaviours of the parents with whom they live. That suggests genes play a small role in religiousness at that age.

Now, researchers led by Laura Koenig, a psychology graduate student at the University of Minnesota in Minneapolis, US, have tried to tease apart how the effects of nature and nurture vary with time. Their study suggests that as adolescents grow into adults, genetic factors become more important in determining how religious a person is, while environmental factors wane.

The study can be found in Journal of Personality (vol 73, p 471)

Continue reading  “Genes contribute to religious inclination”

Posted by Ian Musgrave on March 11, 2005 | Comments (26)

Well, it’s better than boiling mud (1). One of the iconic images of Australia is the Merino sheep, an extremely woolly, arid-land adapted animal that is the backbone of our wool industry. One draw back of their wooliness is that urine and feces accumulate on the sheep’s wool between the hind legs. This attracts flies that lay eggs there, and when the maggots hatch they start eating the sheep alive.

To combat this “fly strike”, Australian farmers have surigally removed the wool-bearing skin between the sheep’s hind legs, a process called Mulesing. This is done without anaesthesia on farms, so the Animal rights group PETA has kicked up a fuss and there is a looming trade boycott on Australian wool.

However, just recently a group of mutant sheep were found on a remote property here in South Australia (listen to the audio presentation for full details). The sheep lack the wool and the folds of skin between the legs found on normal Merinos, and so are relatively immune to fly strike.  It remains to be seen if this beneficial mutation can be bred into Australia’s herd successfully, but it would be amusing if the wrath of PETA was averted by mutant sheep.

(1) The title is taken from comedian John Clarke’s alternative national anthem “God Loves New Zealand, He gave us Boiling Mud”

Posted by Steve on February 16, 2005 | Comments (17)

Here’s a provocative exclusive from Space.com:

Exclusive: NASA Researchers Claim Evidence of Present Life on Mars.

A pair of NASA scientists told a group of space officials at a private meeting here Sunday that they have found strong evidence that life may exist today on Mars, hidden away in caves and sustained by pockets of water.

The scientists, Carol Stoker and Larry Lemke of NASA’s Ames Research Center in Silicon Valley, told the group that they have submitted their findings to the journal Nature for publication in May, and their paper currently is being peer reviewed.

What Stoker and Lemke have found, according to several attendees of the private meeting, is not direct proof of life on Mars, but methane signatures and other signs of possible biological activity remarkably similar to those recently discovered in caves here on Earth.

If confirmed, this could have some serious ramifications for evolution on the early Earth.  Did living things go from Mars to Earth or vice versa?  Are we talking about multiple origin of life events?  Interesting stuff.  I guess we’ll have to live with a mere teaser for now.

Posted by Jim Foley on February 16, 2005 | Comments (1)

For Darwin Day (Feb 12th), the Canberra Skeptics arranged a talk by paleoanthropologist Colin Groves at the National Museum of Australia on the subject of Homo floresiensis, the “Hobbit”. It’s clearly a popular subject; the small lecture theatre was filled to capacity with a few hundred people.

Some scientists have disputed the idea that floresiensis is a new species, suggesting instead that the skeleton is a pathological modern human - Maciej Henneberg, for one, has claimed that it closely resembles a 4000-year-old microcephalic skull found on Crete. Groves showed pictures of that skull and compared it to the hobbit. They did not look very similar to my unqualified judgement, nor, apparently, to the judgement of many qualified scientists. The hobbit femur also has differences from that of any other hominid, and the pelvis flares more than in H. sapiens or H. erectus.

Continue reading  “Homo floresiensis on Darwin Day”

Posted by Nick Matzke on February 9, 2005 | Comments (10)

From the Biology is Cool division at the Thumb.  According to :

Canopy-dwelling ants in the tropical forests of the Americas have adopted a neat way of averting disaster should they fall from their perch. They glide to safety, steering towards their home trunk rather than plummeting to the ground, where they might never see their nest-mates again.

