Recently, new scientific research has contradicted my earlier statements: that while we likely interbred with Neanderthals, very few of their genes were passed on (highlighting the difference between ancestry and gene lineage). However, Svante Pääbo’s team from the Max Planck Institute for Evolutionary Anthropology in Leipzig, suggest that perhaps 4% of some peoples’ genes are from Neanderthals. Homo sapiens and Homo neanderthalis did interbreed. The conclusions come from comparing uncontaminated Neanderthal DNA to living humans, and chimpazees. Surprisingly, Neanderthals and non-African humans share some distinct markers, not found in either chimps or Africans, suggesting interbreeding. The researchers also stress that these where only “genetic markers”, DNA regions supposed not to have any function. If they do not have any function, then Natural Selection can’t work upon them. So, we don’t know if the DNA contributes in any way meaningfully to non-African humans. Any negative traits that Neanderthals may have passed on in their hybrid children, would presumably have been selected against and become extirpated from the gene pool long ago.
(See an amazing interactive website of the neanderthal genome at the Science)
It is amazing to think of two species of humans, first separated over 300 000 years ago, and coming in such (literally) intimate contact again. How many other humans were there? The recent DNA extracted from a 30 – 50 thousand year old finger in a Siberian cave is neither human nor Neanderthal, but something else from its contemporaries. There is also the supposed Homo floresiensis “Hobbit”, indicating that maybe as little as 13,000 years ago, the prehistorical landscape was abloom with many different species of humans. How, I wonder, and what did they think of each other? Did they have such separate lifestyles and separate ecological niches, enabling them to co-habitat the same geographic area, like Pygmy’s and other Africans? Did they raid, trade and communicate with each other? Perhaps. But the Neanderthals quick demise upon the advent of modern H. sapiens upon the North suggests competitive exclusion, and maybe perhaps even violent confrontation.
I can’t help but think what this study means for the perennially touchy issue of “race” among H. sapiens. Probably it means nothing. Regardless of the minor, and apparently non-functional genetic variation introduced by H. neaderthalis, H. sapiens are still remarkably homogeneous in our genes. Most genes came from a few, closely spaced “out-of-Africa” outbursts, starting 70,000 years ago.
Instead of bolstering racist arguments, this study rather helps to lay to rest an even more controversial theory, the Multiregional Hypothesis, which tried to explain how some minor features, like the mandibular cavity, seems to show a continuity from earlier hominids in Europe and Asia to their respective modern humans, by hypothesizing H. sapiens evolved indigenously and in parallel from earlier Hominids who’d already populated Eurasia many millions of years ago. This study by Pääbo gives us a way to reconcile the Multiregional evidence with the Out-of-Africa evidence, that these features common to certain modern “races” and earlier hominids are a result of interbreeding, not separate speciation, and that our genes mostly come through one species from Africa.
I hope they will look for other functionally relevant markers, though racially sensitive, one can easily imagine what a Northern-adapted Neanderthal could offer the northward expanding African humans. But then again, the Neanderthals clearly didn’t have such a great advantage.
> Marine Ecology | Date Science | Scientific Computing
Friday 28 May 2010
Monday 10 May 2010
Mothers Day Tale: Saving a seaturtle
This blog is inspired by a very special mother’s day tale. I was helping with a Seaturtle patrol on a Grenadine Island, witnessing my first ever leatherback: a massive creature relatively unchanged since the Cretaceous, among the dinosaurs. The poor creature was ensnarled in a fisher net, cutting into its own flesh as it struggled to bury its eggs. After a grueling half-hour of sawing, cutting and imploring her to stay, we managed to free her. What a great mother’s day, to let one mother live and give life another day.
The problem is that genetics and morphology show that Birds, once thought of as a grand class on equal rank as mammals, reptiles, etc., is nestled within the Reptile clad. In fact, a goose is more closely related to a crocodile than a turtle, i.e., they share a more recent common ancestor to crocodiles than they do with Turtles. They also share a more recent ancestor with geckos, monitor lizards, caymens, and most of other “reptiles” than the very reptilean-looking Turtles.
The confusion is that the Sauropsids are a very fragmented and persecuted group. Had it not been for the asteroid that whipped clean the dinosaurs, and could have had before us a continuous gradient of morphologies from a crocodile to a cormorant: big and small, scaled and feathered, beaked and toothed, all the extinct intermediates would be obvious to such a lucky taxonomist, who would easily classify all these things --all lizards and birds and dinosaurs -- as being related without batting an eye. Our laymen language would do away with a “reptile” word altogether, instead having something unique for the birds/lizards/dinosaurs (Diapsids) and the turtles (Chelonia).
Perhaps this uniqueness of the sea turtles is their alien allure. Staring into the snapping, jagged maw of the wounded mother, was like staring into an ancient earth.
