Tag Archives: biology

Four Stone Hearth #101 – The Phoenix Edition


This is the Phoenix edition of the Four Stone Hearth.  It’s 100th installment saw the relinquishing of power of the original editor in chief, Martin Rundkvist of aardvarchaeology.  I want to extend my thanks to Martin for turning the Four Stone Hearth into the shining example of what is possible with a Blog Carnival.

We now have a new head-honcho, Aferensis.  Most readers will know him, and know he’ll do a great job at keeping the flame burning for a long time coming.

We’re heading into a new age, and it seems like it is appropriate that this is the 101’st edition.   It’s been speculated that Blog Carnivals are going out of fashion – as evidenced by the demise of a few great ones like The Tangled Bank and The Skeptics Circle.

I think, however, that the blog carnival has an important place in the dissemination of science information to the general reading public.  If nothing else, it provides a hub through which lots of great info can be read that might not have crossed ones radar.  But, it also is a way for bloggers to interact, have fun, and keep the flame of science blogging burning bright – no small issue since most science bloggers are not paid for their blogging.

So, with that in mind here’s the 101’st collection of great blog posts in anthropology:

We’ll start with a hat tip to the previous editor of this blog carnival, Martin Rundkvist, with Archeology 101: Chronology, or, How Can I Get a Date? A good chunk of Creationists base their refusal to believe in human evolution on their total lack of understanding of how scientists date things.  Martin breaks it down for us.

Over at Athropology.net we have a post entitled, “A Curious Look At The 3.39 Million Year Old “Stone Tool Markings” From Dikika, Ethiopia.”  Here’s a quote:

I don’t know who this is worse for, the editors & reviewers over at Nature or the authors of the article who can’t tell the difference between crocodile teeth markings and stone tool modification.

Them sounds like fightin’ words!

You think your neighborhood is bad?  Welcome to Texas:

The family says their dog scared up the monkey under the backyard patio and the creature then chased the woman into her garage – trapping her for over an hour.

Bonvito has two posts.  The first discusses the counterintuitive idea that male primate rank has little to do with reproductive success:

Rhesus females also prefer novel males for mating. This female mate selection is thought to be one of the primary factors why males migrate out of their natal group. The migrating males, who are at the very bottom of the hierarchy, have to be in constant high alert, especially so during the mating season when high ranking males are on guard (i.e., those who are on top are particularly protective of their position on this period).

The second is about Jane Goodall’s connection with Gary Larson’s Far Side.  Is the famous primatologist able to take a joke?

One of the biggest mistakes we make as humans is our tendency to glorify the past and sanitize it.  For instance, we look up to Napoleon and Caesar and totally ignore the horrific violence and death they caused in their selfish pursuits of power.  Judith of Zenobia: Empress of the East takes a hard look at the Peloponnesian War and it’s consequences. A quote:

The bodies of the dying were heaped one on top of the other, and half-dead creatures could be seen staggering about in the streets or flocking around the fountains in their desire for water.

Anthropology is not just about long dead people or exotic tribal societies in Africa.  It’s also about modern cultures and modern living.  Krystal D’Costa, of Anthropology in Practice, has a post about the struggle of keeping the faith during Ramadan and still running a successful food cart business.

While many Muslims choose to slow down during this period, for those who make their livelihood as food cart vendors, it can present a personal challenge: They are surrounded by foods that they themselves cannot eat all day long. It creates a challenge for the individual, but also for the business as they have to rely on sight and smell to gauge flavors

She also has a great post about the odd fact that Nescafe is so popular in coffee producing countries!

… why does Nescafe seem to be popular among coffee producing countries that theoretically have access to their own supply of coffee beans? Anthropologist Kevin Birth offered some suggestions that cover the expenses associated with grinding and brewing beans, but today we’ll look a bit more closely at the relationship between local consumption and consumer identity.

You think the life of an Archaeologist is easy?  Watch out for moose! Magnus Reuterdahl of Testimony of the Spade gives us a glimpse into his world.

