In 1902, Peter Pan first appeared as a character in J. M. Barries "The White Bird." "The White Bird" is mostly about a child, Mamie, who gets lost in Kensington Gardens at night and interacts with the fairies; Peter is merely a minor character, However, this is truly his first appearance. Coincidentally, the confusion between Thimbles and Kisses also appears in this work.
In 1904, Barrie wrote a play entitled "Peter Pan, or the Boy who Wouldn't Grow Up". It was a hit, and the first appearance of the Darling children, Captain James Hook, and the first major appearance of Peter.
In 1911, Barrie wrote a novel version of the play, entitled "Peter and Wendy".
In 1929, Barrie gave the copyright on his novel to his favorite charity - The Great Ormond Street Hospital for Children. They have prospered from numerous movie, stage-play, and musical versions since then, although the strict amount of money that the copyright has earned for the hospital is kept a secret, as per Barrie's wishes.
In 2004, Peter Pan turned 100, and, in honor of this prestigious anniversary, the hospital held a series of celebrations and charities. Among these was a competition for authors to write an official sequel to Peter Pan. The rules stipulated that it must include all the original characters: Peter, Wendy, Hook, Tink, and so on. The winner was Geraldine McCaughrean, and the book is called "Peter Pan in Scarlet".
From a purely personal perspective, I was bothered by the premise of a sequel with the original characters; Wendy, Tink, and Hook are all dead at the end of the novel "Peter and Wendy". At the very least, Hook has been eaten by a crocodile, Wendy has grown up, and Tink has died. Why have another adventure with them in the Neverland when rightfully, it should be Wendy's descendants and some other villian, with some other fairy sidekick or none at all?
However, as you might have guessed, I was given the book yesterday and read it today. So; spoiler alert!
Mrs. McCaughrean's premise makes up for the folly of the contest. Wendy is, indeed, grown up, as are John and the Lost Boys. Tootles is a judge, Nibs a Baronet, and Curly a doctor (all as they should be). It was a refreshing start. McCaughrean has certainly done her research, except for a few apparent but minor mistakes (Girl fairies are white, boys are pink, and the silly little ones who don't know what they are are yellow; you can certainly fly without a shadow or Peter would have died in the beginning of the original novel). She even references the very first appearance in "The White Bird".
The tone, admittedly, is a far cry from Barrie's hands-on narrative style. In fact, I think that the author of "A Series of Unfortunate Events" comes closer to matching Barrie in tone (although in those books I find that often it comes across a little more heavy-handed). One of my favorite things about the original book, and indeed other things I have read by Barrie, is the very real presence of a narratorial character. In "Peter and Wendy", the narrator is as important a character as Peter himself, and reveals a darker, more adult side to the story that is sadly missing in the sequel. The delightful monologues about Mrs. Darling's love for her children, Mr. Darling's pathetic guilt over the loss of his children, and the hints and clues towards Hook's links with the author - these make Peter Pan something that an adult can enjoy as much as a child. Such things are regretfully absent from McCaughrean's sequel.
Indeed, much of the darker side of the original Peter Pan myth has been sadly lost in the sequel. This is something that has certainly happened over the course of time - think of the Disney movie and the modern musicals as compared to the book. Today, even when we try to make a "darker" envisioning of the Pan myth, we come out with the drivel that was the latest attempt at a movie version; sexed up, violent but without purpose, and not emotionally dark at all. Still a children's tale at heart, although admittedly not the kind of children's tale that you would want to tell your children. At least this sequel doesn't do that - it is thoroughly a children's book. Certainly, about halfway through, there is a transformation in Peter towards Jas Hook which might be due to Peter's mercurial, flighty nature and his inability to differentiate between make-believe and reality - but, surprise surprise, that too turns out to be all the doing of Hook and not Peter's own fault at all.
Another thing that we modern readers always seem to be doing is changing Wendy. A particular sentence in the sequel bothered me: "Without the right upbringing, girls can be so... domestic." The original Wendy was nothing if not domestic. Remember the temptation scene, when Peter gets her to run away to the Neverland. He does so by tempting her with, of all things: darning socks, making pockets, tucking children in at night, and telling them stories. "How we should all respect you," he says. And then her introduction to the Lost Boys, in which they ask for a "Nice, motherly sort of person" and she says she fits the bill perfectly? Remember the rather disgusting Father/Mother game that Wendy forces upon Peter, to his dismay? Who is Wendy to be complaining about girls being domestic?
Then again, this is another common problem for modern readers. It is thought, I suppose, that modern little girls would not be able to identify with a female lead who wanted nothing more than to be a mother. At least, that to give them only the example of someone who wanted to be a mother would not be fair to their personalities or would trap them into cultural stereotypes of a woman's place being the kitchen or the nursery. You have only to recall the butchering known as the 2003 movie to know of a Wendy even more distant from her domestic roots. So perhaps I shouldn't be complaining about a grown Wendy who is a motherly sort of person, as she shows herself to be, but has her illusions about not being domestic.
Certainly, in the end, Wendy decides that the thing she wants more than anything is to see her daughter and be a real mother. She mothers everyone throughout the story -- from the grown-up lost boys to Peter to Hook and Smee. She shortens the sleeves on Hook's jacket to give to Peter (although, by rights, she had already made him an outfit out of Hook's old clothing at the end of Barrie's novel) and does other such domestic tasks.
Another thing that McCaughrean does is add to Barrie's universe. It is no longer just the Neverland but instead also a whole other realm; a maze of lost mothers, a sea of a thousand islands, and so on and so forth. It brings to mind the adventuring in "Last of the Great Whangdoodles" rather than Barrie's sort.
