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1

13/7

An image and short film has been encoded in DNA, using the units of inheritance as a medium for storing information.

Using a genome (1) editing tool known as Crispr, US scientists inserted a gif - five frames of a horse galloping (2) - into the DNA of bacteria.

Then the team sequenced (3) the bacterial DNA to retrieve the gif and the image, verifying that the microbes (4) had indeed incorporated the data as intended.

The results appear in Nature journal.

For their experiments (5), the team from Harvard University in Cambridge, Massachusetts, used an image of a human hand and five frames of the horse Annie G captured (6)  in the late 19th Century by the British photography pioneer (7) Eadweard Muybridge.

In order to insert this information into the genomes of bacteria (8), the researchers transferred the image and the movie onto nucleotides (building blocks of DNA), producing a code that related to the individual pixels (9) of each image.

The researchers then employed the Crispr platform, in which two proteins are used to insert genetic code into the DNA of target cells - in this case, those of E.coli bacteria.

For the gif, sequences were delivered frame-by-frame (10) over five days to the bacterial (11) cells.

The data were spread across (12) the genomes of multiple bacteria, rather than just one, explained co-author Seth Shipman, from Harvard University in Massachusetts.

"The information is not contained in a single cell, so each individual cell may only see certain bits or pieces of the movie. So what we had to do was reconstruct (13) the whole movie from the different pieces," Dr Shipman told the BBC.

Image copyright Seth Shipman

Image caption The researchers encoded (14) an image of a human hand into the bacterial DNA

"Maybe a single cell saw a few pixels from frame one and a few pixels from frame four... so we had to look at the relation of all those pieces of information in the genomes of these living cells and say: can we reconstruct the entire movie over time?"

To "read" the information back, the researchers sequenced the bacterial DNA and used custom computer code to unscramble (15) the genetic information, which spits out (16) the images.

The team was able to achieve 90% accuracy: "We were really happy with how it came out," Seth Shipman told me.

Eventually, the team wants to use the technique to create "molecular (17) recorders".

Dr Shipman says these are cells that can "encode information about what's going on in the cell and what's going on in the cell environment by writing that information into their own genome".

This is why the researchers used images and a movie: images because they represent the kind of complex information the team would like to use in future, and movies because they have a timing component (18).

The timing component is important because it would be useful to track (19) changes in a cell and its environment over time.

  1. genome (CN) = the complete set of genetic material of a human, animal, plant, or other living thing
  2. horse galloping
  3. sequence (n):  a series of related things or events, or the order in which they follow each other 
  4. microbes (cn): a very small living thing, especially one that causes disease, that can only be seen with a microscope.
  5. experiments (cn): a test done in order to learn sth or to discover if sth works or is true.
  6. capture (v): to represent or describe sth very accurately using words or images.
  7. pioneer (n): a person who is one of the first people to do sth.
  8. bacteria (n)/ bacterium: a type of very small organism that lives in air, earth, water, plants, and animals, often one that causes disease.
  9. pixels (n) the smallest unit of an image on a television or computer screen.
  10. frame-by-frame
  11. bacterial (adj) caused by, made from, or relating to bacteria.
  12. spread across
  13. to reconstruct (v): to build or create again sth that has been damaged or destroyed.
  14. encode (v) to change sth into a system for sending messages secretly, or to represent complicated information in a simple or short way.
  15. to unscramble (v):  = decode to discover the meaning of information given in a secret or complicated way
  16. to spit out (v): to say sth quickly and angrily
  17. molecular (cn): the simplest unit of a chemical substance, usually a group of two or more atoms
  18. a timing component
  19. to track (v): if a film or video camera tracks in a particular direction, it moves along while it is filming

2

London's Natural History Museum (NHM) has undergone a major revamp (1) with a blue whale skeleton now forming the main exhibit as visitors come through the front door

http://www.bbc.com/news/science-environment-40582046

The marine mammal (2) replaces the much-loved (3) Diplodocus dinosaur, "Dippy", which will soon head out (4) on a tour of the UK.

The museum believes the change will give its image a refresh.

