Hanging out with desert kit foxes

What, what time is it? July? Hell.

I have some catching up to do around here.

While I get less threadrupt, if any of you are available for and interested in a G+ hangout with the Desert Kit Fox project I wrote about this morning earlier this week, back in May, we’ll be doing one at 8:15 PM California time today. Dipika Kadaba and her team will be out at a field study area in the gathering dark, demonstrating how they’re using their drone at night to detect kit fox dens using IR videography. We did a dry run last night and it was impressive.

To join, you can check out my profile here.

I’ll post the youtube version after the show. Here it is:

By the way, if you were meaning to contribute to the Desert Kit Fox Project’s Indiegogo fund, you’ve still got four days to do it. And they’re slightly less than halfway to their goal.

The MFAP Hypothesis for the origins of Homo sapiens

I know you’re thinking we’ve had more than enough discussion of one simplistic umbrella hypothesis for the origin of unique human traits — the aquatic ape hypothesis — and it’s cruel of me to introduce another, but who knows, maybe the proponents of each will collide and mutually annihilate each other, and then we’ll all be happy. Besides, this new idea is hilarious. I’m calling it the MFAP hypothesis of human origins, which the original author probably wouldn’t care for (for reasons that will become clear in a moment), but I think it’s very accurate.

A list of traits distinguishing humans from other primates
DERMAL FEATURES
Naked skin (sparse pelage)
Panniculus adiposus (layer of subcutaneous fat)
Panniculus carnosus only in face and neck
In “hairy skin” region:
 – Thick epidermis
 – Crisscrossing congenital lines on epidermis
 – Patterned epidermal-dermal junction
Large content of elastic fiber in skin
Thermoregulatory sweating
Richly vascularized dermis
Normal host for the human flea (Pulex irritans)
Dermal melanocytes absent
Melanocytes present in matrix of hair follicle
Epidermal lipids contain triglycerides and free fatty acids

FACIAL FEATURES
Lightly pigmented eyes common
Protruding, cartilaginous mucous nose
Narrow eye opening
Short, thick upper lip
Philtrum/cleft lip
Glabrous mucous membrane bordering lips
Eyebrows
Heavy eyelashes
Earlobes

FEATURES RELATING TO BIPEDALITY
Short, dorsal spines on first six cervical vertebrae
Seventh cervical vertebrae:
– long dorsal spine
– transverse foramens
Fewer floating and more non-floating ribs
More lumbar vertebrae
Fewer sacral vertebrae
More coccygeal vertebrae (long “tail bone”)
Centralized spine
Short pelvis relative to body length
Sides of pelvis turn forward
Sharp lumbo-sacral promontory
Massive gluteal muscles
Curved sacrum with short dorsal spines
Hind limbs longer than forelimbs
Femur:
– Condyles equal in size
– Knock-kneed
– Elliptical condyles
– Deep intercondylar notch at lower end of femur
– Deep patellar groove with high lateral lip
– Crescent-shaped lateral meniscus with two tibial insertions
Short malleolus medialis
Talus suited strictly for extension and flexion of the foot
Long calcaneus relative to foot (metatarsal) length
Short digits (relative to chimpanzee)
Terminal phalanges blunt (ungual tuberosities)
Narrow pelvic outlet

ORGANS
Diverticulum at cardiac end of stomach
Valves of Kerkring present in small intestines
Mesenteric arterial arcades
Multipyramidal kidneys
Heart auricles level
Tricuspid valve of heart
Laryngeal sacs absent
Vocal ligaments
Prostate encircles urethra
Bulbo-urethral glands present
Os penis (baculum) absent.
Hymen
Absence of periodic sexual swellings in female
Ischial callosities absent
Nipples low on chest
Bicornuate uterus (occasionally present in humans)
Labia majora

CRANIAL FEATURES
Brain lobes: frontal and temporal prominent
Thermoregulatory venous plexuses
Well-developed system of emissary veins
Enlarged nasal bones
Divergent eyes (interior of orbit visible from side)
Styloid process
Large occipital condyles
Primitive premolar
Large, blunt-cusped (bunodont) molars
Thick tooth enamel
Helical chewing

