Friday, February 02, 2007


Metagenomics: Investigating the invisible life in our environment

A new comparative metagenomics method provides insights into the evolution of the smallest beings on Earth

Microorganisms make up more than a third of the Earth's biomass. They are found in water, on land and even in our bodies, recycling nutrients, influencing the planet's climate or causing diseases. Still, we know surprisingly little about the smallest beings that colonise Earth. A new computational method to analyse environmental DNA samples, developed by researchers at the European Molecular Biology Laboratory [EMBL] in Heidelberg, now sheds light on the microbial composition of different habitats, from soil to water. The study, which will be published in this week's online issue of the journal Science, also reveals that microbes evolve faster in some environments than in others and that they rather rarely change their habitat preferences over time.

Studying microorganisms has proven very difficult in the past, because most naturally occurring types do not grow in the lab. The rapidly growing field of environmental DNA sequencing, called metagenomics [1], now helps to overcome this problem. Instead of analysing the genome of a specific organism, scientists sequence all the DNA they find in environmental samples, ranging from seawater to soil. They collect vast amounts of sequence fragments, which contain genetic information of thousands of species forming communities that colonise a certain habitat.

"We have developed a new and very precise method to classify the microbial communities that are present in a given sample," explains Peer Bork, joint coordinator of the Structural and Computational Biology Unit at EMBL. "We first identify informative DNA sequences in a sample and then map them onto the tree of life, a phylogeny of organisms with sequenced genomes, to find out which microbes are present and where yet unknown species fit into taxonomy and evolution."

In this way, Bork and EMBL alumnus Christian von Mering classified microbial communities present in four very different environments: ocean surface, acidic underground mine water, whale bones from the deep sea and farm soil.

"Most of the DNA we found fits into the evolutionary ancient parts of the tree of life, which means that the organisms are probably not close relatives of the species sequenced and known so far," says von Mering, who carried out the research in Bork's group. "Our novel method complements current classification attempts based on individual RNA molecules and also has additional unique features. It allows us to gain insight into the evolution of microbes in the context of their habitats."

Comparing the datasets from different environments, the researchers discovered that microorganisms evolve at different speeds depending on their habitat. While organisms at the ocean surface evolve fairly rapidly, soil microbes only change slowly throughout evolution, perhaps partly due to long dormancy phases during winter.

In collaboration with Phil Hugenholtz and Susannah Green Tringe from the Joint Genome Institute in Walnut Creek, California, Bork and his colleagues also investigated whether habitat preferences of microbes have remained the same throughout evolution. "It turns out that most microbial lineages remain loyal to a certain environment for long periods of time, only very few are able to adapt to different lifestyles," Bork says. "This tells us that it is not easy to enter a new environment and compete with the established communities in it, which contradicts the longstanding belief that every microbe can potentially live everywhere."

To investigate the invisible life on our planet further, samples of many different environments are being collected and analysed. Metagenomics experiments generating enormous amounts of data and new computational methods extracting meaningful information from it will provide a much better understanding of biodiversity on Earth in future.

Source: European Molecular Biology Laboratory PR 2 February 2007


Based on the Science paper:

Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments

C. von Mering, P. Hugenholtz, J. Raes, S. G. Tringe, T. Doerks, L. J. Jensen, N. Ward, P. Bork
Published online February 1 2007; 10.1126/science.1133420 (Science Express Reports)

The taxonomic composition of environmental communities is an important indicator of their ecology and function. Here, we use a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative and accurate picture of community composition than traditional rRNA-based approaches using polymerase chain reaction (PCR). By mapping marker genes from four diverse environmental data sets onto a reference species phylogeny, we show that certain communities evolve faster than others, determine preferred habitats for entire microbial clades, and provide evidence that such habitat preferences are often remarkably stable over time.


[1] See:

Metagenomics: the science of biological diversity
By K. J. Shelswell

Shelswell, K. J. (2006). Metagenomics: the science of biological diversity. The Science Creative Quarterly, 2. Retrieved February 2, 2007 from

For approximately 4.5 billion years, the Earth has been evolving from a barren volcanic landscape into the vibrant globe full of life that it is today. The first forms of life, small microorganisms, have been found in fossils from 3.5 billion years ago. Around 1.5 billion years ago, motile microorganisms emerged allowing life to migrate to different environments with different environmental conditions like increased exposure to ultraviolet radiation or higher temperatures. Microorganisms began to evolve with the changing environmental conditions of the planet.

These new environmental conditions, acting as selective pressures, drove the evolutionary process. They forced new species of organisms to evolve that were better suited to survival under particular environmental pressures. The evolution of new species generates biological diversity, which is represented by the number of different species in an environment. Over time, the evolutionary process has led to the development of more complex life forms such as trees, fish, and humans. A simple example of biological diversity is a comparison between a human and a monkey...

And the PLoS Computational Biology paper:

Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities
Kevin Chen, Lior Pachter

The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.

Citation: Chen K, Pachter L (2005) Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities. PLoS Comput Biol 1(2): e24 doi:10.1371/journal.pcbi.0010024


Recent posts include:

"Horizontal gene transfer adds to speed and complexity of evolution"

"Shotgun sequencing finds nanoorganisms"

"Cooperation among Micro-organisms"

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Thursday, February 01, 2007


'New Science' to be created at Florida State University Workshop

Genotypes and phenotypes aren't exactly household words outside the realm of the life and biological sciences - yet - but Florida State University biologists mean to integrate those emerging fields into a brand-new science by hiring a "cluster" of world-class scientists who will lead research to connect underlying genetics of organisms to overall appearance and behavior.

On February 2 and 3 at an FSU workshop that will assemble some of the best minds in the fields and feature some high-powered brainstorming, the university will move one step closer to making its "Integrating Genotypes and Phenotypes" initiative a groundbreaking reality.