(News@nature.com)

If you don’t believe it, read the news article, the far-too uncreatively-named Nature paper “Directed aerial descent in canopy ants”, or better yet, watch the video.

How was this fascinating discovery made? 

The discovery was an accident, [Stephen] Yanoviak recalls. “About two years ago I was climbing trees to collect mosquitoes when I was attacked by these ants. I brushed 20 or 30 of them off; they fell down and made a nice J-shaped curve back to the tree.”

(News@nature.com)

Thus a Nature paper was born…

Since you asked, Stephen P. Yanoviak is indeed a Project Steve Steve.

Posted by Nick Matzke on January 24, 2005 | Comments (25)

Creationists often dismiss examples of evolutionary change as “that’s just a loss of information.”  There are many problems with this claim (see also here and here), but here is a new one: it appears that in at least one case, humans evolved by “loss of information” (in this case, loss of a gene) from their apelike ancestors.  Carl Zimmer mentions this in passing in a post on the cell-surface sugars, Neu5Ac and Neu5Gc:

Continue reading  “"Loss of information" in human evolution”

Posted by Nick Matzke on January 17, 2005 | Comments (5)

The European Space Agency has put up a mosaic of the images taken during the Huygens descent.

I think that Huygens landed in the middle of the dark stuff.  If so, the images and data from the surface indicate that this isn’t strictly an “ocean,” rather it is some kind of spongy material.  A giant hydrocarbon bog, perhaps?  Huygens had a GC/MS on board that took samples for 70 minutes, so we should get a quite thorough analysis of the molecular composition of the atmosphere during descent, and the surface material.

The clouds/fog are also very interesting, if they represent “moisture” evaporating off of the “ocean” and then “raining” on the “land” to form the channels.  We may be seeing a complete “hydrologic” cycle, except for the “hydro” part , since the molecules involved are hydrocarbons rather than H₂O.  It appears that a whole new vocabulary will be needed to describe the physical geography of Titan.

See also this article in The Scientist for what astrobiologists are saying:

Continue reading  “Composite image of Titan "coastline"”

Posted by Nick Matzke on January 14, 2005 | Comments (34)

Wow. 

Huygens success = image = drainage pattern = rivers = rain = oceans.

(From CNN.)

Sometimes a picture really is worth a thousand words and a few billion dollars.

Since I need a few more lines to provide space for the image:

Wow.

Wowsers.

(etc.)

Posted by Nick Matzke on January 14, 2005 | Comments (21)

In what is turning out to be a pretty darn good week for science, the Huygens probe from the Cassini spacecraft has apparently entered the atmosphere of the shrouded moon Titan, the parachutes deployed, and data was successfully transmitted.  This blows away all previous surface landings on extraterrestrial bodies and is, well, really cool.

Huygens-Cassini Live Blogging: Titan Touchdown

category - Science
Update: 10:25 Cassini is now sending ‘dummy packets’. The signal has been acquired by JPL/ESA. Good news.

Update: 9:35 JPL Mission briefing. “We know all three parachutes did deploy and the heat shield worked. We know it survived for at least half an hour on the surface of Titan.” Note-some of the data intended for and likely received by Cassini “leaked” all the way to earth, in addition to the carrier signal, indicating data was received from onboard instruments. Cassini should turn to earth and start sending at 10:07 EST. 67 minutes later we begin to download Huygens data. It will take some time to compile

Update: 8:30 ESA/ESOC Mission briefing. Huygens is STILL transmitting earth time. Data Stream appears ‘very rich’. Huygens appears to have survived and is still transmitting well beyond impact/touchdown on Titan’s surface. Cassini will listen for Huygens’s signal as long as there is the slightest possibility that it can be detected. Once Huygens’s landing site disappears below the horizon, there’s no more chance of signal, and Huygens’s work is finished. Cassini-Huygens Data stream is scheduled to commence at 10:07 EST but will not be acquired until 11:14 EST earth time

Update: 7:50 Contact at JPL tells me that Earth bound radio observatory believes they also detected ‘solid’ image data from the DISR . This remains unconfirmed officially.