I have a whole rant about Hook and what she did to Hook, BUT that can be saved for later.
The most important thing, something which supersedes all of the stylistic differences and choices that were made, is that she kept the joy and adventure of the Neverland alive. McCaughrean turned the Neverland into a place where adults can grow young again, rather than just a place for children to go and never grow old. For that, I thank her. She has done it in the style of Roald Dahl, JK Rowling, and other modern children's writers. This book is a fitting sequel to Peter Pan, but just as much a product of its time that Peter Pan originally was. My heart will always be with the original, which I will probably now start reading again. But this one may deserve another read, when I'm looking for a lighthearted romp through second-childhood.
Saturday, December 16, 2006
Wednesday, September 06, 2006
I have submitted to the pressure of corporate America and pop culture
But not enough to get an iPod. (Although if I did, the 4GB nano would be my cup of tea.) Instead, after painstaking research (read: a couple hours online) I found a 4GB small sandisk player much to my liking. Now all that remains is to find a cute skin for it that will wrap around my arm to go running with, and I will camouflage perfectly into the masses of preppy teenagers with their tiny mp3 players. Delightful. But there is something to be said for being able to listen to my music while I'm counting cells or making DNA or doing other repetitive procedures. (I don't need the arm-band skin for that.)
Perhaps my burgeoning desire to seclude my self in my personal cocoon of music stems from spending hours upon end with my family. Don't get me wrong, my family and I never had the sort of melodramatic petulant fights that characterize a stereotypical teenager-hood. They knew that pressuring me into a certain mold, restricting my activities or dictating my behaviors would just end up making me angry and wouldn't end up making me a calmer, happier, more successful child. I knew that if I really screwed up, it would have repercussions in my own life other than having two irate parents. So I toed the line to the extent that was reasonable and my parents got off my back about most things. Instead, my brother went through the angry fights and conflicts with my parents about getting schoolwork done and staying out at night and I was the child who had her head screwed on correctly.
The problem is that when I left, my brother and my parents worked things out. They get along just fine, and while my brother still has the attention to detail reminiscent of "big picture" people everywhere and while I still have tendencies that lean towards professional editor-levels of hair-splitting, my parents are trying to negotiate between the two of us. Generally, what happens is that my brother gets attention and gratitude for things that he half-does, and I get to finish them. Or he messes something up, forgets something, or loses something, and the entire family will go into panic mode to fix whatever it is that is wrong, leaving me behind in the dust. It would be so much nicer if I could just tune everything out and not care about it as much as I do; if I didn't listen to the sounds of their orbits around him. But (at least until the player comes in the mail and I can plug in and zone out) instead I get sucked into the morass of my brother declaring that he knows how to do JavaScript (which he doesn't) or at least can figure it out (which he couldn't) and then get drafted in to fixing it with my limited knowledge of the language or finding a site online which will teach him (or at least give him code to rip off). Of course, when my mother finally just gives him code to copy, he "gets it working" and applauds himself for his skill, which she, for some reason unknown to me, echoes.
I don't really have a conclusion. I was always worst at conclusions. I guess the conclusion is simply that I'm chafing at the bit to get back to college and my real life. Instead of staying here and playing court to my brother. And that I'm getting a new mp3 player, which is going to be sweet.
Perhaps my burgeoning desire to seclude my self in my personal cocoon of music stems from spending hours upon end with my family. Don't get me wrong, my family and I never had the sort of melodramatic petulant fights that characterize a stereotypical teenager-hood. They knew that pressuring me into a certain mold, restricting my activities or dictating my behaviors would just end up making me angry and wouldn't end up making me a calmer, happier, more successful child. I knew that if I really screwed up, it would have repercussions in my own life other than having two irate parents. So I toed the line to the extent that was reasonable and my parents got off my back about most things. Instead, my brother went through the angry fights and conflicts with my parents about getting schoolwork done and staying out at night and I was the child who had her head screwed on correctly.
The problem is that when I left, my brother and my parents worked things out. They get along just fine, and while my brother still has the attention to detail reminiscent of "big picture" people everywhere and while I still have tendencies that lean towards professional editor-levels of hair-splitting, my parents are trying to negotiate between the two of us. Generally, what happens is that my brother gets attention and gratitude for things that he half-does, and I get to finish them. Or he messes something up, forgets something, or loses something, and the entire family will go into panic mode to fix whatever it is that is wrong, leaving me behind in the dust. It would be so much nicer if I could just tune everything out and not care about it as much as I do; if I didn't listen to the sounds of their orbits around him. But (at least until the player comes in the mail and I can plug in and zone out) instead I get sucked into the morass of my brother declaring that he knows how to do JavaScript (which he doesn't) or at least can figure it out (which he couldn't) and then get drafted in to fixing it with my limited knowledge of the language or finding a site online which will teach him (or at least give him code to rip off). Of course, when my mother finally just gives him code to copy, he "gets it working" and applauds himself for his skill, which she, for some reason unknown to me, echoes.
I don't really have a conclusion. I was always worst at conclusions. I guess the conclusion is simply that I'm chafing at the bit to get back to college and my real life. Instead of staying here and playing court to my brother. And that I'm getting a new mp3 player, which is going to be sweet.
Monday, August 07, 2006
Sane Geneticists probably don't have Teleporters
But I don't really have to worry about that.
Today's Narbonic is wonderful. I mean, what's the point of being sane if I can't have my teleporter?
(This is an awesome webcomic that you should read, and will enjoy even if you aren't a slightly unhinged geneticist wondering when her cloning will finally come right and data will start coming in.)
