by

Derwin Darwin II

Thanks to the ingenious workings of my cousin and mentor, Mr. Jules Verne, I have had the opportunity to travel from the present day, indeed, from the present century, far into the future, to a year that by my best surmise is approximately 2007, at which time I was able to converse with numerous members of the society of scientists known (enigmatically to me) as “The Blogos Fear.” From these conversations, I have ascertained numerous proofs, some complete some in process, of the Theories of Organic Change and Natural Selection, as well as Sexual Selection, as have been laid out by my very deservedly famous uncle, Charles Darwin of the Royal Society. I am appreciative of the support and encouragement of the Royal Society, and the publishing house of Periwinkle and Stoat, for the opportunity to lay before you and review these findings from the future. I am also especially appreciative of Cousin Verne for managing to produce this wonderful invention, and especially, for the ability of this invention to work in reverse order such that I have returned safely and soundly to my abode, country, and century, to make this humble report.

The Particle or Unit-based Nature of Inheritance.

It would ultimately have been discovered that the reason offspring resemble their parents is owed to a particle of inheritance called “the gene” and with each gene having a range of variants, not continuous in nature, but rather, existing as alternatives to one another and thus making up the bulk of the variation we see among offspring. It turns out that the particular pieces of inheritance also vary in the way they are “expressed” sometimes working in amazing ways with, and oft against, one another.

This is well understood by study of the phenomenon known as “pliotropy” and in this area of research, the answer to a question so advanced we benighted scholars of the 19th century barely thought to ask it: How did aging evolve? Inasmuch as aging might be described as the loss of (Darwinian) fitness as a function of post-reproductive age, it seems counterintuitive that natural selection could have produced such a phenomenon.

One idea that has gained traction is the theory of so-called antagonistic pleiotropy: A gene that has a beneficial effect early in life, but a bad effect late, can be positively selected. Oft-quoted examples include the prostate and breast, where robust proliferation improves early-life fitness (via effects on reproduction and child-rearing, respectively) but can increase cancer risk (and thereby mortality rate) in old age. I found this interesting set of connundra to have been well explored in the writings of Ouroboros, in particular a piece entitled Conditioned for aging: Antagonistic pleiotropy in essential genes.

Among the more exhuberant individuals, with respect to this “genetic” mode of inheritance, which uses by the way in its operation a molecule called, briefly enough, “DNA,” I found one Dr. Hsien-Hsien Lei, who told me in no uncertain terms, and in a most engaging and interesting manner, “Seven Things I Love about DNA.” By “I” of course I meane He.

Just as I was beginning to develop an understanding that these “genes” were items of inheritance, variable in their nature, made of the molecule DNA, I also was shocked to learn that much of this stuff (this DNA) is considered by some as “Junk.” Not used by the system of inheritance at all. This would be a great joke for my Uncle, who often said that the proof of a lack of Godliness in Nature would be the discovery of things that make little good sense from a designer’s point of view.

This discussion is intensive and widely-ranging. One Dr. Ryan Gregory of the Canadian Provinces (or is it now a Nation, as of this writing I realize I forgot to ask if the Queen, or King still reigned there!) has much to say about it. He discussed the idea of Function, non-function, some function, and a brief history of junk DNA. He further elaborated with the idea that some Junk DNA gets Wired … which in this case is a reference to a discussion in a journal called “Wired” about so-called Junk DNA. He discussed More about ENCODE from Scientific American, a journal, by the way, from our own time I am please to see persists into the future! T. Ryan Gregory also engages into the very nature of being with a discussion of “Because” verses “so that.” Very heady stuff. And, finally, proposes the idea of Inter-lineage selection versus “just in case”. I would recommend reviewing each of these productions in the order provided here, for best results.

Dr. Moran, of whom I speak elsewhere in this manuscript, warned against being Wired on Junk DNA, or at least, explains why our brethren in the fifth estate may have gotten this concept badly wrong in their reporting of it. Even the Panda’s lament that there is So Much Junk in the Genome … and the Press.

