Archive Page 3

16
Nov
10

The Origin of Life: Storytelling or Science?

The events and narratives which follow are mostly fictional. Those parts in bold are historical fiction while those in italics are mostly speculation. Sections which lack any embellishment are my explanations and descriptions.

We shall start from a few billion years after the beginning of time, so not the very beginning, but before anything we would call living (at least on this normal little planet orbiting a normal little start in a relatively quite part of a normal galaxy in a mostly empty portion of the universe). We begin when the planet has cooled enough to sustain standing water on the surface. When was this? Some time between 4.4 and 4.2 billion years ago. Approximately two hundred million years after the collapse of the nebula which formed the Sun. The oldest known fossils date to approximately 3.5 billion years ago. This is where our fictional narrative ends, and it shall be denoted as T=0, for dating purposes, we’ll pretend it is PRECISELY 3.5 billion years ago. This is not to say there is no evidence of biological activity before this time, since the oldest evidence for biological activity (in the form of biochemical markers of biological activity) date to 3.85 billion years ago.

Continue reading ‘The Origin of Life: Storytelling or Science?’

11
Nov
10

What Biogeography Tells Us

Lots of things can be learned from biogeography. Far more than just what species live where. The evolutionary relationship of animals combined with our knowledge of biogeography can assemble a rather interesting interesting map of relationships. Before genetics was well established, biogeography played a large role in determining the relationships of extant closely related species (often not beyond the terrestrially bound kinds) such as reptiles, amphibians, and (excluding Chiroptera and Cetacea) mammals when morphology did not provide enough information, such as the Agkistrodons you should be familiar with by now, if you’ve read my blog at all. Interestingly, genetics alone does not precisely tell us about a fascinating little subspecies/species/whatever the hell taxonomists decide to call it known as Taylor’s cantil (A. bilineatus taylori/A. taylori). It is certainly a species in the sense of the Biological Species Concept (Mayr) and the Cohesion Species concepts (Hull) but not the Ecological Niche Concept (Simpson). More interestingly, where exactly this population fits within the Agkistrodon genus is not fully shown by the genetic data. This is because it appears to be a near-simultaneous three-way split between the subspecies/species of the A. bilineatus group (including A. taylori) and the A. piscivorus group. The Gulf Arc hypothesis postulates that a single interbreeding population of the ancestral A. bilineatus/piscivorus existed around the entire Gulf of Mexico and up the Pacific coast of Central American and Mexico (pretty much it’s present range if you fill in the gaps) and something caused gaps to form in the populations at (very slightly) different times resulting in species that are genetically as dissimilar to each other as they are to any other within the group, but also isolating them and further enhancing all of the distinguishing features which existed among each subpopulation within the entire Gulf Arc. What we know about the changing geography shows the formation of new features which could have resulted in the relatively recent speciation.

It requires both the genetic and geographical information to conclude such a model (genetics alone without any knowledge of the geography (or morphology, ecology, and behavior) would only be capable of indicating A. taylori is a reproductively distinct species from A. bilineatus and A. piscivorus and would be incapable (because of how recent this event was) of demonstrating when this occurred.

03
Nov
10

On the engineering of organisms, or unintelligent design

I’ve been recently confounded by the “argument from remarkable engineering” fallacy against evolution. It is, quite frankly, only puzzling because it is still in use. The Behe-esque argument was made regarding human development and how remarkably elegant and complicated it was, therefor god. Allow me, for a moment, the chance to slam a lid on embryonic development as an example of remarkable engineering.

If you’re like me and just love learning about embryology beyond the point most people would consider sane, I have a few resources for you. It was brought to my attention-yet again-that I can be a bit masochistic when it comes to learning, so I’ll spare you the long list of “shit that breaks” in the genome. If you’ve ever tried to disassemble a lawnmower engine before you were 10 years old, you might find this wikipedia entry as interesting as I did, but since most people won’t or haven’t, I’ll skip it; it’s also just a list of the disorders and associated mutations. It doesn’t break down all the different types since, honestly, there are dozens of specific mutations for any one disorder and it also leaves out quite a few. I kind of wish it also listed the allelic variations as well, but I can’t have everything, now can I?

How can things go wrong in the development of an embryo? Well, you have 6 basic “types” of errors ranging from the not-so-serious to the abortion-inducing (note: I mean spontaneous abortion, not “have an abortion because it will have three eyes, no legs, and be hermaphroditic”–although that is also possible).

  1. Polyploidy (extra copies of chromosomes; I include monosomies here, too)
  2. Mutations (changes in the actual DNA sequence)
  3. Exposure (to either environmental signals or toxins)
  4. Unactivated/deactivated pathways (caused by external or internal interference or mutation)
  5. Overexpression (see  explanation of #4)
  6. Physical trauma (lethal–for the embryo/fetus–oxygen/nutrient deprivation)

To be human is to lack all of the terminating errors and be left only with non-lethal ones. We all have new mutations which our parents did not have; every single one of us has multiple new mutations which could be among any type of mutation: duplications, deletions, frame-shifts, mismatches, etc. Some of us even have trisomies (which are typically lethal) and monosomies (which can be lethal).