Update: 7:46 Data in stream confirmed. Doppler data from one of the onboard instruments was detected via earth bound observatory being transmitted to cassini. Hod damn I think this may have worked folks.

Update: 7:30 AM EST Mission Briefing From ESA/ESOC in Germany, reporting “We have a signal, so we know Huygens is alive”. “Signal was solid for a long time”. “Signal was solid for two hours!”. Confirmed data transmission from Huygens to Cassini by earth bound radio observatories world wide!! Very encouraging!!!!

BBC: Moon mission ‘probably a success’

Cassini webpage: Radio Astronomers Confirm Huygens Entry in the Atmosphere of Titan

Posted by Nick Matzke on October 26, 2004

Remember Cassini, the multibillion dollar spaceship we put in orbit around Saturn back in July?  (If not, see the PT posts Say hello to Phoebe and First decent views of the surface of Titan, and the Cassini website).

Well, it has taken awhile for Cassini to do its first full orbit, but it is back in the inner Saturnian system, and today it completed its first flyby of Titan, the solar system’s largest moon and only moon with a thick atmosphere made of nitrogen and organic compounds.

Cassini will pass within 746 miles of Titan — a mere 10 hour drive on the freeway — and snap up close photos, and image the surface in detail with atmosphere-penetrating radar.

Continue reading  “Titan flyby #1 today”

Posted by Steve on October 9, 2004 | Comments (5)

There’s a new article out about a new breakthrough in controlling pesticide resistant insects in Australia, one which involes trying to shut down their ability to resist pesticides:

Australian and British scientists have achieved a technical breakthrough to help control insects that have developed resistance to common agricultural pesticides, the New South Wales state government said on Thursday.

[…]

“Developed by the NSW Department of Primary Industries and Rothamsted Research in the UK, the technique relies on the use of naturally occurring enzyme inhibitors to disarm an insect’s defense system,” Macdonald said.

“The enzyme inhibitor acts first to shut down an insect’s resistance mechanisms. A few hours later, while the bug’s defenses are still low, the pesticide kicks in.”

Continue reading  “Breakthrough in Pest Control?”

Posted by Pim van Meurs on September 30, 2004 | Comments (20)

A late notice:

After the successful series on ‘Evolution’, PBS has started airing another excellent miniseries, this time on Origins.  (Origins will appear on PBS on Sept. 28-29 at 8:00 p.m. EDT. (Check local listings).)

See Nova Origins website

This series documents in detail the historical trail allowing science to understand the historical links between the Big Bang all the way to our existence.

The website provides a wealth of resources, additional links and interviews.

Continue reading  “Nova: Origins”

Posted by jml on September 13, 2004 | Comments (2)

From EurekAlert:

The morphological complexity of mammals, as compared to invertebrates, is thought to have arisen through advantageous genetic changes that occurred during the course of evolution. A new research study published in the September issue of Developmental Cell suggests that the evolution of higher-order vertebrate organ systems can result from primitive developmental genetic programs that are, in a sense, recycled for entirely new structures.

According to the expression patterns in the fruit fly, Drosophila, the ancestral action of the Hmx gene was limited to the development of the central nervous system (CNS). Dr. Thomas Lufkin from the Genome Institute of Singapore and colleagues show that the mouse Hmx2 and Hmx3 genes have apparently interchangeable functions in CNS development and have overlapping yet distinct functions in the development of the vestibular system of the inner ear, an organ that has no counterpart in Drosophila. The researchers found that when mice are genetically engineered to lack Hmx2 and Hmx3, Drosophila Hmx can substitute for the mouse Hmx3 gene in CNS development and, surprisingly, can also direct development of the inner ear. Therefore, a Drosophila gene can direct formation of an organ system that does not even exist in the Drosophila body.

