What will this mean for Thoughtomics as a blog? Not much, aside from the cosmetic changes: I’ll keep on blogging about evolutionary research, in the same way as I have been doing for the last couple of years.

Aside from Thoughtomics, you will find many other excellent blogs on the new network. Bora Zivkovic has put together a great team of bloggers and blogs. All I can say is that I am very honoured to blog alongside them. Be sure to check out some of my favourites, which include Lab Rat, Culturing Science, the Oceloid and many others.

Please update your bookmarks and feed readers:

New url: http://blogs.scientificamerican.com/thoughtomics/
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Thank you for following Thoughtomics to its new home!

When I think of ‘time travel’, I think of 1985 DeLoreans and flaming skid marks. But the reconstruction of an extinct protein is time travel of a different kind: it provides a glimpse of a distant past, just like a reconstruction of an extinct creature’s skeleton does. In this metaphor, amino acids are the molecular biologist’s bones. Instead of finding out which bone goes where she reassembles protein skeletons by lining up the correct sequence of amino acids.

But how do you bring back an extinct protein from the dead? The earth contains no fossil proteins. They are long gone, as are the ancient strands of DNA that coded for them. Yet modern DNA still contain clues as to what they looked like. How so?

Suppose a linguist wants to reconstruct the Germanic word for apple as it was spoken by Germanic tribes thousands of years ago. This word is just as exitnct as the proteins of our distant ancestors: it has not been written down anywhere, nor has it been spoken by anyone in millennia. The only way our linguist could learn something about its original form is to compare the current incarnations of the word apple in modern Germanic languages.

Appel, apple, æble, Apfel, äpple, eple or eplið

Here’s a list of Germanic apples in a row: apple (English), appel (Dutch), Apfel (German), æble (Danish), äpple, (Swedish), eple (Norse) and eplið (Icelandic). It is obvious that all these apples have some common features, such as the a or e followed by a p. This ubiquity suggests that this letter combination is inherited from the ancestral Germanic word for apple. Other combinations, such as pf in the German Apfel, are unique and derived: pf only ‘evolved’ in the German lineage of apples.

It is via such comparisons that linguists can reverse-engineer extinct words, always with some degree of uncertainty (the proto-Germanic word for apple was eventually reconstructed as apla(z)).

Modern proteins also contain traces of their ancestral shape and form. By comparing the amino acid sequences of a sufficient number of modern proteins, the ancestral protein sequence can be predicted with some confidence.

The authors of the NSMB paper set out to resurrect the ancestor of a a protein family known as the thioredoxins. These small proteins are like a pair of scissors that cut with molecular precision: they can cleave the tight bonds between two sulfur atoms. Such sulfur bridges stabilize a protein’s structure and can be found in all sorts of proteins.

A fossil apple?

The ancestral thioredoxin makes a great target for a reconstruction because all organisms on earth carry the code for one or more thioredoxins in their genome. The advantages of such an ubiqutous distribution are twofold. First of all, the more modern descendants are known, the easier it is to rebuild their common ancestor. If all linguists could work with were Äpfel and epli, reconstructing the proto-Germanic apple would have been more difficult. Second, since the last common ancestor of all life on earth must already have carried a thioredoxin, the trail that these proteins have left behind is billions of years old. It almost leads to the earliest origins of life itself.

For every amino acid that makes up a thioredoxin, the team calculated which of the twenty amino acids was most likely to have occupied this specific spot in ancestral proteins. They did this for a variety of different ancestors, such as the ancestor of all bacteria, the ancestor of eukaryotes, and so on. From these most likely sequences the researchers then produced the most likely proteins, which they subjected to a battery of different tests.

A reconstructed Tyrannosaurus remains dead forever, but a resurrected thioredoxin is just as alive as its modern descendants. They still fold into their proper shape and can still cut sulfur bonds. Not every thioredoxin slices up sulfur-sulfur bonds in the same way, however.

Bacterial thioredoxins have a different cut than the thioredoxins of eukaryotes, the branch of life that includes animals, fungi, and various amoeba-like organisms. Eukaryotic thioredoxins have a deep binding groove that rotate and force the sulfur-sulfur links into a specific position, like a restraint that prevents a patient from moving during surgery. Once the link is in the correct position, the thioredoxin makes the cut. Bacterial thioredoxins also have such a groove, but it is more shallow and bacteria don’t rely on it to break the sulfur bond.

To test the different cutting styles of ancient thioredoxins, the team devised an experiment in which they stretch out a single protein from end to end, like an unwinded ball of yarn.

When the thioredoxin (gray) cuts the sulfur bond (yellow), the protein suddenly increases in length.

The team engineered one sulfur bridge into this thin protein string, which is placed in such a way that part of the thread is locked up in a side loop. When the sulfur link is broken, thanks to a thioredoxin for example, the entire protein strand suddenly increases in length, about 14 nanometers. It is this small jolt that the scientists measured to determine a thioredoxin’s cutting style.

By pulling on one end of the string, it becomes more difficult for thioredoxins with a deep binding groove to break the sulfur bond. The thioredoxin needs to align itself at 180 degrees with the sulfur link, but this becomes harder to do when the protein string is stretched out. Thioredoxins with a more shallow groove can also break sulfur links outside of the groove, and so are less hindered by the pulling force. The researchers suspected that more ancient thioredoxins would have a binding groove that is not as deep and complex as that of modern eukaryotes.

