Life = matter + information. Or does it?

Posted on 09 May 2019 by Mohammed Yahia

This is a guest post by Sarah Hiddleston

{credit}Eileen Haring Woods{/credit}

“We are points of order in a disordered universe. This is an expression of how we feel about being ruled by physics in all our emotions and reactions. It’s how we interpret, describe and live our lives within this system.”

Artist or scientist? These are the words of curator Caroline Wiseman, whose brainchild “Alive in the Universe” found a home at the world’s longest standing contemporary art fair in Venice yesterday. It is a month-long exhibition that seeks to interpret what life is, and rather than reduce it to an equation, surround the viewer with an experience of what that means.

Opening the show is Syrian-born Issam Kourbaj. His three-piece installation is made up of a video of burnt matches, 98 boats made of recycled material and an IV drip. It juxtaposes the energies of fire and water, the flow of death and life, the struggle of a people between the two and the flow of time with the flow of migrants.

“Are we aware of the threads of our lives? I am putting the viewer in a place where many senses are being revisited. Each material sends new signals of information.”

Collaborating alongside him is Ruth Padel, a British poet whose book The Mara Crossing (2012) elucidates detailed comparisons in the way life organizes itself. Whether in cell biology, ornithology or human history, it is with the passage of migration that life begins, she says.

“There are two main reasons cells migrate in our bodies: One to create a new life, and two to defend the body –if we get a new cut the corpuscles and others rush to the site of trauma,” she explains. There’s an interesting parallel to be drawn with people migrating – a vigorous society is constantly replenished by the outside. Human civilization began with migration out of Africa. The first cell arrived on the planet, whether from the sea or outer space, and it colonized other places. The first great land migrants were trees. DNA from the oldest oak trees in Britain shows they came from the Spanish peninsula.”

Living things migrate because life becomes impossible or there’s a desire to make a better life. Birds in or near the Arctic get too cold and fly south. When the south becomes too crowded and they need to breed they return to the Arctic where there are lots of insects – a protein-rich diet for their offspring. It’s a bit heartbreaking but if you overlay the maps of bird migration routes and human migration routes across the Mediterranean, it’s the same. They take the passages where water is smallest – the straits of Gibraltar, or through Sicily, Malta.

Venice, Ruth says, represents the wasp waist of information flow between north and south in history. Both she and Kourbaj will find new resonance for their work in the interconnectivity of the space around them. “My interest will be in the relationship of my work to the water, and to the tourist boats and the gondola boats,” says Kourbaj, “in scale and in meaning, and in contradictions, they will have a new charge.”

For Wiseman, this too is interesting: “What I am trying to do through creativity is put order into things. The more I thought about what this order could be, the more I found that it is the life force, it is evolution.”

Life seems coupled to flow, movement, change, transformation: information in whatever form – the passage of energy, the replication of DNA within biological cells, to animal migrations and the organization of human societies.

You can watch a video about Kourbaj’s work here: https://www.youtube.com/watch?v=vpUOx-wTUz4

Probing a new algae species for clues into plant adaptation

Posted on 12 Sep 2017 by Pakinam Amer

An investigation of the genome and phenome of a green alga called Chloroidium sp. UTEX 3007 has revealed, for the first time, certain adaptive traits that help algae acclimate to desert environments.

But what sets apart this new species, which scientists at the New York University Abu Dhabi (NYUAD) have discovered and sequenced, from other types of green algae?

Nature Middle East talks to Kourosh Salehi-Ashtiani, associate professor of biology and managing director at the Center for Genomics and Systems Biology at NYUAD, to find out.

Nature Middle East: What does your new study add to the body of knowledge that we have of green microalgae?

Kourosh Salehi-Ashtiani: Green microalgae or Chlorophyta live in myriad forms and are believed to be the progenitors of land plants. Many scientists around the globe are involved in active research programs to understand the ecological roles of these organisms as well as to utilize them for biotechnology. Despite the importance of micro-algae, relatively few species have been profiled at the genomic and phenomic levels.

These species are mostly from temperate zones, with very little information available on any alga from the subtropical geographies, such as the environment of the United Arab Emirates (UAE). Our study, however, sets a new standard for understanding the biology of micro-algae, and how Chloroidium has evolved to cope with the environmental challenges unique to the region.

NME: Was there anything particularly surprising about Chloroidium?

KSA: Yes. Its ability to thrive on both freshwater and high-salinity growth media and its ability to assimilate an array of uncommon carbon compounds for heterotrophic growth [which is growth through an energy pathway in which an organism that cannot manufacture its own food uses sunlight or inorganic compounds to produce carbohydrates, proteins and fats from carbon dioxide, in order to survive].

