… is written in our genes. The following was posted in a comment on Pharyngula (a popular science blog) in response to a lone creationist who decided to brave the ire of a thousand snarky science geeks in the spirit of "open debate". It is reproduced here with the kind permission of the author (who posts as Ein Sophistry and currently has no site for me to link to).

Humans and chimpanzees share around 98% of their DNA. Now, it may be (and has been) argued that common genes reflect merely common function, common features designed (intelligently) for common environments. The first and easiest point to make against this claim is simply that common function needn’t at all require common materials. A bird’s wing and a butterfly’s wing arise during development from different tissue and have different genetic underpinnings, but both enable the organism to stay aloft and get around adequately. Biologists make a distinction between homology and analogy, where the former refers to structures that arise from common embryonic tissue and the latter to structures that serve a common function. The posited argument from common function can only explain structures which are both homologous and analogous; it cannot account for non-homologous analogs like the aforementioned wings or non-analogous homologs (structures which develop from the same tissue but serve different functions) such as bird wings and our arms or the fins of a fish. Further, it is difficult for this explanation to make sense of the fact that chimpanzees have more DNA in common with us than with gorillas, though gorillas share the chimpanzees’ forested environment while we are generally savannah creatures. The doctrine of common function would seem to predict that cetaceans (dolphins, porpoises, whales) would have more genetic material in common with, say, sharks than with the ruminants from which they are thought by biologists to be descended. While I don’t know if any representative genomes from these three types of organisms have been fully sequenced yet, I can’t imagine that many people would place any money on the shark.

But there is a much more powerful counter-argument to the doctrine of common function. It concerns what’s come to be called "junk DNA." The vast majority of our genome is in fact never read, never translated into proteins. It serves no function, at least none specified by a nucleotide sequence. There would be no reason, then, to expect commonalities in nucleotide sequence between the junk DNA of apes and that of humans. Troublingly, such commonalities do in fact exist and I will explain a few of those so far discovered.

There are two types of junk sequences I want to talk about here: retrogenes and pseudogenes. Retrogenes are sequences from retroviruses which have been inserted into the host’s genome. As you may recall, viruses cannot reproduce on their own; they must use the host’s replication machinery. When a virus inserts itself into a coding region of DNA, the host cell begins to manufacture copies of the virus, which will eventually burst through the cell and go on to infect its neighbors in similar fashion. Another, less destructive, way for a virus to get copied, though, is to insert its genome into a non-coding region of the host’s DNA. It becomes effectively a part of the host’s genome and is copied along with it prior to each cellular division. Now, for this virus to be passed on to the next generation, it must infect the gametes (sex cells), or the embryological precursors thereof. There are at present seven known retrogenes shared by humans and chimpanzees (For detailed treatments of some of these see: Bonner et al. 1982; Svensson et al. 1995; and Sverdlov 2000). Further, these retrogenes are present in the same locations in chimpanzee and human genomes. Common descent can easily make sense of these commonalities, but what of the alternatives? It is enough of a stretch to say that, absent common descent, a single virus infected the germ line of these two species in the same genomic locations out of the billions of possible locations, but to argue that this happened independently at least seven times strains credulity to a point far beyond what any rational being should allow.

Pseudogenes are formerly functional genes that have been disabled by random mutation. One such pseudogene shared by all primates is known as ψη-globin, which used to play a role in hemoglobin function. This pseudogene is found in the same chromosomal locations across primate species. Further, the mutations which disabled this gene are the same and are found at the same places within it (Goodman, et al. 1989). Another pseudogene, common to humans and chimpanzees, coded for a steroid called 21-hydroxylase. Humans and chimps actually have both a functional and a nonfunctional copy of this gene (the likely result of a type of mutation called gene duplication). The nonfunctional copies of both humans and chimps are missing identical sets of eight base pairs (Kawaguchi et al. 1992). If these species did not inherit these pseudogenes from a common ancestor, they would have had to independently acquire the same mutations in the reproductive cells (because, again, the mutations would have had to be passed on) at precisely the same locations on precisely the same genes–a vanishingly small probability. Still another example, shared by humans and the great apes, codes for the enzyme L-gulano-gamma-lactone oxidase, which allows its bearer to synthesize vitamin C. The disabling mutation in this gene is why we (and the great apes) must get vitamin C from our diets. Here again, in each species, the gene exhibits the same errors in the same locations. The only other mammal in which this gene is known to be broken is the guinea pig— and, as expected, the mutation is different and is in another location, for guinea pigs are not recent concestors.

