Female Triumvirate of Evolution Experts

Technical Fiction: A Proposal

2011-01-30T21:50:00.027-06:00

Rev. Barky and I canceled our cable more than a year ago, not just because of all of the crap on regular television, but because of all of the crap on so-called "science shows." The last good science documentary that I watched on cable television was "How the Earth Was Made." (It is a tour of history through the Precambrian and I highly recommend it!)

We were disgusted by the inaccuracies, the cliches, the inexplicable appeals to asteroids in impending apocalyptic collision with earth or the Bigfoot "expeditions" with dancing graphics and metrosexuals with hair gel doing their Blair Witch act, talking into a spotlight and a camera about how scared they were. (As someone who was a Bigfoot enthusiast when I was twelve, all I could think was, "What would Rene Dahinden or Peter Byrne think of these losers?" Scared! I wish Bigfoot existed! I'd run ahead and tell the big guy that he needs to pick up a digital camera and film the crazy humans for a change.)

Moreover, we are sick of these apparently ubiquitous cliches that seem to happen even in so-called "science fiction": aggressive computers that can be outwitted by being asked to solve a paradox; sparking and exploding electronics; fires that are bright (in reality they are dark) and from which people run upright (the heat and pressure from standing up in a hot fire can kill you before the smoke does); logical people/aliens/robots who discover emotions just by trying really hard (I would like to see the opposite happen for a change); aliens taking human bodies (although I wrote such a story, and the novel Those Who Watch also handles this idea quite well); computers that make a teletype noise when they display print; the scream of a hawk whenever a scene is outside; a character throwing a gun at an opponent once s/he has run out of bullets; cars skidding to a stop; and other tiresome crutches.

There is a natural tension between fiction and reality in literature, but hard science fiction is an attempt to reconcile the two in order to explore certain ideas. Thus I stumbled upon what I think is a new form of fiction, at least as explicitly proposed: Technical Fiction. My idea behind this is that the writer would refrain from falling back upon such literary crutches, and when presented, as writers so often are, with the choice of moving the story along or wrestling with an inconvenient, plot-mangling fact, the writer would deal with the fact even if it derailed the story. The writer would choose to tell a different story, an organic one arising from this fact, instead of glossing over it.

However, technical fiction goes even farther than this. Instead of reducing the story to another soap opera about (often unrealistic) humans, technical fiction will be the first genre since surrealism and science fiction to elevate the machine and the object to the level of character. My work this summer at the Smithsonian National Air and Space Museum solidified for me the ideas that had been simmering since I read the works of Robert Desnos and Andre Breton, who often featured objects as their main characters: that planes, space ships, engines, kites, gliders, cars, and turbines could be as beloved as literary heroes, and in a very real sense were heroes to many people. Their stories, their "characters" would be accurately captured in technical fiction.

However, technical fiction need not be limited only to technology: algorithms and modules of code can be included. However, a very important point to make here is that I would also include accurate representation of sex and sexuality as technical fiction. For a long time I have been troubled by the apartheid between Hollywood/independent films and porn; the former presents sex/uality in an appallingly naive manner while doing a very good job in creating arresting romantic situations and appealing characters; porn is ostensibly more realistic, but today it has become mechanical, a function performed by Brazilian waxed, boob-jobbed, faux blondes and men who have no appeal to me whatsoever. Cunnilingus, fellatio, missionary pos, and doggie - it's the same damn thing all the time. Lather, rinse, and repeat.

Writers like me who wish to write realistically about sex, love, and sensuality, using real people, real men and women, are writing a form of technical fiction as well. I would like to combine the ability to involve the audience in a good story and a romantic situation with more frankness about sex. (The first thing I would change: no one in porn smiles any more! At least in the 1980s, the women would have these glazed, ridiculous over-smiles, but now everyone is so serious. It's joyless, and annoying.)

What kind of stories would we start to tell if, instead of taking poetic license, we pushed ourselves to work through all of the inconvenient facts? I have two projects in the works right now. I don't know if they will be successful, but their progress will be posted here for you to see and comment upon.

(At least this time I hopefully will not be getting spam bots to the comments section of my blog begging me to put my peer-reviewed paper online for lazy, cheating college/graduate students to plagiarize!)

Blogging the Writing of the Peer-Reviewed Paper, Part 5

2010-05-14T15:45:00.004-06:00

Because I have been contacted by various and sundry nefarious term paper mills, who are (if they are to be believed, and who knows?) chomping at the bit for me to post my drafts, I have decided against posting them.

Perhaps I was naive about the amount of evil out there, lurking to shake money out of misguided college students who think they can cheat their way to a dream career. Honesty is the best policy! If you don't develop your voice, and if you allow your lack of confidence in yourself tempt you to cheat, you steal the future from yourself.

At any rate, my paper has been sent to The American Archivist for peer review. I will continue to blog my experiences with this process if the editor gives me permission to do so.