BEHAVIORAL/PHYSIOLOGICAL
Nocturnal activity
Particular about place of defecation
Good swimmer, no fear of water
Extended male copulation time
Female orgasm
Short menstrual cycle
Snuggling
Tears
Alcoholism
Terrestrialism (Non-arboreal)
Able to exploit a wide range of environments and foods

RARE OR ABSENT IN NONHUMAN PRIMATES:
Heart attack
Atherosclerosis
Cancer (melanoma)

First, the author of this new hypothesis provides a convenient list of all the unique traits that distinguish humans from other primates, listed on the right. It falsely lists a number of traits that are completely non-unique (such as female orgasm and cancer), or are bizarre and irrelevant (“snuggling”, really?). It’s clearly a selective and distorted list made by someone with an agenda, so even though some items on the list are actually unusual traits, the list itself is a very poor bit of data.

But set those objections to the list aside for a moment, and let’s consider the hypothesis proposed to explain their existence, the MFAP Hypothesis of Eugene McCarthy, geneticist. I will allow him to speak for himself at length; basically, though, he proposes that the way novel traits appear in evolution is by hybridization, by crosses between two different species to produce a third with unique properties.

Many characteristics that clearly distinguish humans from chimps have been noted by various authorities over the years. The task of preliminarily identifying a likely pair of parents, then, is straightforward: Make a list of all such characteristics and then see if it describes a particular animal. One fact, however, suggests the need for an open mind: as it turns out, many features that distinguish humans from chimpanzees also distinguish them from all other primates. Features found in human beings, but not in other primates, cannot be accounted for by hybridization of a primate with some other primate. If hybridization is to explain such features, the cross will have to be between a chimpanzee and a nonprimate — an unusual, distant cross to create an unusual creature.

For the present, I ask the reader to reserve judgment concerning the plausibility of such a cross. I’m an expert on hybrids and I can assure you that our understanding of hybridization at the molecular level is still far too vague to rule out the idea of a chimpanzee crossing with a nonprimate. Anyone who speaks with certainty on this point speaks from prejudice, not knowledge.

Let’s begin, then, by considering the list in the sidebar at right, which is a condensed list of traits distinguishing humans from chimpanzees — and all other nonhuman primates. Take the time to read this list and to consider what creature — of any kind — it might describe. Most of the items listed are of such an obscure nature that the reader might be hard pressed to say what animal might have them (only a specialist would be familiar with many of the terms listed, but all the necessary jargon will be defined and explained). For example, consider multipyramidal kidneys. It’s a fact that humans have this trait, and that chimpanzees and other primates do not, but the average person on the street would probably have no idea what animals do have this feature.

Looking at a subset of the listed traits, however, it’s clear that the other parent in this hypothetical cross that produced the first human would be an intelligent animal with a protrusive, cartilaginous nose, a thick layer of subcutaneous fat, short digits, and a naked skin. It would be terrestrial, not arboreal, and adaptable to a wide range of foods and environments. These traits may bring a particular creature to mind. In fact, a particular nonprimate does have, not only each of the few traits just mentioned, but every one of the many traits listed in th sidebar. Ask yourself: Is it is likely that an animal unrelated to humans would possess so many of the “human” characteristics that distinguish us from primates? That is, could it be a mere coincidence? It’s only my opinion, but I don’t think so.

Look at the description of the putative non-primate parent in the last paragraph above. What animal are you thinking of? It’s probably the same one McCarthy imagined, which is why I’ve decided that this explanation for human origins must be called the Monkey-Fucked-APig hypothesis, or MFAP for short.

Let’s be perfectly clear about this. McCarthy’s hypothesis is that once upon a time, these two met and had sex,

angrypigangrychimp

And that they then had children that were…us.

That’ll learn me. I thought this South Park clip was a joke.