"Great things are expected to come from the Integrating Genotype and Phenotype cluster and the exceptional people we hope to recruit for it," said FSU College of Arts and Sciences Dean Joseph Travis. "A major challenge of biology is to integrate genomic-level data with the phenotype of the whole organism. This bold move will essentially create a 'new science' and put FSU at its forefront, and the workshop is a key next step in that process."

The upcoming workshop will feature top FSU researchers such as evolutionary geneticist David Houle and internationally renowned scientists from universities such as Yale and Columbia and other institutions worldwide. It kicks off Friday at 8:30 a.m. (2 February 2007) and runs throughout the afternoon in room 499 of Dirac Science Library on the FSU campus. Sessions will continue Saturday, beginning at 9 a.m. in the Pavilion Room at Wakulla Springs State Park.

Invited speakers include science luminaries such as Indiana University's Rudy Raff, a chief architect of the merging of developmental and evolutionary biology into a new field called "evo-devo," [1] and the University of Arizona's Rich Jorgensen, who discovered a genetic phenomenon known as RNA silencing.

The planned "Integrating Genotypes and Phenotypes" cluster hire comprises one of several innovative cluster hire projects being undertaken across a range of disciplines at FSU - critical components of the university's ambitious Pathways of Excellence goals.

With Pathways as a blueprint, said Travis, FSU biological science department faculty are busy laying the groundwork for an eventual cluster hire of eight faculty members with diverse but complimentary research interests. This cluster would be expected to collaboratively drive the Integrating Genotype and Phenotype initiative to generate a rare degree of focused talent and extraordinary results.

"We are endeavoring to bring together two of the most exciting areas in biology - recently discovered systems of inheritance and gene regulation that fall outside the traditional genetic paradigm, and the use of evolutionary thinking to interpret all of life," said Houle, an associate professor in the FSU biology department and co-organizer of the upcoming workshop. "Success in this effort will finally allow us to understand the vast amount of information in the human genome, and potentially to transform the way biology is done."

The challenge, added Houle, is to generate interdisciplinary interactions between researchers with very different research traditions. "This FSU workshop will bring together the stars of two fields in pursuit of common language and goals that can bring this innovative FSU initiative to fruition."

More information at "Integrating Genotype and Phenotype: a planning workshop" and also see "Scientific Justification"

Source: FSU News Release "FSU will host biologists from around the world to create 'new science'" (January 2007)


[1] The evolution of evo-devo biology
Corey S. Goodman, Bridget C. Coughlin
PNAS | April 25, 2000 | vol. 97 | no. 9 | 4424-4425

Introduction: Once seen as distinct, yet complementary disciplines, developmental biology and evolutionary studies have recently merged into an exciting and fruitful relationship. The official union occurred in 1999 when evolutionary developmental biology, or "evo-devo," was granted its own division in the Society for Integrative and Comparative Biology (SICB). It was natural for evolutionary biologists and developmental biologists to find common ground. Evolutionary biologists seek to understand how organisms evolve and change their shape and form. The roots of these changes are found in the developmental mechanisms that control body shape and form. Developmental biologists try to understand how alterations in gene expression and function lead to changes in body shape and pattern. So although SICB only recently validated evo-devo as an independent research area, evo-devo really started over a decade ago when biologists began using an individual organism's developmental gene expression patterns to explain how groups of organisms evolved.

To highlight this emerging field, the PNAS Editorial Board has sponsored a special feature on Evolutionary Developmental Biology. This evo-devo special feature contains eight Perspective articles and a review that examine evo-devo's progress to date, as well as 15 research articles that add new information and focus on the most recent evo-devo biology trends. The majority of the research articles were submitted directly to the PNAS office through our Track II system, and were evaluated by an Editorial Board member. After the initial screening, papers were assigned to an Academy Member-editor who oversaw a process where research manuscripts were rigorously peer-reviewed by experts in the field.


A recent post: "Balancing Robustness and Evolvability"

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Wednesday, January 31, 2007


Astrobiology: Dig deeper to find Martian life

Astrobiology: A UCL-led study has found that probes designed to find life on Mars do not drill deep enough to find the living cells that scientists believe may exist well below the surface.

Although current drills may find essential tell-tale signs that life once existed on Mars, cellular life could not survive the radiation levels for long enough any closer to the surface of Mars than a few metres deep - beyond the reach of even state-of-the-art drills."

The study, published in the journal 'Geophysical Research Letters', maps out the cosmic radiation levels at various depths, taking into account different surface conditions on Mars, and shows that the best place to look for living cells is within the ice at Elysium (see "ESA's Mars Express sees signs of a 'frozen sea'" below), the location of the newly discovered frozen sea on Mars.

Lead author Mr Lewis Dartnell, (UCL Centre for Mathematics and Physics in the Life Sciences and Experimental Biology - CoMPLEX), said: "Finding hints that life once existed - proteins, DNA fragments or fossils - would be a major discovery in itself, but the Holy Grail for astrobiologists is finding a living cell that we can warm up, feed nutrients and reawaken for studying."

"It just isn't plausible that dormant life is still surviving in the near-subsurface of Mars - within the first couple of metres below the surface - in the face of the ionizing radiation field. Finding life on Mars depends on liquid water surfacing on Mars, but the last time liquid water was widespread on Mars was billions of years ago. Even the hardiest cells we know of could not possibly survive the cosmic radiation levels near the surface of Mars for that long."

Survival times near the surface reach only a few million years. This means that the chance of finding life with the current probes is slim. Scientists will need to dig deeper and target very specific, hard-to-reach areas such as recent craters or areas where water has recently surfaced.

Dr Andrew Coates (UCL Space and Climate Physics) said: "This study is trying to understand the radiation environment on Mars and its effect on past and present life. This is the first study to take a thorough look at how radiation behaves in the atmosphere and below the surface and it's very relevant to planned missions. The best chance we have of finding life is looking in either the sea at Elysium or fresh craters."