It wants to be known more for its living science than its old fossils (5).

The museum employs hundreds of researchers who engage in (6) active study on a day-to-day basis (7)

Yes, they use the 80 million-odd specimens (8)kept at the South Kensington institution, but their focus is on learning new things that bare down (9) on the modern world. In that sense, the blue whale is regarded as the perfect emblem (10)

The specimen (11) is being given the name "Hope" as a "symbol of humanity's power to shape a sustainable future".

Blue whales are now making a recovery following decades of exploitation (12) that nearly drove them out of existence.

The exhibits that will support the blue whale

How the whale was prepared for display

Whaling's 'uncomfortable' scientific legacy (13)

Whales reached huge size only recently

The Natural History Museum is closed to the public all day Thursday for final preparations

Staff have spent months preparing the 126-year-old skeleton for its new role.

First, it had to be removed from its old hanging (14) space in the mammals gallery (15)

Then it had to be cleaned and in a few places repaired and strengthened. And finally, it had to be re-hung (16) from the iron girders (17) that support the ceiling in the Waterhouse building's spectacular (18) Hintze Hall.

The BBC was given exclusive access to (19) the whole process, and a Horizon documentary (20), narrated (21) by Sir David Attenborough, will go out on BBC Two at 21:00 BST on Thursday.

The film will air at about the same time as the NHM's patron, the Duchess of Cambridge, and Sir David, inaugurate (22) the new exhibit at a gala reception (23).

A great many people were involved in the make-over (24), but the promotion of the whale represents something of a personal triumph (25) for Richard Sabin, the museum's principal curator (26) of mammals.

He championed the change and suggested the dynamic (27) lunge-feeding pose (28) that the whale now assumes. 

It was on a visit to the NHM in 1976, as a boy of 10, that Richard first saw the skeleton in its old display position. He describes that experience as transformative (29)

"I was absolutely blown away," he told BBC News. "I remember running up the stairs to the balcony and asking an attendant if the whale skeletons in the gallery were real. And she said 'yes, and not only that you can still see these animals in the ocean today'.

"I got home and the very next day I headed down to  (30) the public library to try to find as many books as I could on whales. It was, to coin a phase, a defining moment."

For the Horizon film, Richard can be seen tracing the history of the specimen - meeting the descendants (31) of the Irish fisherman who despatched (32) the animal with a makeshift (33) harpoon (34)after it had beached off County Wexford in March 1891. But he also travels to North America, to the Pacific Coast, to join the Cascadia Research Group as they track migrating blue whales.

The group, co-founded by John Calambokidis, attaches tags to the giant creatures. Held on by suction (35)cups, these devices record the behaviour of the whales, even capturing (36) 4K video as they dive underwater.

The team is learning key facts that will help conserve (37) the majestic animals (38), which went to the brink of (39) oblivion (40) thanks to 20th Century hunters.

"We've discovered that blue whales spend twice as much time at the surface at night than they do in the day," John told Horizon.

"That's the period when they're most vulnerable to ship strikes (41) . That identified right there that we need to be most concerned about ships and their transiting through blue whale areas at night rather than the day."

For Richard, the observation  (42)of whales in the Pacific confirmed his desire to see the conservation icon put centre-stage (43)at his museum back in London.

"It's been an honour (44) and a privilege (45) to work with the specimen that inspired me all those years ago - to breathe new life into it; to inject science from the field into it; to display it in a much more meaningful way.

"I honestly believe it will take people's breath away when they see it.

"Thursday is going to be an amazing day for everyone involved; I am sure there will be plaudits (46) for what we've done. But I can't wait for Friday morning when the first families, the first schoolchildren, walk through the door and I get to hear what they've got to say about what they see."

Fans of Dippy should not despair (47). After the dinosaur's two-year tour of Britain, it will return to a make-over (48) of its own.

The skeleton, which is actually only a plaster cast (49), will be fashioned (50) again in bronze (51) and placed in the east garden in front of the museum.

You can watch a trail for Horizon: Dippy and the Whale. After broadcast on BBC Two, the programme will be available on the iPlayer.