NME: Can you tell me more about your comparative study of Chloroidium and land plants?

KSA: Our phenomic and genomic data suggests that Chloroidium has a close relationship with higher plants and may live an intermittent epiphytic lifestyle, in other words, it may live on the surface of plants when such an opportunity arises. We show the Chloroidium is able to uptake many different sugars. Now, if you think where an alga is likely to find sources of sugar, plant and plant material become the most obvious candidates.

NME: In your paper you mention that Chloroidium harbors “unique protein families involved in osmotic stress tolerance and saccharide metabolism,” would you mind explaining this to our readers?

KSA: It is known that many organisms, when faced with increased osmolarity or typically high salt concentrations, they start to accumulate sugars internally. The Chloroidium’s genome contains unique genes implicated in the accumulation and breakdown of uncommon sugars. It hasn’t been previously known how organisms accumulate and break down these sugars; our study clarifies this.

NME: What are some of the future applications of your findings now that we have this new species, with a robust and flexible biology, especially with regards to conservation and understanding the effects of climate change?

KSA: In light of the environmental hazards befalling much of Southeast Asia that have been caused, at least partly, by razing high-biodiversity rainforests to cultivate oil palm, we chose to particularly emphasize Chloroidium’s ability to accumulate palm-like oil. The fatty acid profiles of oil palm or Elaies guiensis and Chloroidium are virtually identical.

NME: So this discovery may, in the future, help in providing an alternative to palm oil?

KSA: Definitely. Cultivation of oil palm has been associated with deforestation, if not devastation of rainforests in Southeast Asia. It’s why many European countries are banning the use of oil palm in their products. We think this alga may provide an environmentally-friendly alternative to cultivation of oil palms once further developed.

The origins of cats

Posted on 06 Jul 2017 by Pakinam Amer

One of the cat skeletons excavated from a site in Egypt.{credit}© Hierakonpolis Expedition{/credit}

A new study reveals some fascinating insights into the origin story of the cat, arguably the internet’s most favorite creature and a cherished companion to countless humans.

Paleogeneticist Claudio Ottoni and his peers from KU Leuven and the Royal Belgian Institute of Natural Sciences have been collecting DNA from several archaeological sites in an attempt to track down the origins and trace the ancient journeys of the domestic cat.

The scientists unearthed over 200 cat skeletons from sites in Africa, Europe and the Near East and scrutinized DNA from feline skin, hair, bones and teeth that date back to between 100 and 9,000 years ago.

The result? A revelation about how cats dispersed in the ancient world. According to the study, the domestic cat we know today originated in ancient Egypt and the Near East.

Back then, the cats had stripes, not spots – the latter cropped up during the Middle Ages, but not before. The Middle Ages is also when the cat’s coat color had started to become variant.

The ancient felines were domesticated some 10,000 years ago, mostly by farmers wishing to chase away rodents from their fields. When the farmers moved, the cats moved with them. They also spread across the old world through trade, hopping on ships to protect stocks from vermin, and jumping from one port to the next, eventually covering long distances, and traveling far and wide. Now, the domestic cat is present on all continents except Antarctica.

The cats can all be traced back to one Felis silvestris, also known as the African wildcat, originally a feral, territorial and solitary hunter. Both the Near Eastern and Egyptian populations of Felis silvestris, according to the study, contributed to the gene pool of the domestic cat at different historical times.

The last dinosaur on Earth?

Posted on 24 Apr 2017 by Pakinam Amer

This is a guest blogpost by Aya Nader.

Chenanisaurus barbaricus comes from the end of the dinosaurs’ reign.{credit}N.R. Longrich{/credit}

Scientists have discovered remains of one of the last dinosaurs on Earth, in Morocco. About 66 or 67 million years old, Chenanisaurus barbaricus comes from the very end of the prehistoric animals’ reign.

Along with species like Tyrannosaurus rex and Triceratops, it would have been there to watch the asteroid impact that wiped out the dinosaurs.

Previously, the scientists have found only a few teeth, but now they have fossils that comprise part of the dinosaur’s jaw, which is unusually deep, suggesting a powerful bite, and a large body.

The remains were found in Ouled Abdoun, a phosphate sedimentary basin in Morocco.

Chenanisaurus is one of the only dinosaurs to have been found from this time period in Africa, and one of the youngest known members of the group, says corresponding author of the study Nicholas R. Longrich. “We have a pretty good picture of latest Cretaceous dinosaurs from North America and Asia, but very little from Africa, so it helps fill in our picture of what the fauna looked like at this time.”