Remarkably, despite the clear demonstrating of Uncle Charles’ theories by the very existence of this “Junk” the bible waivers run amok, even in this century of epitomal modernosity, as lamented by the Hoofnagles in their pamphlets More prediction of the past — from the future! and Sal Cordova Quote Mines Nature (I’m Shocked!) which deal with the relationship between so called “Junk DNA” and so called “Intelligent Design Creationism.” Whatever that is.

What a fight these “moderners” are having over nothing! Alas, as in my day and the days of my fathers and grandfathers, going back to the ages of darkness and beyond, the preachers seem unable to keep to their own stables, and run amok among the masses waiving and thumping their bibles in the very face of reason and science. I have to agree with one strange man I met in my travels to the future, a Paul (PZ) Myers, clearly a giant in his own time, much feared as one in my day would fear the Bishop Wilberforce himself, but for different reasons, when he (Dr. Myers) exclaims: I’ts Junk. Get over it! as his response to this kerfuffle.

What is most fascinating to me is that decades, not years, and indeed nearly a century after I’m told the “gene” was discovered — only now in this future time — scientists endevor to actually observe and count all of them. I’m not sure what they were thinking for the previous decades. I was told this: “As recently as five days ago, I penned a post about what the Human Genome Project (HGP) had and had not accomplished. I wish I could say that I had written that with the full knowledge that it would be a great primer for a piece about the genome discoveries released today by ENCODE , the NIH follow-up effort to the HGP. I would be lying if I did.” and referred to the pamphlet “What did ENCODE decode?”

The Not So Lowly Worm and Other Matters

It is well known that my venerable Uncle Darwin was among the first philosphers of nature to write extensively about worms. I was thrilled to find out that research on worms continues well into the future. I met a rather skeptical alchemist, who in his toil travels back to the beginnings of C. elegans research, to study a new type of mutant as well as its genetic interactions with other known mutations, all now very much used in 20th century C. elegans labs … a mutation known as roller - or simply rol.

“Many cases of mutations leading to morphological changes are known in higher organisms, but genetic analysis can only be done in a few systems such as mice and Drosophila. In these cases the molecular events leading to the morphological alterations are difficult to ascertain. Nematodes are simple eukaryotes that have some of the major organ systems found in higher organisms. This makes them desirable and relevant animals for study. The nematode Caenorhabditis elegans is used in experimental studies because it is easy to manipulate in the laboratory, has a short generation time, and is accessible to genetic manipulation (Brenner, 1974).”

This self styled alchemist is expert at describing the very nature of worm-research in a highly recommended piece called there is a reason why they call ‘em rollers…

This sort of work relates to the concept that the fullest understanding of evolution requires an examination of the process of development, and much of this effort is apparent in this far away century. The research performed about one year prior to my ‘untimely’ arrival by our colleagues Takahishi and Yamanaka will be, it is claimed by my colleague Alex Palazzo of The Daily Transcript the basis for the former’s receipt of nothing less than a Nobel Prize. The research proposes to reveal how to transform any cell into a stem cell. Of most astounding import is the approach the authors take to their important work. I agree wholeheartedly with Dr. Palazzo that anyone interested in the proof of evolution over alternative theories should Read this stem cell paper!

Lord Kelvin’s Revenge?

I found much to my delight that the calculations of Dr. Kelvin, which so depressed my good Uncle owing to the conflict in estimations of the age of the earth, are completely overthrown in this future century. I was never able to ascertain or understand the reasons for this overthrow of the Great Lord Kelvin’s calculations, but was able to find that his fundemental properties of the physical nature of matter and energy were at least partly intact.

I learned this during a visit to an establishment called The Old Curiosity Shop, and by reading an item On Micelles, Vesicles and Artificial Cells. This is a collection of thoughts on the principles of entropy, energy and equilibrium expressed in the context of self assembly of surfactant molecules. This is a very interesting and highly recommended discussion at the interface between the very physics of life and life itself.