Blogging the Writing of the Peer-Reviewed Paper, Part 4

2009-04-11T22:48:00.004-06:00

Terry Eastwood does articulate a comprehensive archival theory. However, Eastwood’s theory also has a flaw, namely his rejection of selection (appraisal and reappraisal, weeding, deaccessioning). Eastwood’s own concept of “uniqueness,” in contrast to that of Roberts, defines archives as documentation of relationships, and as such, even a record duplicated, tripled, etc. in one collection deserves preservation to manifest each instance, since each gives the record a different context, and thus a larger importance in the fonds as a whole. Eastwood’s definition is problematic for archival theory, and this paper will demonstrate that selection, far from being an invasive action, is a necessary component of archives, and that Eastwood’s uniqueness concept contradicts the other principles in his theory.

Eastwood’s archival theory identifies five characteristics of archives: impartiality (capturing the creator’ biases), authenticity, naturalness, interrelatedness, and uniqueness (Eastwood, 1992). Uniqueness, however, negates the other qualities. Eastwood states:

Each document has a unique place in the structure of an archives. Copies of the document may exist in the same archives or in others. Each one is unique in its place. Being there signifies its relationship to activity and to the other documents accumulated in the course of that activity. So every archival document, whether existing in more then copy or not, is unique. (Ibid, 128)

Rather this fifth quality should be termed redundancy. One can demonstrate the flaw in Eastwood’s model by imagining the natural extreme of his logic—for example, an archives constructed from one original document which is photocopied. There are now two documents, both enjoying a unique relationship with the other. The photocopy is photocopied; now there are at least three unique relationships (actually nine total). Continue to photocopy each new photocopy in succession. Would we have an archives? According to Eastwood’s theory, yes[3]—it would be the impartial, authentic, natural, and interrelated evidence of an action (such as it is), with each document enjoying a unique relationship to all others! Yet our “archives” would also contribute no more information than the original document. Weeding by the creator would produce no more impartiality than not weeding; even disrupting original order would make little difference. Eastwood’s theory is thus incomplete in that relies upon human intuition to define an archives, and therefore Eastwood has not adequately answered the claim by Roberts that archives are a practice that one learns “on the job” (Roberts, 1990, 111), utilizing training and intuition, needing no theory. What is missing here? Selection.

Eastwood could still argue that pruning admittedly redundant information still erases a unique relationship within the archives that the creator included, thus removing a sort of information. However, given the backlog crisis in archives, how likely is it that creators prune their own collections to preserve multiple duplicates? Rather, Eastwood may have succumbed, and would consequently lead researchers, to a fallacious conclusion via the “file-drawer effect”—the creation of a relationship where one does not exist, a false correlation arising from mere coincidence.

Archival redundancy could lead a researcher to go on what is known in research as a “fishing expedition” (Hoofnagle, 2000). That is, the researcher, having found what he or she thinks is a significant outcome (the same document keeps showing up in different places—it must have all that much more importance!), concludes a meaningful finding and gathers further evidence of that, when in fact there will be, in any collection, a certain amount of false positives due to mere chance. This is articulated in John P.A. Ionanidis’s essay, “Why most published research findings are false,” [4] and reiterated by the experience of the editors of the Public Library of Science (PLoS):

[I]f you study anything, anything with statistics you’re going to find statistically significant correlations. In fact if you found nothing that would be strange as you would predict that if you study enough variables, roughly 5% should be statistically significant just by chance, and the nature of the scientific literature and the “file-drawer effect” is that this number goes up as researchers are more likely to publish big effects and “file away” the papers showing no effect even though the results are true (Hoofnagle, 2009).

Hoofnagle’s piece refers especially to false statistical correlation, but there is no reason to deny that if we study anything, anything with relationships (and statistics reveal relations) we would find false positives, qualitative correlations that Eastwood terms uniqueness. It is not true that only proximity preserves relationships in an archives. Each record enjoys an intellectual relationship with every other record in the archives, and therefore, any documents repeated in the archives bear their most significant relationships to each other. This relationship mirrors the “uniqueness” of that archives of photocopies in our thought-experiment, and is mere redundancy which should, and must, be purged to honor Eastwood’s theory.

Until we have more data to contradict these conclusions, our thought-experiment of photocopies suggests that selection, not uniqueness, is necessary to archives. Far from detracting from the authenticity, naturalness, and interrelatedness, careful pruning of a collection enhances these qualities. An archives is selection incarnate, because like an ecosystem it is collaborative and organic.

[3] However, this is a reductio ad absurdum and thus a playful thought-experiment rather than an argument: no archivist would really draw such a conclusion from Eastwood’s theory, and it is not the author’s intent to suggest that Eastwood demands it.
[4] Available at http://medicine.plosjournals.org/

Blogging the Writing of the Peer-Reviewed Paper - 3rd Post

2009-02-21T13:49:00.014-06:00

Roberts, John W. (1990). "Archival Theory: Myth or Reality?" American Archivist, Vol. 53, 110-120.

