Carl Zimmer's Blog, page 74

Mouth War

As we sink into the prime season for colds and flus, it's a good time to remember that most kinds of viruses that invade our bodies aren't interested in us. They attack the bacteria inside us instead.

There are probably 100 trillion microbes inside each of us, such that our bodies are ten microbes for every one human cell. Those tenants probably belong to several thousand species, with a collection of genes that's perhaps a 100 times bigger than the human genome. These microbes live in our guts, lungs, mouths, noses, skin, and many other nooks and crannies. Far from making us sick, they help us in many ways, making food for us, defending us from invaders, and nurturing our immune systems.

These bacteria are also hosts to viruses. In World War I, the Canadian doctor Felix d'Herelle discovered the first virus infecting bacteria while studying the stool of French soldiers sick with dysentery. Once he isolated the bacteria-attacking virus, he could use it to destroy cultures of the dysentery-causing bacteria. He dubbed them bacteriaphages (eaters of bacteria). In the decades since his discovery, scientists have discovered a mind-boggling number of bacteirophages in the ground, the oceans, and even in deep caves. They are, in fact, the most abundant form of life on Earth. Now researchers are turning the tools for identifying bacteriophages back to our own body.

Last year, Jeffrey Gordon and his colleagues looked in the guts of four pairs of identical twins and their mothers and discovered over 4,000 different kinds of viruses among them. Each person had several hundred kinds apiece. Most of these viruses were not predators, like the viruses that attack dysentery-causing bacteria, or the ones the give us a cold. Instead, the viruses merge with their host cell. They can be passed down from one generation to the next; only if they sense danger do these viruses break out of their host.

Gordon and his colleagues made their survey by fishing for snippets of virus DNA. Another way to hunt for bacteria-infecting viruses in our bodies is to look at the bacteria themselves. Bacteria aren't passive victims of viruses; like us, they have an immune system. When a virus invades a bacterium, the host can sometimes stop the parasite before it takes over. It chops up the virus's genes and inserts a small portion of the virus's DNA into a certain section of its own genome.

Once the microbe has captured this viral DNA, it can use it as a template for making a molecular probe. When the virus invades again, the probe latches onto it and quickly guides the microbe's virus-killing proteins to their target. And in a bit of Lamarckian wizardry, the microbe can pass this acquired defense down to its offspring, making them resistant too.

The prisons for these captured pieces of virus DNA are called CRISPRs–an abbreviation for clustered regularly interspaced short palindromic repeats. Mutant viruses that don't match a host's CRISPRs enjoy an evolutionary edge, and so microbes are constantly revising their collection of CRISPRs to fight an ever-evolving enemy.

CRISPRs are still fairly new to science, and it's only been recently that scientists have realized something very cool about them: they are a record of the viruses that a community of bacteria has faced. Taking advantage of this history, David Relman of Stanford University and his colleagues took a look at the microbes that live in the mouth, and catalogued their CRISPRs. They periodically collected spit from four volunteers over the course of sevnteen months. Then they looked for the distinctive sequence of CRISPRs in Streptococcus, a particularly large group of species of bacteria in the mouth.

Relman and his colleagues were able to chronicle a year and a half of relentless warfare. All told, they found several thousand CRISPRs in the patients. A number of them could be found in all four patients, perhaps forming a core of defenses against the most common enemies. But many of the CRISPRs were unique to a single person. For example, in one patient, the scientists found 7447 CRISPRs, 823 of which did not exist in the other subjects. And that patient's CRISPRs changed from month to month, from a low of 174 to a high of 486. The scientists could trace the origin of evolution of new CRISPRs over the seventeen months as well.

It's astonishing for most people to learn there are between 500 and 1000 species of bacteria in their mouths. But now we must begin to get used to the fact that those bacteria are in a constant battle with hundreds–perhaps even thousands–of different viruses. One reason it's such a big surprise is that these battles take place without any noticeable effect on ourselves. But it would be a mistake to think that they have no effect at all. The state of our mouth's ecosystem plays a big role in our overall health. Some species of bacteria that colonize our gums can get into our bloodstream and lead to infections of the heart and other organs, for example. As viruses rework the mouth's ecosystem, our vulnerability to these infections may rise and fall. Unfortunately, Relman's new study does not reveal any simple rules for how to manage the virus-bacterial warfare in our mouths. In fact, the variation from person to person might mean that what rules there are are hidden in a vast amount of complexity. If it's any consolation, we'll have many more surprises to look forward to as we explore our inner jungle in the future.

[Image: Phil Dragash via Flickr/Creative Commons]

The Tangled Bank: One of Choice Magazine's Outstanding Academic Titles of 2010

Hurrah! Choice, the leading magazine for academic book reviews, has named The Tangled Bank: An Introduction to Evolution one of the outstanding academic titles of 2010. Here's a line from the announcement: "These outstanding works have been selected for their excellence in scholarship and presentation, the significance of their contribution to the field, and their value as important–often the first–treatment of their subject."

