Bacteria Made Of Star Stuff

One of the best at explaining science was Carl Sagan. One recurring theme in Sagan’s works can be seen in the quote below:

And we who embody the local eyes and ears and thoughts and feelings of the cosmos we’ve begun, at last, to wonder about our origins. Star stuff, contemplating the stars organized collections of 10 billion-billion-billion atoms contemplating the evolution of matter tracing that long path by which it arrived at consciousness here on the planet Earth and perhaps, throughout the cosmos.

Or consider the video below:

Interesting Science Picture XVIII: Spiders Eat Bats

Call me disturbed.

(Source)

Figure 2. Bats caught by spiders. A – Adult female Avicularia urticans feeding on a Greater Sac-winged Bat (Saccopteryx bilineata) on the side of a palm tree near the Rio Yarapa, Peru (photo by Rick West, Victoria, Canada; report # 1). B – Adult Proboscis Bat (Rhynchonycteris naso) entangled in a web of Argiope savignyi at the La Selva Biological Station, northern Costa Rica (photo by Mirjam Kno¨ rnschild, Ulm, Germany; report # 14). C – Dead bat (presumably Centronycteris centralis) entangled in an orb-web in Belize (photo by Carol Farneti-Foster, Belice City, Belize; report # 12). D – Dead bat (Myotis sp.) entangled in a web of Nephila clavipes in La Sirena, Corcovado National Park, Costa Rica (photo by Harald & Gisela Unger, Ko¨ ln, Germany; report # 17). E – A bat caught in the web of an araneid spider (possibly Eriophora sp.) in Tortuguero National Park, Costa Rica (photo by Cassidy Metcalf, USA; report # 18). F – Live bat trapped in web of Nephilengys cruentata in a thatch roof at Nisela Lodge, Swaziland (photo by Donald Schultz, Hollywood, USA; report # 47). G – Volant juvenile Proboscis Bat (Rhynchonycteris naso) entangled in web of Nephila clavipes photographed in a palm swamp forest near Madre de Dios, Peru (photo by Sam Barnard, Colorado Springs, USA; report # 7). H – Dead bat entangled in web of a female Nephila clavipes in tropical rainforest in the middle of the Rio Dulce River Canyon near Livingston, Guatemala (photo by Sam & Samantha Bloomquist, Indianapolis, USA; report # 11). I – Dead bat (Rhinolophus cornutus orii) caught in the web of a female Nephila pilipes on Amami-Oshima Island, Japan (photo by Yasunori Maezono, Kyoto University, Japan; report # 35). J, K – A small bat (superfamily Rhinolophoidea) entangled in web of Nephila pilipes at the top of the Cockatoo Hill near Cape Tribulation, Queensland, Australia (photo by Carmen Fabro, Cockatoo Hill, Australia; report # 39). The spider pressed its mouth against the dead, wrapped bat, indicating that it was feeding on it. A Nephila pilipes male also present in the web (K) may have been feeding on the bat as well. L – Dead vespertilionid bat entangled in the web of a female Nephila pilipes in the Aberdeen Country Park, Hong Kong (photo by Carol S.K. Liu from AFCD Hong Kong, China; report # 32).

Mutations That Affect Phenotype

Pardon the awkward title of this post. What I would like to do in this post is revisit something I mentioned in the first part of my review of Science and Human Origins in that post I mentioned a paper by Jianzhi Zhang called “Parallel Functional Changes in the Digestive RNases of Ruminants and Colobines by Divergent Amino Acid Substitutions.” The paper looked at mutations in the pancreatic RnNase of ruminants and colobines and found nine mutations in colobine RNase and five -different- mutations in ruminant RNase. The fact that Zhang found fourteen different mutations that affected pancreatic in much the same way prompted Zhang to come up with an estimate of how many different mutations can affect the function of the Rnase. He concluded that this number was somewhere between 16-44. So, of those 16-44 theoretical mutations 14 had been identified.

I have found a more graphic example to illustrate the point. The picture below illustrates the Melanocortin 1 receptor (MC1R)

(Picture Source)

The picture is self explanatory. The black colored dots are mutations that cause melanism, the green dots are mutations linked to coat color changes in rock pocket mice, the red are mutations that cause red fur or hair, the blue are mutations that cause red hair in humans and possibly melanism in other species. Not shown are the mutations in the -COOH that affect coat color in retrievers and other dogs.

The point is that there are many ways to a new function and to say that unless a given specified pathway is followed evolution can’t happen is clearly nonsense.

Majerus and Mundy (2003) Mammalian melanism: natural selection in black and white. TRENDS in Genetics: 19(11)585-588
Zhang (2003) Parallel Functional Changes in the Digestive RNases of Ruminants and Colobines by Divergent Amino Acid Substitutions. Molecular Biology and Evolution 20(8):1310-1317

Interesting Science News

Still working on my review of Science and Human Origins (yes, I have been somewhat lazy when it comes to blogging) in the meantime enjoy the following items.