Here we are at the meat of my objection: Roberts states,

"[A]rchival functions are a process--nothing more. To concentrate too deeply on the process as if it had academic worth or were the essential element in successful archival work trivializes the profession, and threatens to make it arcane and narcissistic [emphasis mine]."

I think that he is party right - one should not "study" incessantly the archival process any more than one should the scientific method - but archival theory does not study the process! Of course not - the scientific method is employed in the study of evolutionary theory. Scientists did not construct this architecture of theory by studying the method - both the theory and the method arose iteratively together. Roberts is making a strawman argument.

From what I have seen of archival theory, theoreticians attempt to articulate the meaning of archives. Yes, in appealing to universal unchanging "truth," to ancient Roman law, and by portraying American archivists almost as heretics, archival theory has become, in my opinion, arcane and narcissistic. Roberts is absolutely correct when he complains:

"Archival theory is largely irrelevant to archival work, promotes an undesirable stratification within the profession, and is intellectually frivolous. Archival theory does two things that are profoundly threatening to clarity of thought: it overcomplicates that which is simple, and it oversimplifieds that which is complicated. It overcomplicates by elevating to the level of philosophy* the easily mastered procedures to archival work, breaking them down into their most minute components and analyzing them far beyond a point of edification. It oversimplifies by reducing to a string of formulas, flow charts, and dicta the multi-faceted demands of learning a topic, a record group, and researcher needs, and integrating that knowledge with a knowledge of other topics, record groups, and a researcher's needs."

Yet in my opinion the reason for this is that what passes for archival theory is not really theory but philosophy. *Roberts even acknowledges this. The philosophy of science is not a scientific theory, and for this reason no real archival theory yet exists that functions as a theory.

However, I am likewise troubled by the writers in Archivaria who inveigh against "Positivism," "impartiality," and "archival science." Many don't see an archival science. Without putting the blame entirely on their appeals to post-modernism (none of the authors believe that a rock thrown at their heads is only a social construct by the dominant paradigm), I think this is nonsense. Of course, we have had to qualify scientific aims and the ideal of objectivity with the observed reality that social constructs filter our attainment of these aims and ideals - but I do not believe for a minute that there is no fact of the matter, no universals to be found in science, whether it be biology or archivism. It seems to me that the words "science," "theory," and "impartiality" (which is mistaken for objectivity) are being thrown around carelessly by archivists.

To return to Roberts, he states at the beginning of this article that Ted Koppel, in speaking to journalism students at the University of Maryland, urged them not to study journalism but to pursue another line of inquiry in order to become a journalist. "Koppel was saying that the key to success in journalism is a knowledge of substance, that journalism as an academic discipline does not deal with substance but only technique, and that the technique itself does not merit a great deal of study because journalism is a trade that can be learned on the job." Immediately I agreed with much of this but had three objections:

1. I never learned about the inverted pyramid/5ws, which I think is a useful construct or method (tune into any cable news show and listen for the who-what-when-where-why and see if you get it first off, rather than a teaser or a "question" posed by the newscaster meant to anger or frighten you into watching a long time for that information), in English Composition or any other class.

2. Just because something is labeled a "trade" does not mean that it can be learned "on the job." People may not remember trade schools and skilled trade apprenticeships anymore since we've exported most of our traditional skilled labor jobs, but no one could walk off the street and immediately get hired as a pipe-fitter or a sheet-metal worker journeyman with the promise that he (it was mostly a he) could learn these skills "on the job." (By Roberts' definition, computer programming is also a "trade.")

3. The true problem may be that certain interdisciplinary skills are not being taught in these "trades" that are not "academic." For example, all journalists should be rigorously drilled in the recognition of logical fallacies! They should also learn proper research and fact checking methods, and some statistics, so that they don't make fools of themselves and spread misinformation, which unfortunately happens more often today.

What do archivists need to learn about their profession - their theory, their science, and the intuition upon which they (as do all scientists) draw? I fear that some archivists are drawing upon "intuition" too much, when these people in their unwillingness to introduce "cold" positivist analysis into their comfortable sphere actually share a methodology that they are unnecessarily reinventing from scratch. Conversely, I also fear that would-be theoreticians are too far removed from the present ad hoc nature of archives. Terry Eastwood, whose article I will examine in the next post, is correct to take Roberts to task for saying that there "is no big picture" in archives, but Eastwood does not supply one himself. Where is the error?

I surmise that archives, despite its long existence, is still a profession that does not know itself, as "natural philosophy" did not sufficiently know itself during the era of Darwin and Mendel. Moreover, I fear that as Darwin and Mendel worked separately, seemingly in work that was mutually unconnected, so today's archivists still work separately, unaware of the transformative power of connection that a proper, scientific theory of archives would bestow. Yes, of course we need to study other disciplines - Darwin needed geology to demonstrate an old earth for there to be enough time for natural selection to work. Darwin could have used the paleontological, genetic, and biochemical knowledge that we have today - but his theory helped to drive the discoveries that his theory needed to become more complete! That's the paradox.