But contrary to this expectation, the experiments revealed that even the most ancient eukaryotic thioredoxins already cut sulfur links in the same way as modern thioredoxins with a deep binding groove. Similarly, ancient bacterial thioredoxins have the same cutting style as modern bacteria. This suggests that thioredoxin chemistry was already established early in evolution and has conserved ever since. Making and breaking sulfur bonds has become such an important foundation of life’s biochemistry, that modern life couldn’t afford to change its nature.

At first glance, a paleoenzymologist looking to reconstruct the distant past might be disappointed to find that today’s protein doesn’t differ from yesterday. But compare his find to that of the explorers who discovered the cave paintings of Chauvet. The realization that early humans already represented animals and humans in an abstract way tells us something about what it means to be human. Extinct enzymes whose inner workings have been preserved teach us what it means to be alive.

Detail of the Chauvet cave paintings

Thanks to @onetruecathal for tweeting the paper

Image credits
Apples on a tree by Imaffo.
Fossil carbon pulp from PaleoSearch.com
Thioredoxin cutting a sulfur bond in a protein string is modified from reference.
Chauvet cave paintings from Wikimedia.

References
Perez-Jimenez R, Inglés-Prieto A, Zhao ZM, Sanchez-Romero I, Alegre-Cebollada J, Kosuri P, Garcia-Manyes S, Kappock TJ, Tanokura M, Holmgren A, Sanchez-Ruiz JM, Gaucher EA, & Fernandez JM (2011). Single-molecule paleoenzymology probes the chemistry of resurrected enzymes. Nature structural & molecular biology, 18 (5), 592-6 PMID: 21460845

This is only possible because Lego bricks are made according to a specific set of design rules. Every stud on every brick is round and has a diameter of 5 mm, for example. In theory, the studs could have any size or shape. They could be shaped as squares, triangles or even little hexagons and work just as well. Yet these alternative, but plausible, Lego bricks don’t exist. The potential space of Lego bricks is much larger than the actual brick space. A Lego brick with square studs will never be made because it would be incompatible with every other Lego brick in existence. The square brick would be an outcast among bricks, unable to connect with its rounder brothers.

The set of dimensions to which every Lego Brick has to abide.

Life on earth is like Lego in this regard, with the exception that life’s building blocks are molecules, not bricks. Of all the molecules that exist in our universe, life only uses a select subset. Every cell and every virus consists of five nucleotides, some sugars, a few lipids and twenty different amino acids. And that’s about it. Every living thing on this planet is made from different combinations of these building blocks.

Life’s building blocks are everywhere on our planet, in every scoop of dirt or every bucket of ocean water. But their presence alone is not enough to distinguish our living planet from a sterile one. Amino acids such as glycine have also been found in some abundance in non-living environments such as meteorites and comets.

What really sets the earth apart, chemically speaking, is the skewed distribution of molecules. In sterile environments, there exists a continuous range of molecules, with a bias for molecules that are stable and easy to form. But life doesn’t produce a range of molecules. Life thrives because it selects and amplifies only those molecules which it needs. Natural selection and historical contingency* shaped the final set of molecules which came to to define life on earth.

Life’s bias in favour of certain molecules might be useful for detecting life on other worlds. While it’s hard to say anything meaningful about alien biochemistry, general principles that apply to life on earth should also apply to life on different planets. Even if aliens are nothing like us earthlings, perhaps the alien set of biomolecules still sets them apart from a non-lving background distribution.

Life selects and amplifies those molecules that serve it well.

The idea that life can potentially be recognized by a skewed distribution of molecules is almost fifty years old. It was first called the ‘Lego Principle’ by the astrobiologist Christopher McKay, but it harkens back to earlier ideas about (alien) life, in particular those formulated by James Lovelock in the 1960s.

The Lego principle sounds logical and sound – but does it hold up outside the realm of theory? Without a second sample of life, opportunities to test the Lego principle in the real world are slim. Still there exists a place where this hypothesis can be tested. I’m not referring to the laboratory or a test tube, but inside a computer core.

There, scientists have created living and evolving organisms. These lifeforms are unrelated to life on earth, and thus provide an opportunity to test the most universal aspects of evolution. One such digital world is Avida. The elementary building blocks (the basic chemistry) of an Avidian organism are simple computer instructions, such as ‘add’, ‘stop’ and ‘substract’. Together, these instructions form a simple computer programme (the organism) that competes with other programmes for computing time in the central processor. By performing certain tasks, doing certain calculation for example, they get more access to computing time.

If the Lego principle is true, Evan Dorn and his colleagues reasoned that the distribution of computer instructions in living Avidians should also differ from that of an ‘abiotic’ background environment ^**. They started out with a virtual world that where mutation rates were high. You can imagine this world as if it is being bombarded with virtual radiation. Living programmes could not survive in the hostile environment: all the useful instructions mutated into gibberish within a few generations. By lowering the mutation rate (or intensity of the radiation) step by step, the Avidians eventually took hold and evolved. After a 1000 generations, Dorn and his colleagues went back and saw how the total distribution of instructions had changed over time.

The change in abundance of certain instructions in Avida over evolutionary time.