“These results demonstrate that the evolution of higher vertebrate characteristics can result from the recycling or redeployment of ‘old’ genes in new parts of the embryo, rather than through mutation of gene protein-coding sequence alone. Old genes can be given a new purpose through ‘reassignment’ to organs undergoing evolutionary advancement. The reassignment likely comes through a shuffling of existing regulatory elements to generate new combinations that are specific to the new organ,” explains Dr. Lufkin.

###

Weidong Wang, J. Fredrik Grimmer, Thomas R. Van De Water, and Thomas Lufkin: “Hmx2 and Hmx3 Homeobox Genes Direct Development of the Murine Inner Ear and Hypothalamus and Can Be Functionally Replaced by Drosophila Hmx”

Developmental Cell, Volume 7, Number 3, September 2004, pages 439-453.

BioMedCentral news report

Posted by jml on August 23, 2004 | Comments (75)

From EurekAlert:

One of the most debated hypotheses in evolutionary biology received new support today, thanks to a study by a scientist at the University of Nevada, Reno. Elissa Cameron, a mammal ecologist in the Department of Natural Resources and Environmental Science, has helped to disprove critics of a scientific theory developed in 1973.

At that time, ecologist Bob Trivers and mathematician Dan Willard said that large healthy mammals produce more male offspring when living in good conditions, such as areas where there is an ample food supply. Conversely, female mammals living in less desirable conditions would tend to have female offspring.  …

She conducted an analysis of 1,000 studies that examined the Trivers-Willard hypothesis and sex ratios in mammals. Her study found that female mammals that were in better body condition during the early stages of conception were more likely have male offspring. Body fat and diet can affect levels of glucose circulating in a mammal’s body, and Cameron suggests that the levels of glucose around the time of conception could be influencing the sex of the animal’s offspring.

“A high-fat diet can result in higher levels of glucose, thereby supporting the hypothesis that glucose may be contributing to the sex of the mammal’s offspring,” Cameron said.

The paper is Elissa Z. Cameron, “Facultative adjustment of mammalian sex ratios in support of the Trivers-Willard hypothesis: evidence for a mechanism” Proceedings of the Royal Society of London, Ser. B.  271, 1723 - 1728 ( DOI: 10.1098/rspb.2004.2773). 

Abstract:

Evolutionary theory predicts that mothers of different condition should adjust the birth sex ratio of their offspring in relation to future reproductive benefits. Published studies addressing variation in mammalian sex ratios have produced surprisingly contradictory results. Explaining the source of such variation has been a challenge for sex-ratio theory, not least because no mechanism for sex-ratio adjustment is known. I conducted a meta-analysis of previous mammalian sex-ratio studies to determine if there are any overall patterns in sex-ratio variation. The contradictory nature of previous results was confirmed. However, studies that investigated indices of condition around conception show almost unanimous support for the prediction that mothers in good condition bias their litters towards sons. Recent research on the role of glucose in reproductive functioning have shown that excess glucose favours the development of male blastocysts, providing a potential mechanism for sex-ratio variation in relation to maternal condition around conception. Furthermore, many of the conflicting results from studies on sex-ratio adjustment would be explained if glucose levels in utero during early cell division contributed to the determination of offspring sex ratios.

Posted by jml on August 11, 2004 | Comments (12)

Studies of the fossil record along with genetic data for Cetacea (Whales, dolphins and their allies) offers some of the best examples of evolutionary studies generating testable, refutable, hypotheses regarding the development of organic diversity. Many readers will perhaps remember Carl Zimmer’s wonderful exposition in At The Water’s Edge (Amazon), but a lot has happened since Zimmer was writing in 1999, with interesting articles appearing in journals such as Systematic Biology, Paleobiology, and Evolution and Development. In the August 12th edition of Nature, a study of the early evolution of whales demonstrates the changes that took place in whales’ outer and middle ears, required for the transition from a land-based to a marine-based existence. From EurekAlert:

The ear is the most important sense organ for modern toothed whales, say scientists, because these whales locate their prey using echolocation. Directional hearing is critical: A blind whale could find food without much trouble; a deaf one would starve.