Roberts argues that archival theory is unlike the theory of quarks, or of plate tectonics, because they deal with indirectly observed behavior, whereas "everything about archival work, theoretically, can be known empirically." Theoretically! He says this without apparent irony. Well, if this is true, then let us know archival science empircially, then! Let us find out, empirically, what archivists really do when they're talking about what they're doing.

Archivists likewise need to document what their real practices are (as opposed to what they think they're doing) and to share this information before we can celebrate, or torpedo, a universal archival theory.

Blogging the Writing of the Peer-Reviewed Paper, 2nd Entry

2009-02-11T19:03:00.014-06:00

I've just completed Caroline Williams' "Studying Reality: The Application of Theory in an Aspect of UK Practice," and as I finished, I thought, "Amused Muse, welcome to the social sciences!"

As I feared, my idea is not original: none other than Barbara Craig has called for a "basic empirical examination of the professional conditions of those who do [archival] appraisal." She has pursued this project in Canada, the preliminary results of which were published in 2004. (Naturally I'm going to get my paws on that.) However, while Williams laments the lack of such a study in the United Kingdom, a limited survey was done.

Archivists doing appraisal in the UK were surveyed as to whether their organization had a formal appraisal policy or guidelines, what they thought the purpose of appraisal was, and their knowledge of or exposure to appraisal theory and how that affected their practice.

Heretofore, I have not been impressed with much of archival theory - for me some of it compares to the niceties and "golden age" nostalgia of the equestrian training and sabre exercises that characterized the Russian military officers just before World War I - but nevertheless, I cannot agree with those hard-core practitioners who argue that the nature of archives is essentially ad hoc, with not enough common ground between individual institutions to merit a broad view. Williams' approach humanizes archival theory and makes it more relevant. Williams identified the "conceptual, long-term aims of some theorists" with regard to archives as:

to "document society"
to "define society's values"
to "provide a representative record of our time"
to "shape the future of our jurisdiction's documentary heritage"
to "serve the interests of justice"

That last point is especially interesting, as I have started reading another article about genocidal archives, such as those used in the Nuremberg Trials and in the aftermath of the conflicts in the former Yugoslavia and in Rwanda. The author of this article expressly advocated that the purpose of archives be to promote the cause of justice. This and Williams' article are the first I've read to put forth justice as a purpose of archives, and a component in archival theory. This would give archives an active role in society, rather than the quaint, "dusty," passive (and "objective") role usually ascribed to them (and usually by non-archivists).

Apparently, the limited survey of UK archivists reveals that they, to avoid what they called "pre-conceived ideas" about the "uniqueness" of their particular repository, eschewed specific guidelines and detailed policies for an "intuitive" appraisal born of experience that was difficult to express, let alone write down. "Some," continued Williams, "acknowledged the difficulties that a lack of guidance could create." I hope so! Williams went on to describe what seemed to me a situation of archivists disconnected from each other, not publishing, and acting as though their archives was completely unique with no overlap or commonality with any other archives, "re-inventing the wheel." Good point!

Of course we must not approach appraisal with preconceived ideas, but we must have an approach. (This is my reply to those, usually conservative religious believers, who argue that we are all ruled by our respective "worldviews" (which they try to equate with theory, when the two are not alike) - one's worldview can be deliberately tentative and subject to an approach, or methodology, that tests and assesses this so-called "worldview.") If we can document the process of writing a novel (or a paper!) we can at the very least set down guidelines that 1) allow for best and consistent practices across staff changes, and 2) allow archivists to communicate with each other and thus test, via publication and communication at conferences, whether their preconceived ideas about so-called preconceived ideas, their worldview, if you will, of archives, is really so unique, so individual, or if there are commonalities about which we can generalize!

Williams does acknowledge the value of experience and "intuition." So do I. Human judgment must enter into appraisal. The best computer indexing program cannot write an adequate index (whereas abstracting programs have produced serviceable abstracts). But without some kind of theory, archives will turn into desert islands of - what kind of methodologies? Cookie-cutter examples of mediocrity, disconnection, and disorganization, I suspect.

However, I cannot believe that the "dynamic tension" of being "practically oriented academics" and "academically oriented practitioners" is a "difficult balancing act." Rather, as Craig says, we do not know enough about how theory and practice inform one another. This is, I suspect, because the archives professionals do not yet thoroughly know their professional practices in various forms of archives around the world. In my view (and this touches upon my hypothesis), archival theory must be understandable, approachable, applicable, and useful to any and all archivists. To mangle that famous quote by Theodosius Dobzhansky, Nothing in archives should make sense except in the light of archival theory.