  1. to revamp: to change or arrange sth again, in order to improve it
  2. marine mammal
  3. much-loved
  4. head out
  5. fossils: the shape of a bone, a shell, or a plant or animal that has been preserved in rock for a very long period.
  6. to engage in:  to take part in or do sth
  7. on a day-to-day basis.
  8. 80 million-odd specimens: -odd: used after a number, especially a number that can be divided by ten, to show that the exact number is not known
  9. to bare down (to bear down): to put more effort into doing sth
  10. emblem (cn): a picture of an object that is used to represent a particular person, group, or idea
  11. specimen (cn): something shown or examined as an example; a typical example
  12. exploitation (un): the use of sth in order to get an advantage from it
  13. legacy (cn): money or property that you receive from someone after they die
  14. hanging (cn): a large piece of cloth, often with a picture on it, that is hung on a wall for decoration
  15. the mammals gallery
  16. re-hung
  17. girder (cn): a long, thick piece of metal or concrete, etc. that suppots a roof, floor, bridge, or other large structure
  18. spectacular (adj): very exciting to look at
  19. exclusive access to
  20. documentary (cn): a film or television or radio programme that gives facts and information about a subject
  21. to narrate: to tell a story, often by reading aloud from a text, or to describe events as they happen
  22. to inaugurate: to put sth into use or action officially
  23. a gala reception: a formal party at which important people are welcomed.
  24. make-over (n): improvement
  25. a personal triumph (n): a very great success, achievement, or victory (= when you win a war, flight, or competition), or a feeling of great satisfaction or pleasure caused by this
  26. curator (cn): a person in charge of a museum, library, etc.
  27. dynamic (adj): continuously changing or developing
  28. pose (n): a particular position in which a person stands, sits, etc. in order to be photographed, painted, etc.
  29. transformative (adj): causing a major change to sth or someone, especially in a way that makes it or them better.
  30. to head down to
  31. the descendants (n): a person who is related to you and who lives after you, such as your child or grandchild
  32. to despatch: to kill someone
  33. makeshift (adj): temporary and low quality, but used because of a sudden need.
  34. harpoon (n): a long, heavy spear (= a long, sharp weapon) attached to a rope, used for killing large fish or whales
  35. suction (un): the act of removing air from a space resulting in a lower pressure in that space, either causing liquid, gases, or other substances to enter, or causing two surfaces to stick together.
  36. to capture: to record or take a picture of sth using a camera
  37. to conserve: to keep and protect sth from damage, change, or waste
  38. majestic (adj): beautiful, powerful, or causing great admiration and respect
  39. on the brink of sth: extremely close to sth
  40. oblivion (un): the state of being completely destroyed
  41. vulnerable to ship strikes: a sudden and powerful hit or attack
  42. observation (n): the fact that you notice or see sth
  43. centre-stage (n): the middle of a theatre stage
  44. honour (n): a quality that combines respect, being proud, and honesty
  45. privilege (n): an opportunity to do sth special or enjoyable
  46. plaudits (usually plural n): praise
  47. to despair: to feel despair about sth or someone
  48. make-over (cn): improvement
  49. a plaster cast (cn); a covering made of plaster of Paris that is put around part of someone's body, forming a hard case to protect them while a broken bone repairs itself
  50. to fashion: to make sth using your hands
  51. bronze (un): a brown metal made of copper and tin

3

US scientists have amassed "planetary-scale" data from people's smartphones to see how active we really are.http://www.bbc.com/news/health-40570442

The Stanford University analysis of 68 million days' worth of minute-by-minute data showed the average number of daily steps was 4,961.

Hong Kong was top averaging 6,880 a day, while Indonesia was bottom of the rankings with just 3,513.

But the findings also uncovered intriguing details that could help tackle obesity.

Most smartphones have a built-in accelerometer that can record steps and the researchers used anonymous data from more than 700,000 people who used the Argus activity monitoring app.

Scott Delp, a professor of bioengineering and one of the researchers, said: "The study is 1,000 times larger than any previous study on human movement.