What they saw was that within a couple of hundred generations, the uniform distribution of instructions at the start of the experiment had changed into a specific signature. Certain commands were favoured, such as the logical operator NAND, while others were purged from the Avidian genomes, like JUMP-F. It is easy to explain why these instructions changed in frequency. The NAND is a vital ingredient of mathematical operations, while JUMP-F instructs the program to jump forward and skip large parts of the original programme. NAND mutations are more useful than JUMP-F mutations, which are often lethal.

But it doesn’t really matter which instructions changed in abundance. The fact that the distribution of building blocks changed when life took over, suggests that such skewed distributions of building blocks are indeed a universal feature of life. So if we want to look for life elsewhere in our galaxy, it seems wise to first try and understand what non-life looks like. By understanding sterile environments, it becomes possible to detect environments that deviate from this sterility. Hopefully, this will make it possible to find life even without knowing on what kind of biochemistry this life is based. Science is cool like that.

* There is no reason to assume that the set of life’s building blocks is the most optimal or has an essential composition. There are instances where life could have picked a different molecules to do the same job. Valine and isovaline are chemically similar, yet the former is everywhere on earth, while the latter is nowhere to be found

^** In their paper, Dorn and colleagues test the slightly different hypothesis that traces of life can be found in a different distribution of molecules, whereas the Lego principle states that life only uses a select subset of natural molecules.

Image credits
Lego bricks and their dimensions by Cmglee
Diagram of abundance of molecules in abiotic and biotic environments from reference 1.
Graph of change in abundance of instructions in Avida from reference 2.

References
McKay CP (2004). What is life–and how do we search for it in other worlds? PLoS biology, 2 (9) PMID: 15367939
Evan D. Dorn, Kenneth H. Nealson, & Christoph Adami (2011). Monomer abundance distribution patterns as a universal biosignature: Examples from terrestrial and digital life J. Mol. Evol. 72 (2011) 283-295 arXiv: 1101.1013v1

Leafcutter bee (Megachile centuncularis) cutting a leaf.

Relatives of the mason bee (their family is called Megachilidae) prefer different natural construction materials. Leafcutter bees line their cells with leaf disks that they cut from leaves with their mandibles, for example. And the carder bees scrape off the tiny hairs that grow on plant leaves to include in their nests. There is no end to the natural resources that the Megachilidae exploit. There are bees that specialize in collecting resin, animal hairs, plant hairs, leaves, mud, petals and pebbles. Confronted with this diverse family of artisan bees, the French entomologist Jean-Henri Fabre asked a simple question: “Why al these different trades?”^*

The answer, ironically, comes from bees that have never learned such a trade: the Fidelia and the Neofidelia, which live in South-America and Africa, respectively. Jessica Litman and her colleagues recently published an updated family tree of Megachilidae. The Fidelia and Neofidelia are placed on the first two branches of this new tree (see below). The differences in their DNA suggest that they shared a common ancestor around 126 million years ago. While the Fidelia and Neofidelia now live on two different continents, separated by the Atlantic, South-America and Africa were still united in the supercontinent of Gondwana at this time. Given their current distribution, it is likely that the ancestor of these two groups lived in Gondwana, before the continents had split up.

Since the ancestor of the Fidelia and Neofidelia is also the ancestor of all the Megachilidae (again, see the family tree), every bee in this family can trace its ancestry back to Gondwana. Man might have come out of Africa, but the mason bee came out of Gondwana.

The Fidelia and Neofidelia have never strayed far from their ancestral territories, whereas their cousins can be found all over the planet. Why is that? Litman suggests that this has everything to do with their nesting behaviour. Unlike their leafcutting and cement mixing cousins, the Fidelia and Neofidelia don’t use any foreign materials in the construction of their nests. Their larvae grow up in underground burrows that lie naked in the sand. Such nests are vulnerable to moist and rain, which can make the mass of pollen rot. This behaviour severely limits a bee’s potential range, for it can only live and breed in environments where seasonal rainfall is low.

One lineage of bees circumvented this problem. It learned how to build nests using foreign materials that protect the larvae and its food. They then escaped the desert, diversified and colonized the wetter half of our planet. These builder bees became the ancestor of modern mason, leafcutter and carder bees. The story of their success can be measured in raw numbers. There are many more species of leafcutter bees and mason bees (3900) than there are Fidelia and Neofidelia (17, including the Pararhophites).

The Fidelia and Neofidelia were already out of the loop when their relatives evolved a more sophisticated nesting behaviour. They still follow the old ways and build their nests with unlined cells, like the ancestral Megachile bee in Gondwana must have done. Biologists call such an ancestral trait a ‘plesiomorphic‘ trait. This does not make the Fidelia and Neofidelia ‘primitive’. One of their traits just happens to resemble the ancestral form.

Further evidence that building simple, unlined nests is the ancestral condition for Megachile bees, comes from the apoid wasps, the wasps from which bees evolved. They also store their paralyzed prey in unlined burrows.

Litman finishes her article with some interesting speculation that the Fidelia and Neofidelia resemble their wasp-like ancestors in another way. They only collect pollen from a subset of flowers: they have to be large and have radial symmetry and stamens that are well exposed. Other Megachiles are not so picky: they happily collect pollen from bilaterally symmetrical flowers for example. Apoid wasps are specialized hunters that hunt for prey that have similar size and stature. They might be programmed to ‘respond to prey of a certain size and behaviour‘. The finicky nature of fideliini could be the heritage of this programmed hunting behaviour. If this is true, this would mean the shift from prey to pollen in the Megachilidae wasn’t the driving factor in the the diversification of bees, as has been suggested previously. Other behaviours evolved first, before bees started to exploit the wide range of flowers available to them.