Archival theory is at present too distant from, and too idealized for, the practice of appraisal. My hypothesis, that we need a comprehensive empirical study of what archivists are actually doing (and not only what they say or what they think they are doing), and what actually happens when archivists leave it all to "intuition," before we can formulate a relevant archival theory, seems to be echoed in both Williams and in Craig. In my paper I hope to support my position with evidence drawn from actual case studies in order to set out a program for such a comprehensive survey.

Blogging the Writing of the Peer Reviewed Paper

2009-02-09T18:18:00.007-06:00

Draft. (Why can't I view the draft?)

Where am I in this process? Really, even though I have a proto-hypothesis, I am still in the process of reading for information and refining my question.

If all goes well with the thesis that I'm developing, I won't have a test (it would involve a lot of surveying), but a plan of action for a test.

At this point, I need to find out more about what is known about the actual implementation of archival theory by its advocates in Europe, and about the actual employment of the methodologies by those who counter that archival theory is too abstract and that Americans, at least, need to focus on methods and practices because we are a less centralized and more diverse culture.

I have gathered around 30 articles/blog posts/book reviews relating to archival theory, appraisal, deaccession, case studies from multicultural perspectives, archival practices in various nations and/or cultures, archival integrity or deceptive practices or statistical anomalies, political pressure on archivists, and interdisciplinary views of archives. At this point, I don't see a need to revise my primitive thesis.

What the hell is she talking about?

Galapagos Diary

2008-03-02T16:31:00.001-06:00

Introduction: Quito

Jerry Falwell Deconverted

Day One: Landing at Baltra

Day One: Las Bachas, Santa Cruz

An *Hic* Aside

Day Two: Espanola

Day Two: Floreana

Day Two: Star-Gazing Stumbling

Richard Dawkins: Responses to God Delusion

Richard Dawkins: Neo-Darwinism, Part I

Day Three: Fernandina

Day Three: Isabella

Photos

Organisms, Groups, and Memes: Vehicles or Replicators? Part 2

2007-03-26T21:58:00.000-06:00

I have never understood Punctuated Equilibrium in the manner that Dawkins, in his chapter, spends considerable time refuting. Evolution is gradualist, as Dawkins says, in the sense that there is no such thing as half an animal. A "transitional fossil" can be a confusing concept, giving one the idea that certain animals are "transitional" as opposed to being "normal" (when in fact every living thing is "transitional"). This misunderstanding is exploited by creationists in their tiresome demand for "transitional" fossils.

P.E. is, essentially, a reinterpretation of the fossil record which turns out not to be as radical or revolutionary as Gould portrayed it to be. Dawkins likens the difference between previous interpretations and the Gould-Eldredge proposal as the difference between walking up a hillside and ascending a staircase. There are no "gaps" in the fossil record, only steps.

Dawkins explores Gould and Eldredge's equation: P.E. + Wright's Rule = Species Selection

Wright's Rule: "The proposition that a set of morphologies produced by speciation events is essentially random with respect to the direction of evolutionary trends within a clade." In other words, in an apparent analogy with mutational randomness, if a species of horse shows marked progression toward larger body size, a new species of horse would not necessarily follow this trend, if Wright's Rule is preserved. As many new species would be smaller than the clade as larger. Therefore, Wright's Rule must be tested.

However, Dawkins points out (quoting Gould): "'If Wright's Rule be valid, and new species of horses arise equally often at sizes smaller and larger than their ancestors, then the trend is powered by species selection. But if new species arise preferentially at sizes larger than their ancestors, then we don't require species selection at all, since random extinction would still yield the trend.' Gould here simultaneously sticks his neck out and hands Occam's Razor to his opponents!" Dawkins adds that he can imagine some major speciational trends of the type described by Cope's Rule,* but points out that this is quite different that the original question, that of individual sacrifice behavior or adaptations "for the good of the species." The difference is between the concept of the group as replicator versus the group as a vehicle for replicators.

Palaeontological major trends, such as the length of horses' legs, are simple, requiring only a few replicator replacements, whether we mean genes or species at this point. However, many more replicator replacements are required for the evolution of a complex adaptation such as those that allowed a land mammal to evolve into whales, for example. Even if such a complex phenomenon could be broken down into smaller evolutionary events, the adaptation involves an interrelated web of changes that group-selectionism just could not produce them without yielding, over and over again, a highly unlikely barrage of parallel beneficial trends. (Indeed, this mistaken idea of group-selectionism could be what some creationists imagine evolution to be, leading them to dismiss evolution as improbable.)

Dawkins writes:

The theory of species selection, growing out of that of punctuated equilibria, is a stimulating idea which may well explain some single dimensions of quantitative change in macroevolution. I would be very surprised if it could be used to explain the sort of complex multidimensional adaptation that I find interesting, the 'Paley watch," or 'Organs of extreme Perfection and Complication' kind of adaptation that seems to demand a shaping agent at least as powerful as a deity. Replicator selection, where the replicators are alternative allels, may well be powerful enough. If the replicators are alternative species, however, I doubt if it is powerful enough, because it is too slow. Eldredge and Cracraft (1980, p. 269) appear to agree.