The team found that the best places to look for living cells on Mars would be within the ice at Elysium because the frozen sea is relatively recent - it is believed to have surfaced in the last five million years - and so has been exposed to radiation for a relatively short amount of time.

The team developed a radiation dose model to study the radiation environment for possible life on Mars. Unlike Earth, Mars is not protected by a global magnetic field or thick atmosphere and for billions of years it has been laid bare to radiation from space. The team quantified how solar and galactic radiation is modified as it goes through the thin Martian atmosphere to the surface and underground.

Taking the known radiation resistance of terrestrial cells combined with the annual radiation doses on Mars, the team calculated the survival time of dormant populations of cells. Some strains are radiation-resistant and are able to survive the effects because, when active, they successfully repair the DNA breaks caused by ionising radiation. However, when cells are dormant, such as when frozen as in the subsurface of Mars, they are preserved but unable to repair the damage, which accumulates to the point where the cell becomes permanently inactivated.

Mr Dartnell said: "With this model of the subsurface radiation environment on Mars and its effects on the survival of dormant cells we have been able to accurately determine the drilling depth required for any hope of recovering living cells. We have found that this suspected frozen sea in Elysium represents one of the most exciting targets for landing a probe, as the long-term survival of cells here is better than underground in icy rock. This could be crucial for the scientists and engineers planning future Mars missions to find life."

Source: University College London, 30 January 2007


Based on the paper:

Dartnell, L. R., L. Desorgher, J. M. Ward, and A. J. Coates (2007), Modelling the surface and subsurface Martian radiation environment: Implications for astrobiology, Geophys. Res. Lett., 34, L02207, doi:10.1029/2006GL027494


The damaging effect of ionising radiation on cellular structure is one of the prime limiting factors on the survival of life in potential astrobiological habitats. Here we model the propagation of solar energetic protons and galactic cosmic ray particles through the Martian atmosphere and three different surface scenarios: dry regolith, water ice, and regolith with layered permafrost. Particle energy spectra and absorbed radiation dose are determined for the surface and at regular depths underground, allowing the calculation of microbial survival times. Bacteria or spores held dormant by freezing conditions cannot metabolise and become inactivated by accumulating radiation damage. We find that at 2 m depth, the reach of the ExoMars drill, a population of radioresistant cells would need to have reanimated within the last 450,000 years to still be viable. Recovery of viable cells cryopreserved within the putative Cerberus pack-ice requires a drill depth of at least 7.5 m.


"ESA's Mars Express sees signs of a 'frozen sea'" - A February 2005 Press Release from the European Space Agency:

Elysium Planitia Frozen Sea (Evolution Research: John Latter / Jorolat)

The above image, taken by the High Resolution Stereo Camera (HRSC) on board ESA's Mars Express spacecraft, shows what appears to be a dust-covered frozen sea near the Martian equator.

It shows a flat plain, part of the Elysium Planitia, that is covered with irregular blocky shapes. They look just like the rafts of fragmented sea ice that lie off the coast of Antarctica on Earth. This scene, taken during orbit 32, is a few tens of kilometres across, and is centred on latitude 5 degrees North and longitude 150 degrees East.

The water that formed the sea appears to have originated beneath the surface of Mars, and to have come out through a series of fractures known as the Cerberus Fossae, from where it flowed in a catastrophic flood.

It collected in a vast area about 800 kilometres long and 900 kilometres wide with a depth of about 45 metres. As the water started to freeze, floating pack ice broke up into rafts. These became later covered in ash and dust from volcanic eruptions in the region.

Ice is unstable at the surface of Mars because of the low atmospheric pressure, and sublimates away (changes straight from ice to vapour without passing through the liquid state) into the atmosphere, but some of the ice rafts appear to have been protected by layers of volcanic dust. While the entire sea froze solid, the unprotected ice between the rafts sublimated to leave 'ice plateaus' surrounded by bare rock.

The sparse cratering of this region shows that it cannot have formed more than about five million years ago, meaning this is a relatively young feature.

The question remains as to whether the frozen body of water is still there, or whether the visible floes are just the remains of the sublimation process. Two observations suggest that the ice is still there: first, the submerged craters are too shallow, indicating most of the ice is still in the craters; and second, the surface is too horizontal - if the ice had been lost, there would be a greater height variation.

Map of Elysium Planitia Frozen Sea (Evolution Research: John Latter / Jorolat)

These findings were presented on 21 February at ESA's Mars Express Science Conference at ESTEC in Noordwijk, the Netherlands, where about 250 scientists from all over the world are discussing the first year of scientific results from Mars Express. The complete scientific paper by Dr J. Murray et al. describing the frozen sea results will be published by the journal Nature in March 2005. [1]

The colour images were processed using the HRSC nadir (vertical view) and three colour channels. The perspective views were calculated from the digital terrain model derived from the stereo channels.

Image Caption: Map showing location of the 'frozen sea' in context


[1] Nature 434, 352-356 (17 March 2005) | doi: 10.1038/nature03379
Evidence from the Mars Express High Resolution Stereo Camera for a frozen sea close to Mars' equator

John B. Murray et al.

It is thought that the Cerberus Fossae fissures on Mars were the source of both lava and water floods two to ten million years ago. Evidence for the resulting lava plains has been identified in eastern Elysium, but seas and lakes from these fissures and previous water flooding events were presumed to have evaporated and sublimed away. Here we present High Resolution Stereo Camera images from the European Space Agency Mars Express spacecraft that indicate that such lakes may still exist. We infer that the evidence is consistent with a frozen body of water, with surface pack-ice, around 5 degrees north latitude and 150 degrees east longitude in southern Elysium. The frozen lake measures about 800 times 900 km in lateral extent and may be up to 45 metres deep - similar in size and depth to the North Sea. From crater counts, we determined its age to be 5 plus or minus 2 million years old. If our interpretation is confirmed, this is a place that might preserve evidence of primitive life, if it has ever developed on Mars.


