What mechanism generates our fingers and toes?

Dr. Marie Kmita and her research team at the IRCM contributed to a multidisciplinary research project that identified the mechanism responsible for generating our fingers and toes, and revealed the importance of gene regulation in the transition of fins to limbs during evolution. Their scientific breakthrough is published today in the prestigious scientific journal Science.

By combining genetic studies with mathematical modeling, the scientists provided experimental evidence supporting a theoretical model for pattern formation known as the Turing mechanism. In 1952, mathematician Alan Turing proposed mathematical equations for pattern formation, which describes how two uniformly-distributed substances, an activator and a repressor, trigger the formation of complex shapes and structures from initially-equivalent cells.

“The Turing model for pattern formation has long remained under debate, mostly due to the lack of experimental data supporting it,” explains Dr. Rushikesh Sheth, postdoctoral fellow in Dr. Kmita’s laboratory and co-first author of the study. “By studying the role of Hox genes during limb development, we were able to show, for the first time, that the patterning process that generates our fingers and toes relies on a Turing-like mechanism.”

In humans, as in other mammals, the embryo’s development is controlled, in part, by “architect” genes known as Hox genes. These genes are essential to the proper positioning of the body’s architecture, and define the nature and function of cells that form organs and skeletal elements.

“Our genetic study suggested that Hox genes act as modulators of a Turing-like mechanism, which was further supported by mathematical tests performed by our collaborators, Dr. James Sharpe and his team,” adds Dr. Marie Kmita, Director of the Genetics and Development research unit at the IRCM. “Moreover, we showed that drastically reducing the dose of Hox genes in mice transforms fingers into structures reminiscent of the extremities of fish fins. These findings further support the key role of Hox genes in the transition of fins to limbs during evolution, one of the most important anatomical innovations associated with the transition from aquatic to terrestrial life.”

Scientists Offer New Way To Look At The Origins Of Life

People have been trying to understand the origins of life on Earth through scientific means since the concept of science began and a pair of Arizona State University researchers suggests in a new report that we’ve been approaching the question incorrectly, almost from the beginning.

In a paper titled, “The algorithmic origins of life,” Paul Davies and Sara Walker proposed that understanding the correct chemical makeup for the origin of life only tells part of the story and scientists should also be focused on how chemical information is organized into life-creating processes.

They equate the shift in perspective to understanding how a computer works. To function, a computer not only needs hardware, akin to life’s chemical makeup, it also needs software, or chemical information.

“When we describe biological processes we typically use informational narratives – cells send out signals, developmental programs are run, coded instructions are read, genomic data are transmitted between generations and so forth,” Walker said. “So identifying life’s origin in the way information is processed and managed can open up new avenues for research.”

“We propose that the transition from non-life to life is unique and definable,” added Davies. “We suggest that life may be characterized by its distinctive and active use of information, thus providing a roadmap to identify rigorous criteria for the emergence of life. This is in sharp contrast to a century of thought in which the transition to life has been cast as a problem of chemistry, with the goal of identifying a plausible reaction pathway from chemical mixtures to a living entity.”

Walker and Davies argue that their approach skirts many issues that have confounded previous efforts to define the origin of life.

Rhesus monkeys cannot hear beat in music

Beat induction, the ability to pick up regularity – the beat – from a varying rhythm, is not an ability that rhesus monkeys possess. These are the findings of researchers from the University of Amsterdam (UvA) and the National Autonomous University of Mexico (UNAM), which have recently been published in the scientific journal PLOS ONE.

The research conducted by Henkjan Honing, professor of Music Cognition at the UvA, and a team of neurobiologists headed by Hugo Merchant from the UNAM, shows that rhesus monkeys cannot detect the beat in music, although they are able to detect rhythmic groups in music. The results of this research support the view that beat induction is a uniquely human, cognitive skill and contribute to a further understanding of the biology and evolution of human music.

(Photograph by Shane Moore)

Genetic Researchers Grow A Fish That Has Legs

The fossil record has a lot of strange stories to tell about the evolution of life on Earth, and one of the strangest is how life moved from sea to land. Though clues from the record give the rough outlines of the story—limbs grew from fins in a series of stages in which fins grew longer and narrower—scientists are still filling in the details, trying to determine what genetic changes might have allowed the limbs to grow.

One of the best ways to learn those details is to reproduce the changes that occurred some 400 million years ago—to virtually back in time and alter the development of the land-goer’s living ancestors and see what happens.

Which is what biologist Renata Freitas and colleagues were up to when they added some extra Hoxd13—a gene known to play a role in distinguishing body parts during embryological development— to the tip of a zebrafish embryo’s fin, and watched as the developing fin kept growing.

Their lab findings led the researchers to hypothesize that the secret to limb development may have been a new element in some lobe-finned fish’s DNA. When present, this DNA element would have helped turn on the Hoxd13 gene on the fish embryo’s fins, leading them to lengthen and grow into limbs.