While their ways might be ancient, they still serve the fideliini well. After all, they are still around in these modern times. And so, as the mason bee mixes her clay and the carder bee combs the leaves, another one still builds her simple nests, just like her ancestors have done for millions of years. Dig on, little friends.

* In his essay on Megachiles, Jean Henri Fabre also gives an answer to his question: “I foresee the answer: they are prescribed by the organization. An insect excellently equipped for gathering and felting cotton is ill-equipped for cutting leaves, kneading mud or mixing resin. The tool in its possession decides its trade.” While a true statement, this is not a great answer. It is akin to answering the question why lions hunt gazelles by saying that lions have claws and gazelles have hoofs. This is not the cause of their predator-prey relationship, it is a consequence.

Leafcutter bee image by Bernhard Plank.

Litman JR, Danforth BN, Eardley CD, & Praz CJ (2011). Why do leafcutter bees cut leaves? New insights into the early evolution of bees. Proceedings. Biological sciences / The Royal Society PMID: 21490010

Some of my favourite posts are The First Trilobite by John McKay, Oiling The Devil’s Darning Needle by Meera Lee Sethi, But did you correct your results using a dead salmon? by Iddo Friedberg and Givin’ props to hybrids by DeLene Beeland. You can read these blog posts online of course, but wouldn’t it be nice to read them in book form, bundled with 52 other great science stories, poems and essays?

You can buy the ‘traditional’ book here and the downloadable e-book here

Disclaimers: I was a judge for this edition, and helped reviewing some of the 900+ contributions. Also, my own blog post ‘Living fossils don’t exist‘ is included in this edition. Obviously, I have not judged my own blog post!

The black and white Great Auk was a beautiful bird of bizarre proportions. Its ribbed beak was huge and unwieldy, its legs were too short and its stubby wings were far too small to carry its big body into the air. In these regards, the Great Auk’s clumsy appearance rivals that of the Dodo. And that’s not the only thing these two birds have in common. For the Great Auk too, was driven extinct by human cruelty and carelessness.

The Icelandic fishermen Sigurðr Islefsson, Jón Brandsson and Ketil Ketilsson saw the last living Great Auks, in June 1844. They promptly killed both birds and destroyed their egg. The bland details of their story, chronicled by the British zoologists Alfred Newton and John Wolley, make it seem as if these birds were killed only yesterday. And indeed, the Great Auk is almost tangible. Whereas all that is left of the dodo are a few bones, 78 stuffed Great Auks and about the same number of their spotted eggs still exist.

Almost tangible, but not quite. There’s only so much you can learn from dead birds and unhatched eggs. No one remembers what their call sounded like or what colour their eyes were. Nor will anyone ever know. The only thing that is left, is to understand the tale of their demise.

Life

If Great Auks looked out of place on land, this is because they belonged in the water, where they caught fish and crustaceans. They were great swimmers and divers, just like their living relatives the Razorbill and the Atlantic Puffin. The shape of their wings and body life are adaptations for a life on and under water, allowing the Great Auks to swim with such ease. They couldn’t fly, but they were masters of what Bengson called “subaqueous flight”.

The flippers of Penguins have a similar shape as the wings of the Great Auk. Penguins are also just as flightless as the Great Auk. This is an example of convergent evolution, since Auks and Penguins independently evolved their streamlined wings.

Great Auks could be found throughout the subarctic Atlantic ocean. Their range extended from the rocky shores of Newfoundland to the British Isles and the coasts of Norway. They were out on sea for most of the year, and only sought out land during their breeding season, which started in late spring. The Great Auk’s choice of breeding sites was limited because of its inability to fly. The only suitable islands were those with ledges or reefs, so that the birds could waddle ashore.

Great Auks lived in large breeding colonies. Some of the larger colonies near Newfoundland must have numbered tens of thousands of birds. Each breeding pair laid a single egg, which had unique spots and markings. Perhaps these markings helped the parents to recognize their own egg on the crowded breeding grounds.

Not much is known about the way the Great Auk raised their chicks. Since other species of Auk share the care for the chicks between both parents, it is likely that Great Auks did the same. Some scientists think that the chicks took to the sea as quick as a few days after hatching, because it would have been difficult for the parents to feed their chicks for much longer, without being able to fly. Finding food out at see and coming back ashore would have costed a lot of energy. On sea, the chicks could be nourished easier. But computer models suggest that Great Auks would have had enough energy and time to feed their chicks for a while, before taking them to sea. This parenting style would have matched that of their closest living relative, the Razorbill, which feeds its chicks until they have a quarter of their adult body weight, before they take them to sea.

Extinction

The unique adaptations that served the Great Auk so well at sea, turned against them in their interactions with man. Their breeding sites were easily accessible from sea, but also easily accessible for humans. Their stubble wings gave them great speed under water, but also meant they could not escape from man’s hungry reach. Wherever they could, humans hunted the Great Auks for their meat, feathers and oil.