"There have been wonderful health surveys done, but our new study provides data from more countries, many more subjects, and tracks people's activity on an ongoing basis.

"This opens the door to new ways of doing science at a much larger scale than we have been able to do before."

Activity inequality

The findings have been published in the journal Nature and the study authors say the results give important insights for improving people's health.

The average number of steps in a country appears to be less important for obesity levels, for example.

The key ingredient was "activity inequality" - it's like wealth inequality, except instead of the difference between rich and poor, it's the difference between the fittest and laziest.

The bigger the activity inequality, the higher the rates of obesity.

Tim Althoff, one of the researchers, said: "For instance, Sweden had one of the smallest gaps between activity rich and activity poor... it also had one of the lowest rates of obesity."

The United States and Mexico both have similar average steps, but the US has higher activity inequality and obesity levels.

Global sleeping patterns revealed by app data

Has wearable tech had its day?

Is that fitness tracker you're using a waste of money?

The researchers were surprised that activity inequality was largely driven by differences between men and women.

In countries like Japan - with low obesity and low inequality - men and women exercised to similar degrees.

But in countries with high inequality, like the US and Saudi Arabia, it was women spending less time being active.

Jure Leskovec, also part of the research team, said: "When activity inequality is greatest, women's activity is reduced much more dramatically than men's activity, and thus the negative connections to obesity can affect women more greatly."

The Stanford team say the findings help explain global patterns of obesity and give new ideas for tackling it.

For example, they rated 69 US cities for how easy they were to get about on foot.

The smartphone data showed that cities like New York and San Francisco were pedestrian friendly and had "high walkability".

Whereas you really need a car to get around "low walkability" cities including Houston and Memphis.

Unsurprisingly, people walked more in places where it was easier to walk.

Image copyright Tim Althoff

The researchers say this could help design town and cities that promote greater physical activity.

minute-by-minute

tackle obesity

 a built-in accelerometer

bioengineering

 ingredient

wealth inequality

fittest

wearable tech

fitness tracker

pedestrian

walkability

 

4

The UK should focus on using waste products like chip fat if it wants to double production of biofuels according a new study. http://www.bbc.com/news/science-environment-40599491

The report from the Royal Academy of Engineering says that making fuel from crops like wheat should be restricted.

Incentives should be given to farmers to increase production of fuel crops like Miscanthus on marginal land.

Even with electric vehicles, biofuels will still be needed for aviation and heavy goods say the authors.

While the European Union has mandated that 10% of transport fuels should come from sustainable sources by 2020, these biofuels have been a slow burner in the UK.

Suppliers are already blending up to 4.75% of diesel and petrol with greener fuel, but doubling this amount will take up to 10 years say the authors of this new report, that was commissioned by the government.

To get to this point, the authors argue that several important changes will need to take place.

While in countries like the US and Brazil biofuels are mainly made from maize or sugar cane, the main sources in the UK are wheat and used cooking oil.

To boost production there will need to be restrictions on crops grown for fuel, say the authors.

Last year according to the Department for the Environment, Food and Rural Affairs (Defra), almost half the land in the UK used for biofuels was used to grow wheat.

When the authors of this study reviewed the global scientific literature, they found that if all the extra emissions involved in changing land use to grow wheat were added in, fuel based on this grain was worse for the environment than regular petrol or diesel.

Image copyright Getty Images

Image caption Even the fat and waste that block sewers could be used to generate biofuel say the authors

"Generally, we know if land use change is involved, do not use wheat to make biofuels, it is higher than petrol in terms of carbon footprint," said Prof Adisa Azapagic from the University of Manchester who chaired the panel that produced the report.

"What we need to understand about agriculture, is that it is different from farm to farm. This is what we have found across the world, how people farm wheat in different ways and the emissions would be different depending on soil, previous carbon stocks and so on, it really is a very complex science."

The study recommends that the government set a cap for all crop-based biofuels to reduce the risk of indirect land use change.

"We would be concerned if we went up to 10% and allowed all of that 10% to come from food based crops, then we would say no, that's not what we're recommending," said Prof Nilay Shah from Imperial College London.