In other news, I am wondering when my cloning will finally come right and data will start coming in. I mean, I understand that one of the few things bacteria are really good at is recombination, but I've been working at cloning this one vector for a good two months with no success whatsoever. I'm way past the third-time's-the-charm rule for ligations, and that appears to be the problem with the last one; the insert just doesn't want to pop in. I know, I've been told a million and one times that the first few months you work in a new lab are never good, even when you're a post doc who knows the procedures like the back of her hand, not to mention being a student fairly well-versed in PCR and gel electrophoresis, and the cutting up of mouse embryos, and perhaps some staining, but without much experience in the land of cloning. Well, I'm getting that.
So during incubations, while randomly surfing the net for something that had enough text I wouldn't feel guilty for reading lots of webcomics at work, I found this. Go ahead and read it, I recommend it as not as puerile and offensive as many articles of its ilk. It tries to be scientific and not necessarily in a bad way. But there's still something wrong, some nagging itch at the back of my mind. The basic point of the article is as follows: 1) Humans and apes are not as similar as previously thought, which implies 2) that humans were, after all, created by God in his image. I know I'm not doing it justice, you should read the article if you want to know the actual argument. I'll just include quotes.
"While many evolutionists proclaim that human DNA is 98% identical to chimpanzee DNA, few would lie by idly and allow themselves to receive a transplant using chimpanzee organs. As a matter of fact, American doctors tried using chimp organs in the 1960s, but in all cases the organs were totally unsuitable."
My problem with the term 'evolutionists' notwithstanding, this argument is as misleading as the statement that "Human DNA is 98% identical to chimpanzee DNA." Most human organs are completely unsuitable for transplantation into other humans -- finding a suitable donor isn't just a matter of matching blood types and going. Immune response to foreign (although still perfectly human) organs and rejection of them is an incredibly serious issue in medicine, which spurs some of the research into stem cells and artificial tissue growth -- the only way to be sure that someone's body won't reject the organ is to regrow an organ from that same person's tissue. Which highlights the fact that "totally unsuitable" in this case might or might not mean functionally different, structurally different, or wracked with differences similar to those between individual humans. As a matter of fact, human hearts and even mouse hearts look very similar (although obviously of different sizes) and function almost identically. The fact that chimp organs cannot be transplanted means next to nothing.
However, after that rocky start, the article goes into even rougher territory when it begins to take issue with the concept that genetic similarity between humans and chimps does exist. Here are some highlights:
"It appears that only about 1.5% of the human genome consists of genes, which code for proteins. These genes are clustered in small regions that contain sizable amounts of “non-coding” DNA (frequently referred to as “junk DNA”) between the clusters. The function of these non-coding regions is only now being determined. These findings indicate that even if all of the human genes were different from those of a chimpanzee, the DNA still could be 98.5 percent similar if the “junk” DNA of humans and chimpanzees were identical. "
This argument just smacks of poor logic. First of all, the pre-genomic sequence homology study was done entirely on a selection of known genes; that was the only way they could do the study. The study (referenced earlier in this article) reported “that the average human polypeptide is more than 99 percent identical to its chimpanzee counterpart” (King and Wilson, 1975, pp. 114-115). A polypeptide is certainly not coded for by junk DNA, as the author of apologetics press's article obviously knew. So we know, and the author knows, that the 98.5% homology, whether true or false, is certainly not accounted for by homology in junk DNA. This argument, then, is purposely misleading. Worse than simply getting the numbers wrong, as an argument of whether humans and chimps are 98% similar, 95% similar, or 80% similar would be -- the author appears here to conciously misrepresent findings he referred to earlier in his article.
Here's another quote they use to back up a claim that DNA similarity isn't all that surprising:
"Because DNA is a linear array of those four bases—A,G,C, and T—only four possibilities exist at any specific point in a DNA sequence. The laws of chance tell us that two random sequences from species that have no ancestry in common will match at about one in every four sites. Thus even two unrelated DNA sequences will be 25 percent identical, not 0 percent identical (Marks, J. 2000, p. B-7)."
This is again entirely misleading. Even though an entirely unrelated sequence would in fact be 25% homologous, homology on the level of 95% for long peptides is still huge. Take a series of 30 bases; what would be required to code 10 amino acids in a protein (hardly anything on the scale of peptides which are at least 30 amino acids in length and usually in the realm of hundreds). In 30 bases, 95% homology means one, maybe two mismatches, as opposed to the seven or eight matches one would expect randomly. The chance that, even in a random population of 100 of these 30-base pair sequences, you would see a sinificant chunk at 95% homology is ridiculously small. Since the difference between the average homologies (25% and 95%) is 40%, in order to get a statistically insignificant result (p-value of 0.05 or higher) you would need a standard deviation between 20 and 30, which is impossible to have with a mean of 95 out of 100 (it would imply some greater than 100% homologies). This is assuming that the researchers aligned only about 100 sequences, which also is probably very false. So the fact that yes, a random sequence will probably be 25% homologous does not mean that the finding that most sequences are around 95% homologous is insignificant in the least. Remember, the original finding is that the average human polypeptide is 99 percent identical with a chimp polypeptide -- not that the total sequence is x% similar.
What I love the most is where this article goes next:
"Therefore a human and any earthly DNA-based life form must be at least 25% identical. Would it be correct, then, to state that daffodils are “one-quarter human”? The idea that a flower is one-quarter human is neither profound nor enlightening; it is outlandishly ridiculous!"