Part 3: Memes

Open Thread on Global Warming

2007-03-19T16:41:00.000-06:00

Hello everyone:

While I finally work on my upcoming installment of The Extended Phenotype, you may have at it about global warming. Just a reminder: I am going to be a lot more strict about enforcing the respectful comments rule than I have been at Amused Muse. The subject is global warming - not each other. Puh-lease! Thank you so much. :-)

First Woman to Win Turing Award

2007-02-23T12:15:00.000-06:00

(AP) -- One of the most prestigious prizes in computing, the $100,000 Turing Award, went to a woman Wednesday for the first time in the award's 40-year history.

Frances E. Allen, 74, was honored for her work at IBM Corp. on techniques for optimizing the performance of compilers, the programs that translate one computer language into another.
This process is required to turn programming code into the binary zeros and ones actually read by a computer's colossal array of minuscule switches.

Allen joined IBM in 1957 after completing a master's degree in mathematics at the University of Michigan. At the time, IBM recruited women by circulating a brochure on campuses that was titled "My Fair Ladies."

Read the rest here.

Organisms, Groups, and Memes: Vehicles or Replicators? Part 1

2007-02-13T23:09:00.000-06:00

An active replicator is that which exerts at least some kind of influence over the likelihood of its being copied. A DNA molecule is a replicator; a piece of sheet music considered valuable enough to be xeroxed can be considered a replicator (Dawkins, p. 83); but an individual organism, sexual or asexual, cannot be considered a replicator.

Here's why.

Because we reject Lamarckism, we know that characteristics acquired during an organism's life cannot be passed down to its offspring. Even in the case of asexual reproduction in which the entire genome is passed down, any acquired features--a lost limb, developmental factors, etc.--is not replicated in the lineage, and in order for the organism as a whole to be called a replicator it must pass these on. "There is a causal arrow," writes Dawkins, "going from gene to bird, but none in the reverse direction." However, the genome of an organism that reproduces asexually could be a candidate for the term "replicator."

Can a species be considered a replicator? Again, Dawkins points out that a species, being mutable, is not comparable to a gene and its alleles. However, the gene pool of a reproductively isolated species could be a candidate.

In examining this possibility, Dawkins explores "differential lineage extinction"--for example, the statistical rates of extinction of ammonites and bivalves that have a high rate of evolving a larger size, say, than those who do not (those that more rapidly increase their size over successive generations are also more likely to die off). However, while these different rates of extinction are a form of selection, they do not drive "progressive evolutionary change" and thus these lineages are not replicators, either. They are merely, as Dawkins terms them, "survivors."

(And at this point, people, I confess I must read the chapter again.)

Part II: Punctuated Equilibrium and Memes

And I Was Going For LeGuin!

2007-01-28T18:09:00.000-06:00

I am:

Samuel R. "Chip" Delany

Few have had such broad commercial success with aggressively experimental prose techniques.

Which science fiction writer are you?

The Active Germ-Line Replicator

2007-01-17T23:23:00.000-06:00

What is a "gene"? Dawkins admits to using the term loosely. In this chapter he tries to nail down the term more precisely, in order to give a clearer, "gene's eye-view" of the replicator as the unit of selection.

In 1957 S. Benzer split the gene into three units: the muton (minimum unit of mutational change); the recon (minimum unit of recombination); and the cistron (roughly equivalent to the unit need for one polypeptide synthesization). Dawkins proposes the optimon (and Ernst Mayr the selectron) as the unit of natural selection.

Dawkins briefly describes Gould's objection to his proposal, and critiques Gould't characterization of the selfish gene replicator as located "below" the level of the individual (which for Gould was the unit of selection), as the species group-unit is located "above" the level of the individual. Dawkins points out that this "single-dimensional ladder" analogy is not apt in that genes are replicators, whereas vehicles (individuals and species) are not. Individual vehicles are selected, but they are not replicators (more on this later). Likewise, replicators are selected by proxy as individuals (vehicles) are selected.

The issue of species versus individual selection is a question of what is to be properly considered a vehicle; the issue of individual/species versus gene selection is a question of what is to be considered a replicator.

"I define a replicator as anything in the universe of which copies are made," says Dawkins. These may be active (displaying some ability to influence their being copied) or passive, "germ-line" (such as gametes), or "dead-end" (somatic). It is the active, germ-line replicator that Dawkins names as his optimon.

Because chromosomes, and the genes within them, are subject to splitting due to crossing-over in sexual reproduction, replicators may consist of various codon lengths, but, depending upon their length and the strength of the particular selective pressure on them, various replicators will have different "half-lives," and the most successful replicators will, by exerting their phenotypic effects, have the longest half-lives with respect to their alleles.