Investigations at the Smallest of Scales

The primitive machines of my Uncles century (and, alas, mine own as well) have given us insight into the workings of the very small, but in the future there would develop an understanding of the nature of life at scales of unimaginable tiny-ness.

One of the most alarming findings is that related to the so-called “bacterium” Clostridium botulinum. This is a rod-shaped Gram-positive bacterium which produces the most poisonous toxin known. Botulinum toxin has a lethal dose of about 1 ng/kg, meaning that a few hundred grams could theoretically kill every person even on the heavily populated Earth of the 21st century! The toxin works by blocking the release of acetylcholine, preventing muscles from contracting. In mammals, this leads to repiratory failure and death, although the toxin is slow acting and takes several days to reach its full effect. I learned a great deal about this alarming substance from the writings of MicrobiologyBytes, in a piece called Botox is Bonkers. I have yet to divine the meaning of this word “Bonkers.”

At this scale, we find the discovery of the very mechanisms of such states as a sense of taste, smell, or one’s very own body temperature, and the reaction our bodies have to these sensations. For years researchers had hypothesized that the detection of temperature would occur through specialized protein sensors in the body, which would most likely be ion channels. Ion channels are proteins that form pores across cell membranes, and specifically allow ions to flow through them, thus controlling an electrochemical gradient. By doing so, the electrical gradients formed can control many biological processes, from vision to muscle contraction and your heartbeat. Vertebrate organisms have evolved, as my Uncle would say, numerous diverse ion channels, all with specific functions, in order to enable these diverse processes. Now, the specific channels that responded to hot or cold temperatures were largely unknown, and it was unclear what made a “sensory cell”. Unknown, that is, until the so called TRP channels were discovered. Indeed, this remarkable find gave me a chill - A cold, cold feeling indeed.

The modern scientist of the 21st century seems to be fixated on the workings of the smallest molecules at this fine scale, including Kinase Structures and Autoinhibition. As more structures are being solved for multimodular signaling proteins, the regulatory kinetics (on, off, and everything in between) is coming into greater clarity. For instance, the recently solved structural basis for allosteric autoinhibition of focal adhesion kinase (FAK), along with the ZAP-70 tyrosine kinase, and the protypical tyrosine kinase Src.

In a State of Alarm

In my travel to the future, I found many things to be different, but much to the chagrin of modernity itself, one thing at least remains absolutely the same: To wit, there are still lawyers. Indeed, they abound. Indeed, attorneys werecircling like sharks over the recent concern about the drug rosiglitazone (brand name Avandia, produced by Glaxo-SmithKine) for treatment of type 2 diabetes. Research by Nissen and Wolski has shown the effect of rosiglitazone on the risk of myocardial infarction and death from cardiovascular causes. Much ado among doctors and even in the American Congress has been made of the safety of this new medication. Bioblog informed me of The misplaced Avanida hysteria. This is an interesting discussion of fallacies in statistical analysis, and of the nature of risk in modern medicine.

Another cause for alarm embedded well in our future is this cycle of events: Science, using principles of physiology and based on the discovered evolutionary relationship among microbial forms, developed a way of fighting infectious disease - an anti-biotic substance, actually, many kinds of substances, mimicking the evolved properties of Yeasts and the like to diminish in number or even kill-off microbial “bacteria” which cause many illnesses. Unfortunately, microbial bacteria reacted to this medical treatment by further evolving resistance to the anti-biotics. I learned of this amazing state of warfare between science and sickness from one Dr. Moran, a leading natural philosopher (though somewhat of a detractor from my Uncle, in that he refuses to call himself a “Darwinist” … an assertion that Uncle Charles would certainly find appropriate and amusing!) Dr. Moran has written two excellent pieces on this topic: Penicillin Resistance in Bacteria: Before 1960 and Penicillin Resistance in Bacteria: After 1960.