These are but a few examples. Most mammals are highly olfactory creatures, hence adaptations like a long snout and a wet nose. Primate evolution has exhibited a marked decrease in reliance on the sense of smell, as exhibited by the gradual reduction in snout length and the loss of the wet nose (still retained in lemurs, the most primitive living primates). Humans have nearly 100 different olfactory genes, yet around 70 of them are inactivated pseudogenes (Rouquier, et al 2000). Why would we have all these useless genes devoted to olfaction if we were built from scratch and not descended from ancestors for whom olfaction was much more important?

Now, as I’ve said, humans and chimps have vastly similar genomes. One conspicuous difference, though, is in the number of chromosomes present. Our haploid chromosome number is 23, while that of chimpanzees and the other great apes is 24. How do we explain this? Chromosomes are not uniform in structure, and when stained with certain dyes will exhibit distinctive banding patterns which may be used to gauge similarities or detect abnormalities. The following picture compares the banding patterns of human chromosome 2 (chromosomes are numbered according to their size, 1 being the largest) and two chromosomes (called 2p and 2q) each from chimpanzees, gorillas, and orangutans.

You can see that there are many similarities, most notably between the patterns of the human and chimp chromosomes. This led researchers to hypothesize that earlier versions of the two chromosomes possessed by the apes shown above had fused to create our chromosome 2 in one of our ape-like ancestors (Yunis, et al 1980; Yunis & Prakash, 1982). Is there any evidence for this?

There is, but it will require a little more background explanation. When the enzymes responsible for the replication of DNA get to the end of a strand, there’s nothing for them to hold on to, and so they fall off without being able to replicate the last few nucleotides. Because this would quickly degrade the genome (and the organism harboring it), chromosomes have long, non-coding strings on their ends called telomeres, which serve to prolong the destruction of the coding genetic material (what manifests to us as the process of aging). Our telomeres consist of a specific six-base pair section repeated over and over: thymine-adenine, thymine-adenine, adenine-thymine, guanine-cytosine, guanine-cytosine, and guanine-cytosine. Interestingly, we find these telomeric regions in the middle of our chromosome 2, right at the expected point of fusion. Further, the bases and the sequence even reverse in the middle of this region (remember that the two DNA strands are anti-parallel), indicating the presence of both a trailing and a leading telomere (as from two different chromosomes) (Ijdo, et al. 1991).

There is more. There is a region of the chromosome called a centromere, which is crucial to proper cell division. These are the slightly constricted regions in the chromosomes shown in the above image. Our chromosome 2 contains remnants of a second centromere corresponding to the centromere seen on the lower chimpanzee chromosome (Avarello, et al. 1992).

Each of these lines of evidence is individually quite powerful. Take them all together, though— along with the morphological, geographical, and fossil evidence— and the force of the argument becomes tremendous. Common descent is the only thing that can satisfactorily account for the discussed similarities.

__________

Avarello, R., A. Pedicini, et al. (1992). "Evidence for an ancestral alphoid domain on the long arm of human chromosome 2." Hum Genet 89(2): 247-9.

Bonner, T. I., C. O’Connell, et al. (1982). "Cloned endogenous retroviral sequences from human DNA." PNAS 79: 4709.

Goodman, M., B. F. Koop, et al. (1989). "Molecular phylogeny of the family of apes and humans." Genome 31 (316-335).

Ijdo, JW., A. Baldini, et al. (1991). "Origin of human chromosome 2: an ancestral telomere-telomere fusion." PNAS 88(20): 9051-5.