The study documents how hearing in these whales evolved. The research is based on cetacean fossils representing four groups of early whales. The earliest cetaceans, pakicetids (those that swam in ancient seas 50 million years ago), used the same sound transmission system as did land mammals, and so had poor underwater hearing. More recent cetaceans, remingtonocetids and protocetids (those that lived 43-46 million years ago), retained the land-mammal system, but also developed a new sound transmission system.

“The fossils document the ways in which cetacean hearing has changed, starting with ear fossils of whales’ land ancestors and ending with the ear of near-modern looking whales,” said Hans Thewissen, an anatomist at the Northeastern Ohio Universities College of Medicine (NEOUCOM). Thewissen and NEOUCOM researcher Sirpa Nummela led the study.

The newer system was similar to that of modern whales. The later whales could hear better in water than pakicetids could, and could also hear in air, but hearing in both media was compromised by the existence of two systems. With the advent of basilosauroids (approximately 40 million years ago), the old land-mammal ear disappeared, and the modern cetacean sound transmission system began its development. Although basilosaurids were not echolocators (they lacked the sound-emission equipment of later echolocators), they had taken a major step forward in refining underwater sound reception.

The paper in question is S. Nummela et al. “Eocene evolution of whale hearing” Nature Vol 430, No 7001, pp 776-778 (doi:10.1038/nature02720). Abstract reads:

The origin of whales (order Cetacea) is one of the best-documented examples of macroevolutionary change in vertebrates. As the earliest whales became obligately marine, all of their organ systems adapted to the new environment. The fossil record indicates that this evolutionary transition took less than 15 million years, and that different organ systems followed different evolutionary trajectories. Here we document the evolutionary changes that took place in the sound transmission mechanism of the outer and middle ear in early whales. Sound transmission mechanisms change early on in whale evolution and pass through a stage (in pakicetids) in which hearing in both air and water is unsophisticated. This intermediate stage is soon abandoned and is replaced (in remingtonocetids and protocetids) by a sound transmission mechanism similar to that in modern toothed whales. The mechanism of these fossil whales lacks sophistication, and still retains some of the key elements that land mammals use to hear airborne sound.

Those with access to the journal can read the article here

Posted by jkrebs on July 19, 2004 | Comments (2)

The description of our site in the right sidebar says that “The Panda’s Thumb is the virtual pub of the University of Ediacara,” and the University of Ediacara (U of E) is “an online virtual University dedicated to the study of the origins of life in the cosmos.”

At the U of E site, Chris Nedin explains where the name “Ediacara” came from

The name “Ediacara” (pronounced Edi-ak-ra) comes from the Ediacara fauna, the first example of multicelled metazoans found in the fossil record. The significance of the fauna was first realized by geologists in South Australia, who found abundant fossils at the Ediacara Hills in the Flinders Ranges, about 650 km north of Adelaide. They realized that not only did the fauna contain jellyfish, soft corals and possibly worms and proto-arthropods, similar to modern forms, but that the fauna was significantly older than any other animal fossils yet found (600-540 million years old), even predating the Cambrian explosion. Whilst debate still continues as to the exact nature of the fauna, few now doubt that at least some of the forms represent examples of modern animal groups. The origin of the metazoa and thus all animal groups must now be placed even further back in time, and may never be found, since it is thought that the precursor organisms were miofaunal - tiny worm-like organisms living in the interstitial spaces between sand grains and thus having little chance of fossilizing.

“Ediacara” thus represents not only a major milestone in the history life on Earth, but also in the history of the Internet, being - as it is - the worlds first virtual university.

Apropos of this explanation, here’s a really neat story from the internet today.  See here for the whole story and some neat pictures.