There aren’t many terrestrial rocks from the latest Cretaceous that are exposed in Africa, he elaborates.

“What we do have is mostly marine rocks in Morocco and Angola, for example. That may be related to the fact that the sea levels were high at the end of the Cretaceous, so much of Morocco is underwater.”

There are a fair number of terrestrial fossils from this time period in Madagascar, he adds, but Madagascar isn’t really part of Africa. It broke off of India, Australia, and Antarctica in the middle of the Cretaceous.

Yet, the Moroccan phosphates are among some of the richest fossil beds in the entire world, according to Longrich. “So the upshot is that if you want to find a dinosaur from this time in Africa, the best place to look is in the marine rocks.”

Chenanisaurus is one of the youngest known members of its group.{credit}N.R. Longrich{/credit}

2016: Editor’s choice

Posted on 31 Dec 2016 by Pakinam Amer

Extracts from selected news and feature articles published this year.

Astrophysics

An international team of scientists, including from New York University Abu Dhabi (NYUAD), managed to directly observe structural components of one slowly rotating star, thanks to asteroseismology. This new technique, 10,000 times more precise than its predecessor, reveals a star’s flatter, rounder contours and different rotational speeds. It allows scientists to ‘see’ the nature of the stellar interior with very high precision.

Marine science

In an unprecedented study on non-model organisms in captivity, scientists from Saudi Arabia, Australia and Norway were able to create large sequence datasets on how reef fish and their offspring react to the phenomenon of decreasing pH levels, called ocean acidification, brought on by climate change. Acidification happens due the uptake of atmospheric carbon dioxide. “The amount of sequencing data we generated is unparalleled for a non-model organism,” says Timothy Ravasi, the senior author of the paper. Scientists discovered that the offspring of some reef fish can tolerate acidification by adjusting their circadian rhythm to night time function throughout the day.

Ecology and evolution

An international consortium of researchers analysed the coding portions of genes, or “exomes”, belonging to 1,794 nationals of Greater Middle Eastern (GME) countries, a region spanning from Morocco in the west to Pakistan in the east. “As expected for a region so rich in history and at the crossroads of many civilizations, the Middle East ‘variome’ [the set of genetic variations in a given population] suggests mixing with other populations, although the percentage varies greatly depending on which subpopulation you look at,” says geneticist Fowzan Alkuraya from Saudi Arabia’s King Faisal Specialist Hospital and Research Center. Northwest African genes were found in people across northern Africa, most likely representing the Berber genetic background. Arabian Peninsular genes were observed in nearly all GME peoples studied, possibly the result of the Arab conquests of the seventh century. Similarly, Persian expansion in the fifth century into the Turkish peninsula, the Syrian Desert region and parts of northeast Africa probably accounts for the Persian and Pakistan genetic signal present in the peoples of those regions. The peoples of the Syrian Desert and Turkish peninsular regions show the highest levels of mixing with European populations.

Geology

Shallow, dense magma reservoirs may be responsible for the most hazardous type of volcano on Earth, according to a new study. Ivan Koulakov and colleagues, including scientists from Saudi Arabia, present a fresh seismic model, based on studying magma paths beneath the Toba volcano in Indonesia, which last erupted some 74,000 years ago. The model explains why the magma system under Toba causes large, devastating eruptions, and how such large volumes of magma are generated.

Archaeology

“We always say it can’t get any worse, and then it does — and that’s the hardest part,” says Allison Cuneo, project manager for the American Schools of Oriental Research’s Cultural Heritage Initiative (CHI), which documents the loss of Syrian heritage. CHI reported 851 incidents of damage to cultural heritage between September 2015 and August 2016, mostly concentrated in areas of northern Syria controlled by forces opposed to President Bashar al-Assad. With such extensive damage, there “is so much data on destruction to report, it’s like holding the ocean back with a broom,” says Michael Danti, the academic director of CHI.

Environment

A world atlas of artificial night sky brightness, published earlier this year in Science Advances, captured the extent to which we are smothered in light. It reveals Kuwait, Qatar, United Arab Emirates and Saudi Arabia as the most light-polluted places to live on the planet, topped only by Singapore. More than half of people living in Israel and Libya live through extremely bright nights, and the widest connected twilight zone in the world is along the Nile Delta in Egypt. No more can people in Kuwait and Qatar see the glowing band of the Milky Way from their homes. For more than 97 per cent of people in the United Arab Emirates, Israel, and Egypt, this is also true. “The night sky is the beginning of our civilization. It leads to all religions, philosophy, science, literature and the arts. The cultural significance of a sky full of stars is huge. The new generations have lost this source of inspiration,” says Fabio Falchi, of the Italian Light Pollution Science and Technology Institute’s Fabio Falchi, who led the study.