Instead, the report suggests that renewed emphasis be placed on developing waste. In the UK we produce 16 million tonnes every year, enough to double our current biofuel supplies. A third of that waste is called green waste, a quarter of it is agricultural straw.

The authors believe there is great scope for expansion in the use of unavoidable waste, such as used cooking oil, forest and sawmill residues, the dregs from whisky manufacture, even so-called "fatbergs" from sewers could play a role.

However the study warns that care must be taken to avoid giving people perverse incentives to create waste just to cash in on biofuels.

Image copyright Getty Images

Image caption Aviation and shipping are likely to need to use liquid biofuels for many years to come

"There have been some examples where people have used virgin cooking oil as a source of biofuel because it was cheaper than used cooking oil so we need to make sure we avoid these market distortions that unfortunately do happen," said Prof Azapagic.

The government should also aim to remove any incentives for the use of materials in biofuels that involve deforestation or the drainage of peat land. Incentives should be put in place to encourage farmers to grow crops like Miscanthus and short rotation coppice wood on marginal land.

If we want to double the amount of biofuel we are using over the next decade, say the authors, the government will have to stump up some cash.

"If you've got a ready supply of used cooking oil it is not very challenging or expensive, if your alternative is to go clear some land and plant Miscanthus and all the processing that goes with that, then the prices are going to be different," said Prof Roger Kemp, a professorial fellow from Lancaster University.

"We wouldn't be getting up to anything like 10% if it was purely a market based thing."

fuel

 marginal

aviation

 sustainable sources

 blending

greener fuel

maize

boost

biofuels

grain

sewers

carbon footprint

 from farm to farm

agricultural straw

fatbergs

distortions

deforestation

short rotation

stump up

 a professorial fellow

5

Canaanites survived Biblical 'slaughter', ancient DNA shows http://www.abc.net.au/news/science/2017-07-28/ancient-dna-shows-canaanites-survived-biblical-slaughter/8749264

The ancient Canaanites, who according to the Bible were commanded (1) to be exterminated (2), did not die out, but lived on to become modern-day (3) Lebanese, according to the first study to analyse their DNA.

Key points

  • DNA reveals that modern Lebanese are direct descendants (4) of ancient Canaanites
  • Despite tumultuous history, there has been substantial genetic continuity in the Near East across the past 3,000 to 4,000 years
  • European additions to Lebanese ancestry (5) occurred around 3,750-2,170 years ago
  • Study also provides clues (6) about ancient Phoenicians

The Bronze Age Canaanites lived between 3,000 and 4,000 years ago in the region now encompassed (7) by Israel, Lebanon, Syria and Jordan.

Despite being the first group known to use an alphabet (8) , and appearing many times in the Bible, the Canaanites left few written records.

The ancient Canaanites were buried in what is now Sidon in Lebanon 

(Supplied: Dr Claude Doumet-Serhal)

Now, in research published today in the American Journal of Human Genetics, an international team of geneticists (9) has mapped the mass migrations that occurred in this tumultuous (10)region by "reading" the DNA of the region's ancient and modern inhabitants (11).

"What is exciting was that we can see the genetic continuity (12) between the Bronze Age population and the present-day populations," said Dr Marc Haber of the Wellcome Trust Sanger Institute in the UK.

The study found that over 90 per cent of the ancestry of modern-day people from Lebanon was derived from the Canaanites.

"We know from history that after the Bronze Age, the region was under a lot of expansions (13) and conquests (14), and you would expect that those would have brought new gene (15) flow, but in the DNA we see that the present-day (16) population did not change too much from the Bronze Age population."

Analysis of genetic traits (17) found the ancient Canaanites would have looked very similar to today's Lebanese population, except perhaps a little darker in skin tone.

Extracting DNA from ancient skulls

To track the changes over time, Dr Haber and his colleagues compared five whole genomes (18)  recovered from human remains found in the area of the ancient Lebanese city of Sidon, with the genomes of 99 Lebanese living in the region today.