See the Sunday, December 10, 2006 post "NASA Images Suggest Water Still Flows in Brief Spurts on Mars"

Video: "Mars Discoveries - Liquid Water and Impact Craters" (03.19)


Other posts include:

"The Mars Phoenix Lander: Piercing Together Life's Potential"

"Earth-like planets may be more common than once thought"

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Tuesday, January 30, 2007


Anthropologist confirms 'Hobbit' a separate species (+ BBC Video)


1) Anthropologist confirms 'Hobbit' indeed a separate species: News + Related Paper
2) The Mystery of the Human Hobbit: BBC Horizon Video (49 minutes)
3) Excerpts from "What is the Hobbit?"


1) Anthropologist confirms 'Hobbit' indeed a separate species: News + Related Paper

After the skeletal remains of an 18,000-year-old, Hobbit-sized human were discovered on the Indonesian island of Flores in 2003, some scientists thought that the specimen must have been a pygmy or a microcephalic - a human with an abnormally small skull.

Not so, said Dean Falk, a world-renowned paleoneurologist and chair of Florida State University's anthropology department, who along with an international team of experts created detailed maps of imprints left on the ancient hominid's braincase and concluded that the so-called Hobbit was actually a new species closely related to Homo sapiens.

Now after further study, Falk is absolutely convinced that her team was right and that the species cataloged as LB1, Homo floresiensis, is definitely not a human born with microcephalia - a somewhat rare pathological condition that still occurs today. Usually the result of a double-recessive gene, the condition is characterized by a small head and accompanied by some mental retardation.

"We have answered the people who contend that the Hobbit is a microcephalic," Falk said of her team's study of both normal and microcephalic human brains published in the January 29 issue of the journal PNAS (Proceedings of the National Academy of Sciences of the United States) [1].

The debate stemmed from the fact that archaeologists had found sophisticated tools and evidence of a fire near the remains of the 3-foot-tall adult female with a brain roughly one-third the size of a contemporary human.

"People refused to believe that someone with that small of a brain could make the tools. How could it be a sophisticated new species?"

But that's exactly what it is, according to Falk, whose team had previously created a "virtual endocast" from a three-dimensional computer model of the Hobbit's braincase, which reproduces the surface of the brain including its shape, grooves, vessels and sinuses. The endocasts revealed large parts of the frontal lobe and other anatomical features consistent with higher cognitive processes.

"LB1 has a highly evolved brain," she said. "It didn't get bigger, it got rewired and reorganized, and that's very interesting."

In this latest study, the researchers compared 3-D, computer-generated reconstructions of nine microcephalic modern human brains and 10 normal modern human brains. They found that certain shape features completely separate the two groups and that Hobbit classifies with normal humans rather than microcephalic humans in these features. In other ways, however, Hobbit's brain is unique, which is consistent with its attribution to a new species.

Comparison of two areas in the frontal lobe, the temporal lobe and the back of the brain show the Hobbit brain is nothing like a microcephalic's and is advanced in a way that is different from living humans. In fact, the LB1 brain was the "antithesis" of the microcephalic brain, according to Falk, a finding the researchers hope puts this part of the Hobbit controversy to rest.

It's time to move on to other important questions, Falk said, namely the origin of this species that co-existed at the same time that Homo sapiens was presumed to be the Earth's sole human inhabitant.

"It's the 64,000 dollar question: Where did it come from?" she said. "Who did it descend from, who are its relatives, and what does it say about human evolution? That's the real excitement about this discovery."

Source: University of Florida/PhysOrg

[1] Falk, D.; Hildebolt, C.; Smith, K.; Morwood, M.J.; Sutikna, T.; Jatmiko; Saptomo W.E.; Imhof, H., Seidler, H. & F. Prior. Brain shape in human microcephalics and Homo floresiensis
Published online before print February 2, 2007
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0609185104


Because the cranial capacity of LB1 (Homo floresiensis) is only 417 cm3, some workers propose that it represents a microcephalic Homo sapiens rather than a new species. This hypothesis is difficult to assess, however, without a clear understanding of how brain shape of microcephalics compares with that of normal humans. We compare three-dimensional computed tomographic reconstructions of the internal braincases (virtual endocasts that reproduce details of external brain morphology, including cranial capacities and shape) from a sample of 9 microcephalic humans and 10 normal humans. Discriminant and canonical analyses are used to identify two variables that classify normal and microcephalic humans with 100% success. The classification functions classify the virtual endocast from LB1 with normal humans rather than microcephalics. On the other hand, our classification functions classify a pathological H. sapiens specimen that, like LB1, represents an {approx}3-foot-tall adult female and an adult Basuto microcephalic woman that is alleged to have an endocast similar to LB1's with the microcephalic humans. Although microcephaly is genetically and clinically variable, virtual endocasts from our highly heterogeneous sample share similarities in protruding and proportionately large cerebella and relatively narrow, flattened orbital surfaces compared with normal humans. These findings have relevance for hypotheses regarding the genetic substrates of hominin brain evolution and may have medical diagnostic value. Despite LB1's having brain shape features that sort it with normal humans rather than microcephalics, other shape features and its small brain size are consistent with its assignment to a separate species.


2) The Mystery of the Human Hobbit: BBC Horizon Video 2005

"Is the hobbit a new human species or nothing more than a modern human with a crippling deformity?"

From the BBC website:

On the far-flung island of Flores, in the Indonesian archipelago, a team of archaeologists happened upon a tiny 18,000-year old skeleton. It was no more than a metre tall. They assumed they have found the remains of a young girl. But other signs suggested she was in fact much older. They had discovered one of the smallest human adults ever found.

As the dig continued, the evidence unearthed got stranger. The diggers found elephants the size of cows, rats the size of dogs, lizards the size of crocodiles. It was like stepping with Alice into Wonderland. It was not just the humans that were peculiarly sized, everything large had shrunk and everything small had grown.