Kawaguchi, H., C. O’hUigin, et al. (1992). "Evolutionary origin of mutations in the primate cytochrome P450c21 gene." American Journal of Human Genetics 50: 766-780.

Rouquier, S., A. Blancher, et al. (2000). "The olfactory receptor gene repertoire in primates and mouse: Evidence for reduction of the functional fraction in primates." PNAS 97: 2870-2874.

Svensson, A. C., N. Setterblad, et al. (1995). "Primate DRB genes from the DR3 and DR8 haplotypes contain ERV9 LTR elements at identical positions." Immunogenetics 41: 74.

Sverdlov, E. D. (2000). "Retroviruses and primate evolution." BioEssays 22: 161-171.

Yunis, J. J., J. R. Sawyer, K. Dunham. (1980). "The striking resemblance of high-resolution g-banded chromosomes of man and chimpanzee." Science 208(6): 1145-1148.

Yunis, J. J., O. Prakash. (1982). "The origin of man: a chromosomal pictorial legacy." Science 215(19): 1525-1530.

… is the title of a book I’m going to write, which I’ll finish in about a year, and as I’m crossing the street to discuss cover art with the publisher I’ll get run down by a fiery redhead on a moped, causing me light injuries and starting a relationship which will cause me to disavow everything I’ve just written about the joys of being single and having all my time to myself.

I went to see U2 last night with friends (after getting last minute tickets, I am not a giant U2 fan) and for much of the night felt conspicuously sans partner, having instead to settle for discreetly ogling the young hotties. There was one song which seemed set up to make people get all emotional and wrap their arms tightly around their loved ones, and rarely have I felt more alone (ironically that song was One… or maybe that’s not ironic— who the hell knows with irony).

Things that are great about being single (and living alone): No one messes with your stuff; no one hassles you to do anything; no one gets annoyed when you don’t come to bed; no one gets upset when you see a movie without them; no one comes home after a bad day and brings you down with them; no one expects you to reassure them about their insecurities; no one makes you feel like the worst person in the universe by pointing out you’ve said or done something insensitive; no one gets jealous if you flirt with someone else.

Things that aren’t: No one hassles you to do anything, so you don’t do anything; there’s no sleepy girl to wrap you in her loving arms — thank you Whitlams for that annoyingly appropriate lyric—; no one gets excited with you about seeing a movie; no one expects you to be there for them after a hard day, and no one is there for you; there’s no one to share your insecurities with, and no one to remind you how important you are (to them); there’s no one to hide behind when flirting turns out to be ill-advised.

Things that are just weird: Smells. I find myself getting attached to my own scent. In lieu of a significant other I seem to be chemically bonding with myself, so I can pick up my own shirt from the day before, hold it to my face and be strangely comforted by the familar smell of moi.

Dating is also weird, as in virtually impossible for me. Like other singles I sign up with the dating sites and agonize over creating a profile which will portray me as confident but not smug, sensitive but not wet, intelligent but not intimidating. Unlike other singles I find it hard to actually follow up on any contacts I make, so usually end up ditching it again after a month or two. As everyone knows, chemistry is vital, and pheromones do not travel well via email and IM, so it’s almost a guaranteed disappointment— and I just haven’t the stomach to play the numbers. Last time I went out with someone via such a service I think I fell in love with two other people we just happened to run into. My rational mind has limited say in who I yearn for, so no matter how good a match on paper it probably isn’t going to work for me.

Acceptable comments [just barely] for someone who changes their hair color dramatically:

Comments which cross the line:

1. You so ugly!
2. You’re not going to leave it like that are you?
3. It’s great to see you’re still doing the kind of crazy stuff we all left behind years ago.

Is it mean that I felt the need to correct this image? I think my version is a lot closer to reality— not that Tom Cruise has ever visited reality… boom-tsshh!

(source image here)

One day I was flying around when a renowned museum curator was murdered. He had no clothes on and so that helped me find clues to the murdering monk. He was sad because he only did what his father told him but it was still bad. We stole a box from the bank and eventually got away. There was a combination lock inside but then the monk came back and we had to jump on a plane for England and we tied him up and brought him too. Then we eventually found what the combination was and I pretended to break it so I could go and find the treasure for myself, but when I went there it was gone… It was under the big glass pyramid all along!