One thing that struck me in reading McCarthy’s claim is how they are so similar to the claims of the soggy ape fans — they even use the very same physiological and anatomical features to argue for their delusion. For instance, I’ve read aquatic ape proponents’ arguments that the shape of our nose is adaptive for streamlining and for preventing water from flowing into the nostrils while propelling ourselves forward through the water…but compare that to the MFAP.

Neither is it clear how a protrusive cartilaginous nose might have aided early humans in their “savannah hunter lifestyle.” As Morris remarks, “It is interesting to note that the protuberant, fleshy nose of our species is another unique feature that the anatomists cannot explain.” This feature is neither characteristic of apes, nor even of other catarrhines. Obviously, pigs have a nose even more protuberant than our own. In a pig’s snout, the nasal wings and septum are cartilaginous as ours are. In contrast, a chimpanzee’s nose “is small, flat, and has no lateral cartilages”. A cartilaginous nose is apparently a rare trait in mammals. Primatologist Jeffrey Schwartz goes so far as to say that “it is the enlarged nasal wing cartilage that makes the human nose what it is, and which distinguishes humans from all other animals.” The cartilaginous structure of the pig’s snout is generally considered to be an “adaptation” for digging with the nose (rooting). Rooting is, apparently, a behavior pattern peculiar to pigs. Other animals dig with their feet.

Point, MFAP. Of course, just as I would point out to aquatic ape people, we do have an explanation for the nose: recession of the facial bones associated with reduced dentition, along with retention of the bones associated with the respiratory apparatus. The protuberant nose is simply a ridge made apparent by the receding tide of our chewing apparatus. McCarthy uses evidence as badly as does every wet ape fan.

Now, why won’t this hybridization claim work? Well, there are the obvious behavioral difficulties, even if it were cytogenetically possible. We’d have to have pigs and chimps having sex and producing fertile offspring, and those human babies (remember, this is a saltational theory, so the progeny would have all the attributes of a third species, ours) would have to be raised by chimps. Or pigs. I don’t think either is a reasonable alternative, and a band of chimps would probably be no more charitable to a helpless fat blob of a baby than Mr Wu’s pigs.

However, no one reasonably expects pigs and chimps to be interfertile. The primate and artiodactyl lineages have diverged for roughly 80 million years — just the gradual accumulation of molecular differences in sperm and egg recognition proteins would mean that pig sperm wouldn’t recognize a chimpanzee egg as a reasonable target for fusion. Heck, even two humans will have these sorts of mating incompatibilities. Two species that haven’t had any intermingling populations since the Cretaceous? No way.

pig-chimp_lca

But further, even if the sperm of one would fuse with the egg of another, there is another looming problem: chromosome incompatibilities. Pigs have 38 chromosomes, chimpanzees have 48. Cells are remarkably good at coping with variations in chromosome number, and even with translocations of regions from one chromosome to another; and further, pigs and people even retain similar genetic arrangements on some of their chromosomes. There are pig chromosomes that have almost the same arrangement of genes as a corresponding human chromosome.

But there are limits to how much variation the cell division machinery can cope with. For instance, with fewer chromosomes than we primates have, that means you need to line up multiple primate chromosomes to match a single pig chromosome (this pairing up is essential for both mitosis and meiosis). Look at pig chromosome 7, for instance: it corresponds to scrambled and reassembled bits of human chromosomes 6, 14, and 15.

Blocks of conserved synteny between pig and human. (a) Pig SSC7 to human chromosomes 6, 14 and 15. (b) HSA13 compared to pig chromosome 11. Block inversions between pig and human are denoted with broken lines. Contig coverage is depicted by bars in the center of SSC7 and HSA13.

Blocks of conserved synteny between pig and human. (a) Pig SSC7 to human chromosomes 6, 14 and 15. (b) HSA13 compared to pig chromosome 11. Block inversions between pig and human are denoted with broken lines. Contig coverage is depicted by bars in the center of SSC7 and HSA13.

Maybe that would work in mitosis within the hybrid progeny — you’d have three chromosomes from the human/chimp parent twisted around one chromosome, but they would be able to pair up, mostly, and then separate to form two daughter cells. But meiosis would be total chaos: any crossing over would lead to deletions and duplications, acentric and dicentric chromosomes, a jumble of broken chromosomes. That would represent sterile progeny and an evolutionary dead end.

