I moved to ScienceBlogs earlier this year. If you want to catch up on what you missed, buy my new book and get 80 of the best blog posts from the last year. From Mexican-waving bees to snow-making bacteria, from the neuroscience of jazz to the psychology of voting, the book covers some of the coolest, most exciting and most ground-breaking discoveries from 2008. Click the image for more.

This is a quick reminder for anyone still subscribing to the old feed to update your feed-readers. I’ve now moved to ScienceBlogs and I’d hate to lose any readers along the way. I’m sticking to the original mission statement and if anything, I’m writing even more than before.

Here are the new details:

URL: http://scienceblogs.com/notrocketscience/

Feed: http://feeds.feedburner.com/scienceblogs/notrocketscience

And a wee taster of some of the new material so far:

• How sharks, penguins and bacteria find food in the big, wide ocean
• Immune snakes outrun toxic newts in evolutionary arms races
• Punishing slackers and do-gooders
• The machine that identifies images from brain activity alone
• Moths remember what they learn as caterpillars?
• What happens in the brain of an improvising jazz musician?
• Snow-making bacteria are everywhere
• Communicating chimps and talking humans show activity in same part of the brain
• Japanese moths hit by male-killing virus
• Effects of invading island rats ripple across land and sea

You’ll need to update your bookmarks and/or feed readers.

URL: http://scienceblogs.com/notrocketscience/

Feed: http://feeds.feedburner.com/scienceblogs/notrocketscience

I want to assure current readers that the blog is not going to change, (well, except in look). Even though the blog will have some academic neighbours, my mission statement of making science interesting and fun to as many people as possible remains the same and the pitch of the writing won’t change.

I still have full freedom to write about whatever I like and if anything, I’m hoping that the scrutiny of a tight community of experienced bloggers, many of whom are hardcore scientists, will push me to ensure an even higher level of accuracy in what I’m putting out.

So for the moment a massive round of thanks to everyone who continues to read and support this blog. The growing traffic and the generally positive comments from people are really gratifying and I’m really excited about the next step.

In a couple of weeks, the new blog should be ready, I’ll post up the new URL, raise my hands in the air, say “Begin Phase Two!” and cackle maniacally.

The closest evolutionary cousins of the vertebrates are simple aquatic creatures such as the jawless lancelets and the sac-like, immobile sea squirts. How did these simple body plans diversify into the vast array of sophisticated forms wielded by today’s fish, amphibians, reptiles and mammals?

Gene number

Many scientists have suggested that the answer lies in the number of our genes. At three different points, the vertebrate genome (its full suite of genes) experienced a massive jump in size as huge chunks of genes – possibly the entire lot – were duplicated. The first of these coincided with the origins of the group itself and the second happened alongside the rise of the first jawed fish, setting them and their descendants aside from more ancient jawless forms like the lampreys.

So far, there seems to be a tidy connection between gene number and complexity, but the third round of duplication is a bit of a stumbling block. It happened at some point during the evolution of the bony fishes and while this group proceeded to radiate into a multitude of different shapes, their basic body plan stayed essentially the same. No big jump in complexity there.

Indeed, as the full genome sequences of more and more species are revealed, it’s becoming clear that the basic genetic toolkit that controls the development of animal bodies is remarkably consistent across the kingdom. Even the genome of a sea anemone, one of the simplest and most ancient animals on Earth, is strikingly similar to that of vertebrates.

In this light, it’s looking increasingly unlikely that the advent of new genes can account for the large rise in vertebrate complexity. Now, Alysha Heimberg and colleagues from Dartmouth College have proposed a new theory, centred around tiny molecules called microRNAs.

MicroRNAs

First, a quick crash course in molecular biology. Genes are made up of stretches of DNA, which acts as a sort of molecular code To be of use, the code is read and transcribed into a related molecule called RNA. This transcript is used as instructions for building proteins that go on to do useful jobs around our cells.

But large reams of RNA are never translated into proteins. Vertebrates genomes in particular are rife with these non-coding stretches, and we have over 10 times more of them than invertebrates like worms and flies. These stretches of code are often labelled as “junk” but it’s an unfair and inaccurate term. It is now clear that they have very important roles indeed.

MicroRNAs are a particular group of non-coding RNA that has captured the interests of scientists. They are tiny, much smaller than the average piece of protein-coding RNA, and the equivalent of a long word nestled within a single page in a shelf of books. These minute molecules control other genes and carefully determine which are switched on and which are turned off.