This argument just sets my teeth grinding in my mouth. First of all, it is more likely for "any earthly DNA-based life form" to be 0% identical with humans as it is for it to be 50% identical with humans if you espouse the idea that these similarities are purely random, so the statement that any life-form "must be at least 25% identical" is blatantly false and shows a disgusting lack of knowledge of statistical probability. I could go into that, but it's probably best that I don't. Secondly, in all probability, humans share a lot more than 25% of their DNA with daffodils. While E. Coli is probably a better example of what this author wanted to choose -- something arguably entirely unrelated to humans -- certain incredibly essential proteins, such as Ribosomal proteins, tRNAs, polymerases, and so-called "house-keeping" genes are incredibly similar between E. Coli and humans, which very well might boost the homology level above 25%. And it is significant -- it supports the idea that we share distant ancestry not just with chimpanzees, who in the scheme of things look like us, use tools like us, and even have some sort of rudimentary language like us, but indeed even with things as alien and apparently different as a tiny prokaryote.
Here's another gem: "The truth is, if we consider the absolute amount of genetic material when comparing primates and humans, the 1-2% difference in DNA represents approximately 80 million different nucleotides (compared to the 3-4 billion nucleotides that make up the entire human genome). To help make this number understandable, consider the fact that if evolutionists had to pay you one penny for every nucleotide in that 1-2% difference between the human and the chimp, you would walk away with $800,000. Given those proportions, 1-2% does not appear so small, does it? "
First, using the same reasoning: if you were given one penny for every nucleotide which stayed the same between human and chimp, you would walk away with $39,200,000. Given those proportions, 800 thousand seems rather small, doesn't it?
I could use actual logic, but it doesn't seem worth it.
Now the author changes the subject slightly and talks about chromosomal organization: "It would make sense that, if humans and chimpanzees were genetically identical, then the manner in which they store DNA also would be similar."
You mean, like, chromosomes with centromeric heterochromatin (regions of inactive DNA at the center of the chromosome, full of short tandem repeats) and telomeric ends (regions of inactive DNA at the end of the chromosome to protect the genes within from degradation), organized in a nucleus with specific regions of activity/inactivity, packed around histones, with certain alterations on the histones that make the DNA more accessible to proteins and certain alterations that make the histones hold the DNA tighter and keep it away from proteins? Something like that? Oh, wait, that is shared not only between chimps and humans but also more distant species. As opposed to, say, bacterial DNA which is simply floating in the cytoplasm in a large loop attached to the cellular inner membrane, or viral DNA which is jammed into a protien coat and sometimes not even DNA at all but RNA instead? Similar DNA storage?
But no, the author is here talking about the number of chromosomes: "All cells that possess a nucleus contain a specific number of chromosomes. Common sense would seem to necessitate that organisms that share a common ancestry would possess the same number of chromosomes. However, chromosome numbers in living organisms vary from 308 in the black mulberry (Morus nigra) to six in animals such as the mosquito (Culex pipiens) or nematode worm (Caenorhabditis elegans) [see Sinnot, et al., 1958]. Additionally, complexity does not appear to affect the chromosomal number. The radiolaria (a simple protozoon) has over 800, while humans possess 46. Chimpanzees, on the other hand, have 48 chromosomes. A strict comparison of chromosome numbers would indicate that we are more closely related to the Chinese muntjac (a small deer found in Taiwan’s mountainous regions), which also has 46 chromosomes."
First of all, how would common sense seem to necessitate that organisms that share a common ancestry possess the same number of chromosomes? Oh, because "To remove even one chromosome would potentially remove the DNA codes for millions of vital body factors." True. But what about two chromosomes fusing? An example being a recombination event between homologous parts of nonhomologous chromosomes (such as the end repeats, maybe?) at some point in germ line generation. The repetitive elements would be partially removed, oh no, and we would be left with one germ line cell which doesn't mature because it is missing quite a bit of DNA and one germ line cell which has fewer chromosomes. It isn't common. It isn't very likely. But it's possible; and we're not talking about one person and one generation here -- we're talking about millions upon millions of germ line cells times just as many generations. With so many chances, what's not to say that this happened? Certainly, most apes will breed to give apes and humans will breed to give humans. But given an isolated population, and perhaps something to select for in that recombination, maybe a gene suddenly not being in the repressive environment of the telomere and overexpressing, allowing for more (or different) development in certain parts of the brain, etc... You can get somewhere. They're still not humans, but they're on the way.
However, the next part gets better. "Amazingly, the authors found that only 48.6% of the whole human genome matched chimpanzee nucleotide sequences. [Only 4.8% of the human Y chromosome could be matched to chimpanzee sequences.] This study compared the alignments of 77,461 chimpanzee sequences to human genomic sequences obtained from public databases."
Okay, remember all of that "junk", "non-coding" DNA they were talking about earlier? Where 98.5% of the human genome could be identical to chimps and still have no coding sequence involved? Well, here's the hitch: those genomic sequences include the junk DNA, regions that don't code for proteins and hence aren't really strictly conserved over time. Of course you have binding sites in there, little bits of conserved sequences amid general lenghts of spacing DNA and unconserved sequences, but you don't have long stretches of homology because there's no reason to have that homology. If anything, the fact that the figures vary so much, that less than half of the whole genome is homologous, but that actual coding sequences, changes in which would have concrete effects, are conserved over time to a much greater extent supports the fact that changes HAPPEN, and the ones that don't effect much stick around or go away depending on random chance, but the ones tht are helpful stay there and the ones that are harmful go away. It argues for evolution, not against it.