For those who don’t know, Eric Michael Johnson, formally of the Primate Diaries on ScienceBlogs.com, is in exile.  Well … he’s in blogging exile.  And he decided he was going to go on tour.  His most recent stop is at Anthropology in Practice where he talks about the cultural divides of Myspace and Facebook, functional racism, and class. Great stuff.

In the wake of many teens departure Boyd describes what was left behind as the formation of a digital ghetto. Abandoned Myspace profiles “often fell into disrepair, covered in spam, a form of digital graffiti [as] spammers took over like street gangs.” In contrast, Facebook was seen as a virtual gated community with the “same values signaled by the suburbs.” The class bias represented in this was extremely telling in 2009 when Facebook and Myspace converged with roughly equal numbers of visitors. A New York Times story about this convergence was titled “Do You Know Anyone Still on Myspace?” This confession by the author is extremely revealing. Given data showing equal traffic his preference was to make assumptions based on his network of friends, a trend that is likely to be pervasive throughout the mainstream media on stories that are much more important.

A Primate of Modern Aspect has a piece about ape sex, the human inability to stay objective, and evolutionary psychology.

Here’s the thing that gets me all riled up when I read these sorts of op-eds: Lots of people study primate sexuality.  It’s a fascinating field.  And who the primates are having sex with is only part of the fun.  We know about stress, group dynamics, cognition, and general evolutionary theory because of the good, hard work of these people who are driven by curiosity. But for some reason, the only time primate sexuality gets any attention is when we turn it into a debate about how humans should be having sex.

We never say, “Hey, those muriquis are too promiscuous.  Don’t they know that all of their close evolutionary cousins are polygynous?  If they just did what came naturally to them, they’d have a lot less psychological stress.”  Or, “Those gibbons are so sexually repressed.  If they just gave in to their natural predilection for promiscuity, I bet those nasty gibbons would have fewer territorial disputes and gibbon society would be much more peaceful.”

Help! These Baboons need a name.

A Hot Cup of Joe deconstructs the PseudoArchaeology of Glenn Beck.

It should be no surprise that, since he has little grasp on the rest of reality, that Glenn Beck would fare any better at understanding archaeology.

Anna of Anna’s Bones adds the third installment to her “Stripped” series:

I felt the blood rush towards my head. Everything was upside down. I adjusted my hands according to yoga instructions I had been given many years ago – “you have a very long back” I had been told. I tilted my head to the side to meet 50 pairs of very confused eyes staring intently at me… I was, after all, doing downward dog in a Paleoanthropology workshop.

In DIY Knapping, at A Very Remote Period Indeed, we get a nice video showing how hard this practice really was.

Kris Hirst discusses Gary Feinman’s photo essay on About.com on a Regional Survey in China:

Mick Morrison has a post about the teaching of Archaeology, digital learning, and blogging (rather relevant to a blog carnival, I dare say!).

Finally, here is a picture of John Hawks, a Paleoanthropologist who clearly loves his job:

Clash of the Titans: Mature vs New Science


John Hawks takes a paragraph of a new book by William Burroughs, “Climate Change in Prehistory,” and runs with it.   It has to do with the clash between mature sciences and emerging new sciences.  Here’s the paragraph Hawks refers to:

It is often easier to write with confidence on fast-developing and relatively new areas of research, such as climate change and genetic mapping, than to review the implications of such new developments for a mature discipline like archaeology. Because the latter consists of an immensely complicated edifice that has been built up over a long time by the painstaking accumulation of fragmentary evidence from a vast array of sources, it is hard to define those aspects of the subject that are most affected by results obtained in a completely different discipline. Furthermore, when it comes to many aspects of prehistory, the field is full of controversy, into which the new data are not easily introduced. As a consequence, there is an inevitable tendency to gloss over these pitfalls and rely on secondary or even tertiary literature to provide an accessible backdrop against which new developments can be more easily projected (Burroughs 2005:10).