Continue reading  “Exquisite fossils from the Ediacaran”

Posted by jml on July 15, 2004

From ScienceDaily:

Comparing primate genomes is an approach that can help scientists understand the genetic basis of the physical and biochemical traits that distinguish primate species. James Sikela and colleagues, for example, collected DNA from humans, chimpanzees, bonobos, gorillas, and orangutans to identify variations in the number of copies of individual genes among the different species. Their work is published in this month’s issue of the open-access journal, PLoS Biology.

Overall, Sikela and colleagues found more than 1,000 genes with changes in copy number in specific primate lineages. All the great ape species showed more increases than decreases in gene copy numbers, but humans showed the highest number of genes with increased copy numbers, at 134, and many of these duplicated human genes are implicated in brain structure and function.

Because some of these gene changes were unique to each of the species examined, they will likely account for some of the physiological and morphological characteristics that are unique to each species. One cluster of genes that amplified only in humans was mapped to a genomic area that appears prone to instability in human, chimp, bonobo, and gorilla. This region has undergone modifications in each of the other descendent primate species, suggesting an evolutionary role. In humans, gene mutations in this region are also associated with the inherited disorder spinal muscular atrophy. This fact, along with the observation that there are human-specific gene duplications in this region, suggests a link between genome instability, disease processes, and evolutionary adaptation.

The research paper is available at the Public Library of Science - abstract is below:

Given that gene duplication is a major driving force of evolutionary change and the key mechanism underlying the emergence of new genes and biological processes, this study sought to use a novel genome-wide approach to identify genes that have undergone lineage-specific duplications or contractions among several hominoid lineages. Interspecies cDNA array-based comparative genomic hybridization was used to individually compare copy number variation for 39,711 cDNAs, representing 29,619 human genes, across five hominoid species, including human. We identified 1,005 genes, either as isolated genes or in clusters positionally biased toward rearrangement-prone genomic regions, that produced relative hybridization signals unique to one or more of the hominoid lineages. Measured as a function of the evolutionary age of each lineage, genes showing copy number expansions were most pronounced in human (134) and include a number of genes thought to be involved in the structure and function of the brain. This work represents, to our knowledge, the first genome-wide gene-based survey of gene duplication across hominoid species. The genes identified here likely represent a significant majority of the major gene copy number changes that have occurred over the past 15 million years of human and great ape evolution and are likely to underlie some of the key phenotypic characteristics that distinguish these species.

Posted by jml on July 12, 2004 | Comments (2)

From EurekAlert:

A butterfly’s wing is a uniquely visual exhibition, not only of the aesthetics of nature, but of the machinery of evolution. Biologists have long appreciated that butterfly wing patterns dramatically exemplify the intricate interplay between genes and the environment — as the patterns evolve to give butterflies advantages in evading predators and attracting mates.

In a paper in the July 13, 2004, issue of Current Biology, biologists Robert Reed and Michael Serfas add a new piece to the evolutionary puzzle of the butterfly wing. By comparing among species the molecular machinery that controls wing development, the researchers are revealing how the regulation of two key genes has evolved in association with specific color patterns. The color patterns they studied vary among species, existing in a continuum including simple lines, teardrops and rounded spots.

Robert D. Reed and Michael S. Serfas (2004) “Butterfly Wing Pattern Evolution Is Associated with Changes in a Notch/Distal-less Temporal Pattern Formation Process” Current Biology 14(13): 1159-1166. doi:10.1016/j.cub.2004.06.046

I’ll leave it to PZ to perhaps comment on this :), but below is the abstract of the paper.