There is evidence that Great Auks were already hunted in prehistoric times. But the earliest accounts of their wholesale slaughter date to the 16th Century. From this time onwards, massacres have been described where birds were killed by European sailors, hundreds at a time. The most horrible account of such a massacre comes from the journal of one Aaron Thomas. He describes what happened on Funk Island, near Newfoundland, which hosted one of the largest colonies of Great Auks. Ironically, Funk Island is now a protected wildlife sanctuary.

If you come for their Feathers, you do not give yourself the trouble of killing them, but lay hold of one and pluck the best of their Feathers. You then turn the poor Penguin^* adrift, with their skin naked and torn off, to perish at his leisure.

While you abide on this Island you are in the constant practize of horrid crueltys for you not only Skin them Alive, but you burn them Alive also, to cook their bodies with. You take a kettle with you into which you put a Penguin or two, you kindle a fire under it, and this fire is absolutely made of the unfortunate Penguins themselves. Their bodys being oily soon produce a Flame; there is no wood on the island.

~Journal of Aaron Thomas (1794), aboard the H.M.S. Boston
quote from The Great Auk (1999) by Errol Fuller

* Great Auks were called penguins long before European sailors gave the birds on the southern hemisphere the same name. Penguins are named after Auks, not the other way around.

It is obvious that Great Auks could not survive such sustained butchering for long. Their numbers plummeted until all the large colonies had disappeared by the turn of the 19th century. By then, the last retreat of the Great Auk was Geirfuglasker, a small islet near Iceland where they would breed in the early summer months. Fishermen occasionally came to Geirfuglasker to hunt and plunder, but the island was remote and its currents treacherous enough to provide relative safety.

That is, until disaster struck in 1830. During a period of volcanic activity, Geirfuglasker sank into sea entirely. The birds that survived this upheaval sought a new home, and found it on the island of Eldey. This island was just as desolate and barren as Geirfuglasker, but it had one big disadvantage: it was much closer to the Icelandic coast, and thus more accessible.

A Great Auk egg. These eggs were heavily sought after by European naturalists.

Fishermen hunted down most of Great Auks that lived on Eldey. They were spurred on by naturalists in Europe who began to realize that the Great Auk was becoming rare. They commissioned fishermen to obtain dead birds and eggs for their collections. For what better way to impress your Victorian colleagues than with a stuffed Great Auk on your desk, or one of its spotted eggs in your cabinet? This sudden popularity as a gentleman’s collector’s item would be the final push that the Great Auk could no longer take.

It was the  merchant Carl Siemsen who contracted the party of fourteen men that would set out to kill the last Great Auks in 1844. When they had rowed close to the island, they quickly saw the two large birds. Three men landed on the island. Not soon after, one bird was cornered against the cliff wall. One bird tried to escape via the water. Both were caught and strangled. “I took him by the neck as he flapped his wings. He made no cry when I strangled him”, is what the fisherman Sigurðr would remember later. It was only after the birds had been killed, that the men discovered their egg had been broken. Eldey too, is now a protected bird reserve.

Did the death of this breeding couple mean the last Great Auks had died? Was their egg the last hope of an entire species? Could the Great Auk be saved? Maybe. Probably not. Perhaps a few Great Auks still existed out on sea or on some isolated island. But as a species, the Great Auks was doomed long before 1844. The Great Auk was a colonial and social bird, that relied on large numbers of its kind to be successful.

The conservation biologist Michael Soulé once compared the death of the last individual of a species to the final punctuation mark in a book, or the final curtain of a play: it was not this death itself that mattered, but the story that preceded it. Only by learning the story, can we learn how and why species become extinct. Still, I think the tale of the last Great Auk deserves to be told. It doesn’t really matter where she lived, or when she died. She lived. She died. If she did not have a peaceful death in life, at least she will have one in fiction.

She had seen much in her long life. Her colony had fallen apart when she was only four years old. Her mate was clubbed to death not long after the confusion that ensued. Now, she was old and alone. She no longer caught as much fish as she once did. When the summer months finally came, her instincts drove her out of the sea, to her old home. As she waddled ashore, she saw no others of her kind. She never did. Far from the other birds, she found a vacant spot on the rocks,  in the shadows of the cliffs. She lowered her head and closed her eyes. The last Great Auk slowly sank into her final sleep. The sounds of the birds and beating waves morphed into the the calls of a thousand Great Auks. So this is where they went. Finally, she was home.

Top: The Last Stand, by Error Fuller. Fuller is an artist and writer who wrote a beautiful book on the Great Auk. Image used with his permission.
Middle: Alca Impennis, drawing by the ornithologist and artist John Gould. Image in the common domain.
Bottom: Great Auk egg, drawing by naturalist Adolphe Millot. Image in the common domain.

The final paragraph was inspired by the description of the death of the last Dodo by David Quammen, in Song of the Dodo (p. 275).

The earliest ancestors of the blue whale fed themselves differently. They still had teeth, and no baleen. Some modern whales still have teeth (the Odontoceti – literally ‘toothed whales’), but they form a separate group from the baleen whales (Mysticeti) who have replaced all their teeth with baleen. This transition to toothlessness is documented by multiple fossil whales. Each of these fossils provides a snapshot of what must have been gradual change.