Hawks makes the point that this paragraph’s suggestion that a new science in facing resistance from an entrenched mature science can lead to one of two possible conclusions

1. … and therefore the simple conclusions of the immature sciences may be wrong.


2. … and therefore those wishy-washy archaeologists had better get their act together.

He comes to the defense of (what he calls) the mature science of archaeology.  In this defense he points out …

What marks a "mature" discipline is the emergence of informed critiques focused on the limits of methods of analysis. When archaeology was immature, before the 1950s or so, almost all archaeologists were simple (some say "naive") positivists. They excavated and found the traces of ancient people, just as today’s archaeologists do. And what they found was what there must have been. Find a handaxe, you know people made handaxes; find a temple, you know they worshipped gods of some kind. Dig in a mound, find a grave, you know that the people had rituals associated with death that required substantial non-subsistence directed labor.

Notice his definition of “mature”:  An emergence of informed critiques, focused on the limits of methods of analysis.  This isn’t a horrible definition (I’ll argue for a different one below).  He goes on:

Of course, today’s archaeologists tend to be positivists, too. There’s no sense twiddling around with hypotheses that will never be testable. The religion of Neandertals? Well, it’s one thing to speculate about it, but the fact is that it’s devilishly hard to test hypotheses about religion from the material remains of any pre-monumental culture. In the absence of information, we may as well stick to the facts.

But there’s a deeper sense in which archaeologists have a much more complicated view of their evidence. Archaeology has gone through many periods where different researchers developed and applied distinctive analytical techniques. These techniques have often been incommensurable. Sometimes they settle debates. For example, the systematic study of skeletal element representation and cutmark taphonomy has gone far toward testing (and verifying) the occurrence of hunting in some Early Pleistocene contexts. The hunting versus scavenging debate still goes on, with renewed emphasis on active or confrontational scavenging. But knowledge advanced by means of analytical critique.



What is a “Mature” Science?

Now, I don’t want to sound like a curmudgeon, but I would never call Archeology a mature science.  At least not by my definition (which I’ll outline in a second).  It is an adolescent science, albeit an exciting one on the verge of maturity. 

I define a field to be "mature" if and only if it has a reasonably well developed empirical AND theoretical side.  Without both, you are only half a science.   

(OK, I used the ambiguous word "reasonably" in my definition.  And this opens the door for questions about what we mean by that.  But, that’s the way laws should be written – with room for interpretation.)

I’ve found most people I talk to about this (in the sciences) to be rather hostile to my definition.  I suspect the reason is that if we take it to be strict, there is only ONE mature science – Physics.  (I include engineering in physics as applied-physics, the way that we include medicine in biology as applied-biology.)  The reason is that it is the only science that has serious mathematics and theoretical work being done “in house”.  They don’t rely on Mathematicians to do the hard labor for them.  There IS great work being done on the theoretical side of a lot of other sciences, but nearly all of it is done by Mathematicians and Physicists. 

Let’s go into more detail as to what I mean in my definition:

Empirical Science


The empirical side of science is what everyone thinks of when they think of science.  That is, when YOU think “science”, I’m guessing that you’re thinking of guys in white lab coats pouring boiling blue liquid into a beaker.  This side of science is well developed in nearly every field save for economics (that’s a whole different discussion – and a strange one at that). 

This side of science is all about hypothesis testing, data collection, and statistical and other methods to deal with the vast amount of data that is gathered.  That is, this is the “get your hands dirty” part of science.  It’s why most people who go into science went in to it in the first place.  They loved all that went with it.  Primatologists love to hang out with primates, Chemists love to mix chemicals, Archaeologist love to dig in the dirt. 

As I discussed in my article on Karl Popper, a science must have a robust empirical side in order to test hypothesis.  Without it, we have no way to know if we’re just blowing smoke or not.

What most sciences don’t have (and some refuse to take seriously) is a serious theoretical side of their field. 