I also found that, for better or worse, the method of critique so well advanced by my Uncle is alive and well in the distant future. I met a William (Bill) Eley, who was actively engaged in a critique of a paper written with the title: “Changes in Bird Abundance in Eastern North America: Urban Sprawl and Global Footprint” published in Bioscience. Mr Eley’s forcefull critique of this study is called “How to do Bad Science” and I can only assume he is being cynical in his choice of title!

Apparently, the engineers … those whose toileous labours give us the Steam Engine and the Improved Vehiculator Findibulum Machines and the like, have gotten into the business of engineering the very “genetic” basis of life, manipulating the “DNA” to produce more desirable results. Astoundingly, many 21st century thinkers object, in an apparently entirely modern phenomenon of not always trusting science. Goodness me. I heard concerns from one S.A. Smith on Genetically Modified Rice, which she claims, is “going to kill us alllllllll!!!” Additionally, this engineering of genes seems to be applied as well to the subject of health. Members of a group called, interestingly, “The Conspiracy Factory” have written about Genetic engineering meets vaccinology: or how to get the attention of all kinds of protesters.

And while we are on the subject of alarming disease, I was much informed and, indeed, enamored with the thoughtful discussion of one Dr. Tara Smith regarding that to which she refers as The Outbreak that Shaped the Course of History. Halfway through her exposition it suddenly dawned on me that she was speaking of the Great Cholera Outbreak of 1854, the very plague that took the life of my landlord, Ezekial Fuderwudder, and his cousin the baker, who’s name I cannot at the moment recall. Apparently, dear readers, our theories of the nature of this disease, as a product of the spread of Miasma, have been overthrown by scientists of the future! Will wonders never cease!

The Birds and the Bees, and the Fairer Sex

I had the great pleasure of meeting the delightful Annalise Paaby, proof personified of one assertion to which I have always adhered despite the protestations of many of my good Uncle’s colleagues: Members of the fairer sex often have something worthwhile to say, and in our age of Queen Victoria often underachieve in their role of house mate and servant to man. The charming Annalise asked me the question: “Have you heard about the honeybee crisis?” and went on to explain that sometimes beekeepers discover that their hives have dwindled or gone extinct over the winter. Such events are usually rare, however, and multiple colony collapses are typically local phenomena. But across America, beekeepers are now reporting alarming numbers of hive deaths. A 20% loss over the winter is normal, but beekeepers in California report losses up to 60% and losses have been even higher in Texas and on the east coast. This alarming state of affairs clearly causes us to ask the question: Is the golden age of beekeeping over?

I also had the opportunity to dine with a woman so studied in the concept that members of the fair sex can and should carry out investigations in the area of natural philosophy that she has changed her very own name to Grrrrl Scientist. This endearing juxtaposition of a feminine appellation and the growlings of a territorial beast truly set my own heart aflutter, and made me consider, if ever so briefly, prolonging my visit to this odd and distant century. Grrrrl is a truly renaissance scholar, and has broad and divers interests. I was regaled with examples of her excellent photography and informative stories of Cicadas and their Plead for Love, The Psychedelic Fluorescent Purple Frog found in far away Suriname, An Ancient Fossil Mushroom Preserved in Amber, Efforts to Save from Extinction the Northwest American Spotted Owl, the discovery of a Giant Roadrunner-like Dinosaur Fossil, and the story of the Slow Loris, a primate she claims is Too Cute to Live.

She also told me the oddest story of an attempt at surgery that revealed a most unusual result, which she has written up in a piece that is far too singular for my own comprehension: Vancouver Surgeons Perform Surgery on .. a Vulcan?