The Tangled Bank: One of Choice Magazine's Outstanding Academic Title of 2010

Hurrah! Choice, the leading magazine for academic book reviews, has named The Tangled Bank: An Introduction to Evolution one of the outstanding academic titles of 2010. Here's a line from the announcement: "These outstanding works have been selected for their excellence in scholarship and presentation, the significance of their contribution to the field, and their value as important–often the first–treatment of their subject."

The Loom's Top Ten of 2010

Happy New Year to one and all. 2010 has been a busy one here, full of tattoos, duck privates, and cannibal Neanderthals. Here are the top posts of the year at the Loom…

1. Kinkiness Beyond Kinky (Why Darwin would have loved the extreme genitals of ducks)

2. Simply Impossible (An uncanny illusion)

3. The X-Woman's Fingerbone (The Denisovans–the first shoe. Here's the second)

4. Oh Pepsi, What Hath Thou Wrought? (A science blogging trainwreck that led to the birth of several new blog networks)

5. Linux vs E. coli (Networks in computers and cells)

6. Dawn of the Picasso Fish (A fossil fills in the evolution of flounders)

7. I For One Welcome Our Microbial Overlords (How the microbiome may control our behavior)

8. Skullcaps and Genomes (The Neanderthal genome turns up in the most unexpected places. Like in Craig Venter)

9. Feathers That Sing (Another example of sexual selections' creative powers)

10. Of Arsenic and Aliens (which is then followed by this)

Vaporware human evolution update

I've updated my post on the supposed evidence of Homo sapiens in Israel 400,000 years ago. We have a better idea of where this worldwide meme got started, and what the scientist behind the paper thinks about what happened…

Missing Links, George Will, and Other Train Wrecks: My Keynote Talk at NECSS

Last year, I gave the keynote lecture at the first annual Northeast Conference on Science and Skepticism in New York. It was a nerve-wracking experience, given that James Randi was originally slated to give the keynote, but was too ill at the time to attend. So I brought some of my favorite head-slapping tales of the dysfunctional relationship between science and the media, from global warming disinformation to so-called missing links. My goals for the talk were laughter, tears, and a glimmer of hope.

NECSS has now posted the video of all the talks at both their 2009 and 2010 meetings. I took a look at my talk, and it's (sadly) just as relevant today (cough, arsenic, cough, ancient Homo sapiens teeth) as it was when I originally delivered it.  So I've embedded it below (it's also here). You may find the Q and A afterwards as interesting as I did: the audience had thought as long–and, in many cases, longer–about these issues as I had.

Unfortunately, the video is a bit marred by my fondness for throwing way too many words on the screen. So if you want to take a closer look at my slides (and follow their links), I've posted a pdf file of my slides here. [Update: Let's try that again .]

Be sure to check out the other NECSS videos if you have a chance, such as the talk by Dr. Paul Offit on the real harm vaccine scares can cause.

Missing Link, George Will, and other Train Wrecks: My Keynote Talk at NECSS

Last year, I gave the keynote lecture at the first annual Northeast Conference on Science and Skepticism in New York. It was a nerve-wracking experience, given that James Randi was originally slated to give the keynote, but was too ill at the time to attend. So I brought some of my favorite head-slapping tales of the dysfunctional relationship between science and the media, from global warming disinformation to so-called missing links. My goals for the talk were laughter, tears, and a glimmer of hope.

NECSS has now posted the video of all the talks at both their 2009 and 2010 meetings. I took a look at my talk, and it's (sadly) just as relevant today (cough, arsenic, cough, ancient Homo sapiens teeth) as it was when I originally delivered it.  So I've embedded it below (it's also here). You may find the Q and A afterwards as interesting as I did: the audience had thought as long–and, in many cases, longer–about these issues as I had.

Unfortunately, the video is a bit marred by my fondness for throwing way too many words on the screen. So if you want to take a closer look at my slides (and follow their links), I've posted a pdf file of my slides here.

Be sure to check out the other NECSS videos if you have a chance, such as the talk by Dr. Paul Offit on the real harm vaccine scares can cause.

[http://vimeo.com/18222690]

Losing our germs: My last podcast

On my new podcast, I talk to Martin Blaser of New York University about Helicobacter pylori, best known as the microbe that causes ulcers. It's also an ancient passenger in our stomachs, and has evolved a delicate balance with its human hosts. In fact, Blaser is worried by the disappearance of H. pylori from the modern world, thanks to antibiotics and hygiene. We may have to pay a price for its extinction, in the form of higher rates of asthma, esophageal cancer, and perhaps even obsesity. Check it out.