It got me thinking about Reptiles. The very word is troubling to taxonomists, unlike the monophyletic mammals, it is not so neat and tidy. The Chelonia, the turtle/terrapin/tortoise clad, split off of from the Diapsids (the group containing all other lizards, dinosaurs, birds and crocodiles) some 200 million years ago, contained within the Sauropsids, the class generally thought of as reptiles.
The problem is that genetics and morphology show that Birds, once thought of as a grand class on equal rank as mammals, reptiles, etc., is nestled within the Reptile clad. In fact, a goose is more closely related to a crocodile than a turtle, i.e., they share a more recent common ancestor to crocodiles than they do with Turtles. They also share a more recent ancestor with geckos, monitor lizards, caymens, and most of other “reptiles” than the very reptilean-looking Turtles.
The confusion is that the Sauropsids are a very fragmented and persecuted group. Had it not been for the asteroid that whipped clean the dinosaurs, and could have had before us a continuous gradient of morphologies from a crocodile to a cormorant: big and small, scaled and feathered, beaked and toothed, all the extinct intermediates would be obvious to such a lucky taxonomist, who would easily classify all these things --all lizards and birds and dinosaurs -- as being related without batting an eye. Our laymen language would do away with a “reptile” word altogether, instead having something unique for the birds/lizards/dinosaurs (Diapsids) and the turtles (Chelonia).
Perhaps this uniqueness of the sea turtles is their alien allure. Staring into the snapping, jagged maw of the wounded mother, was like staring into an ancient earth.
A mother's day gift: saving a leatherback
Midnight, Mother’s Day 2010: At the beach, we killed our lights upon emerging from the dark forest, knowing how skittish seaturtles are to flashes of light on potential nesting sights. After a few moments adjusting to the darkness, the white foam of the surf, and the coral-grain sand become relatively bright beacons on the dark, midnight island. Then we see it: 6 feet voluminous dome, in dark contrast to the sand. Thought we can’t see its details, the size and smell mean only one thing: a nesting leatherback burying her eggs.
We’re on Union Island, a small Grenadine Island in the Caribbean, on a turtle patrol to monitor the population and protect against poachers. We approach the ancient turtle from the rear and turn on redlight, to which they’re insensitive. I crack a smile as I see the back flippers strain dexterously in an ancient ritual to move sand about the nest.
But all is not as it should be. The scales buckle and purse to the tug of a thin, taut thread. The turtle is covered in a net. Its face and front flippers are a horrifying sight, as the fishing net has found its complex peace ensnarling its entire front, cutting into pinkish flesh and carapace. What can the sad creature do, but try to live on, try to satisfy its unrelenting urge to live and pass on new life. It surely would not have lived much longer.
We moved quickly. She had finished and was trying to leave, digging massive flippers into the sand and throwing us off as it drove its tonnage towards the sea. We cut and sawed at the convoluted knots, and begged the creature to stand still. It frothed and groaned to the molestation. I tried to lure it back to the beach with the mesmerizing red light.
In time we see it free, and with new-found mobility she made a quick dash to the breakers and was gone. I thought "what a perfect way to celebrate mother’s day", by letting one ancient mum live and to give life another day.
It was also an appropriate introduction to seaturtles. This is the sad norm for most of them: dangled, choking, and drowning in the littered, despoiled seas we have wrought. They’re numbers are on the brink of extinction, an accomplishment that 110 millions years of dangerous and variable Earth’s could not trump. I hope they outlive us.
Monday 3 May 2010
You are descended from Viruses, not Apes
The blog title is a cheeky play on a chapter in the Matt Ridley book, Genome, which compares the fact that our genome has more genes of useless viral origin than genes which actually code for something useful: only 4% of the human genome actually do something (99% of which is the same as our closest relatives, the chimpazees), while a whopping 21% is composed of self-propagating remnants from retrograde viruses (e.g., LINEs, see Griffiths Introduction to genetic analysis 2009). We’ve been hijacked. Does this make you feel incredulous, or give you a sense of awe? No doubt it does, so long as you adhere to the illusion that you are some cohesive whole, and that “your” genes exist solely for your benefit. A view more in line with the facts, however, is that the “I” is just the accidental ambassador for a troublesome nation of genes.
I like this fact as a way to set the context for two paradigm-smashing themes in evolution and genetics, namely, a) our genome is a demonstrably flawed “set of instructions” (if viewed through the lens of a “Designer”), and b) We, or rather, “I”, the seemingly unified human individual, is merely a vehicle for the selfish propagation of many genes, among them with great schisms and outright war, competing to do what they exist only to do: getting themselves duplicated.