But we wouldn’t have to even get that far. Human and chimpanzee chromosomes are even more similar to one another, and there are no obvious chromosomal barriers to interfertility between one another. If hybridization in mammals were so easy that a pig and a chimp could do it, human-chimp hybrids ought to be trivial. Despite rumors of some experiments that attempted to test that, though, there have been no human-chimp hybrids observed, and I think they are highly unlikely to be possible. In this case, it’s a developmental problem.

For example, we have bigger brains than chimpanzees do. This is not a change that was effected with a single switch; multiple genes had to co-evolve together, ratcheting up the size in relatively incremental steps. So you could imagine a change that increased mitotic activity in neural precursors that would increase the number of neurons, but then you’d also need changes in how those cells are partitioned into different regions, and changes in the proliferation of cartilage and bone to generate a larger cranium, and greater investment in vascular tissue to provide that brain with an adequate blood supply.

Development is like a ballet, in which multiple players have to be in the right place and with the right timing for everything to come off smoothly. If someone is out of place by a few feet or premature by a few seconds in a leap, the dancers could probably compensate because there are understood rules for the general interactions…but it would probably come off as rough and poorly executed. A hybrid between two closely related species would be like mixing and matching the dancers from two different troupes to dance similar versions of Swan Lake — everything would be a bit off, but they could probably compensate and muddle through the performance.

Hybridizing a pig and a chimp is like taking half the dancers from a performance of Swan Lake and the other half from a performance of Giselle and throwing them together on stage to assemble something. It’s going to be a catastrophe.

But here’s the deal: maybe I’m completely wrong. This is an experiment that is easily and relatively cheaply done. Human sperm is easily obtained (McCarthy probably has a plentiful supply in his pants), while artificial insemination of swine is routine. Perhaps McCarthy can report back when he has actually done the work.


Humphray SJ, Scott CE, Clark R, Marron B, Bender C, Camm N, Davis J, Jenks A, Noon A, Patel M, Sehra H, Yang F, Rogatcheva MB, Milan D, Chardon P, Rohrer G, Nonneman D, de Jong P, Meyers SN, Archibald A, Beever JE, Schook LB, Rogers J. (2007) A high utility integrated map of the pig genome. Genome Biol. 8(7):R139.

Last chance for the soggy apes

I’m getting more than a little tired of the long-running wrangle on the wet ape hypothesis thread. I’m closing it and opening a new thread here, with a few rules:

  • No more pointless dismissals of comments from either side as mere opinion or evidence-less, even if they are.

  • Absolutely NO copy-pasting of arguments from other sites. If you’re not going to engage in conversation, but just want to unthinkingly recite rote claims from elsewhere, go away. That will be considered a bannable offense in this thread.

  • If you want to reply to a previous comment, actually reply to it. That involves thinking about and addressing the points in that comment. That means actually backing up your claims with evidence.

  • You’ve got one page of comments to do it all in. If this thread hits 500 comments, I’m simply closing it. You’re done.

  • If you try to run out the clock and spew lots of itty-bitty repetitive posts, I will ban you.

  • If you just snipe and run, I will delete your comment. So be substantive, or shut up.

OK? OK. Go to it.

I expect this thread will promptly die now that the obtuse and refractory proponents of paleontological nonsense are prohibited from regurgi-posting and are expected to actually have a dialog about the evidence. They may surprise me, but they probably won’t.

Besides, Space Ape Rules.

It’s a species-wide problem!

The results of a world-wide analysis of violence against women reveals that it’s common, it’s widespread, and it’s serious.

Three in ten women worldwide have been punched, shoved, dragged, threatened with weapons, raped, or subjected to other violence from a current or former partner. Close to one in ten have been sexually assaulted by someone other than a partner. Of women who are murdered, more than one in three were killed by an intimate partner.