With this episode, the American Society for Microbiology is bringing the Meet the Scientist podcast series to a close. In the coming year, they're going to be focusing their online efforts on some new projects you can look forward to on the Microbe World web site. (And they'll be keeping all the episodes of Meet the Scientist on the site.) I've had a wonderful time over the past year hosting the podcast, and I'd like to thank all the scientists who shared their work with me and all the people at ASM who made this experience possible.

100 Trillion Connections–For Free!

Scientific American has pulled my article on the complexity of brain networks out in front of their paywall. Check it out!

Update: Ack! For some people, it seems to be behind a paywall. I'll get it onto carlzimmer.com when I get a chance.

Oldest Homo sapiens fossil? Journalistic vaporware

[image error]I've been baffled by the spread of a non-story over the past couple days, about the supposed discovery of the oldest fossil of our species, doubling the age of our species from 200,000 years to 400,000 years and overturning the generally-accepted idea that Homo sapiens evolved in Africa.

Here's a typical report, from the Associated Press:

Researchers: Ancient human remains found in Israel

JERUSALEM—Israeli archaeologists said Monday they may have found the earliest evidence yet for the existence of modern man, and if so, it could upset theories of the origin of humans.

Got it?

The hook for this story is the publication of a paper in the American Journal of Physical Anthropology. Did the reporters who hyped this story actually look at the paper itself? I have to wonder.

Let me quote a few pieces from it. You tell me where the scientists actually claim they have identified 400,000 year fossil of Homo sapiens.

Here is the abstract (I'll define a few terms and give context afterwards):

This study presents a description and comparative analysis of Middle Pleistocene permanent and deciduous teeth from the site of Qesem Cave (Israel). All of the human fossils are assigned to the Acheulo-Yabrudian Cultural Complex (AYCC) of the late Lower Paleolithic. The Middle Pleistocene age of the Qesem teeth (400–200 ka) places them chronologically earlier than the bulk of fossil hominin specimens previously known from southwest Asia. Three permanent mandibular teeth (C1-P4) were found in close proximity in the lower part of the stratigraphic sequence. The small metric dimensions of the crowns indicate a considerable degree of dental reduction although the roots are long and robust. In contrast, three isolated permanent maxillary teeth (I2, C1, and M3) and two isolated deciduous teeth that were found within the upper part of the sequence are much larger and show some plesiomorphous traits similar to those of the Skhul/Qafzeh specimens. Although none of the Qesem teeth shows a suite of Neanderthal characters, a few traits may suggest some affinities with members of the Neanderthal evolutionary lineage. However, the balance of the evidence suggests a closer similarity with the Skhul/Qafzeh dental material, although many of these resemblances likely represent plesiomorphous features.

These teeth are from a site that's between 400,000 and 200,000 years old in Israel called the Qesem Cave. Archaeologists have been working at the site for years now, bringing forth tools that some kind of hominin was using to cut up meat. Now researchers have found a few teeth from the site, in the older layers.

Hominins–that is, species closer to us than to chimpanzees–left fossils during this period all over the Old World, from South Africa to England to Java. They all clearly belong to our own genus, Homo. They share a number of key traits, including big brains, small teeth, and many other subtler but more diagnostic traits. But which species of Homo do they belong to? Here's where things get tricky. A lot of fossils in East Asia are similar enough to one another that they're considered one species, called Homo erectus. But some fossils from China from this age don't fall so neatly into this group. Are they another species? Are they just an odd subspecies of H. erectus? A firm answer is hard to find.

Over in Europe, hominins first arrived 1.2 million years ago. At 400,000 years ago, the fossil record in Europe includes a species known as Homo heidelbergensis. Among other things, it is the first species known to make wooden spears. Some fossils from Asia and Africa resemble H. heidelbergensis, too.

Now, let's turn the clock forward on each continent…

In Europe, the H. heidelbergensis fossils start to look a lot like Neanderthals. By about 200,000 years ago, the fossil record in Europe contains full-blown Neanderthals.

In Asia, H. erectus holds on 200,000 years ago, although there are other fossils that look like they might belong to H. heidelbergensis.

In Africa, H. heidelbergensis and other hominins give way to the first full-blown Homo sapiens fossils. These are fossils that have a number of different traits that link them clearly to us, and distinguish them from other hominins. (Here are details on two important ones: Omo and Idaltu)

There were probably other lineages of hominins living at the same time as well–such as the Denisovans of East Asia.

What about the region around Israel, where the new teeth come from?

The fossil record offers a picture of hominins evolving in Africa, and pulses of new lineages rolling out through Israel and neighboring regions, and then onward to Europe and Asia. Some 1.4 million years ago, for example, a species of early Homo left fossils in Israel at a site called Ubeidiya. At several sites in and around Israel, paleoanthropologists have found fossils and tools dating back 400,000 to 200,000 years ago–the same period as the Qesem site.  Unfortunately, the fossils are mostly fragments that might belong to a number of different species. The tools are equally ambiguous.