Further digging uncovered spear points scattered among the bones of the pygmy elephants that appear to have been roasted on fires. It seemed that their tiny human must have been a skilled and intelligent hunter. Yet when they looked more closely at her skeleton, they discovered her brain was smaller than any other known human and no bigger than a chimpanzee's...


3) Excerpts from "What is the Hobbit?"

An open access/free PLoS Biology article by the science writer Tabitha M. Powledge.

Citation: Powledge TM (2006) What Is the Hobbit? PLoS Biol 4(12): e440 DOI: 10.1371/journal.pbio.0040440

Who - or what - is Homo floresiensis? The tiny hominid bones, which a joint Australian-Indonesian team unearthed in 2003 on the Indonesian island of Flores, have quickly become as celebrated (and derided) as any find in the tempestuous history of human paleontology. The mystery that shrouds these ancient skeletons, nicknamed hobbits after the diminutive characters in J. R. R. Tolkien's novels, seems to deepen with every study published. Two main camps have emerged, each certain they can settle the question. But many other paleoanthropologists confess they still have no idea.

H. floresiensis Discovered

The discovery team declared their find a new human species, H. floresiensis, based primarily on a single near-complete skeleton of one very small individual with a very small brain, known as LB1. Compared to H. sapiens, LB1, whose age was estimated from tooth wear at about 30 years, was only one meter tall - about the size of a 4-year-old H. sapiens child - with a brain the size of a newborn's. Although there are also fragments of eight other small individuals, they provide no information about brain size, nor is much skeleton preserved. Nonetheless, they possess a combination of features never before seen in human fossils, which makes it credible that a previously unknown population of people smaller than today's pygmies lived on Flores between 90,000 and 12,000 years ago.

Stone tools found at the site raise the possibility that hobbits had culture, even though LB1's brain size would make a chimpanzee sneer. H. floresiensis, the discovery team claimed, could be the first human example of island dwarfing. This phenomenon, thought to be evolution's response to limited resources, is known for other mammals, including dwarf elephants from Flores itself. But this is not the only possible conclusion. A long-awaited paper [2], which appeared online in Proceedings of the National Academy of Sciences of the United States of America (PNAS) on August 23, 2006, offers a radically different interpretation of these skeletal remains.

...The Hobbit's Brain

A March 2005 paper in the journal Science, whose authors include a subset of the discovery team, reported that a virtual endocast of LB1's cranium, which has brain features imprinted on it, suggested that hobbits were not simply miniature versions of sapiens or erectus, but still may have had human-like thinking abilities because the prefrontal cortex and temporal lobes seemed expanded. The region, known as Brodmann area 10, is thought to be the seat of higher cognitive processes like memory, communication, and planning.

By contrast, Holloway, who has also studied an LB1 endocast, says the brain's small size and some other features hint at pathology. Parts of area 10 called the gyri recti seem too thin, he reports, and he has never seen a human endocast so flattened out before, which also suggests abnormality. Like several other researchers, Holloway has tried (and failed) to find direct correspondences between LB1's cranium and those of people with microcephaly. Microcephaly, meaning simply small head, is an umbrella term for a miscellany of conditions with scores of different genetic and environmental causes and myriad manifestations. The most recent study, published online in Anatomical Record on October 9, 2006, concludes that "it is not possible to match any of these syndromes exactly with the LB1 fossil," although the authors argue that some microcephalic syndromes share features with LB1, including stature, head size, and anomalies of jaw and teeth. As all the studies point out, nothing so far unearthed in the clinical literature or the fossil record matches LB1's peculiar head. Those negatives, of course, don't rule out deformity, especially deformity unique to the hobbits; isolated populations routinely develop distinctive abnormalities.

Debbie Argue of Australian National University (Canberra, Australia) and co-authors of an October 2006 paper in the Journal of Human Evolution say LB1 is probably not microcephalic, and they endorse the designation of a new species. They also say the hobbits are not pygmy-like. They suggest instead (as have others) that, whereas LB1's cranium is not like anything else in the hominid fossil record, some other hobbit bones resemble much older early human (but non-Homo) fossils known only from Africa - the Australopithcines.

[2] Pygmoid Australomelanesian Homo sapiens skeletal remains from Liang Bua, Flores: Population affinities and pathological abnormalities
T. Jacob et al.
Published online before print August 23, 2006, 10.1073/pnas.0605563103

Liang Bua 1 (LB1) exhibits marked craniofacial and postcranial asymmetries and other indicators of abnormal growth and development. Anomalies aside, 140 cranial features place LB1 within modern human ranges of variation, resembling Australomelanesian populations. Mandibular and dental features of LB1 and LB6/1 either show no substantial deviation from modern Homo sapiens or share features (receding chins and rotated premolars) with Rampasasa pygmies now living near Liang Bua Cave. We propose that LB1 is drawn from an earlier pygmy H. sapiens population but individually shows signs of a developmental abnormality, including microcephaly. Additional mandibular and postcranial remains from the site share small body size but not microcephaly.


Related posts include:

"Komodo Dragons: News, Video, Further Reading"

"Bad News For Tolkien Fans - Flores 'Hobbit' Is Just A Miniman"

"Compelling evidence demonstrates that 'Hobbit' fossil does not represent a new species of hominid"

"Flores' Hobbits Update: New hominid species may be early version of Homo sapiens"

"Homo floresiensis - 'No Hobbits in this Shire'"

"The hullabaloo about hobbits"

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Horizontal gene transfer adds to speed and complexity of evolution

It's a mystery why the speed and complexity of evolution appear to increase with time. For example, the fossil record indicates that single-celled life first appeared about 3.5 billion years ago, and it then took about 2.5 billion more years for multi-cellular life to evolve. That leaves just a billion years or so for the evolution of the diverse menagerie of plants, mammals, insects, birds and other species that populate the earth.