Several early baleen whales such as Janjucetus and Mammalodon still had fully developed, enamel-covered teeth. Eomysticetus had already exchanged its teeth for baleen plates. But it is Aetiocetus, that captures this evolutionary change in its entirety. This was a whale that still had teeth, but that also carried baleen, as small modifications in its skull reveal.

Whale embryos also contains hints that their distant ancestors once bore teeth. They still grow tooth buds that disappear before the young whale is born. Charles Darwin must have had the toothed ancestors of whales on his mind when he wrote the following sentence in the Origin of Species:

What can be more curious than the presence of teeth in foetal whales, which when grown up have not a tooth in their heads; or the teeth, which never cut through the gums, in the upper jaws of unborn calves?
~Charles Darwin, On the origin of species.

Reconstruction of Aeitocetus that lived 25 million years ago. This wale had both teeth and baleen.

Aside from the evidence from fossils and whale embryos, the loss of enamel-capped teeth also left traces in the genomes of modern whales. All reptiles and mammals have genes that produce proteins that mineralize the enamel of teeth. Since baleen whales have no teeth as adults, they have no need for these proteins. Over time such unnecessary genes tend to acquire mutations that impair the protein. This is exactly what happened in baleen whales. In all species of baleen whale, up to three tooth genes turned into pseudogenes (remnants of genes that can no longer produce a functional protein, but are still recognizable as former genes).

But there is something strange about how these mutations are distributed: every species of whale has a different set of mutations. Humpback whales have a mutated enamelin gene, for example. Blue whales carry a different mutation in enamelin. And sei whales have a mutation in a different tooth gene altogether.

Such an uneven distribution of mutations can mean a couple of things. One explanation could be that all the baleen whales lost their enamel independently from each other, due to different mutations in each lineage. Another possibility is that an hitherto unknown mutation that can be found in all baleen whales is responsible for the loss of enamel. Enamel-covered teeth would have been only lost once by the common ancestor of baleen whales. The fossil evidence supports this scenario: the distribution of toothed baleen whales is not nearly as patchy as the distribution of tooth gene mutations.

Scientists from the University of California suspected a gene called MMP20 might contain the mutation that had been overlooked so far. This gene seemed to be a good candidate, because the MMP20 protein is involved in processing tooth proteins such as enamelin and ameloblastin. A mutation in MMP20 could affect multiple enamel proteins downstream. Moreover, humans and mice that have a defective MMP20 gene develop bad and brittle enamel (amelogenesis imperfecta).

The family tree of whales, including extinct relatives. Baleen whales (top) and some pygmy sperm whales (bottom) have mutations in their tooth genes. Every orange symbol denotes a mutation; different letters represent different genes.

The team initially screened four different species of baleen whales for mutations in MMP20. They hit the jackpot right away. In all four whales, a stretch of DNA (a SINE) had inserted itself right inside MMP20, splitting the gene in two. When they extended their search to other species, they found that whale after whale had the same DNA insertion inside MMP20. This ubiquity gives a clear message: it is this insertion that rung the death knell for the whale’s teeth.

But the researchers discovered that some pygmy sperm whales (Kogia), that belong to the branch of toothed whales, also carry mutations in their MMP20 genes. These pygmy sperm whales are also known to have enamel-less teeth. But whereas baleen whales first lost MMP20 before the other tooth genes mutated, these sperm whales seem to have lost the tooth protein enamelin first, with MMP20 now having mutated secondarily in some individuals.

So here are two lineages of whales, caught in the act of evolving on different, but similar paths. Evolution is sometimes criticized for not being amenable to experimental scrutiny in the lab, but the pygmy sperm whales prove these critics wrong. As the authors note, “mammalian diversity presents a unique laboratory, complete with replicated experiments.” Life herself presents us with a multitude of ingenious experiments. It is up to us to interpret them. Personally, I couldn’t imagine a more exciting science.

Reconstruction of Aetiocetus by the great paleoartist Carl Buell. Check out his website here. Image used with his permission.
Whale phylogeny from reference, whales also drawn by Carl Buell.

Meredith RW, Gatesy J, Cheng J, & Springer MS (2011). Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales. Proceedings. Biological sciences / The Royal Society, 278 (1708), 993-1002 PMID: 20861053

Molecular biologists study life at its tiniest scale. Their world is both fascinating and mysterious, but I never regarded it as beautiful. Beauty is the domain of those fields of biology that study exotic creatures and ancient fossils, and not that of those who study nature with a microscope and a pipette. Or so I thought. My view changed when, at the end of my second year in college, one of my teachers showed the following video to our class:

Suddenly, the cell came to life. It became a bustling city where proteins and molecules were doing their jobs, and through their collective actions sustain a complex, living machine. Thanks to the great writers that contributed blog posts for this edition, I can present you a taste of all the wonderful things that happen within our cells.

Imagine a cell. Today, an animal cell will do. Our imagined cell is not floating in empty space. It is embedded into a matrix of proteins and sugars. This matrix provides support, but is also flexible enough to bend and stretch when needed. Michael Scott Long from phased writes how deforming this elastic matrix can make it easier for cancer cells to grow deeper into tissues.