Astronomy

The Qatar Exoplanet Survey (QES) has discovered three new “exoplanets” outside our solar system. The planets, named Qatar-3b, Qatar-4b and Qatar-5b, are hot Jupiters: they are similar in size to Jupiter (11 times the size of Earth) and orbit very closely to their respective suns. They are located some 1400 to 1800 light years away from Earth and can be seen in the same part of the sky as the Andromeda Constellation, best observed in autumn in the northern hemisphere.

How changing sex helps “Nemo” survive and adapt

Posted on 26 Oct 2016 by Pakinam Amer

Laura Casas, House of Wisdom guest blogger and King Abdullah University of Science & Technology (KAUST) marine biologist, talks to us about the orange salt water fish and how it used a marvelous evolutionary mechanism to conquer the seas.

{credit}Fran Saborido-Rey{/credit}

How did a small, very bright, colorful fish that’s a poor swimmer become extensively distributed in tropical waters from the Indian to the western Pacific Oceans, including the Great Barrier Reef and the Red Sea?

Two processes have potentially played a role in the successful evolutionary adaptation of clownfishes: a mutual relationship with anemones – flower-like marine animals and relatives to corals – which provides shelter and protection in exchange for nourishment, plus their capacity to change sex when their partner dies, preventing the need for dangerous travel across the reef.

While the different aspects of this mutual relationship have been unveiled in dozens of studies, very little has been known about the mechanisms that orchestrate sex change in fishes.

Our new study at KAUST provides insights into the genetic mechanism governing social sex change in fish, using the Red Sea endemic species of clownfish, Amphiprion bicinctus, as a model in its natural habitat.

Clownfishes are monogamous, living in social assemblages as pairs or social groups consisting of a dominant female, always the largest in size, surrounded by her male partner and a variable number of immature juveniles of smaller size. They display a strong social hierarchy based on size; these hierarchies function as queues for breeding, so when a dominant female of a social group dies, all subordinates seize the opportunity to ascend in rank.

This way, the male is always poised to become female and rapidly changes sex to assume the vacated position, while the biggest juvenile rapidly matures into a male ensuring the ability to produce new generations without abandoning the anemone.

ClownfishExperiments_Credit_ThamerSHabis (3)

{credit}Thamer S. Habis{/credit}

The confinement of an animal, however, is known to alter its normal behaviour but traditionally sex change has been studied using aquarium experiments. In our study, we localized sixteen families living on the exposed side of Al-Fahal reef, in the Central Red Sea and removed all the females to trigger the sex change process.

One sex-changing individual was sampled every five days for 1.5 months to cover the full time course of the sex change process and their transcriptional responses were assessed using RNA sequencing.

Our results show a response in the male´s brain which starts two weeks after the female’s disappearance and lasts for two additional weeks.

During this period, there is a marked down-regulation in deferentially expressed genes of sex-changing individuals, compared to mature males and females. We identify a large number of candidate genes, both well-known and novel potentially playing a role in sex change.

Based on our results, we propose a picture of the genetic mechanisms that take place during the sex shift: the aromatase gene known as cyp19a1 plays a central role by modulating the balance between estrogen and androgen signaling. Aromatase is involved in the production of estrogen.

The genes sox6 and foxp4 may play a role in regulating the expression of aromatase and/or other genes involved in steroid production at the brain level. The genes cyp19a1 and foxl2 play a pivotal role in the activation of the female pathway driving the sex gland transformation from testis to ovary during sex change, while Sox8, Dmrt1 and Amh are important for testis maintenance.

The results have not only provided important insight into the main genetic mechanism governing sex change and sex gland restructuring in hermaphrodite flowers or animals, but also detailed information on specific genes involved during every step of the process. Our study is the first genome-wide study in a social sex-changing species in its natural habitat and the dataset generated is a valuable genomic resource for a species with virtually no genetic information available in public datasets.

Future work would ideally explore whether the genetic processes underlying sex change in hermaphrodites is evolutionary conserved. We need to deepen our knowledge of the unexplored genetic mechanisms underlying such sex change.

As well, only a deep understanding of the genetic processes governing reproduction in hermaphrodites will allow us to anticipate how reproductive success might be affected by the temperature rise in coming years as a consequence of the climate change and give us a chance to conserve and protect the sea’s biodiversity.

House of Wisdom

a blog from Nature Middle East

Category Archives: Evolution