These grim statistics come from the first global, systematic estimates of violence against women. Linked papers published today in The Lancet and Science assess, respectively, how often people are killed by their partners and how many women experience violence from them. And an associated report and guidelines from the World Health Organization (WHO) in Geneva, Switzerland, along with the London School of Hygiene and Tropical Medicine and the South African Medical Research Council in Pretoria, estimates how often women suffer sexual violence from someone other than a partner, gauge the impact of partner and non-partner violence on women’s health and advise health-care providers on how to support the victims.

We’re thinking beings, and we’re aware of the problem (although a lot of people are in denial) — we ought to be able to change this behavior. And speaking as a biologist, it would be an interesting change, shifting the intra-specific social dynamics in powerful ways that would affect the course of our future evolution. Come on, who doesn’t want to do an experiment on our own species? Especially one that reduces fear and increases security?

(via August Berkshire)

Obama says weasel words

Wasn’t it nice of Obama to say a few words about the environment yesterday?

President Barack Obama said Tuesday that the proposed Keystone XL pipeline project from Canada to Texas should only be approved if it doesn’t worsen carbon pollution.

The $7 billion pipeline has become a contentious issue, with Republicans touting the jobs it would create and demanding its approval and environmentalists urging the Obama administration to reject it, because it would carry carbon-intensive oil from Canadian tar sands to the Texas Gulf Coast.

"Allowing the Keystone pipeline to be built requires a finding that doing so would be in our nation’s interests," Obama said in a speech on climate change at Georgetown University. "Our national interest would be served only if this project does not significantly exacerbate the problem of carbon pollution."

So of course the Keystone XL pipeline will be immediately shut down, because of course building a leaky, fault-prone pipe full of toxic sludge across the country to further feed our appetite for burning carbon based fuel will exacerbate the problem of carbon pollution.

You mean he hasn’t shut it down?

I’m betting he’s going to wait for some industry-funded committee to issue a piece of paper with a few token concessions, and then announce that his requirements have been met: “Why, yes, we’ve got this big dirty pipe gurgling petroleum into the nation’s fuel tank, but that doesn’t mean we’re going to burn it.”

>

It’s summer head-asplodey time!

Gang, don’t try this at home. I’m a trained professional, so I can get away with it, although I do face extreme risk of brain damage.

I am reading two books at once. OK, that part isn’t too scary, I’m actually just alternating between the two — an hour with one at lunch time, an hour or two with another before bed. I trust you all are able to do this, no problem.

It’s the pairing that is the killer. In one corner, I’m reading the marvelously detailed, juicy, thought-provoking The Cambrian Explosion: The Construction of Animal Biodiversity by the highly regarded scientists, Erwin and Valentine. In the other corner, the tedious and misleading Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design by the highly self-regarded philosopher and creationist apologist, Stephen Meyer.

Some would say I’m mad to do this; others would say the shock of the combination will drive me mad. They are both right, I fear.

I’m only a few chapters into each so far. The Erwin & Valentine book is terrific — a bit dense and technical, but full of the right stuff. I’m learning a great deal; it starts with material I’m not at all familiar with, the geochemistry of the pre-Cambrian. The point is to set the stage, to explain the environment in which the Cambrian explosion will occur, and also most importantly, to explain how scientists know what the world was like between a billion and 500 million years ago.

It also discusses real controversies and real science. For example, there was a world-wide shift in ocean and atmospheric chemistry during this period: was it primarily an abiotic process, or did the expansion of bacterial forms and the emergence of multicellular life contribute significantly?

We haven’t even gotten to the fossils yet, let alone the biology! I’m appreciating the education, though — the story simply cannot be understood without this background material. It’s also fueling an interest in, of all things, geology. I may have to read more about this subject.

The Meyer book, on the other hand…maybe it’s best that I am reading it in conjunction with some real science. The contrast is jarring and enlightening.

The first bit of this book is an extended whine about how no one understood his last book, Signature in the Cell, which was another gloppy bit of tripe from a mediocre mind with a magnificent ego. That book was entirely about the origin of life, he says, and how it’s impossible to create new information with undirected processes; everyone thought it was about how undirected processes can add information to existing organisms, but it wasn’t, and this new book about the Darwin’s Doubt and the Cambrian explosion is the one that is going to show that’s impossible, too. So he begins by repetitively reciting the same bogus assertions he made in his previous book.