It now becomes obvious why no individual, nor even an individual's genome, can be considered a replicator.

In the next chapter, Dawkins explains what individuals and species are, and why species also cannot be defined as replicators.

Menopause and Mountain Sickness

2006-12-25T21:13:00.000-06:00

Dr. Marco sent me the link to his paper.

Arms Races and Manipulation, Part 2

2006-12-15T23:33:00.000-06:00

If evolution can be viewed as a sort of “arms race,” one often assumes that if an animal manipulates another, the victim will, via random mutation and natural selection, develop counterstrategies to escalate the arms race rather than capitulate. However, Dawkins shows several examples of how this is not necessarily so.

For example, the foster parents of the cuckoo continue to feed their changeling “child” despite the obvious absurdity of a tiny Garden Warbler straining to feed a cuckoo several times its size. Why doesn’t the Warbler recognize this incongruity, when apparently some host parents of cuckoos can indeed recognize flaws in the cuckoo’s egg mimicry? Why does the host parent recognize the parasitic egg but not the more obvious parasitic changeling fledgling bird?

Dawkins’s answer is that natural selection does not act uniformly at all times in any animal’s life. Selective pressure may be stronger at some points in the life cycle than others, or natural selection may have no effect on evolution even if a beneficial mutation were to arise. As an example of the first case, Dawkins points out that recognition of a cuckoo egg in one’s nest gives the host parent the chance to gain an entire breeding cycle, whereas recognition of the incongruous fledgling would buy at most a few days, and that probably too late for the host parent to breed again. Moreover, the actions of the cuckoo, its exaggeratedly gaping mouth, its size, could indeed act as a “drug” on the foster parent, no less than the song of a male nightingale acts as a drug on the female reproductive cycle (and, incidentally, upon the poet’s imagination).

However, a fascinating example of how an animal’s victimhood can be perpetuated is exemplified by slave-making ants. Some species of ants spend a great deal of their time raiding the nests of others and carrying off the larvae and pupae, which subsequently hatch in the new nest and begin to labor for their “masters.” This is a disturbing and puzzling development. Why don’t the enslaved worker ant colonies develop a resistance to the strange environment, filled with others not their genetic sisters—for example, by evolving a genetic disposition to cease work (to go on “strike”) when in a strange queen’s lair?

Remember that worker ants do not reproduce. Therefore, any beneficial mutation that arose in the enslaved ants would not be passed on to the rest of their home nest. At any rate, the raids do not happen often enough to destroy the victims utterly, who are under little selective pressure to evolve complex adaptive countermeasures against slave-making behavior on the part of others that, while aggressive, does not threaten the existence of the nest. An uneven battle ensues, in which the slave-making ants can be said to win the war.

Dawkins indicates that this situation is not unlike the phenomenon of a certain species of hybrid frog, which has one set of chromosomes that is jettisoned in meiosis and one set that is passed on to its offspring. The set of chromosomes (dead-end replicators) that is jettisoned in the hybrid frog is perpetuated in the pure bred species that carries two sets of these chromosomes (which become germ-line, not dead-end, replicators in this species). Thus, any beneficial mutation in the dead-end replicator line will be passed on in the pure bred species that contains two sets of these chromosomes (because in this species these sets of chromosomes are not dead-end replicators), but will not be passed on in the hybrid species. The situation of the enslaved ants is like that of the hybrid species of frog: their genes have phenotypic effects and can even be selected, but they will not be transmitted in the hybrid species, and thus are irrelevant to that particular species' evolution.

Arms Races and Manipulation, Part 1

2006-12-15T23:29:00.000-06:00

Dawkins' purpose in his book The Extended Phenotype is to dash the concept that the individual is the unit of selection, that is, the idea that, among other things, individuals act in a manner as to increase copies of itself. (Ann Coulter, for example, in her crap book Godless asks why, if evolution is true, she doesn't want to have children. Once again, she has mistaken evolutionary theory for a naive "for the good of the species" caricature of evolution. I should think that organisms (i.e., Dembski) manipulating other organisms (i.e., Coulter) into believing in creationism would be a prime example of said manipulation.)

Organisms may consistently work against their own interests (inclusive fitness) through being manipulated by another organism. Examples of manipulators are angler fish and cuckoos.

Although it's easy to assume that one animal manipulating another is only a temporary phenomenon until the other animal evolves some method of fighting back (that is, that the manipulation is a "time-lag" phenomenon--see my post on constraints on perfection), in reality the manipulator can in fact succeed continuously under certain conditions. An example of this is intraspecific manipulation (manipulation within the species, particularly kin-manipulation). Examples are parents manipulating their offspring, and offspring manipulating their parents.

Altruism is defined here, in a biological sense, as a behavior that favors other individuals (their inclusive fitness) at the expense of the actor.