Much of the rest of the article goes on about similarities between the great apes that are missing in humans, pointing to a tighter link among the great apes and an increased distance from humans. However, all of these arguments simply fail to be persuasive. Why should I believe this is evidence that humans had special creation by God when I can simply account for this difference by an earlier divergence from the great apes?
Finally, a part of the article that I loved almost the most: "After studying tissues and blood samples from the great apes, and sixty humans from various ethnic groups, Muchmore and colleagues discovered that human cells are missing a particular form of sialic acid (a type of sugar) found in all other mammals (1998, 107[2]:187)."
Interestingly enough, the particular form of sialic acid referenced here is commonly hypoexpressed in the brain, indicating that it is not amenable to brain development. Also interestingly, sialic acid can be released from cells and travel through the bloodstream to be picked up by other cells. What does this mean? Less (or, perhaps, none) of this cell marker in humans could very will be helpful to the increase in brain development and intelligence -- sounds like something evolution would select for, right? Especially in humans, where tool-making and intelligence had, for a long time, a direct impact on how much food you had and thereby how many children you had. Conveniently enough, the mutation in a hydroxylase protein that accounts for the lack of this form of sialic acid occurred in between the split between chimps and humans but before the divergence between neanderthals and humans -- exactly the right place to be looking for the development of human intelligence.
On another note, an interesting coincidence is that this hydroxylase protein is still expressed in humans, still at a lower level in the brain, but is non-functional. Why would God make humans with an ineffective version of this gene, expressed in exactly the same places? To confuse scientists? Or maybe this enzyme and its expression is a relic from a distant past.
I'm sure that a simple literature search such as the single google search I did on "sialic acid" would return interesting results in response to many of the other arguments in this article. I don't really have the time or energy for it, but this kind of pseudo-science really just gets on my nerves. It's perfectly fine in my opinion to cling to an irrational view that we are special, that we were created in God's image. It's nice to think you're better than the bacteria in your belly or the dogs on the street or the monkeys in the zoo. It's nice to think that all the other miraculous organisms were created for us to rule over and use.
But I think that in many ways it is simpler, and more beautiful to think that we are similar, that we came from the same place. Of course I look at the evidence before me in fossil records, in DNA homology, in skeletal similarities and vestigial limbs (such as our tailbones), and I see evidence for a common ancestor and evolution. But even on a spiritual level, there is something incredibly powerful about the idea of a common ancestor for all life. It puts you firmly as part of the beauty of the world, instead of placing you outside as an observer and overseer. That human life is as beautiful and simple and natural as a flower sprouting from the ground is, in my mind, just as magical as the idea that the flower was made for us and we were made to be like God.
Today's Narbonic is wonderful. I mean, what's the point of being sane if I can't have my teleporter?
(This is an awesome webcomic that you should read, and will enjoy even if you aren't a slightly unhinged geneticist wondering when her cloning will finally come right and data will start coming in.)
In other news, I am wondering when my cloning will finally come right and data will start coming in. I mean, I understand that one of the few things bacteria are really good at is recombination, but I've been working at cloning this one vector for a good two months with no success whatsoever. I'm way past the third-time's-the-charm rule for ligations, and that appears to be the problem with the last one; the insert just doesn't want to pop in. I know, I've been told a million and one times that the first few months you work in a new lab are never good, even when you're a post doc who knows the procedures like the back of her hand, not to mention being a student fairly well-versed in PCR and gel electrophoresis, and the cutting up of mouse embryos, and perhaps some staining, but without much experience in the land of cloning. Well, I'm getting that.
So during incubations, while randomly surfing the net for something that had enough text I wouldn't feel guilty for reading lots of webcomics at work, I found this. Go ahead and read it, I recommend it as not as puerile and offensive as many articles of its ilk. It tries to be scientific and not necessarily in a bad way. But there's still something wrong, some nagging itch at the back of my mind. The basic point of the article is as follows: 1) Humans and apes are not as similar as previously thought, which implies 2) that humans were, after all, created by God in his image. I know I'm not doing it justice, you should read the article if you want to know the actual argument. I'll just include quotes.
"While many evolutionists proclaim that human DNA is 98% identical to chimpanzee DNA, few would lie by idly and allow themselves to receive a transplant using chimpanzee organs. As a matter of fact, American doctors tried using chimp organs in the 1960s, but in all cases the organs were totally unsuitable."
My problem with the term 'evolutionists' notwithstanding, this argument is as misleading as the statement that "Human DNA is 98% identical to chimpanzee DNA." Most human organs are completely unsuitable for transplantation into other humans -- finding a suitable donor isn't just a matter of matching blood types and going. Immune response to foreign (although still perfectly human) organs and rejection of them is an incredibly serious issue in medicine, which spurs some of the research into stem cells and artificial tissue growth -- the only way to be sure that someone's body won't reject the organ is to regrow an organ from that same person's tissue. Which highlights the fact that "totally unsuitable" in this case might or might not mean functionally different, structurally different, or wracked with differences similar to those between individual humans. As a matter of fact, human hearts and even mouse hearts look very similar (although obviously of different sizes) and function almost identically. The fact that chimp organs cannot be transplanted means next to nothing.