Abstract:: In butterflies there is a class of “intervein” wing patterns that have lines of symmetry halfway between wing veins. These patterns occur in a range of shapes, including eyespots, ellipses, and midlines, and were proposed to have evolved through developmental shifts along a midline-to-eyespot continuum. Here we show that Notch (N) upregulation, followed by activation of the transcription factor Distal-less (Dll), is an early event in the development of eyespot and intervein midline patterns across multiple species of butterflies. A relationship between eyespot phenotype and N and Dll expression is demonstrated in a loss-of-eyespot mutant in which N and Dll expression is reduced at missing eyespot sites. A phylogenetic comparison of expression time series from eight moth and butterfly species suggests that intervein N and Dll patterns are a derived characteristic of the butterfly lineage. Furthermore, prior to eyespot determination in eyespot-bearing butterflies, N and Dll are transiently expressed in a pattern that resembles ancestral intervein midline patterns. In this study we establish N upregulation as the earliest known event in eyespot determination, demonstrate gene expression associated with intervein midline color patterns, and provide molecular evidence that wing patterns evolved through addition to and truncation of a conserved midline-to-eyespot pattern formation sequence.

Posted by Nick Matzke on July 3, 2004 | Comments (4)

In case you’ve been living in a box somewhere, the NASA/ESA spacecraft Cassini-Huygens successfully fired its rockets on July 1, slowing down enough to be captured by Saturn’s gravity and enter a highly elliptical orbit around Saturn.  If the rocket burn had failed, Saturn’s gravity boost would have given Cassini enough velocity to escape the solar system, so this was a fairly important part of the 7-year mission.

Cassini threaded a gap in the rings (twice), flew within one Saturn-diameter of Saturn, and took some ultra-close snapshots of Saturn’s rings.  Soon afterwards, Cassini made a moderately close Titan flyby, getting the first decent images of the surface of the solar system’s second-biggest moon.

Clicking these thumbnails will take you to the full resolution version on the NASA website.

As you can see (left), in the wavelengths of visible light (400-700 nanometers), Titan appears covered in impenetrable red haze.  However, by using longer infrared wavelengths (2000, 2800, and 5000 nanometers), the Cassini cameras can peer through the haze.

Continue reading  “First decent views of the surface of Titan”

Posted by Nick Matzke on June 13, 2004 | Comments (6)

I am mostly a biology person, and PT is mostly a biology blog, but I think we can all take a moment to have a gasp at the results of the first moon flyby of the Cassini-Huygens mission to Saturn. 

Quite an improvement over the last few days, eh?  Check the continually-updated latest images from Cassini page at JPL, where you can view the images at almost whatever resolution you desire.  The Cassini team will probably be adding images rapidly from now on.

Continue reading  “Say Hello to Phoebe”

Posted by jml on April 20, 2004 | Comments (1)

The discovery in microbes of two oxygen-packing proteins, the earliest known ancestors to hemoglobin, brings scientists closer to identifying the earliest life forms to use oxygen.

Hemoglobins are ubiquitous in Eukarya and Bacteria but, until now, have not been found in Archaea. A phylogenetic analysis of the recently revealed microbial family of globin-coupled heme-based sensors suggests that these sensors descended from an ancient globin-only progenitor, or a protoglobin (Pgb). Here, we report the discovery and characterization of two Pgbs from the Archaea: ApPgb from the obligately aerobic hyperthermophile Aeropyrum pernix, and MaPgb from the strictly anaerobic methanogen Methanosarcina acetivorans. Both ApPgb and MaPgb bind molecular oxygen, nitric oxide, and carbon monoxide by means of a heme moiety that is coordinated to the protein through the F8 histidine (histidine 120). We postulate that these archaeal globins are the ancestors of contemporary hemoglobins.

1. Tracey Allen K. Freitas, Shaobin Hou, Elhadji M. Dioum, Jennifer A. Saito, James Newhouse, Gonzalo Gonzalez, Marie-Alda Gilles-Gonzalez, and Maqsudul Alam, “Ancestral hemoglobins in Archaea” Proceedings of the National Academy of Sciences published April 19, 2004, 10.1073/pnas.0308657101 [link].

EurekAlert press release.

Posted by jml on April 16, 2004 | Comments (1)

[Via Boing Boing]

A brain study released today shows that the human ability to appreciate aesthetics is based in the prefontal cortex, part of the brain involved in decision making. The scientists at the Balearic Islands University in Spain came to this conclusion by imaging their subjects’ brains while looking at art and photography. According to the study, quoted in Scientific American, “‘a phylogenetic change in the prefontal cortex could give way to the decorative and artistic profusion’ in humans.”