I’ve seen a few movies in the past few weeks and not really mentioned here, so some condensed reviews follow (all links are to Wikipedia entries, because official sites are always too flash-heavy, and IMDB is such a useless pile of poo that I’ve decided to boycott it):

Brick — excellent must see teenage detective noir. Has been compared to Donnie Darko, mainly on the basis that it has both style and substance.

Kenny — Excellent Australian film that will hopefully get a wider release with positive reviews. I’d call it documentary-style more than a mockumentary, since the latter has very negative connotations to me (ie piss-take). Kenny is a plumber who installs and maintains portable toilets, and is one of the most likeable (and believable) characters I’ve seen in an Australian film in ages.

Jackass Number Two — Utterly repulsive and yet still I laughed a lot. To clarify, I think this is a very bad film, which will have a very negative influence on dumb young men, but that doesn’t mean it isn’t funny. There seems to be a particular propensity for vomit in this one, especially from Bam Marguera who will dive into a scene just so he can upchuck on film.

Little Miss Sunshine — I thought I’d already mentioned this one, but must have been in email. The dysfunctional family tag might make you groan but it does it really well. There wasn’t a character I didn’t warm to.

Monster House — A pleasant surprise, with some genuinely creepy moments. It even had a little of the Spielberg touch to it (producer credit) harking back to the The Goonies.

Ah, what a week. I am delighted to see that there is finally a change in the political wind— well done US Democrats, even though I have no idea what your policies are, you are not beholden to the neocons, and that’s enough for now. It’s a pity the world had to get this insanely fucked up before people decided it was time to maybe take some of the power away from those in charge.

Anyone who has dabbled in Photoshop has probably wondered at some time what the hell all the blending modes actually do. With this in mind I created the following swatches some time ago, to help me select the most appropriate modes for creating mockups of shading and lighting effects.

The samples here illustrate the result of blending the following two images (disregarding the color specific blends for now).

A

B

What I find striking about the results is that many of them have discontinuities, which seems a little crappy to me. Eg overlay and hard light, which both appear to be based on combinations of multiply and screen simply stuck together.

	Multiply: A*B
	Screen: 1-(1-A)*(1-B)
	Overlay: if (A<0.5) 2*A*B else 1-2*(1-A)*(1-B)
	Soft Light: ???
	Hard Light: if (B<0.5) 2*A*B else 1-(1-A)*2(1-B)
	Color Dodge: A/(1-B)
	Color Burn: 1-(1-A)/B
	Darken: min(A,B)
	Lighten: max(A,B)
	Difference: |A-B|
	Exclusion: 0.5-2*(A-0.5)*(B-0.5)

It’s incidental arson day (aka Guy Fawkes) here in NZ so should be fun to see the sky light up, assuming the rain stays away (it’s possible). It’s still weird to see fireworks for sale in regular supermarkets, since they were banned many years ago in Australia. I nearly bought a box full myself, just because they were there, but then I saw something even better, something I have wanted since ages ago:

Yep, it’s a good ol’ fashioned plasma ball (or lamp). Way fun to finally have one, I’m already experimenting with wrapping the globe in foil, which seems to turn it into a sort of poor man’s Van der Graaf generator. Now I just need to create a Leyden jar and I’ll have my own FCC non-compliant indoor fireworks kit!

Speaking vaguely of NZ, there is one thing I really hate about it here, and it’s not the weather— It’s the goddamn television. More specifically, it’s the fact that about 20% of air time appears dedicated to infomercials, while the same amount again is reserved for hocking extortionate and retarded SMS "services". Apparently for only $4.50 I can purchase myself, via TXT, a horrible smiley, a horrible background image, a horrible ringtone or a horrible subscription to a competition to win what appears to be a fourth generation iPod with a sterling silver back (which means it looks just like any other iPod, only for some reason the backplate is made of a ridiculously heavy and expensive metal instead of strong, light aluminium).

I still love this recut "Shining" trailer…