However, after that rocky start, the article goes into even rougher territory when it begins to take issue with the concept that genetic similarity between humans and chimps does exist. Here are some highlights:
"It appears that only about 1.5% of the human genome consists of genes, which code for proteins. These genes are clustered in small regions that contain sizable amounts of “non-coding” DNA (frequently referred to as “junk DNA”) between the clusters. The function of these non-coding regions is only now being determined. These findings indicate that even if all of the human genes were different from those of a chimpanzee, the DNA still could be 98.5 percent similar if the “junk” DNA of humans and chimpanzees were identical. "
This argument just smacks of poor logic. First of all, the pre-genomic sequence homology study was done entirely on a selection of known genes; that was the only way they could do the study. The study (referenced earlier in this article) reported “that the average human polypeptide is more than 99 percent identical to its chimpanzee counterpart” (King and Wilson, 1975, pp. 114-115). A polypeptide is certainly not coded for by junk DNA, as the author of apologetics press's article obviously knew. So we know, and the author knows, that the 98.5% homology, whether true or false, is certainly not accounted for by homology in junk DNA. This argument, then, is purposely misleading. Worse than simply getting the numbers wrong, as an argument of whether humans and chimps are 98% similar, 95% similar, or 80% similar would be -- the author appears here to conciously misrepresent findings he referred to earlier in his article.
Here's another quote they use to back up a claim that DNA similarity isn't all that surprising:
"Because DNA is a linear array of those four bases—A,G,C, and T—only four possibilities exist at any specific point in a DNA sequence. The laws of chance tell us that two random sequences from species that have no ancestry in common will match at about one in every four sites. Thus even two unrelated DNA sequences will be 25 percent identical, not 0 percent identical (Marks, J. 2000, p. B-7)."
This is again entirely misleading. Even though an entirely unrelated sequence would in fact be 25% homologous, homology on the level of 95% for long peptides is still huge. Take a series of 30 bases; what would be required to code 10 amino acids in a protein (hardly anything on the scale of peptides which are at least 30 amino acids in length and usually in the realm of hundreds). In 30 bases, 95% homology means one, maybe two mismatches, as opposed to the seven or eight matches one would expect randomly. The chance that, even in a random population of 100 of these 30-base pair sequences, you would see a sinificant chunk at 95% homology is ridiculously small. Since the difference between the average homologies (25% and 95%) is 40%, in order to get a statistically insignificant result (p-value of 0.05 or higher) you would need a standard deviation between 20 and 30, which is impossible to have with a mean of 95 out of 100 (it would imply some greater than 100% homologies). This is assuming that the researchers aligned only about 100 sequences, which also is probably very false. So the fact that yes, a random sequence will probably be 25% homologous does not mean that the finding that most sequences are around 95% homologous is insignificant in the least. Remember, the original finding is that the average human polypeptide is 99 percent identical with a chimp polypeptide -- not that the total sequence is x% similar.
What I love the most is where this article goes next:
"Therefore a human and any earthly DNA-based life form must be at least 25% identical. Would it be correct, then, to state that daffodils are “one-quarter human”? The idea that a flower is one-quarter human is neither profound nor enlightening; it is outlandishly ridiculous!"
This argument just sets my teeth grinding in my mouth. First of all, it is more likely for "any earthly DNA-based life form" to be 0% identical with humans as it is for it to be 50% identical with humans if you espouse the idea that these similarities are purely random, so the statement that any life-form "must be at least 25% identical" is blatantly false and shows a disgusting lack of knowledge of statistical probability. I could go into that, but it's probably best that I don't. Secondly, in all probability, humans share a lot more than 25% of their DNA with daffodils. While E. Coli is probably a better example of what this author wanted to choose -- something arguably entirely unrelated to humans -- certain incredibly essential proteins, such as Ribosomal proteins, tRNAs, polymerases, and so-called "house-keeping" genes are incredibly similar between E. Coli and humans, which very well might boost the homology level above 25%. And it is significant -- it supports the idea that we share distant ancestry not just with chimpanzees, who in the scheme of things look like us, use tools like us, and even have some sort of rudimentary language like us, but indeed even with things as alien and apparently different as a tiny prokaryote.
Here's another gem: "The truth is, if we consider the absolute amount of genetic material when comparing primates and humans, the 1-2% difference in DNA represents approximately 80 million different nucleotides (compared to the 3-4 billion nucleotides that make up the entire human genome). To help make this number understandable, consider the fact that if evolutionists had to pay you one penny for every nucleotide in that 1-2% difference between the human and the chimp, you would walk away with $800,000. Given those proportions, 1-2% does not appear so small, does it? "
First, using the same reasoning: if you were given one penny for every nucleotide which stayed the same between human and chimp, you would walk away with $39,200,000. Given those proportions, 800 thousand seems rather small, doesn't it?
I could use actual logic, but it doesn't seem worth it.
Now the author changes the subject slightly and talks about chromosomal organization: "It would make sense that, if humans and chimpanzees were genetically identical, then the manner in which they store DNA also would be similar."
You mean, like, chromosomes with centromeric heterochromatin (regions of inactive DNA at the center of the chromosome, full of short tandem repeats) and telomeric ends (regions of inactive DNA at the end of the chromosome to protect the genes within from degradation), organized in a nucleus with specific regions of activity/inactivity, packed around histones, with certain alterations on the histones that make the DNA more accessible to proteins and certain alterations that make the histones hold the DNA tighter and keep it away from proteins? Something like that? Oh, wait, that is shared not only between chimps and humans but also more distant species. As opposed to, say, bacterial DNA which is simply floating in the cytoplasm in a large loop attached to the cellular inner membrane, or viral DNA which is jammed into a protien coat and sometimes not even DNA at all but RNA instead? Similar DNA storage?