Dawkins believes that parents who manipulate their children have an advantage over parents who do not, but states that parents do not have any built-in advantage over their children by the mere fact of their being parents.

The Extended Phenotype - Constraints on "Perfection"

2006-12-15T23:23:00.000-06:00

One of the flaws in Ann Coulter's arguments in Godless is the fact that she believes that mutations arise already labeled neutral, beneficial, or non-beneficial, as if God had willed it so. Mutations do not arise in a vacuum, however, and any mutation is potentially any of these. When one says that a mutation (or adaptation) is beneficial, this must be taken in context with the vehicle's (organism's) genetic structure, environment, the existence of predators and competitors, the potential costs of this benefit as opposed to other benefits that could have evolved instead, etc. That a mutation carries an advantage in its particular context does not mean that the resulting adaptation is perfect, or that "things came together in perfect harmony" (as I often hear people say), or that the adaptation would even be considered adequate given fewer external constraints!

"It is simply meaningless to speak of an absolute, context-free, phenotypic effect of a given gene."--Dawkins

6 Constraints on "Perfection," or 6 Objections to Naive Adaptationism

-Time lags--the animal observed is "out of date," built under the influence of genes selected in an earlier era under different conditions. (The "lag load")

-Historic constraints--natural selection, having no foresight, modifies existing structures for new uses, leading in many cases to an obviously suboptimal formation, which nevertheless carries an advantage over no such formation at all.

Two species can respond to the "same selective forces in slightly different ways." --Lewontin

-Available genetic variation--"No matter how strong a potential selection pressure may be, no evolution will result unless there is genetic variation for it to work on."

-Constraints of Costs and Materials--adaptive organization is a "tangle of compromises."-Imperfections at one level due to selection at another--again, natural selection has no foresight.

-Mistakes due to environmental unpredictability or "malevolence"--adaptation to conditions is statistical in terms of success; moment-by-moment changes in an environment can trip up even the most successful animal. Moreover, manipulation of one animal by another can exploit the victims abilities, which in this context become disadvantages. The "loser" of this arms race may develop the ability to resist such manipulation; may find the manipulation beneficial to itself as well or may shape it to be such; or may actually go extinct, which does not necessarily benefit the aggressor.

Women Not Funny? Now, That's Funny!

2006-12-15T22:50:00.000-06:00

Christopher Hitchens needs to get out more. He's turning into a pompous old fart. He doesn't think women are funny - can you imagine? hasn't he ever watched Judge Judy? - and he invokes pop evolutionary psychology to defend his point.

Hoo-boy, the next batch of self-help books (Men are from Mars, Women are from Penis, uh, Venus) are going to be something else (Men are Happyloids, Women are Dippyloids)!

Kristine launches her silly salvo.

I love to make people laugh. (And to inspire "sudden art." I am, after all, the Amused Muse.)

The Extended Phenotype - Introductory Summary

2006-12-15T16:03:00.000-06:00

-There is survival value in the "packaging of life into discrete units" called "vehicles" or organisms.

-We can speak of "adaptations as being 'for the benefit of' something, but that something is best not seen as the individual organism" but the "active, germ-line replicator" which are not selected directly, but by proxy.

-A behavior pattern "can be treated like an anatomical organ."

-A species or "group" is not the unit of selection, and gene selectionism is not genetic determinism.

Regarding the defining of what constitutes an adaptation, Dawkins first takes on the concept of extreme adapationism and identifies three proposed constrants on "perfection" (or optimal function) that he finds less persuasive:

-Neutral mutations, which are changes in polypeptide structure having no effect on enzymatic activity of the protein, and thus having no phenotypic effect at all.

(Biochemical controversy: Do all gene substitutions have phenotypic effects?)
(Adaptationist controversy: Is this phenothypic effect the result of natural selection?)
Though it is possible to a phenotypic effect to be selectively neutral, beware human subjectivity in these judgements. Genetic drift plus natural selection may result in more optimal function than just the effects of natural selection alone.

-Allometry, which is the disproportionate growth of a characteristic (such as a large head in small humans and in large ants).

-Pleiotropy, which is the possession by one gene of more than one phenotypic effect.

Introducing a New Blog - Science and Women

2006-12-14T23:45:00.000-06:00

John A Davison told me: "Why don't you join up with the other two multisexual femme fatales to complete the female triumvirate of evolution experts. Then you might found a colony on the island of Lesbos where you can spend the rest of your useless lives admiring one another with GAY abandon."

To me, that rather reeks of, "I'm not into girls." Well, neither am I, not in the pre-biblical sense that JAD means. However, this comment, plus a debate going on about women in science gave me an idea.

How about a blog devoted to science--just science--by women--just women?

Men can view and comment, but this is about (smashing) women smashing stereotypes. How about it?

Of course, I wish to have more than three women posting, so I suppose the triumvirate could refer to the concept of triangulation.

I will keep my posts on The Extended Phenotype at Amused Muse but will migrate them here as well.