Recently, they have been implicated in the development of cancer and heart disease but Heimberg has assigned them with the altogether more congenial role of fuelling the rise of vertebrate complexity.

Organisation vs. recruitment

Our repertoire of microRNAs far outstrips those of invertebrates, and over 50 families arose during the course of vertebrate evolution. Once added, new microRNAs are incredibly stable over time and unlike other parts of the genome, they are very rarely altered or lost. These traits allowed Heimberg to create an accurate microRNA family tree, charting the addition of these controlling molecules as the vertebrate lineage rose and branched out.

To do this, Heimberg scoured the genomes of several vertebrates for microRNA sequences. She looked at species from humans to chickens to sharks, along with some of our evolutionary cousins – the lancelets and sea squirts.

Heimberg found that the genomes of vertebrates have been massively fortified with microRNAs. A massive number of new families exploded into being during a short span of time when the vertebrate dynasty first evolved some 500 million years ago. This rapid acquisition occurred slightly ahead of the gene-duplication event, which then served to increase the diversity of microRNAs within each family.

This key period marked the height of microRNA innovation and the vertebrates have never since acquired new families so quickly at any other point during their history. To Heimberg, the timing is no coincidence. Many of these new microRNAs are also found in parts of the body like the liver and pancreas that are unique vertebrate inventions, or organs like the brain that are considerably more sophisticated than those of their invertebrate counterparts.

It seems then, that the complexity of the vertebrate body stems from ancient innovations in the control of genes rather than the bulk addition of new ones. Our genes instruct a workforce of proteins, and rather than adding more staff, we simply redeployed the existing personnel in new and ground-breaking ways.

Reference: Heimberg, A.M., Sempere, L.F., Moy, V.N., Donoghue, P.C., Peterson, K.J. (2008). MicroRNAs and the advent of vertebrate morphological complexity. Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0712259105

Images – tiger by Anant

Because of the way our education system works, this process of hard studying has become almost synonymous with the act of learning, and the inevitable tests and exams that bookend this ordeal merely assess how much information has stuck.

But a new study reveals that the tests themselves do more good for our ability to learn that the many hours before them spent relentlessly poring over notes and textbook. The act of repeatedly retrieving and using learned information drives memories into long-term storage, while repetitive revision produced almost no benefits.

Studying vs. testing

To separate the effects of studying and testing on memory, Jeffrey Karpicke from Purdue University and Henry Roediger III from Washington University in St Louis set a group of local university students to a simple learning exercise.

At first, all of them were asked to study 40 pairs of English words and their Swahili equivalents, such as boat and mashua and were then tested on each pair to see how many they could remember. The students were then split into four groups who were put through three more rounds of studying and testing but with important differences.

For Group 1, the three further rounds were exactly like the first. For Group 2, any recalled pair of words were dropped from the study lists but were still tested. Group 3 faced the opposite condition – their correct answers were dropped from the subsequent tests but they were still asked to study them. And finally, Group 4′s correct answers were omitted both from later study sessions and later tests.

This fourth situation most closely mirrors what conventional wisdom tells us to do. Once something is learned, that’s the end of the story and our attentions should focus on trickier facts that haven’t been so amenable to memory.

After four rounds, the students had done an almost perfect job. Almost all of them remembered almost all of the 40 word pairs and all four groups picked up the words at the same rate.

Testing times

The successful students were sent away, but Karpicke and Roediger reconvened them one week later for a final test of their rudimentary Swahili vocabularies. All the students from the four groups had predicted that in a week’s time, they would remember about half of the words they had learned. But the reality was very different – two of the groups achieved much higher scores than the others.

Repeated testing was the critical factor. The first two groups were repeatedly tested on all the word pairs regardless of whether they successfully remembered them or not. A week later, they still remembered 80% of the words they had learned and Group 2, who didn’t have to study words they correctly remembered did just as well as Group 1, who had to pore over the full lists.

Students in the last two groups were not tested on words once they had remembered them correctly once, and they suffered for it. After a week, they remembered only about a third of the 40 pairs. Even Group 3, who repeatedly studied every pair in every study period fared much worse in the long run than Group 2, who studied selectively but were tested comprehensively.