But no, the author is here talking about the number of chromosomes: "All cells that possess a nucleus contain a specific number of chromosomes. Common sense would seem to necessitate that organisms that share a common ancestry would possess the same number of chromosomes. However, chromosome numbers in living organisms vary from 308 in the black mulberry (Morus nigra) to six in animals such as the mosquito (Culex pipiens) or nematode worm (Caenorhabditis elegans) [see Sinnot, et al., 1958]. Additionally, complexity does not appear to affect the chromosomal number. The radiolaria (a simple protozoon) has over 800, while humans possess 46. Chimpanzees, on the other hand, have 48 chromosomes. A strict comparison of chromosome numbers would indicate that we are more closely related to the Chinese muntjac (a small deer found in Taiwan’s mountainous regions), which also has 46 chromosomes."
First of all, how would common sense seem to necessitate that organisms that share a common ancestry possess the same number of chromosomes? Oh, because "To remove even one chromosome would potentially remove the DNA codes for millions of vital body factors." True. But what about two chromosomes fusing? An example being a recombination event between homologous parts of nonhomologous chromosomes (such as the end repeats, maybe?) at some point in germ line generation. The repetitive elements would be partially removed, oh no, and we would be left with one germ line cell which doesn't mature because it is missing quite a bit of DNA and one germ line cell which has fewer chromosomes. It isn't common. It isn't very likely. But it's possible; and we're not talking about one person and one generation here -- we're talking about millions upon millions of germ line cells times just as many generations. With so many chances, what's not to say that this happened? Certainly, most apes will breed to give apes and humans will breed to give humans. But given an isolated population, and perhaps something to select for in that recombination, maybe a gene suddenly not being in the repressive environment of the telomere and overexpressing, allowing for more (or different) development in certain parts of the brain, etc... You can get somewhere. They're still not humans, but they're on the way.
However, the next part gets better. "Amazingly, the authors found that only 48.6% of the whole human genome matched chimpanzee nucleotide sequences. [Only 4.8% of the human Y chromosome could be matched to chimpanzee sequences.] This study compared the alignments of 77,461 chimpanzee sequences to human genomic sequences obtained from public databases."
Okay, remember all of that "junk", "non-coding" DNA they were talking about earlier? Where 98.5% of the human genome could be identical to chimps and still have no coding sequence involved? Well, here's the hitch: those genomic sequences include the junk DNA, regions that don't code for proteins and hence aren't really strictly conserved over time. Of course you have binding sites in there, little bits of conserved sequences amid general lenghts of spacing DNA and unconserved sequences, but you don't have long stretches of homology because there's no reason to have that homology. If anything, the fact that the figures vary so much, that less than half of the whole genome is homologous, but that actual coding sequences, changes in which would have concrete effects, are conserved over time to a much greater extent supports the fact that changes HAPPEN, and the ones that don't effect much stick around or go away depending on random chance, but the ones tht are helpful stay there and the ones that are harmful go away. It argues for evolution, not against it.
Much of the rest of the article goes on about similarities between the great apes that are missing in humans, pointing to a tighter link among the great apes and an increased distance from humans. However, all of these arguments simply fail to be persuasive. Why should I believe this is evidence that humans had special creation by God when I can simply account for this difference by an earlier divergence from the great apes?
Finally, a part of the article that I loved almost the most: "After studying tissues and blood samples from the great apes, and sixty humans from various ethnic groups, Muchmore and colleagues discovered that human cells are missing a particular form of sialic acid (a type of sugar) found in all other mammals (1998, 107[2]:187)."
Interestingly enough, the particular form of sialic acid referenced here is commonly hypoexpressed in the brain, indicating that it is not amenable to brain development. Also interestingly, sialic acid can be released from cells and travel through the bloodstream to be picked up by other cells. What does this mean? Less (or, perhaps, none) of this cell marker in humans could very will be helpful to the increase in brain development and intelligence -- sounds like something evolution would select for, right? Especially in humans, where tool-making and intelligence had, for a long time, a direct impact on how much food you had and thereby how many children you had. Conveniently enough, the mutation in a hydroxylase protein that accounts for the lack of this form of sialic acid occurred in between the split between chimps and humans but before the divergence between neanderthals and humans -- exactly the right place to be looking for the development of human intelligence.
On another note, an interesting coincidence is that this hydroxylase protein is still expressed in humans, still at a lower level in the brain, but is non-functional. Why would God make humans with an ineffective version of this gene, expressed in exactly the same places? To confuse scientists? Or maybe this enzyme and its expression is a relic from a distant past.
I'm sure that a simple literature search such as the single google search I did on "sialic acid" would return interesting results in response to many of the other arguments in this article. I don't really have the time or energy for it, but this kind of pseudo-science really just gets on my nerves. It's perfectly fine in my opinion to cling to an irrational view that we are special, that we were created in God's image. It's nice to think you're better than the bacteria in your belly or the dogs on the street or the monkeys in the zoo. It's nice to think that all the other miraculous organisms were created for us to rule over and use.
But I think that in many ways it is simpler, and more beautiful to think that we are similar, that we came from the same place. Of course I look at the evidence before me in fossil records, in DNA homology, in skeletal similarities and vestigial limbs (such as our tailbones), and I see evidence for a common ancestor and evolution. But even on a spiritual level, there is something incredibly powerful about the idea of a common ancestor for all life. It puts you firmly as part of the beauty of the world, instead of placing you outside as an observer and overseer. That human life is as beautiful and simple and natural as a flower sprouting from the ground is, in my mind, just as magical as the idea that the flower was made for us and we were made to be like God.
Wednesday, May 31, 2006
I don't like change. I never have; from the time that I was three years old and raging against the fact that soon I wouldn't be in preschool but would be at home for the summer - even that much change was too much. It's not a good thing about my personality or a bad thing about my personality, it's just a thing that I have. I don't like change.
