Short, sharp summary

Larry Moran has a simple list of the 5 basics you need to understand about junk DNA. It’s short and sweet; I’d like to see a creationist, who are often weirdly antagonistic to the whole idea of junk DNA, deal with these basic facts before they start ranting against the observations and conclusions.

  1. Genetic Load

    Every newborn human baby has about 100 mutations not found in either parent. If most of our genome contained functional sequence information, then this would be an intolerable genetic load. Only a small percentage of our genome can contain important sequence information suggesting strongly that most of our genome is junk.

  2. C-Value Paradox

    A comparison of genomes from closely related species shows that genome size can vary by a factor of ten or more. The only reasonable explanation is that most of the DNA in the larger genomes is junk.

  3. Modern Evolutionary Theory

    Nothing in biology makes sense except in the light of population genetics. The modern understanding of evolution is perfectly consistent with the presence of large amounts of junk DNA in a genome.

  4. Pseudogenes and broken genes are junk

    More than half of our genomes consists of pseudogenes, including broken transposons and bits and pieces of transposons. A few may have secondarily acquired a function but, to a first approximation, broken genes are junk.

  5. Most of the genome is not conserved

    Most of the DNA sequences in large genomes is not conserved. These sequences diverge at a rate consistent with fixation of neutral alleles by random genetic drift. This strongly suggests that it does not have a function although one can’t rule out some unknown function that doesn’t depend on sequence.

I’m also relieved to see that the anti-junk fanatics tend to gravitate towards Larry’s blog and leave the rest of us mostly alone.


I got up early this morning and rushed over to the lab to suck on tanks — danios lay demersal eggs that sink to the bottom of the tank, and you can just siphon them up — and…nothing but fish poop. I have a sad face. It was probably overly optimistic since we only have a few adults yet and they’ve just been plunked into the system, but I had hopes. They look so happy! (Zebrafish visibly respond to stress by going pale, and as soon as these guys hit the tanks their little stripes were vividly dark blue).

Water quality is good, but now I’m channelling my grandmother and starting to fuss over their diet. They need to eat and get fat and good rich fatty food is just the ticket. We’ve got the brine shrimp hatchery bubbling and those should be ready tomorrow, and I’m going to be giving them a range of tropical fish foods. We will plump these little creatures up so they can give me more than just feces to look at in the morning.

We’ve also ordered a couple of defined wild type lines — at $20/pair, so we expect thoroughbreds — so the colony population should climb soon, which will help. Then, observations and experiments and breeding and colony expansion.

You asked, I deliver the fish porn

Since everyone insisted, here’s a photo of our incipient zebrafish system, built by my student Josh.


What it is is a set of ordinary plastic shelving with some custom built plastic trays to catch water overflow, and then an array of simple 2-3 liter tanks (the smallest size Kritter Keepers, if you must know — you can get them for about $2 each). There is a 110 liter reservoir tank down below, with an immersible pump that can generate a flow of about 1900 gallons/hour, currently greatly throttled down since we only have a few tanks in place. Water is pumped out of the reservoir to two places: 1) towards the ceiling, where the PVC plumbing splits — with valves, we can select to have the water pumped right out to the sink nearby, or to a bypass line that just has the water going up and back down, or in normal operation, to a line that has a big hunk of 3″ PVC pipe packed with bioballs and charcoal for filtering, and 2) to a big bucket of sand for additional filtration. Water is just flowing all over the place here.

Most importantly, the main outflow line is tapped in 3 spots to some irrigation hose leading to six of these nifty little widgets that provide a trickle of water out nine smaller drip lines, which lead to the fish tanks. It’s amazing what you can find in hydroponics gear. If ever Minnesota legalizes marijuana, I could also cycle fish water (mmm, rich & tasty fish poop) into racks of plants and pay for all this stuff.

Here’s a quick and dirty diagram if that explanation doesn’t help. Not that the cartoon will necessarily help, either. Blue circles are valves. Arrows indicate the direction of water flow.


It’s been running for a couple of weeks solid with no problems (I wish I could say the same for the backup system we set up yesterday, which blew gaskets all over the place and made a mess overnight), so we’ve actually put a few fish in there. With any luck, we’ll have embryos this week!

Next phase begins!

We think our fish facility is complete now. We have run it through the fishless cycling process. Now I have to drive 60 miles to get some cheap pet store danios to give it the live test, so I’m going to be offline for a bit.

Once those are thriving and we’re totally confident that everything is going to work, we’ll be ordering a bunch of defined strains and raising those up…and doing our preliminary baseline analyses on the embryos. It’s progress! Science marches on!

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
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

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

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
– 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

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.
Absence of periodic sexual swellings in female
Ischial callosities absent
Nipples low on chest
Bicornuate uterus (occasionally present in humans)
Labia majora

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

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

Heart attack
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,


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.


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.