While on the subject of birds and bees, it is notable that not only are the bees in some sort of trouble but so are the birds. I was tickled to see that the venerable Mr. Audubon, in the future, will have a whole society named after him, and I’m told by one Mr. Bergin, a well respected Biologizer of Birds, that The National Audubon Society just dropped a bombshell of a report detailing 20 common North American birds whose populations have declined over the last 40 years. The list of birds, all of which have lost at least half their populations in just four decades, is both surprising and disconcerting, indicating that even the most robust species may be vulnerable to our rough and thoughtless treatment of this planet. It is indeed saddening to these Common Birds in Decline.

Uncle Darwin was rapt with the chickens and other birds, their plumage and their ways of nature. The future, little could he know, holds much beyond the imaginable in the area of understanding the behavior, or perhaps I should say, behavioral ecology, of these and other creatures. Obsessed as he seems to be with the reproductive arts (a veritable Lawrence in a Lab coat?) is one Mr. Matt M. (as I shall call him) who drew to my attention research on the sexual practices of the chicken. Of which he apparently knows a great deal, as exposed, as it were, in his writings “Wanna Score? Try her in the morning…”

Nay, the Earth Still Yields

My Uncle once remarked “At the rate these museum keepers are digging, there will be no fossils left for future generations to find in their own explorations.” But nay, my own exploration of the future reveals, happily, that there is still plenty of digging left to do, and furthermore, that many scientists of the 21st century … paleontologists as they call themselves … are happily geologizing across this vast globe. Indeed, I met a self-styled Godless Serbian Jew with the odd name Coturnix who has been musing on the observation that the skeletons of the ancient dinosaurs are oft found with their heads turned up and back in relation to the main line of their bodies. I asked him the obvious question: Why are dinosaur fossils’ heads turned up and back? His answer was both amusing and informative.

The Grand View of Life and Matters of Faith and Reason

Owing largely to my venerable Uncle’s original propositions about the interrelatedness of all living things, it is satisfying to see the pursuit of the science of life in the grandest scale in the 21st century. And, it is thus not surprising to read of awe and wonder in the writings of such as Emmett Duffy, who waxes poetic (or at least prosaic) about a hypothesized “Ocean Soul”

I met a group of wise scientists who told me they would welcome the insights of people with more economics expertise than they felt able to muster regarding the issue of Agricultural Biodiversity. The question is whether to specialize in the growth of one crop, or diversify to grow many, in reference to crops grown for the production of fuel as well as food. These Agricultural Biodiversity experts ask about “Invasion of the agro-bread-heads” as well as The Value of Organic Farming” and the value of Agricultural Subsidies.

Also at the grand scale, where we find spirituality and religion both overlapping with and oft conflicting with science (to which I can attest having witnessed so many encounters between that bulldog of a man Huxley and the bible thumping followers of Paley and the like!) there is no end, it seems to this eternal conflict. Even as reason prevails in medicine and other areas of applied science, there seem to be those held over to insist on the literacy of the old texts and belief in ancient myth. I was brought up to date on this conundrum of modern life by a gentleman named Jeremy Bruno, who speaks of Evangelicals vs. Anthropogenic Global Warming.

Some complain, in the ultra modern 21st century, that it seems that everything done is potentially saving the world. If you believe advertising, that is. The mighty no-brains of the advertising “industry” have noticed that modern people seem to care that the planet upon which we live might be in fatal breakdown. So they have decided to use this worry in order to sell us stuff we don’t need. What heroes they are…Paddy K writes a “blogg” shall I say “pamphlet” on Saving the World (again) addressing this concern.

Afterward

I note with pleasure that the next edition of The Tangled Bank will be hosted at Aardvarchaeology. An artifact digging ant-eater? Will wonders never cease!

I presume, unless disabused of this thought, that you may send your entries for Number Eighty Three to PZ Myers or to the Aardvark Blog itself or to host@tangledbank.net.

And I note with trepidation that many entries, obviously were sent for this publication, and it is quite possible that one or more were skipped. If that is the case or if you feel otherwise that I, in my humble efforts, have done you an injustice, then please send a note to my assistant at laden002 AT umn.edu … and he’ll fix it right away.

D.D.