Between the tangled proteins of the extracellular matrix, we find our cell. The lipids of its cellular membrane are bobbing up and down. Before we enter our cell, we’d better ring the bell. Not only would it be impolite to barge in – it would also be nigh impossible. The lipid membrane is a formidable barrier to all kinds of ions, proteins and other molecules. The cell’s doorbells are its signalling receptors that raft on the lipid sea. When a molecule binds this receptor, the word of its arrival gets spread on the other side of the membrane via signal molecules that are released. Lab Rat wrote a post on these signal molecules, which appear to be more complex and versatile than was previously known.

Some molecules, such as the hormones estradiol and testosterone, have no need for doorbells: they can pass the membrane on their own. Once they are in the cell, a protein ferry picks them up and brings them straight to the cell’s core, where all the DNA is located. Once it is there, the molecule switches on certain genes and turns off others. But why use the ferry boat at all? Why don’t the molecules bind the DNA themselves? Over at the It Takes 30 blog, Becky Ward gives the answer in a blog post on the signalling networks. There you will also read that the entire mechanism is way more complex than I just summarized (over 100 molecules are involved in the entire process!).

While we’re in the cell’s nucleus, we might as well look around us and see what’s going on here. Katie Pratt explains: the information that lies in the DNA is read and converted into RNA. These RNA molecules contain the instructions for making functional proteins. But some RNAs lack these instructions. Their sole purpose is to regulate the activity of other genes. Scientists use these RNAs to silence the genes they want to study. They even think about using them to repress the genes of virusses such as HIV, as a potential therapy. Head over to Katie’s blog to find out more.

Our imagined cell is not infected by HIV, luckily. We can safely follow a messenger RNA molecule as it squeezes through the nuclear pore on its way to the ribosome. There, its encoded message is translated into an enzyme. Enzymes are pipelines of our cell. By catalyzing chemical reactions, they can direct the flow of small molecules within the cell. Christopher Dieni on Bitesizebio tells you everything you want to know about enzymes. Seriously, it’s a great overview of all the things that enzymes do and don’t do, so go check it out!

That’s it for this month’s edition of The MolBio Carnival. I hope you enjoyed the journey. You can check future hosts and past editions on the Carnival’s home page. Be sure to subscribe to the RSS feed to receive notifications and summaries when new editions of the Carnival are posted. Also, you are welcomed to submit your best molbio blog articles to the next edition of The MolBio Carnival, which will be hosted by Alex from Alles was lebt.

The classification of worms got off to a false start thanks to Carl Linnaeus, the great-grandfather of taxonomy. After he had given mammals, reptiles, birds and fishes their own groups, he divided the remaining invertebrates (animals without a spine) into just two categories: insects and Vermes, or worms. Anything that was not an insect therefore was, by necessity, a worm. In this way Linnaeus lumped a diverse group of creatures was together into a single class. Corals, jellyfish, squids, worms themselves and other soft-bodied animals were all members of the bloated Vermes. Stephen Jay Gould famously described the Linnaean class of Vermes as a taxonomic wastebucket.¹

The taxonomists that came after the Linnaeus spent a lot of time cleaning out this wastebucket. One of the first biologists to study worms in detail was Jean-Baptiste Lamarck. He liberated the ringed worms, or annelids, from the Vermes and placed them into their own, unique group. He recognized that their segmented body plan, gut, nerve cord and blood vessels make them different from other worm-like creatures without these features, such as snails and flatworms.

Tomopteris, a free-living worm belonging to the Errantia. When they are disturbed, they release glowing particles from their parapodia.

Later, in 1866, the French naturalist Quatrefages further divided the ringed worms into the Sedentaria and the Errantia. Not only do these two groups differ in their way of life, with the Errantia being free-living predators and the Sedentaria immobile filter feeders, they also differ in the way they look. The parapodia (little worm legs) of Sedentaria are smaller and less pronounced than those of Errantia for example.

This classification was used for over a century, but it was dismissed as an ‘arbitrary grouping’ that was used only for ‘practical purposes’ by biologists in the 1970s². They argued that the similarities of Sedentaria and Errantia arose due to convergence, rather than reflecting a deep evolutionary split. In other words, they argued that some worms look the same because they have a similar way of life, and not because they are closely related. Just like the wings of a bird and and bat wings look similar even though the common ancestor of birds and bats had no wings. The revisionists came up with a new classification that featured a split between the bristled worms (polychaetes) and the collared worms (clitellates, which includes the famous and noble earthworm).

But when Torsten Struck and his colleagues analyzed hundreds of genes of 34 different species of ringed worms, they didn’t find this split. Instead, they found that most worms belonged to two groups that mirror the nineteenth century groupings of Errantia and Sedentaria³. The different lifestyles of the two groups aren’t arbitrary. On the contrary, they are the reflections of an ancient crossroads in the evolution history of ringed worms!

The new family tree of Annelids (red), showing that Sedentaria (blue) and Errantia (green) are distinct groups.

This means the end for the bristled worms as taxonomic group. Earlier studies already hinted that something was amiss, but Torsten Struck was surprised to see the revised classification from the 70s rejected with such confidence. This makes clear what the biggest problem is of classifying life solely on the way it looks: you cannot distinguish whether a certain feature was never there in the first place, or whether it became lost during evolution later on. Genes, if you look at enough of them, don’t have this problem, .

Take the collared worms, who adapted to a life in freshwater and in the earth. They lost the parapodia and bristles of their marine ancestors and evolved many changes in the way they reproduce. If you would classify earthworms based on these characteristics, they would appear to be more distantly related to other bristled worms than they really are.