Which makes me really hate to own up to the fact that things I loved at the beginning of the year I'm fed up with now. I guess part of it is leading a group - this was my first year in a leadership position. It's difficult getting through a year and leading a group with people who either want to commit too much or don't commit at all, who have too much at stake with the group or who simply aren't invested. It's even harder when you're incredibly invested in the group. But I still feel like something could have been done differently so that the group I loved at the beginning of the year wasn't just a dark cloud hanging over my head right now. I hate admitting the change - and I don't believe that that change is necessary.
Objectively, when I look back, I think I did a good job. I started out with a group of two returning members, myself and one other, and the group now is a fairly tight-knit group of eleven. Two are graduating and leaving, one will probably drop out, but most of the rest of us are likely staying. We've done as much and been as active this year as in any previous year, perhaps moreso because this year is the first time we've released a CD. Hopefully the CD sales will push us back out of the debt that we were in going into the year, as the people who were leading the group before me didn't really pay attention to deadlines to get funding from the University. All of that says that I did a good job in what was an incredibly hard situation.
But the problem is that I go to rehearsal and I feel two things: first, that no one thinks I'm doing a particularly good job, and second, that if I do less than what I'm doing now they would think I was doing an actively bad job. All of which makes me dislike rehearsals and the group.
The problem is, at base, my hatred for change. Because although I know that I don't like the group as it is, and I know that I'm sick and tired of how the group is working, I feel like I should be just as in love with the group as I was when I agreed to be leader at the beginning of the year. I feel like nothing should have changed, because I don't like change - I'm scared of change, and so I'm scared of admitting that I don't like the group as it is right now and stepping down or leaving entirely. At the same time, I know that the best move for me mentally is probably to do one of those things, and in all likelihood I should just leave the group and say good riddance to a frustration and a sink for my money, time, and energy.
How's that for an introduction? I don't like the aesthetics of beginnings and introductions, they feel false and contrived - nothing really starts or ends in life; as things are now, all cells come from other cells and all organisms from other organisms. So there are no new beginnings and there are no real endings, there are only changes. That might explain my hatred for change - every change is an ending, if you want to read it that way. Every change is the end of some story, as every story can only end in a change of focus -- we stop paying attention, therefore it is over. In preschool, admitting that the schoolyear was being exchanged for summer was tantamount to saying that the story of that year in preschool was ending, over, that I wouldn't be able to go back to it and to be that same person with those same friends. Every summer is a little bit like that for me now, there's a thought that next year will be different (because it will) and that since I can't go back I can't continue the story. And for the group, which I had so many grand dreams about and so many hopes for, leaving it or stepping down as leader is tantamount to saying that those dreams and hopes are forfeit, that's not how the story worked out, because the story is over -- things changed.
Well, things change, as much as I hate admitting it. And to the extent that things change, things end.
Which makes me really hate to own up to the fact that things I loved at the beginning of the year I'm fed up with now. I guess part of it is leading a group - this was my first year in a leadership position. It's difficult getting through a year and leading a group with people who either want to commit too much or don't commit at all, who have too much at stake with the group or who simply aren't invested. It's even harder when you're incredibly invested in the group. But I still feel like something could have been done differently so that the group I loved at the beginning of the year wasn't just a dark cloud hanging over my head right now. I hate admitting the change - and I don't believe that that change is necessary.
Objectively, when I look back, I think I did a good job. I started out with a group of two returning members, myself and one other, and the group now is a fairly tight-knit group of eleven. Two are graduating and leaving, one will probably drop out, but most of the rest of us are likely staying. We've done as much and been as active this year as in any previous year, perhaps moreso because this year is the first time we've released a CD. Hopefully the CD sales will push us back out of the debt that we were in going into the year, as the people who were leading the group before me didn't really pay attention to deadlines to get funding from the University. All of that says that I did a good job in what was an incredibly hard situation.
But the problem is that I go to rehearsal and I feel two things: first, that no one thinks I'm doing a particularly good job, and second, that if I do less than what I'm doing now they would think I was doing an actively bad job. All of which makes me dislike rehearsals and the group.
The problem is, at base, my hatred for change. Because although I know that I don't like the group as it is, and I know that I'm sick and tired of how the group is working, I feel like I should be just as in love with the group as I was when I agreed to be leader at the beginning of the year. I feel like nothing should have changed, because I don't like change - I'm scared of change, and so I'm scared of admitting that I don't like the group as it is right now and stepping down or leaving entirely. At the same time, I know that the best move for me mentally is probably to do one of those things, and in all likelihood I should just leave the group and say good riddance to a frustration and a sink for my money, time, and energy.
How's that for an introduction? I don't like the aesthetics of beginnings and introductions, they feel false and contrived - nothing really starts or ends in life; as things are now, all cells come from other cells and all organisms from other organisms. So there are no new beginnings and there are no real endings, there are only changes. That might explain my hatred for change - every change is an ending, if you want to read it that way. Every change is the end of some story, as every story can only end in a change of focus -- we stop paying attention, therefore it is over. In preschool, admitting that the schoolyear was being exchanged for summer was tantamount to saying that the story of that year in preschool was ending, over, that I wouldn't be able to go back to it and to be that same person with those same friends. Every summer is a little bit like that for me now, there's a thought that next year will be different (because it will) and that since I can't go back I can't continue the story. And for the group, which I had so many grand dreams about and so many hopes for, leaving it or stepping down as leader is tantamount to saying that those dreams and hopes are forfeit, that's not how the story worked out, because the story is over -- things changed.
Well, things change, as much as I hate admitting it. And to the extent that things change, things end.
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