"One of the most exciting parts of the research was to get DNA out of the specimens (19)" Dr Haber's colleague Chris Tyler-Smith said.

Depending on the environment, the DNA in bones decays at different rates and the Lebanese coast is both warm and moist (20), which isn't good for preservation.

To extract enough DNA for the study, the researchers targeted bone found at the base of the human skull, which is extra dense (21) and was very recently identified as a good source of DNA long after it has decayed (22) elsewhere in the skeleton( 23)

DNA may help solve Phoenician mystery

Alan Cooper of the Australian Centre for Ancient DNA said the study was hard evidence that God's biblical command, as described in the Book of Deuteronomy, to "totally destroy" the Canaanites, was not carried out.

"Clearly the Bible's wrong in the sense of the Canaanites being smited, they were clearly not smit (24) too well," Professor Cooper, who was not involved in the research, said.

Professor Cooper said the new study provides valuable insight into when shifts in the population occurred in the Near East in ancient times. (25)

Who were the ancient Egyptians?

DNA from mummies (26) reveals that some ancient Egyptians shared very little of the ancestry that dominates (27) the heritage (28) of modern Egyptians.

Genomic changes occurred between 6,600 and 3,550 years ago — with input from migrants (29) from the east genetically related to Copper Age Iranians — and again between 3,750 and 2,170 years ago with the introduction of Eurasian ancestry.

Professor Cooper said the genetic continuity Dr Haber and his colleagues found also helps to solve the mystery of the Phoenicians.

"The Phoenicians, as the natural descendants of the Canaanites, were such a mystery," he said.

"They were all over the Mediterranean but we couldn't find any skeletons to gather their DNA from, and there didn't seem to be any natural cultural descendants.

"Therefore, to find that the area in which they were located, which is Lebanon and the surrounding Levant, actually has the same genetics today, shows that while the culture's transmogrified (30), the people stayed much more statically in place than the cultures would have suggested."

  1. command: to deserve or get something good, such as attention, respect or a lot of money.
  2. exterminate: to kill all the animals or people in a particular place or of a particular type.
  3. mordern-day (adj): relating to people or things from modern times and not from a time in the past
  4. descendant (n): a person who is related to you and who lives after you such as your child or grandchild
  5. ancestry (n): your ancestors who lived a long time ago, or the origin of your family
  6. clue (n) a sign or some information that helps you to find answer to a problem, question, or my stery
  7. to encompass: to include different types of things
  8. alphabet (n) a set of letters arranged in a fixed order, used for writing a language
  9. geneticists (n) a person who studies genetics
  10. tumultuous (adj): very loud, or full of confusion, change, or uncertainty
  11. inhabitants (n): a person or annimal that lives in a particular place
  12. genetic continuity (n): the fact of sth continuing for a long period of time without being changed or stopped
  13. expansions (n): the increase of sth in size, number, or importance
  14. conquests (n): the act of conquering a country, area, or situation
  15. gene (n) a part of the DNA in a cell that controls the physical development, behaviour, etc. of an individual plant or animal and is passed on from its parents
  16. present-day (adj): existing now
  17. traits (n): a particular characteristic that can produce a particular type of behaviour.
  18. genomes (n) the complete set of genetic material of a human, animal, plant, or other living thing 
  19. specimens (n) something shown or examined as an example; a typical example
  20. moist (adj) slightly wet, especially in a good way
  21. dense (adj) having parts that are close together so that it is difficult to go or see through
  22. to decay (v): to become gradually damaged, worse, or less; to cause sth to do this
  23. skeleton (n): the frame of bones supporting a human or animal body
  24. to smite (v): to hit someone forcefully or to have a sudden powerful or damaging effect on someone.
  25. in ancient times.
  26. mummies: a dead body that is prevented from decaying by being treated with special substances before being wrapped in cloth
  27. to dominate (v): to have control over a place or person
  28. heritage (UN): features belonging to the culture of a particular society, such as traditions, languages, or buildings, that were created in the past and still have historical importance.
  29. to transmogrify (v): to change or be changed completely