The study’s results are as amazing as they are counter-intuitive. They showed that where long-term memory is concerned, the act of repeated studying brings essentially no benefits, especially once a piece of information can already be dredged up from memory. Repeated testing, on the other hand, is of paramount importance, even for facts that can already be successfully recalled.

Implications

If this seems like an obvious conclusion in retrospect, consider the fact that the students themselves were unaware of it. All of them predicted that they would score about 50% in the final test where in fact, the average scores were either substantially higher or lower.

Indeed, surveys have shown that very few students use self-testing as a strategy for revision. When they do, it’s more to work out what they have or have not learned rather than as an active part of the process. And once they have successfully memorised something, they tend to drop it from further practice.

Karpicke’s and Roediger’s study makes a case for tests and exams to move away from their crude use as assessment tools. Currently, they are stressful and high-stakes affairs, deployed at the end of academic terms to mark an endpoint of the learning process. Perhaps, if they were used in a more continuous and informal capacity, they could actually contribute too.

Photos by Gabriel Pollard, Michael Surran and Milford

Reference:Karpicke, J.D., Roediger, H.L. (2008). The Critical Importance of Retrieval for Learning. Science, 319(5865), 966-968. DOI: 10.1126/science.1152408

The success of bats hinges on two key abilities: their mastery of flight, a feat matched only by birds and insects; and echolocation, the ability to navigate their way through pitch-blackness by timing the reflections of high-pitched squeaks. For evolutionary scientists, the big question has always been: which came first?

The ‘clawed bat’

Until now, fossil bats haven’t provided any clues for all of them show signs of both echolocation and flight. But a stunning new fossil, discovered by Nancy Simmons from the American Museum of Natural History is an exception and it provides a categorical answer to the long-running debate – the earliest bats could fly but could not echolocate.

The new creature hails from the Green River in Wyoming and is known as Onychonycteris, meaning “clawed bat”. Its fossils date back to about 52.5 million years ago and by comparing it to other prehistoric bats, Simmons found that it is the most ancient member of this lineage so far discovered. It acts as a ‘missing link’ in bat evolution, much like the famous Archaeopteryx hinted that birds may have evolved from dinosaurs.

Onychonycteris was clearly a capable flyer. Its wings are remarkably similar to those of today’s bats, with the exception of small claws at the end of its digits that modern bats lack. But the really exciting part of the new fossil is the size of its cochlea – the coiled tube that allows mammals to hear. Relative to the size of their head, all bats that use echolocation have massively enlarged cochleae and the two traits are so tightly linked that large cochleae have been used to show that other prehistoric bats were also echolocators.

Not so for Onychonycteris. The dimensions of its skull revealed that its cochlea was too small to have supported echolocation and was closer in size to those of flying foxes, large bats that favour vision over echolocation. It provides direct evidence that bats mastered the art of flying before they developed a way of navigating through the dark.

Flight or echolocation

When the flight-echolocation debate first started, the “echolocation-first” camp had the upper hand. According to this school of thought, the earliest bats used echolocation from tree perches to detect and snatch passing insects, and indeed, the most primitive of modern bats sometimes use this technique. The ancestral bats then evolved long, webbed arms and fingers to better catch their prey and eventually took to jumping after them.

However, this theory has since run into troubled times. It turns out that echolocation – which involves producing very loud bursts of sound – takes a lot of energy and it’s something that a perching bat cannot afford to keep up for long. A flying bat on the other hand, has no such difficulties. On each stroke of their wings, bats are contracting the powerful lung muscles that power their ultrasonic shouts so that if they time their flaps and squeaks correctly, echolocation is effectively free.

Other parts of the fossil provide clues about Onychonycteris‘s lifestyle. Its strong hind legs and wing claws suggest that it was an agile climber and could have scampered through branches on all fours.

The proportions of its limbs are closest to the modern mouse-tailed bats, which fly with an undulating style that alternates true flight with gliding. Onychonycteris may have also used this efficient tactic and it may have been a stepping stone from gliding to proper continuous flight.

Daytime hunter

But how could Onychonycteris have found its way through the air without echolocation to guide it? Perhaps it was a daytime flier and relied on vision to find its way around. Its descendants may have been forced to become nocturnal when the birds came to power towards the end of the dinosaurs’ reign, some 65 million years ago.