First facial reconstruction of the Indonesian ‘Hobbit’ unveiled

Scientists at this week’s Australian Archaeological Conference have unveiled the face of Homo floresiensis— more commonly referred to as the ‘Hobbit’ — for the first time. Specialist facial anthropologist Dr. Susan Hayes used forensic facial approximation techniques to build out a female skull specimen discovered in 2003 in Flores, Indonesia. Other bones have been found since, revealing that these Hobbits were only about three and a half feet tall— just like the creatures of J.R.R. Tolkien lore that will hit the big screen later this week. Homo floresiensis populated the island of Flores between 95,000 and 17,000 years ago, but it’s not yet clear where the species falls within the human evolutionary tree. Although she’s pleased with the final results, Hayes says that the reconstruction was far from easy— “she’s not what you’d call pretty, but she is definitely distinctive.”

What howler monkeys can tell us about the role of interbreeding in human evolution

Did different species of early humans interbreed and produce offspring of mixed ancestry?

Recent genetic studies suggest that Neanderthals may have bred with anatomically modern humans tens of thousands of years ago in the Middle East, contributing to the modern human gene pool. But the findings are not universally accepted, and the fossil record has not helped to clarify the role of interbreeding, which is also known as hybridization.

Now a University of Michigan-led study of interbreeding between two species of modern-day howler monkeys in Mexico is shedding light on why it’s so difficult to confirm instances of hybridization among primates—including early humans—by relying on fossil remains.

The study, published online Dec. 7 in the American Journal of Physical Anthropology, is based on analyses of genetic and morphological data collected from live-captured monkeys over the past decade. Morphology is the branch of biology that deals with the form and structure of animals and plants.

The two primate species in the study, mantled howler monkeys and black howler monkeys, diverged about 3 million years ago and differ in many respects, including behavior, appearance and the number of chromosomes they possess. Each occupies a unique geographical distribution except for the state of Tabasco in southeastern Mexico, where they coexist and interbreed in what’s known as a hybrid zone.

Human Evolution Enters an Exciting New Phase

“Most of the mutations that we found arose in the last 200 generations or so. There hasn’t been much time for random change or deterministic change through natural selection,” said geneticist Joshua Akey of the University of Washington, co-author of the Nov. 28 Nature study. “We have a repository of all this new variation for humanity to use as a substrate. In a way, we’re more evolvable now than at any time in our history.”

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Origin of intelligence and mental illness linked to ancient genetic accident

Scientists have discovered for the first time how humans – and other mammals – have evolved to have intelligence. Researchers have identified the moment in history when the genes that enabled us to think and reason evolved.

This point 500 million years ago provided our ability to learn complex skills, analyse situations and have flexibility in the way in which we think. Professor Seth Grant, of the University of Edinburgh, who led the research, said: “One of the greatest scientific problems is to explain how intelligence and complex behaviours arose during evolution.”

The research, which is detailed in two papers in Nature Neuroscience, also shows a direct link between the evolution of behaviour and the origins of brain diseases. Scientists believe that the same genes that improved our mental capacity are also responsible for a number of brain disorders.

"This ground breaking work has implications for how we understand the emergence of psychiatric disorders and will offer new avenues for the development of new treatments," said John Williams, Head of Neuroscience and Mental Health at the Wellcome Trust, one of the study funders.

The study shows that intelligence in humans developed as the result of an increase in the number of brain genes in our evolutionary ancestors. The researchers suggest that a simple invertebrate animal living in the sea 500 million years ago experienced a ‘genetic accident’, which resulted in extra copies of these genes being made.

This animal’s descendants benefited from these extra genes, leading to behaviourally sophisticated vertebrates – including humans. The research team studied the mental abilities of mice and humans, using comparative tasks that involved identifying objects on touch-screen computers.

Researchers then combined results of these behavioural tests with information from the genetic codes of various species to work out when different behaviours evolved. They found that higher mental functions in humans and mice were controlled by the same genes.

How the animals lost their sensors

For free-living organisms, the ability to sense and respond to the outside environment is crucial for survival. Eukaryotes, such as animals and plants, often have highly complex network systems in place to monitor their surroundings and respond effectively, but bacteria have developed a remarkably simple system. It’s called the ‘Two Component System’ because it literally relies on just two components; a sensor and a responder. The sensor picks up the signal, communicates this to the responder, which then causes the effect.

The picture above shows this process happening. The ‘communication’ of the message from the sensor to the responder, as shown by the coloured arrows, is carried out by transferring phosphate molecules. The signal interacting with the sensor causes the sensor to autophosphorylate (phosphorylate itself) and then pass the phosphate molecule onto the responder to trigger the response. The letters “H” and “D” are the actual amino-acids being phosphorylated; Histadine and Aspartate.

Although Two-Component Systems (TCS) are found in all three superkingdoms of life (archaea, bacteria and eukaryotes) they are suspiciously absent from the animal kingdom. Plants have them, as do fungi and several protazoa, but they just aren’t present in animals. For this reason they’ve been looked into as potential antibiotic targets as knocking out the Two-Component Systems of most bacteria is fatal.

Why don’t animals use TCS? To answer this you have to start looking at the evolution of the system itself, because despite being nominally present in eukaryotes such as plants and fungi, TCS are used very differently. Bacteria use TCS for sensing a wide variety of signals; stress, metabolism, nutrient regulation, chemotaxis, pathogen-host interactions etc. In eukaryotes on the other hand they are used sparingly; for ethylene responses and photosensitivity in plants and osmoregulation in fungi and slime moulds.

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