Theoretical Science


Theoretical Science is all about hypothesis generating.  Darwin’s theory of natural selection is an example of a work of theoretical science.  Einstein was a theoretical physicist, and the theory of relativity is a work of theoretical science also. 

As a field gets more developed, theoretical science converges more and more toward mathematical and computational work.  That is, the models become so complicated that only the tools of mathematics and computer science are able to deal with them.

Don’t get this confused with statistics.  We need complex statistical models to deal with the data collected by empirical scientists.  But, theoretical scientists don’t deal with data – at all.  Sure, they may be inspired by data.  But, the point is that they are developing theories about how the world works that are then able to be tested.    They follow lines of implication – if this is true, then this other thing MUST be true.  It is logical philosophy, mathematics, theorem-proof. 

No science is totally devoid of theory.  Obviously.  Paleoanthropologist gave us the “out of Africa” theory which has proven to be rather robust.  But, no science other than physics has a dedicated “in house” world of theoreticians who’s ONLY job is to follow lines of implications and thereby generate new and diverse hypothesis. 

Theoretical physics predicted Black holes before they were seen on a telescope.  They predict things like an expanding universe.  They predict dark matter, super strings, etc.  All of this is done by physicists who are not passed off by their empirical counterparts as “just” mathematicians, or “arm chair” physicists. 

They do their job with very complex mathematics.  Some times the experimental physicists will prove them right … sometimes wrong.   But, the important point is that they are full fledged members of the physics community. 

In most other sciences, theoretical (and especially mathematical) work is met with skepticism and sometimes outright disdain.  If you do ONLY theoretical work, then you are not really a member of this science at all … you’re a mathematician.  A real scientist DOES something.  They do field or lab work.  They get their hands dirty.  Blah, blah, blah …

Why Are Most Sciences So Hostile to Mathematics, and What Can We do About It?

I suspect the reason why most sciences have been traditionally so hostile to treating mathematical modeling as a serious part of their field is simply because most of the members of that science haven’t ever taken any serious math.  Oh, they may have taken a calculus class or two, but let’s get real.  Calculus is a FRESHMAN level class for math, physics, and engineering students.  There is an entire world of mathematics that comes after that that is hard to describe to people who haven’t seen it (imagine explaining what “red” means to a blind man).

Of course, this is changing.  Chemistry has always been in second place to Physics as the most mathematical of sciences.  They had to be.  Now Biology is catching up.  Theoretical Biology is (in my opinion), hands down, the most exciting emerging field (it’s been emerging for about 25 years).  But, still most of the work is done by math people, not biologists. 

What’s wrong with that?  Why not just let mathematicians do the work, and leave scientists alone to do the dirty stuff?

There are 2 reasons. 

  1. Mathematicians have their own work to do.
  2. Scientists and Mathematicians can’t communicate properly with one another.

First, contrary to popular belief amongst many scientists, Mathematicians are not here to serve you.  Yes, oftentimes they come up with highly useful tools that scientists find they can’t live without.  But, mathematicians generally get into math for its own sake … not because they care so much about furthering some particular science. 

Second, even amongst those mathematicians who DO get in on the action of a particular science, it’s often impossible for them to communicate with the members of said science.  This goes both ways.

Mathematicians are frustrated by the total lack of knowledge of even basic mathematical skill by scientists, and scientists are shocked at how little mathematicians know about the basics of their field. 

What physicists have figured out is that if you train your own theoreticians, then you can train them from the get-go to be able to communicate with the experimenters. They’ll know the big problems in the field, they’ll know the history, the language, the nuts and bolts.  Similarly, they train ALL physicists up to a threshold level of mathematical maturity, even the ones who become experimenters.  This way, everyone can talk to everyone else. 

So far, no other field has ever gotten this right.  They only train empirical scientists.  The only math required is what any advanced high school kid can do.  And as such, the theoretical side of their field is grossly underdeveloped. 