The type of information present in living cells — that is, “specified” information in which the sequence of characters matters to the function of the sequence as a whole — has generated an acute mystery. No undirected physical or chemical process has demonstrated the capacity to produce specified information, starting from “purely physical or chemical precursors”. For this reason, chemical evolutionary theories have failed to solve the mystery of the origin of first life—a claim that few mainstream evolutionary theorists now dispute.

Simply rebutted: random peptides exhibit catalytic activity. There’s a process that starts from “purely physical or chemical” precursors and uses the information defined by the sequence of amino acids to produce a naturally selectable function. And I’m sorry, but what is an example of a non-physical, non-chemical process in biology?

Are we done yet?

Of course not. Meyer is going to drool out a few hundred pages of drivel that will only convince the gullible, the ignorant, and the already dedicated creationists. There is not one bit of substance in the book so far; just rehashed Intelligent Design creationist talking points. This “specified information” of which he speaks is undefined and unmeasurable — it’s the phrase they flap at anyone who challenges their claim of have concrete evidence against evolution.

Meyer then dives into more misleading statements, such as that the Cambrian biota just erupted abruptly into the fossil record, with no precursors — surely you don’t expect a creationist to explain the geological and biological context of the pre-Cambrian/Cambrian, as Erwin and Valentine do? That would take work and knowledge, which Meyer lacks. Nick Matzke at the Panda’s Thumb has torn into the superficiality and wrongness of Meyer’s arguments already — go read that if you want to see ID arguments taken down a notch.

Otherwise, wait a bit and somewhere in my looming frantic schedule I’ll be reading deeper into The Cambrian Explosion…and I see that the next section is titled “The Record of Early Metazoan Evolution”. I think I’ll trust Ervin and Valentine’s competence over Meyer’s religiously driven ignorance.

If this combo does not hurl me down the stairs of madness into the abyss of total chaotic brain-scrambling, there’s a third book gazing ominously at me from the bookshelf. I’ve been asked to consult with Tony Ortega, who runs an anti-scientology website on a public evisceration of Scientology: A History of Man by L. Ron Hubbard. It’s a “cold-blooded and factual history of your last 76 trillion years” — it contains Scientology’s version of evolution. I’m pretty sure I’ll be curled into a fetal ball, gibbering, by August.

Misandry In Teh Animule Kingdom!!!!7!

Misandry, polyandry, whatever. I know it’s some kind of -andry. Hordeling Ron Sullivan and her partner in crime Joe Eaton have been spending a lot of time in the San Joaquin Valley of late, and Joe has a new post up on Ron’s blog riffing on their recent frequent sightings of Swainson’s hawks. It turns out that the hawks engage in behavior that completely undermines the traditional institution of marriage as Gahd intended:

Polyandry, it seems, is not that unusual in buteos and related hawks. It’s more or less standard for the Galapagos hawk, which genetic studies indicate is the Swainson’s closest relative. (The i’o or Hawai’ian hawk is also near kin. Swainson’s is typically a long-distance migrant, with most of the population traveling from the North American plains to the Argentine pampas every year. You can see how accidental colonization of remote islands might happen.) Polyandrous mating groups also occur in the more distantly related Harris’s hawk. The advantage? Male raptors often provide prey for their incubating mates and nestlings. A female with two male providers would have a better chance of successfully fledging her brood.

The MRAs were right all along: it’s all about the child support. How dare those ladyhawks go against biology? Don’t they understand about gathering berries?

Anyway, it’s a good post by a longtime favorite natural history writer. And the post title proves that Parentheses Matter.

Speaking of people writing good stuff at the Coyot.es Network, we’ve added two new blogs over there: “InyoOwnWay” by Owens Valley biologist Mike Prather and “Miracle or Mirage?” by renewable energy maven Patrick Donnelly-Shores. We’ve got another new addition pending once she answers her email.