Something really interesting happened later in Israel, between about 130,000 and 50,000 years ago. It appears that Homo sapiens, having evolved in Africa, expanded tentatively into the Near East for the first time.  Fossils of tall, slender Homo sapiens turn up at a site called Skhul/Qafzeh. But then they vanish, replaced for tens of thousands of years by Neanderthals. Only later does Homo sapiens expand again out of Africa, and this time they don't retreat. Instead, it's the Neanderthals that disappear from the Near East, dwindling away to refuges such as Spain before becoming extinct.

The new paper documents the struggle of the scientists to figure out who the Qesem teeth belong to. In some ways, they seem more like Neanderthal teeth. In others, they seem more like the choppers of Homo sapiens, as represented by the Skhul/Qafzeh fossils. The authors tilt towards a relationship with Homo sapiens, but mostly because the teeth are "plesiomorphous." That term refers to a trait the was already present before the origin of a group of species. It does not refer to a trait that closely links all individuals that have it into a single lineage.

Here's a simple example of what this means. Let's say you find a fossil at a site where you had already found dogs and birds. The new fossil has four legs. In that respect, it's more like a dog than a bird.

But it would not make sense for you to conclude that the fossil was a dog. The common ancestor of dogs and birds had four legs, and birds evolved into two-legged animals. But alligators have four legs, too, and they're closer to birds than to dogs. All those four legs really tell you is that the fossil isn't a bird.

The Qesem teeth–in some respects–lack distinctive Neanderthal features. Perhaps they are human. Or perhaps they belong to some other hominin, like a Denisovan.

Here's how the scientists end their paper:

There are three scenarios that might account for the morphological details in the Qesem teeth. The first one is of a local archaic Homo population occupying southwest Asia during the Middle Pleistocene, to which the Qesem specimens would be attributed. Perhaps relevant in this regard, the Qesem lithic assemblages studied to date indicate a local origin, with no evidence of African and or European cultural affinities (Barkai et al., 2005; Gopher et al., 2005; Barkai et al., 2009). Albeit the lack of other diagnostic Middle Pleistocene SW Asian teeth, considering the evidence in its entirety, we believe that the Qesem ''package'' is more Skhul/Qafzeh like, even if some of its features are plesiomorphous.

The second scenario is one of long-term in situ evolution of Neanderthals in southwest Asia. The presence of shoveling and a lingual tubercle in the stratigraphically younger maxillary teeth may be indicating the emergence of the Neanderthal morphological pattern during the Middle Pleistocene in southwest Asia. This would parallel the situation documented in Europe, where the Neanderthal evolutionary lineage has been shown to have roots extending deep into the Middle Pleistocene (Arsuaga et al., 1997; Stringer and Hublin, 1999; Bischoff et al., 2007). Under this scenario, southwest Asia would represent one regional subpopulation within the wider geographic range of the evolving Neanderthal lineage. Nonetheless, the large and well dated samples of fossil humans from Skhul/Qafzeh that post-date the Qesem specimens but predate most of the Neanderthal specimens from the region do not show an accentuation of Neanderthal features.

The third scenario is that more than one Pleistocene human taxon is represented within the Qesem dental sample. The mandibular teeth are stratigraphically deeper (older) but are smaller and lack plesiomorphous features identified in the chronologically later specimens. The differences between these chronologically disparate samples may reflect a population or species level distinction, and may involve population replacement on a local scale.

Resolution of these alternative scenarios must await further discoveries of additional and more complete Middle Pleistocene remains from southwest Asia. Nevertheless, the Qesem specimens represent an important contribution to the growing sample of Pleistocene human fossils from this circum-Mediterranean region of the Old World.

Nowhere in this conclusion do the authors say that these teeth belong to Homo sapiens. Nowhere do they say they have just doubled the age of our species. Nowhere do they say that our species evolved in the Near East, not in Africa. There are only some vague hints that the teeth might be "Skhul/Qafzeh-like." Or they might be something else.

While the paper itself is non-commital in its conclusions, it contains lots of good detail about the teeth, which is why it probably got accepted at the American Journal of Anthropology. Who knows how some reporter got the idea that scientists had discovered the oldest fossils of Homo sapiens. It does seem that one of the authors has played footsie with reporters, offering some tasty quote-bait.

"It's very exciting to come to this conclusion," said archaeologist Avi Gopher, whose team examined the teeth with X-rays and CT scans and dated them according to the layers of earth where they were found.

He stressed that further research is needed to solidify the claim. If it does, he says, "this changes the whole picture of evolution."

The logical thing a reporter should then do is ask, "How exciting can this conclusion be, when you never actually made it in the paper?"

The illogical thing to do is to declare the these teeth could "rewrite the evolutionary history of our species."

[Image: AP Photo/Oded Balilty]