We would normally turn to Onychonycteris‘s eyes for clues for nocturnal animals that fly by sight, like the flying foxes, have large eye sockets. Unfortuantely, that will have to wait until the discovery of new fossils. The top half of the skulls that Simmons used were found crushed. While their ear cavities have already told us much about the evolution of bats but their eyes sockets will tell no tales.

Image courtesy of Nature

Reference: Simmons, N.B., Seymour, K.L., Habersetzer, J., Gunnell, G.F. (2008). Primitive Early Eocene bat from Wyoming and the evolution of flight and echolocation. Nature, 451(7180), 818-821. DOI: 10.1038/nature06549

Shuffling the genetic deck

Sex chromosomes aside, every person has two copies of each gene, one inherited from their father and one by their mother. Not every gene will be in correct working order, but there’s a good chance that a faulty copy will be offset by a functional one from the other parent.

However, if two parents are closely related, there’s a higher-than-average chance that they will already share some of the same genes and a similarly increased chance that their child will receive two defective copies. That can be very bad news indeed and in cases where important genes are affected, the results can include miscarriage, birth defects or early death.

Sex, then, is a shuffling of their genetic deck and theoretically the more closely related the partners are, the greater the chance that their child will be dealt a dud hand. And yet, some studies have found that some closely related couples actually do better than distant relatives in terms of the number of children they manage to raise. This trend is certainly unexpected and the big question is whether it is the result of biology or money.

Wealth or genes

In societies where close relatives marry, these unions tend to happen at a relatively early age and they provide avenues for families to retain wealth and land within bloodlines. These related couples enjoy the health benefits enjoyed by the rich as well as more time in which to raise a larger family. Together, these two effects could more than make up for any disadvantages wrought by their genes.

Earlier studies have done little to clear the confusion. They have mostly been conducted in parts of the world like India, Pakistan and the Middle East where marriage between close relatives is relatively frequent, but which are also home to enormous gulfs between the richest and poorest members of society. With demographics like these, sorting out the relative contribution of socioeconomics and biology is difficult.

To do that, what you need is a country with a small population where couples are reasonably closely related and with a very shallow gradient between rich and poor. Ideally, you’d also want this country to have excellent family records dating back several years. In short, you’d want to base your study in a country almost exactly like Iceland.

200 years of Iceland

Iceland is home to a tiny population of just over 300,000 people who enjoy a level of social equality that is almost unparalleled elsewhere in the world. Wealth, family size and cultural practices are fairly uniform. The country is also home to uniquely impressive geneaological records that allow today’s Icelanders to track their family trees with exacting precision for centuries. These records are supplemented by thorough medical records and thousands of willingly donated genetic samples.

Agnar Helgason from deCODE Genetics, a pharmaceutical company located in Reykjavik, made good use of these records to study over 160,000 Icelandic couples since 1800. At this time, Iceland was still a poor agricultural nation and close-knit rural communities meant that on average, couples were related at the level of third or fourth cousins.

Since then, the country has prospered into a wealthy industrial one and the growing population has shifted to a mainly urban way of life. In doing so, people became more likely to find partners who were more distantly related and by 1965, couples were only related at the level of fifth cousins on average

As expected, Helgarson’s study unveiled the dangers of close inbreeding. While the most closely related couples had the highest number of children, many of them failed to live long enough to have children of their own and in the long run these couples had the fewest grandchildren.

But surprisingly, distantly related couples were at a disadvantage too. In fact, Helgarson found that couples related at the level of third cousins eventually fostered the largest families. For example, among women born between 1800 and 1824, those partnered with men who were third cousins had an average of 4 children and 9 grandchildren, while those partnered with a distant eighth cousin had just 3 children and 7 grandchildren. For starting large families, very distant relatives were just as poor prospects as very close ones.

Over the 200 years included in the study, Iceland has seen a steep decline in both fertility and relatedness between couples. And despite all that, for every 25-year period the Helgarson looked at, the same pattern held – couples who were moderately closely related ended up with the largest number of descendants.

Implications

These remarkably consistent results have convinced Helgarson that the counterintuitive effect must have some biological foundation. Its exact nature will have to wait for another study and for now, we are left only with speculation.

It could be that a child’s immune system may be more compatible with its mother’s if its father is reasonably closely related to her. Alternatively, a union between distant relatives could serve to splinter groups of beneficial genes that have evolved in close association with each other.