Consider the most common protein gene in the human genome, Reverse Transcriptase gene, which has no useful application for us or our cellular machinery, but is employed by retroviruses such as HIV. Reverse Transcriptase takes RNA (say, from a virus), transcribes it into DNA, wherein other enzymes can inserts it into our genome. Why do we have a gene that does nothing else but potentially insert viral RNA into our genome? Other genes have done away altogether with their viral middleman, such as Retro-Transposons, and do nothing but replicate themselves with Reverse Transcriptase.
(See a video on Reverse Transcriptase and HIV)
These facts, and others, such as 96% of the human genome being “junk DNA”, challenge all attempts to “make common sense” of the genome. Forget all the info/media analogies you’ve heard about the genome, such as it being like a blueprint, a recipe, an instruction manual, or a program for proteins. The genome is absurdly far from being a coherently “authored” document. For example, an analogous “Instructions Manual For How to Build a Protein”, would make Pulitzer Prize-winners of the most hopefully convoluted IKEA Instruction Manuals in comparison:
“At least [Instruction Manuals] do not insert… five copies of the Schiller’s Ode to Joy, or a gargled version of a set of instructions for how to saddle a horse. Nor do they generally include five copies of a complete set of instructions for how to build a machine that would copy out just that set of instructions. Nor do they break the actual instructions you seek into twenty-seven different paragraphs interspersed with long pages of irrelevant junk, so that even finding the right set of instructions is a massive task. Yet, that is a description of the human Retinoblastoma gene, and as far as we know, it is typical of human genes: 27 brief paragraphs of sense, interrupted by 26 long pages of something else”(Matt Ridley, in Genome).
This is because our genome is a document which wrote itself, rather being Authored, Designed, or Created. And (to extend the absurd analogy) rather than the whole document having its own interest at heart, individual paragraphs are clamouring and competing for selfish verbosity.
Some genes increase themselves in the greater gene-pool by genuinely improving their hosts’ chances of staying alive and reproducing, such as genes which code for language or blood-clotting. Other’s do it by hijacking our DNA-replication machinery.
The point is that the focus of evolution is not at the species-level, nor even at the individual-level, but at the level of the gene. Just like it is wrong to say that natural selection promotes traits which benefit the species (consider 2-tonne male Elephant Seals pulverizing young pups – even their own – in their frantic race to rape females), so too does natural selection sometimes promote genes which are bad for the individuals who harbour them (but are good at getting the gene’s replicated more, so all the better).
How to think of this gene-level view of evolution and natural selection? One way is to build family trees for each individual gene. As an organism, you have a unique family tree which branches backwards in time with 2 parents, 4 grandparents, 8 great-grand-parents, 16 great great-grand-parents, and so on, all of which, more or less, contributed a corresponding proportion of their genome to you. However, each individual gene has a different story: each copy came from only 1 parent, 1 grand-parent, 1-great-grand-parent, and so on ad infinitum. This difference between genetic lineage and ancestry is key to understanding evolution. For example, we may have genes whose origins do not show up at all in the parental ancestry, such as from viruses. Likewise, we may have ancestors who contribute next to nothing of our genome, but nonetheless mated with one of our great-, great-, great- … grand-mothers. For example, African Homo sapiens likely interbred with European Neanderthals passing on hybrid-children, but the children with proportionally more H. sapiens genes were favoured by natural selection, until the exo-species genes were culled away. (This is one way to reconcile the seemingly contradictory evidence for an “Out-of-Africa” hypothesis that all homo sapiens are descended from Africa, and the Multi-Regional hypothesis, that Homo sapiens evolved from different Homo erectus variants already in different parts of the globe. Nearly all of our genes have a family-tree that traces them back to the march of H. sapiens spreading out of Africa. But, some people have features which seem to come from Neanderthals, such as the mysterious bridged-form of the mandibular nerve canal, present in 6% of Europeans today, but no where else. Very little else of the neanderthals’ genes survived.)
In future blogs, I’ll discuss how this flawed genome with its various competing genes can explain many mysteries of the human experience.
See Genome by Matt Ridley.
I like this fact as a way to set the context for two paradigm-smashing themes in evolution and genetics, namely, a) our genome is a demonstrably flawed “set of instructions” (if viewed through the lens of a “Designer”), and b) We, or rather, “I”, the seemingly unified human individual, is merely a vehicle for the selfish propagation of many genes, among them with great schisms and outright war, competing to do what they exist only to do: getting themselves duplicated.
Consider the most common protein gene in the human genome, Reverse Transcriptase gene, which has no useful application for us or our cellular machinery, but is employed by retroviruses such as HIV. Reverse Transcriptase takes RNA (say, from a virus), transcribes it into DNA, wherein other enzymes can inserts it into our genome. Why do we have a gene that does nothing else but potentially insert viral RNA into our genome? Other genes have done away altogether with their viral middleman, such as Retro-Transposons, and do nothing but replicate themselves with Reverse Transcriptase.