New studies by Rice University scientists suggest a possible answer; the speed of evolution has increased over time because bacteria and viruses constantly exchange transposable chunks of DNA between species, thus making it possible for life forms to evolve faster than they would if they relied only on sexual selection or random genetic mutations.

"We have developed the first exact solution of a mathematical model of evolution that accounts for this cross-species genetic exchange," said Michael Deem, the John W. Cox Professor in Biochemical and Genetic Engineering and professor of physics and astronomy.

The research appears in the January 29 issue of Physical Review Letters.

Past mathematical models of evolution have focused largely on how populations respond to point mutations - random changes in single nucleotides on the DNA chain, or genome. A few theories have focused on recombination - the process that occurs in sexual selection when the genetic sequences of parents are recombined.

Horizontal gene transfer (HGT) is a cross-species form of genetic transfer. It occurs when the DNA from one species is introduced into another. The idea was ridiculed when first proposed more than 50 years ago, but the advent of drug-resistant bacteria and subsequent discoveries, including the identification of a specialized protein that bacteria use to swap genes, has led to wide acceptance in recent years.

"We know that the majority of the DNA in the genomes of some animal and plant species - including humans, mice, wheat and corn - came from HGT insertions," Deem said. "For example, we can trace the development of the adaptive immune system in humans and other jointed vertebrates to an HGT insertion about 400 million years ago."

The new mathematical model developed by Deem and visiting professor Jeong-Man Park attempts to find out how HGT changes the overall dynamics of evolution. In comparison to existing models that account for only point mutations or sexual recombination, Deem and Park's model shows how HGT increases the rate of evolution by propagating favorable mutations across populations.

Deem described the importance of horizontal gene transfer in the work in a January 2007 cover story in the Physics Today [1], showing how HGT compliments the modular nature of genetic information, making it feasible to swap whole sets of genetic code - like the genes that allow bacteria to defeat antibiotics.

"Life clearly evolved to store genetic information in a modular form, and to accept useful modules of genetic information from other species," Deem said.

The research is supported by the Defense Advanced Research Projects Agency.

Source: Rice University News Release 'Does evolution select for faster evolvers?' 01/29/2007


Based on the paper:

Physical Review Letters 98, 058101 (2007)
Phase Diagrams of Quasispecies Theory with Recombination and Horizontal Gene Transfer
J.-M. Park and M. W. Deem

We consider how transfer of genetic information between individuals influences the phase diagram and mean fitness of both the Eigen and the parallel, or Crow-Kimura, models of evolution. In the absence of genetic transfer, these physical models of evolution consider the replication and point mutation of the genomes of independent individuals in a large population. A phase transition occurs, such that below a critical mutation rate an identifiable quasispecies forms. We show how transfer of genetic information changes the phase diagram and mean fitness and introduces metastability in quasispecies theory, via an analytic field theoretic mapping.


[1] M. W. Deem, Mathematical Adventures in Biology, invited feature article, Physics Today 60 (January 2007) 42-47

Opening paragraph: The contemplation and resolution of questions at the interfaces of biology, mathematics, and physics promise to lead to a greater understanding of the natural world and to open new avenues for physics. The choice of questions in this article, most of them related to the statistical behavior of biological systems, reflects my own research interests. But it also reflects my belief that some of the unresolved issues in the mathematics of biology are related to the diversity, randomness, variation, and correlations in biology. With luck, physics-based approaches may shed further light on those issues.


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Thinking with the spinal cord?

Two scientists from the University of Copenhagen have demonstrated that the spinal cord uses network mechanisms similar to those used in the brain. The discovery is featured in the current issue of the journal Science.

The research group behind the surprising results consists of Professor Jorn Hounsgaard and Post.doc Rune W. Berg from the University of Copenhagen, and Assistant Professor and PhD Aidas Alaburda from the University of Vilnius. The group has shown that spinal neurons, during network activity underlying movements, show the similar irregular firing patterns as seen in the cerebral cortex.

New approach

Our findings contradict conventional wisdom about spinal cord functions, says Rune W. Berg from Department of Neuroscience and Pharmacology at the Faculty of Health Sciences. Until now, the general belief was that the spinal networks functioned mechanically and completely without random impulses. The new discovery enables researchers to use the theory on cortical networks to explore how spinal cords generate movements.

Still puzzled by movement

How humans are able to move at all remains a puzzle. Our muscles are controlled by thousands of nerve cells in the spinal cord. This entire, complex system must work as a whole in order to successfully create a single motion. The new research shows that even if we repeat a certain motion with high accuracy, the involved nerve cells never repeat their activity patterns. This particular observation reflects the organisation of the nerve cells of the cerebral cortex.

Source: University of Copenhagen


Based on the paper:

Balanced Inhibition and Excitation Drive Spike Activity in Spinal Half-Centers

Berg et al.
Science 19 January 2007: 390-393
DOI: 10.1126/science.1134960

Many limb movements are composed of alternating flexions and extensions. However, the underlying spinal network mechanisms remain poorly defined. Here, we show that the intensity of synaptic excitation and inhibition in limb motoneurons varies in phase rather than out of phase during rhythmic scratchlike network activity in the turtle. Inhibition and excitation peak with the total neuron conductance during the depolarizing waves of scratch episodes. Furthermore, spike activity is driven by depolarizing synaptic transients rather than pacemaker properties. These findings show that balanced excitation and inhibition and irregular firing are fundamental motifs in certain spinal network functions.


Other papers of interest:

The evolution of the spinal cord in primates: evidence from the foramen magnum and the vertebral canal
MacLarnon A
Journal of Human Evolution, Volume 30, Number 2, 1996, pp. 121-138(18)

Based on evidence from the foramina magna of two Eocene adapid species, Adapis parisiensis and Leptadapis magnus, it has previously been suggested that the spinal cord increased in size during primate evolution (Martin, 1980). However, it is shown here that foramen magnum size is not related simply to spinal cord size. The adapid group as a whole had a wide range of relative foramen magnum size, which is very difficult to explain. Unlike the foramen magnum, vertebral canal dimensions provide quite good indication of spinal cord dimensions.