The study’s implications for societal taboos against marriages between close cousins is open for debate. Certainly, it doesn’t mean that singletons should be sifting through their phone books on the hunt for attractive third cousins. However, the relatively poor reproductive success of distant relatives has the potential to explain the massive decline in fertility in many countries the world over.

In the time that Iceland has gone from rural agriculture to urban industry, its population growth has slowed and its fertility rates have declined, a trend shared by a slew of other nations. Helgarson suggests that this could, at least in part, be due to people finding ever more distantly related partners.

Image: Wedding photo by Claude Renault

Reference: Helgason, A., Palsson, S., Guthbjartsson, D.F., Kristjansson, t., Stefansson, K. (2008). An Association Between the Kinship and Fertility of Human Couples. Science, 319(5864), 813-816. DOI: 10.1126/science.1150232

For the next week, you’ll hear tumbleweeds blowing through this blog as I will be on holiday. I’m going to Whistler, Vancouver, where I will be sticking two flimsy strips of wood to my feet and throwing myself down a mountain at high speed. I see it as a challenge to both cold and gravity.

I’ll be writing a few things while I’m there so expect some good stuff the week after. For the moment, feel free to scour the Site Index for oldies-but-goodies or have a look at my Review of 2007 for more focused recommendations.

A word about comments: This blog’s comments policy are set so that anyone who’s had a comment previously approved can post more, but any newbies have to be moderated first. If you’ve never commented here before and your comment doesn’t show up until next week, that’s why.

Languages are often compared to living species because of the way in which they diverge into new tongues over time in an ever-growing linguistic tree. Some critics have claimed that this comparison is a superficial one, a nice metaphor but nothing more.

But the new study by Quentin Atkinson, now at the University of Oxford, suggests that languages evolve at a similar stop-and-start pace, which uncannily echoes a long-standing theory in biology, known as ‘punctuated equilibrium’. The theory’s followers claim that life on Earth also evolved at an uneven pace, full of rapid bursts and slow periods.

Famously championed by the late Stephen Jay Gould, the punctuated equilibrium theory suggests that most species change very little over time and big evolutionary changes are concentrated at rare moments where new species branch off from existing lineages. Together with colleagues from the US and New Zealand, Atkinson found similar patterns in three of the worlds’ largest families of languages.

Three families

They compared lists of words from the Indo-European group, which include English and Hindi; the Bantu group, consisting of several hundred African languages; and the Austronesian group, which includes over a thousand tongues from Indonesia, Papua New Guinea and the Polynesian islands. Between them, these three families account for a third of all the world’s languages.

Of course, languages borrow words from each other all the time and indeed, 50% of English words are loans from French and Latin. That was a potential pitfall of the study and Atkinson avoided it by only considering basic words such as numerals, body parts and pronouns that are very unlikely to have been co-opted from another tongue.

For each group, Atkinson built a family tree showing how newer languages split off from ancestral ones. The trees mirrored those that biologists use to chart the evolutionary relationships between species.

In the model, the birth of new languages is represented by new branches on the tree and the length of each branch depends on the difference in vocabulary between the new tongue and its parent one. The greater the changes, the longer the branch.

In each family tree, Atkinson saw that the parts of the tree with the most branches also had the longest ones. So groups that spawned the highest number of new languages also diverged most significantly in their repertoire of words. That’s the pattern you would expect if the birth of new languages triggered bursts of rapid evolution. If the pace of evolution was more constant, the number of branch points would have no effect on overall branch length.

The need for speed

These rapid bursts accounted for 31% of the vocabulary differences between Bantu speakers, 21% of the differences in Indo-European languages and 10% of the variation in the Austronesian group. For comparison, team estimated that these fast and slow evolutionary cycles explained about 22% of the genetic differences between biological species.

As they split from each other, new sister tongues begin to adopt new words at a fast pace and these are probably accompanied by equally quick changes in pronunciation, spelling and grammar. As their identities become clearer, the pace of change slows.

Atkinson thinks that this process happens when different groups of people try to establish distinct social identities by exaggerating differences in language. American English may have developed along these lines and the need for a unique identity was at the forefront of Noah Webster‘s mind when he published his first American Dictionary of the English Language in 1828. “As an independent nation, our honour requires us to have a system of our own, in language as well as government,” he said.

For more on the evolution of language, have a look at this post on the evolution of the past tense in English verbs.