Interesting Science Picture XVI

The story:

“Scientists have collected tens of thousands of fossils at this site in recent decades,” notes co-author Dr. Stephan Schaal of the Senckenberg Naturmuseum in Frankfurt, “but only these turtles are known to occur in pairs, a total of nine so far.” Detailed analysis of the fossil material revealed that each pair consists of a female and male individual. More importantly, even though the males typically face away from the females, the tail of some male individuals can be found wrapped under the shell of the female. “There is no doubt in my mind,” says Dr. Joyce, “These animals died some 47 million years ago in the act of mating. No other vertebrates are known to have died during this important biological process and then been fossilized.”

Source: W. G. Joyce, N. Micklich, S. F. K. Schaal, T. M. Scheyer. Caught in the act: the first record of copulating fossil vertebrates. Biology Letters, 2012; DOI: 10.1098/rsbl.2012.0361

Gorilla Genome Sequenced!

The gorilla genome has been sequenced and yields some interesting insights on human evolution. The research is reported in Nature. The article is open access. Here is the abstract:

Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human–chimpanzee and human–chimpanzee–gorilla speciation events at approximately 6 and 10 million years ago. In30%of the genome, gorilla is closer tohuman or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing.Wealso compare the western and eastern gorilla species, estimating an average
sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.

Shark Bites Whale

Phys.Org mentions an interesting article published in the International Journal of Osteoarchaeology. The article concerns a fragment of a whale rib, dating to the Pliocene, that shows evidence of a shark bite. In this case the rib also displays evidence of having survived the attack. From Phys.Org:

I’ll Never Make Fun of Online Gamers Again!

Online gamers have solved an interesting problem in AIDS research:

“We wanted to see if human intuition could succeed where automated methods had failed,” said Dr. Firas Khatib of the University of Washington Department of Biochemistry. Khatib is a researcher in the protein structure lab of Dr. David Baker, professor of biochemistry.

Remarkably, the gamers generated models good enough for the researchers to refine and, within a few days, determine the enzyme’s structure. Equally amazing, surfaces on the molecule stood out as likely targets for drugs to de-active the enzyme.

Cool!

The Genetics of Stay at Home Vs “Exploratory” Butterflies

Science Daily has a fascinating bit on butterflies called Butterflies That Explore and Colonize New Habitats Are Genetically Different from Cautious Cousins.This extended quote from the press release is fascinating:

In the new study, another gene variant also stood out as an important indicator of butterfly flight ability. New-population females were more often missing a small part of the succinate dehydrogenase gene (Sdhd) and this small deletion was associated with the ability to maintain flight for a greater duration. “The Pgi gene variant seems to be associated with sprinting, and the Sdhd gene variant appears to be associated with endurance,” Marden said. “It’s easy to see why these traits and their associated genes would be found at higher frequencies in new populations. Better flight ability allows certain butterflies to be able to reach and settle new habitat patches.”

Wheat, the paper’s lead author, said, “We already knew about Pgi from previous work in other butterflies and what has been done so far in the Glanville fritillary butterfly. Now with Sdhd we have two genes in the same carbohydrate-metabolism pathway containing alleles of major effect for ecologically important traits.” Marden also commented on the differences in gene expression involving protein dynamics. “Butterflies obtain protein only during larval feeding, whereas the adults rely on nectar, from which they obtain only carbohydrate,” he said. “The timing and level of expenditure of stored proteins is one way to manipulate life history in a species where no more protein will be available to the adult.”

The paper is being published in Molecular Ecology, if someone has access and can send me a copy I would appreciate it. The paper can be found here:

Christopher W. Wheat, Howard W. Fescemyer, J. Kvist, Eva Tas, J. Cristobal Vera, Mikko J. Frilander, Ilkka Hanski, James H. Marden. Functional genomics of life history variation in a butterfly metapopulation. Molecular Ecology, 2011; DOI: 10.1111/j.1365-294X.2011.05062.x

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Orangutan Genetics: Begging for an Article

There are a couple of interesting articles on Orangutan genteics out. The first, published in Nature (and is open acess), announces the sequencing of the Orangutan genome. Results are kind of interesting. From Science Daily (I haven’t had a chance to read the Nature article yet):

However, in a surprising discovery, the researchers found that at least in some ways, the orangutan genome evolved more slowly than the genomes of humans and chimpanzees, which are about 99 percent similar.

“In terms of evolution, the orangutan genome is quite special among great apes in that it has been extraordinarily stable over the past 15 million years,” says senior author Richard K. Wilson, PhD, director of Washington University’s Genome Center, which led the project. “This compares with chimpanzees and humans, both of which have experienced large-scale structural rearrangements of their genome that may have accelerated their evolution.”