Again, this IS changing.  Most of the hard sciences are making strides fast, but it will take a lot more time. But, because of the reasons outlined above, I can’t call Archaeology a “mature” science. 

Are You Trapped in an Extinction Vortex? Beware of Inbreeding

A new article with a catchy title (I’m a sucker for those) in BMC Evolutionary Biology using the endangered shorebird the southern dunlin (dunlins Calidris alpina schinzii) as an example looks for evidence of why inbreeding and it’s associated loss of genetic variation are causes of extinction. 

I’m not gonna say this article is telling us much that we don’t already know.  But, its refining the reasons why inbreeding has such negative effects by using longer term studies and genetic markers. 

Here’s the abstract: (Bold is mine)

Inbreeding and loss of genetic diversity are expected to increase the extinction risk of small populations, but detailed tests in natural populations are scarce. We combine long-term population and fitness data with those from two types of molecular markers to examine the role of genetic effects in a declining metapopulation of southern dunlins Calidris alpina schinzii, an endangered shorebird.

The decline is associated with increased pairings between related individuals, including close inbreeding (as revealed by both field observations of parentage and molecular markers). Furthermore, reduced genetic diversity seems to affect individual fitness at several life stages. Higher genetic similarity between mates correlates negatively with the pair’s hatching success. Moreover, offspring produced by related parents are more homozygous and suffer from increased mortality during embryonic development and possibly also after hatching.

Our results demonstrate strong genetic effects in a rapidly declining population, emphasizing the importance of genetic factors for the persistence of small populations.

One of the consequences of such a study has to do with conservation.  If we ignore the negative genetic effects of small population size, we are not paying attention to one of the driving factors present in extinction.   That is, as soon as a population gets below a certain threshold in numbers, then the risk of serious inbreeding is imminent.  This only furthers the downward spiral toward extinction. 

The species find themselves in a catch 22.  They need to have a larger population to  lower their incidence of inbreeding.   But, they need to breed more to get that larger population.

Why Biology Needs Mathematical Models

John Hawks reviews Peter Turchin’s 1998 book, Quantitative Analysis of Movement.

I tend to lecture about genetic models, for which there is a great value in simplicity (point 3), but which may require quite complicated extensions to handle reasonable biological populations (point 2). In that connection, some reasonable people go to extremes of interpretation — sometimes claiming that the data necessitate some assumption on the basis of a very simplified model, and in other cases claiming that no model can apply to the complex history of the population. It is our task (my task) to determine which factors are important and conceivably affect results, and which will always be too weak to influence the interpretation of the data (point 1). And the end will often be to discover evidence for values in past human populations for which we have no direct means of estimating aside from genetic variation (point 5).


Makes me want to read.  More here

Evolution in the High School Science Class

John Hawks discusses the trouble with the lack of Evolution teaching in High School Biology classes.

What really does concern me is the absolute minimal amount of time that high school biology courses spend on evolution. Without evolution, biology really lacks any mechanism to talk about cause and variation — dissecting a fetal pig may help show you how the body works, but it can’t show you why different individuals should vary, or why drugs should have different reactions in different people, why genetic disorders shouldn’t happen very often, but why they sometimes happen anyway, why hybrid corn works but hybrid dairy cattle don’t, and why oil just broke $130 a barrel and is still rising. In other words, important stuff — the sort of basic consumer knowledge of biology that we want future citizens to know.

Physics is still searching for its grand unifying theory.  Biology already has it:  Evolution.  To not cover Evolutionary Biology is to pull the spine out of the “why” questions that make biology so interesting.

This is a deep division, which also exists at the university level. There are a large group of “science-friendly” people who do not understand evolutionary biology, and who do not have a practical idea of its importance. These people are without a doubt against teaching creationism in science courses, but they cannot be for evolution except in the most nebulous sense, because they have no more than a nebulous idea of what evolution is. Unfortunately, some professional biologists, geneticists, and other scientists are among this group.