[article]

Posted by jml on April 14, 2004 | Comments (2)

An interesting article in this week's edition of Nature suggests that at least in some fish, alterations in a single gene bring about evolutionary change in the form of limb (fin) loss.

Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks
MICHAEL D. SHAPIRO, MELISSA E. MARKS, CATHERINE L. PEICHEL, BENJAMIN K. BLACKMAN, KIRSTEN S. NERENG, BJARNI JÓNSSON, DOLPH SCHLUTER & DAVID M. KINGSLEY
Nature 428, 717–723

Eurekalert press release
Original Article
Discussion by Shubin & Dahn

Posted by Wesley R. Elsberry on April 1, 2004

I received notice through the MARMAM listserve of two upcoming meetings open to the public on marine mammals and public policy. I will append the announcements.

The U.S. Marine Mammal Commission will host a meeting of the Advisory Committee on Acoustic Impacts on Marine Mammals, to be held April 28-30, 2004, in Arlington, VA. See this page for the meeting agenda and instructions for public comment.

The U.S. Marine Mammal Commission will host a workshop on the vulnerability of beaked whales to anthropogenic sound, to be held April 13-16, 2004, in Baltimore, MD. The public may attend as observers to this technical meeting. An agenda and information page will be posted for the meeting.

The schedule of upcoming meetings of the Marine Mammal Commission.

Continue reading  “Marine Mammals and Public Policy - Two Meetings”

Posted by jml on March 30, 2004

[Disclaimer: I am a co-author of the research discussed below, but I felt it would be of interest to the community particularly as it may help clarify hominid relationships]

A paper by Charlie Lockwood (of University College London), Bill Kimbel (of Arizona State University) and I (also of ASU) just published in this weeks Proceedings of the National Academy of Sciences titled "Morphometrics and hominoid phylogeny: Support for a chimpanzee-human clade and differentiation among great ape subspecies," finds a strong agreement beween morphological and genetic variation among great apes when using a specific bone of the skull (the temporal) and a specific set of techniques (geometric morphometrics and distance-based tree generation). As the temporal bone is often well preserved in fossil hominids, we suggest that this combination of techniques may allow the inference of accurate phylogenies (i.e. congruent with genetic data) from such material. All very exciting, as it re-affirms the importance of morphological data in the phylogentic analysis of extinct hominids and opens up a range of possibilities for future studies, in that we feel reasonably confident that morphological trees thus derived using fossil material have a strong relationship to the patterns we would get if genetic data were available from the fossils.

Continue reading  “Reconstructing Human Origins”

Posted by jml on March 25, 2004 | Comments (24)

A paper published online in Molecular Biology and Evolution claims to have "rigorous proof that [junk DNA was] added to DNA 'late' in the evolution of life on earth--after the formation of modern-sized genes, which contain instructions for making proteins" according to a press release from the National Institute of Standards and Technology, whose Center for Advanced Research in Biotechnology (CARB) was involved with the research (link)

The press release states:

Research from the CARB group appears to resolve a debate over the "early versus late" timing of the appearance of introns. Since introns were discovered in 1978, scientists have debated whether genes were born split (the "introns-early" view), or whether they became split after eukaryotic cells (the ones that gave rise to animals and their relatives) diverged from bacteria roughly 2 billion years ago (the "introns-late" view). Bacterial genomes lack introns. Although the study did not attempt to propose a function for introns, or determine whether they are beneficial or harmful, the results appear to rule out the "introns-early" view.

The CARB analysis shows that the probability of a modern intron's presence in an ancestral gene common to the genes studied is roughly 1 percent, indicating that the vast majority of today's introns appeared subsequent to the origin of the genes. This conclusion is supported by the findings regarding placement patterns for introns within genes. It long has been observed that, in the sequences of