The canal dimensions of two other adapid species, Notharctus tenebrosus and Smilodectes gracilis , are compared with the vertebral canal and spinal cord dimensions of modern primates. The cervical and thoracic spinal cords of these notharctine species were relatively smaller than those of any modern primate, and a spinal cord of modern relative dimensions could not have fitted through the fossil thoracic vertebral canal. On the other hand, the lumbar spinal cord of the notharctines was within the relative size range of modern species. The increase in the size of the cervical and thoracic regions of the spinal cord that has occurred during primate evolution is probably related to locomotor control of both the forelimb and the hindlimb. Forelimb innervation apparently increased as well as the flow of neural information to and from the hindlimb and the brain.

Size increase in the corticospinal tract and dorsal columns may have been important, affecting the agility and coordination of movement, including fine digital movement. Evidence from the vertebral canal therefore supports the suggestion from previous work that spinal cord size has increased during primate evolution in association with increasing sophistication of locomotor control.


The scaling of gross dimensions of the spinal cord in primates and other species
MacLarnon A.
Journal of Human Evolution, Volume 30, Number 1, 1996, pp 71-87(17)

Previous work on quantitative aspects of the evolution of the spinal cord suggests either that the cord has undergone considerable evolutionary changes, or that it is invariable and somatic. Variation in gross dimensions of the spinal cord is investigated here, mostly in mammals, including new data on 12 primate species, plus some bird and amphibian species.

Allometric analyses demonstrate that spinal cord size varies little relative to body size in mammals, including primates. Some gross locomotor differences, but not others, are associated with small differences in relative cord dimensions. Birds, on average, have slightly smaller spinal cords than mammals relative to body size; amphibians may have much smaller spinal cords. On the basis of present evidence, spinal cord weight in mammals scales to body weight with an exponent of 0?69. This is significantly different from the scaling exponent of 0?75 for brain weight to body weight. Therefore, metabolic explanations developed to explain the scaling of brain size are not applicable to the spinal cord.

However, the scaling exponent calculated for spinal cord weight is compatible with its scaling to body weight as a surface area to a volume, which may be important for functional interpretation of the scaling of somatic innervation. Simple brain:cord ratios should not be used as measures of relative brain size or intelligence, as the two parts of the central nervous system scale to body size with different exponents, and, at least between classes, because relative spinal cord size also varies. Analysing brain weight relative to spinal cord weight allometrically gives a functionally meaningful assessment of brain size relative to the level of neural communication between the brain and body.

Mammals have both large relative brains and cords compared with other classes, which may be required for the sophisticated control of their mode of locomotion. Some species, including the haplorhine primates, have expanded their brain sizes beyond this common level for increased cognitive capacity.


Proceedings of the National Academy of Sciences U S A. 1983 October; 80(19): 5936-5940.
Ontophyletics of the nervous system: development of the corpus callosum and evolution of axon tracts.
M J Katz, R J Lasek, and J Silver

The evolution of nervous systems has included significant changes in the axon tracts of the central nervous system. These evolutionary changes required changes in axonal growth in embryos. During development, many axons reach their targets by following guidance cues that are organized as pathways in the embryonic substrate, and the overall pattern of the major axon tracts in the adult can be traced back to the fundamental pattern of such substrate pathways. Embryological and comparative anatomical studies suggest that most axon tracts, such as the anterior commissure, have evolved by the modified use of preexisting substrate pathways.

On the other hand, recent developmental studies suggest that a few entirely new substrate pathways have arisen during evolution; these apparently provided opportunities for the formation of completely new axon tracts. The corpus callosum, which is found only in placental mammals, may be such a truly new axon tract. We propose that the evolution of the corpus callosum is founded on the emergence of a new preaxonal substrate pathway, the "glial sling," which bridges the two halves of the embryonic forebrain only in placental mammals.


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Sunday, January 28, 2007


Fish can determine their social rank by observation alone, study finds

A male fish can size up potential rivals, and even rank them from strongest to weakest, simply by watching how they perform in territorial fights with other males, according to a new study by Stanford University scientists. The researchers say their discovery provides the first direct evidence that fish, like people, can use logical reasoning to figure out their place in the pecking order.

The study, published in the January 25 edition of the journal Nature, is based on a unique experiment with cichlids (SIK-lids), small territorial fish from Africa.

"In their natural habitat, male cichlids are constantly trying to ascend socially by beating each other up," said study co-author Russell D. Fernald, professor of biological sciences at Stanford. "It would be really valuable for them to know in advance who to pick a fight with."

The Nature experiment was designed by lead author Logan Grosenick (2005 Recipient of The Firestone Medal for Excellence in Undergraduate Research), a graduate student in statistics at Stanford, and Tricia S. Clement, a former postdoctoral fellow. Their goal was to determine whether territorial fish use a type of reasoning called "transitive inference," (*See below) in which known relationships serve as the basis for understanding unfamiliar ones.

"Transitive inference is essential to logical reasoning," Fernald explained. "It's something that kids generally figure out by age 4 or 5 - Mary is taller than Fred, Fred is taller than Pete, therefore Mary is taller than Pete. It's been demonstrated in primates, rats and some bird species, but how and why it evolved in animals is a matter of debate."

Aggressive bouts

In the experiment, the Stanford team used a popular laboratory fish called Astatotilapia burtoni, one of many cichlid species that inhabit Lake Tanganyika in eastern Africa. A. burtoni males are extremely territorial and regularly engage in aggressive fights, the outcome of which determines who gets access to food and mates.