(See a video on Reverse Transcriptase and HIV)
These facts, and others, such as 96% of the human genome being “junk DNA”, challenge all attempts to “make common sense” of the genome. Forget all the info/media analogies you’ve heard about the genome, such as it being like a blueprint, a recipe, an instruction manual, or a program for proteins. The genome is absurdly far from being a coherently “authored” document. For example, an analogous “Instructions Manual For How to Build a Protein”, would make Pulitzer Prize-winners of the most hopefully convoluted IKEA Instruction Manuals in comparison:
“At least [Instruction Manuals] do not insert… five copies of the Schiller’s Ode to Joy, or a gargled version of a set of instructions for how to saddle a horse. Nor do they generally include five copies of a complete set of instructions for how to build a machine that would copy out just that set of instructions. Nor do they break the actual instructions you seek into twenty-seven different paragraphs interspersed with long pages of irrelevant junk, so that even finding the right set of instructions is a massive task. Yet, that is a description of the human Retinoblastoma gene, and as far as we know, it is typical of human genes: 27 brief paragraphs of sense, interrupted by 26 long pages of something else”(Matt Ridley, in Genome).
This is because our genome is a document which wrote itself, rather being Authored, Designed, or Created. And (to extend the absurd analogy) rather than the whole document having its own interest at heart, individual paragraphs are clamouring and competing for selfish verbosity.
Some genes increase themselves in the greater gene-pool by genuinely improving their hosts’ chances of staying alive and reproducing, such as genes which code for language or blood-clotting. Other’s do it by hijacking our DNA-replication machinery.
The point is that the focus of evolution is not at the species-level, nor even at the individual-level, but at the level of the gene. Just like it is wrong to say that natural selection promotes traits which benefit the species (consider 2-tonne male Elephant Seals pulverizing young pups – even their own – in their frantic race to rape females), so too does natural selection sometimes promote genes which are bad for the individuals who harbour them (but are good at getting the gene’s replicated more, so all the better).
How to think of this gene-level view of evolution and natural selection? One way is to build family trees for each individual gene. As an organism, you have a unique family tree which branches backwards in time with 2 parents, 4 grandparents, 8 great-grand-parents, 16 great great-grand-parents, and so on, all of which, more or less, contributed a corresponding proportion of their genome to you. However, each individual gene has a different story: each copy came from only 1 parent, 1 grand-parent, 1-great-grand-parent, and so on ad infinitum. This difference between genetic lineage and ancestry is key to understanding evolution. For example, we may have genes whose origins do not show up at all in the parental ancestry, such as from viruses. Likewise, we may have ancestors who contribute next to nothing of our genome, but nonetheless mated with one of our great-, great-, great- … grand-mothers. For example, African Homo sapiens likely interbred with European Neanderthals passing on hybrid-children, but the children with proportionally more H. sapiens genes were favoured by natural selection, until the exo-species genes were culled away. (This is one way to reconcile the seemingly contradictory evidence for an “Out-of-Africa” hypothesis that all homo sapiens are descended from Africa, and the Multi-Regional hypothesis, that Homo sapiens evolved from different Homo erectus variants already in different parts of the globe. Nearly all of our genes have a family-tree that traces them back to the march of H. sapiens spreading out of Africa. But, some people have features which seem to come from Neanderthals, such as the mysterious bridged-form of the mandibular nerve canal, present in 6% of Europeans today, but no where else. Very little else of the neanderthals’ genes survived.)
In future blogs, I’ll discuss how this flawed genome with its various competing genes can explain many mysteries of the human experience.
See Genome by Matt Ridley.
6 months in the Grenadines
I’m living in the
This is the first time in about 7 years that I’m spending my summer in doors, which is challenging both psychologically and to my gut, but in a way, kind of welcome, given that the dry Grenadines are a scorching 30 degrees all the time, and it only gets worse. This is quite the contrast to the last 3 summers, which have included a very different repertoire of environments and activities, such as photographing polar bears, prancing across snow drifts, and falling through ice. At least the sea is modestly cool here, and I spend most of my outdoor snorkeling on real coral reefs, in various states of bleaching and overfished, but nonetheless exciting to a northerner, in the same way that a German tourist might gawk at a cedar in
I work at the Sustainable Grenadines Inc, on a CIDA-backed Internship through the Coady International Institute at St. Francis Xavier University, mostly assisting local groups to organize, get funding and carry out their activities. My favourite group is a band of mostly school teachers you've made a quasi-successful macro-algae mariculture cultivation, processing and sales cooperative! I’m also hoping to start a bird monitoring project. I seem to be busy all the time, which is great.
More on the culture and history of the
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