With the new family tree in hand, Torsten Struck could reconstruct what the ancestors looked like (apparently, they were really cute!). The reconstruction of the ancestor of Errantia shows that it was already well adapted to a mobile and predatory way of life. It had well-developed antennae, two pairs of eyes (“‘all the better to see you with, my dear”) and parapodia which it used to move around quickly. The evolution of Sedentaria show the opposite trend. Their ancestor had no antennae and reduced parapodia. Other sensory organs were lost in different lineages of Sedentaria.

Meet the really cute ancestors of annelids, Errantia and Sedentaria

Scientists who use worms as model organisms should pay close attention to these results. The marine ragworm, or Platynereis dumerilii, has recently come in vogue for studying how eyes and organs evolved in animals. Many of its characteristics, like its large antennae and sensory palps, seem to be more characteristic of the family of Errantia, and not for the ringed worms as a group. Torsten Struck writes: “None of the model organisms alone will reveal the ancestral conditions which were present in Annelida. You can only achieve this with a comparative approach that includes several organisms.”

Tomopteris picture by Uwe Kilis.
Annelid phylogeny from reference 3.
Ancestral reconstruction adapted from reference 3

1 Gould, SJ (2001). A Tree Grows in Paris: Lamarck’s Division of Worms and Revision of Nature, The Lying Stones of Marrakech
2. FAUCHALD, K., & ROUSE, G. (1997). Polychaete systematics: Past and present Zoologica Scripta, 26 (2), 71-138 DOI: 10.1111/j.1463-6409.1997.tb00411.x
3. Torsten H. Struck, Christiane Paul, Natascha Hill, Stefanie Hartmann, Christoph Hösel (2010). Phylogenomic analyses unravel annelid evolution Nature

The rare, subterranean orchid Rhizanthella gardneri.

By living underground, the remarkable Rhizanthella is somewhat protected from drought and desiccation. The orchid had to make a Faustian deal to receive this protection: without the light of the sun to nourish it, the orchid became a parasite.

Rhizanthella parasitizes a species of fungus, which lives on the roots of the broom bush Melaleuca uncinata. The relationship between the fungus and broom bush is harmonious. They both produce something that the other needs. The bush captures sunlight and converts it to sugars, which it exchanges for minerals that the fungus takes up from the soil. But the orchid? It grows near the roots of the broom bush, so that it can exploit its fair trade agreement by stealing nutrients from the fungus.

This subterranean and parasitic lifestyle is a big change from normal plant life. Other plants use their green chloroplasts to obtain energy from the sun via photosynthesis. But underground, Rhizanthella no longer needed its chloroplasts. Its leaves turned purple instead of green.

Still, the chloroplasts endured. They might no longer be green, but they have other functions that prevented Rhizanthella from doing them away entirely. Photosynthesis normally overshadows these other roles, but a parasitic plant like Rhizanthella presents the perfect opportunity to peek at this hidden, far side of the chloroplast.

A recent census of the genes inside Rhizantella‘s chloroplasts turned 37 genes. This a big drop from the more than hundred genes that chloroplasts normally have. In fact, with only three dozen genes, Rhizantella‘s chloroplasts are some of the most gene-poor chloroplasts known. The genes that were no longer necessary in the chloroplast were purged from its genome or moved to the cell’s nucleus. All its photosynthesis genes went missing, for example.

Parasites like Rhizanthella are perfect for peering at the far side of the chloroplast, which are the organelles that are responsible for photosynthesis in other plants.

More interesting than the genes that are no longer there, are the genes that remain. The majority of them are somehow involved in manufacturing proteins. Nine chloroplast genes code for RNAs that carry amino acids, and two genes are responsible for stringing these amino acids together into proteins, for example.

Another gene, with the poetic name accD, codes for a part of a protein that produces fatty acids that are part of cellular membranes. The other parts of this protein are coded for by genes that are located in the cell’s nucleus, but the entire protein has to be put together inside the chloroplast. This could be the reason why accD managed to keep its spot inside the chloroplast: as long as at least one part is represented by a gene inside the chloroplast, the larger protein can still be assembled.

A deep incorporation into the cellular infrastructure seems to have been the ticket to survival for the 37 genes that remained. For now, at least. But getting rid of these superfluous genes also means that there is no way back for Rhizanthella and other parasites. It will never be able to absorb the light of the sun again. This can be a dangerous strategy, because a parasite’s fate will always be in the hands of other species. For Rhizantella the dependency on the fungus and broom bush comes on top of its dependence on termites for pollination of its flowers and mammals for the dispersal of its seeds. With so many delicate interactions with other species, no wonder it’s so rare.

Rhizanthella picture by Jean Hort.
Picture of rain on a castor oil plant by Fozzeee.

Dixon, K. (2003). Plate 468. Rhizanthella Gardneri Orchidaceae Curtis’s Botanical Magazine, 20 (2), 94-100 DOI: 10.1111/1467-8748.00378

Delannoy E, Fujii S, des Francs CC, Brundrett M, & Small I (2011). Rampant Gene Loss in the Underground Orchid Rhizanthella gardneri Highlights Evolutionary Constraints on Plastid Genomes. Molecular biology and evolution PMID: 21289370