"Males that repeatedly lose fights are unable to hold territories and consequently descend in social status," the authors wrote. "Success in aggressive bouts is therefore crucial to male reproductive fitness, and the ability to infer the relative strength of rivals before engaging them in potentially costly fights should be highly adaptive."

When A. burtoni males fight, it's easy to spot the winner. Mature males have a menacing black stripe, or eyebar, on their face. After a fight, the winner retains his showy appearance, but the loser's eyebar temporarily disappears as he tries to flee his more aggressive opponent.

The Stanford team took advantage of this reversible transformation by staging a series of short fights between male cichlids. All of the combatants used in the experiment were the same size. During one-on-one combat, the fish whose eyebar disappeared was declared the loser.

After each bout, the loser was separated from his opponent and put back in his original tank. Within minutes, his eyebar returned, and he looked like all the other dominant males again.

Bystanders and rivals

The fights were staged in a square tank divided into several compartments. A lone male observer - the "bystander" - was placed in a cubicle in the center of the tank. Surrounding him were five smaller compartments, each with a solitary male rival identified simply as A, B, C, D or E. Researchers made sure that the bystander and his five potential rivals had never met.

Although the bystander remained alone in his cubicle and never swam with the others, he was allowed to observe a series of fights between rival pairs - A vs. B, B vs. C, C vs. D, and D vs. E. Researchers manipulated the fights so that A would dominate B, B would dominate C, and so forth down the line.

"These fights, taken together, imply the dominance hierarchy [where] A is greater than B is greater than C is greater than D is greater than E," the authors wrote. But did the bystander really comprehend this intricate pecking order, and if so, would he use that knowledge to make logical decisions about the same fish paired in new relationships?

To find out, eight different bystanders were tested in the familiar square tank and in a new setting - a rectangular aquarium with three adjacent compartments. In each test, a bystander was placed in the middle compartment between two sets of rivals that he had never seen together - A and E (AE), and B and D (BD). At this point in the experiment, all the rivals had recovered from earlier losses, so their physical appearance was similar, right down to the eyebar. From the point of view of the bystander, therefore, each rival looked like a winner.

Using a video camera, researchers recorded which rival the bystander approached first, and the overall time he spent next to each of them. "Previous experiments in A. burtoni and other fish have shown that time spent in tank quadrants adjacent to a particular male indicates bystander 'preference,' and that bystanders spend more time near the rival they perceive to be weaker," the authors explained.

Losers and winners

The results were dramatic. Virtually all of the bystanders swam to the weaker rival first and stayed near him for a significantly longer period of time. In the AE tests, bystanders preferred E, the wimpiest of all the losers, over A, the top fish in the tank. In the more subtle BD tests, most bystanders chose D over B, even though these two rivals were ranked very close together on the dominance hierarchy.

"These results show that fish do, in fact, use transitive inference to figure out where they rank in the social order," Fernald said. "I was amazed that they could do this through vicarious experience, just by watching other males fight. In Lake Tanganyika, where conditions change all the time, it would be advantageous for a male to know who the new boss is going to be and who his weakest rivals are. Our experiment shows that male cichlids can actually figure out their odds of success by observation alone. From an evolutionary standpoint, transitive inference saves them valuable time and energy."

The results raise the possibility that fish brains might contain the rudimentary neuronal circuitry for transitive inference that appeared later in birds and mammals. "Any animal that has evolved a social system that requires combat among males will have some kind of eavesdropping capability allowing them to surreptitiously draw inferences about their social rank," Fernald said. "Cognitive capacities that evolved in fish may contribute to human transitive inference, or perhaps this capacity evolved independently. The question remains unresolved."

The Nature study was supported with grants from the National Institutes of Health.

Related video

Source: Stanford Report, Stanford University News Service, January 25th 2007


Based on the journal Nature paper:

Fish can infer social rank by observation alone (p429)
Logan Grosenick, Tricia S. Clement and Russell D. Fernald

Opening paragraph

Transitive inference (TI) involves using known relationships to deduce unknown ones (for example, using A greater than B and B greater than C to infer A greater than C), and is thus essential to logical reasoning. First described as a developmental milestone in children, TI has since been reported in nonhuman primates, rats and birds. Still, how animals acquire and represent transitive relationships and why such abilities might have evolved remain open problems.

Here we show that male fish (Astatotilapia burtoni) can successfully make inferences on a hierarchy implied by pairwise fights between rival males. These fish learned the implied hierarchy vicariously (as 'bystanders'), by watching fights between rivals arranged around them in separate tank units. Our findings show that fish use TI when trained on socially relevant stimuli, and that they can make such inferences by using indirect information alone. Further, these bystanders seem to have both spatial and featural representations related to rival abilities, which they can use to make correct inferences depending on what kind of information is available to them.

Beyond extending TI to fish and experimentally demonstrating indirect TI learning in animals, these results indicate that a universal mechanism underlying TI is unlikely. Rather, animals probably use multiple domain-specific representations adapted to different social and ecological pressures that they encounter during the course of their natural lives.

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*Colin Allen's Transitive inference in animals: Reasoning or conditioned associations? appears in the book "Rational Animals?":

Abstract (available via Allen's Curriculum Vitae webpage)

It is widely accepted that many species of nonhuman animals appear to engage in transitive inference, producing appropriate responses to novel pairings of non-adjacent members of an ordered series without previous experience of these pairings. Some researchers have taken this capability as providing direct evidence that these animals reason. Others resist such declarations, favouring instead explanations in terms of associative conditioning. Associative accounts of transitive inference have been refined in application to a simple 5-element learning task that is the main paradigm for laboratory investigations of the phenomenon, but it remains unclear how well those accounts generalise to more information-rich environments such as social hierarchies which may contain scores of individuals, and where rapid learning is important. The case of transitive inference is an example of a more general dispute between proponents of associative accounts and advocates of more cognitive accounts of animal behaviour. Examination of the specific details of transitive inference suggests some lessons for the wider debate.

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