The first of these includes Down syndrome (trisomy 21), Trisomy-22, Edwards syndrome (trisomy 18), Patau syndrome (trisomy 13), and pretty much one for every chromosome, although many (including Patau syndrome) result in miscarriage. For survival of the embryo with one of these trisomies which often result in miscarriage requires genetic chimerism where the founder cells are two fertilized ova rather than only one–this can result in non-identical twins or a single chimera. Chimeric individuals can survive with a trisomy which would normally result in death since the other cell line is capable of “filling the gaps” where the trisomy-containing cells could not, such as in many functions of the kidneys or heart or liver (depending upon the trisomy). None of these, I would say, are marvels of engineering.

As mentioned previously, every last one of us has a mutation of some kind, so to say that “human” is a specific genotype with no variation is to miss the point entirely.

[tangent] The “human genome project” was actually an “average human genome project” which did nothing to elucidate the subtleties and complications involved. An example of a complication is the following: hypothetically, an individual can have the mutation for sickle cell anemia, but if another mutation exists (such as an increase in α2γ2 hemoglobin production as opposed to α2β2), then the person develops (almost) normally. Almost because the γ subunit gives a slightly higher oxygen affinity than the β subunit. This is essential due to fetal blood needing to “steal” oxygen from the maternal blood supply.[/tangent]

We are, above all, products of a procedural development, and as new types of cells arise procedurally, they influence the development of additional ones through the same processes of feedback. Procedural development, as a bottom-up process, is inherently unstable and easily broken. How easily? Consider that the removal of a specific single molecule at the beginning of an open reading frame can result in the lack of an entire protein or multiple proteins (if the initial one is a promoter or enhancer or regulatory protein, it could be hundreds). If this (these) protein (s) is/are necessary for survival of that particular cell line or used in a (or many) vital process(es),not all are, then the cell or organism will die. Is this a good design?

The mutations which do arise in all organisms result in evolution, but evolution is, for lack of a better phrase, all about mistakes. These mutations which an organism can live with (and reproduce) are those that rise to higher frequency within the breeding population.

There is an illusion of design resulting from non-lethal mutations being selected AGAINST, not for. Those alleles which confer relative advantage result in decreased success of other alleles in the same population. The previous sentence is VERY important. If a population is isolated, only the alleles present in that population will be subject to any selective pressure unique to that population.

Since mutations arise randomly, and genetic drift “noise” can further complicate the evolutionary history of an organism. The end results of these processes may look, on the outside, to be finely engineered organisms, but the deeper one delves into the anatomy and genetics of an organism, the more of a mess it becomes.

22
Jul
10

Way too busy

Ok, so I can finally start doing a bit of blagging again. I have a few photos to share, but first, it’s a mysterious mystery.

Can you find this guy?

He’s hiding somewhere in this image:

You’ll probably have to view the image full size…

I found him just before I went to cut grass.

23
Jun
10

Raining oil?

It’s certainly possible youtube user HistoryTours is correct in saying Louisiana experienced oil rain. If you listen to television and news meteorologists, oil doesn’t evaporate, but this certainly isn’t correct. The boiling point of light oils (pentane and lighter) is below the current temperature of the Gulf of Mexico. It is possible that this fell along with the water which evaporated from the same area. Below are several of the videos which he uploaded. I have requested additional information from him and hope to keep everyone up to date.It is definitely in the New Orleans area. Thanks to Stacy for the pointer.

22
Jun
10

Want a miracle?

Then get off your fucking knees and grab a shovel, donate some money, wash some birds, or even just buy a candle.

Quit praying and do something.

/rant

26
May
10

Some conclusions on “the cause”

Having investigated the current ecological disaster extensively, I can tell you now that the problem is almost exclusively the fault of BP and was caused by a breach of procedure and trying to hurry along the drilling of the well and possibly not even drilling the well properly.

Here is what a finished well is supposed to look like before the mud is pumped out:

Green=platform
Blue=riser
Red=BOP
Grey=casing
Black=oil reservoir

Notice how the casing goes all the way through the reservoir? This is done to prevent a blowout of a finished well. Once the well is put finished, oil is produced by perforating (poking a hole) in the casing. If oil is leaking from a well that was in the process of being finished, it wasn’t finished. If you get an abnormal reading in one pressure test and a normal one on a subsequent test, don’t just ignore that abnormal test; something is happening you dumbasses. If you put in 5 barrels of fluid and get back 15, you’ve probably got a leak. If you shut down a pump and pressure increases, there is a problem. BP did a sloppy job on the drilling process and in its rush to move Deepwater Horizon off the well so it could be produced, completely and utterly fucked it up. As a result of this and numerous other smaller spills, botches, and fuck ups which BP has been cited for, I propose a means to alleviate such future problems.

BP is required to pay out of pocked for the entire cost of clean-up. BP is not allowed to produce this well or sell any of the crude which is recovered from the cleanup. Instead, another company should be given this well and the oil salvaged. The EPA should confiscate this well and donate it to another company; the one which receives this gift should be the one with the best environmental and safety record. Half of the profit from this well and the oil from the cleanup should go to the states affected by this spill. (The remaining half, of course, goes to the company that takes environmental and personnel safety seriously)

I think, in this instance, gross negligence is easily provable, thus BPs liability for cleanup costs is not set at the $75 million mark. BP (as a large, multibillion dollar a year company), I think, could make an excellent example of a large company being held accountable for its mistakes. The cost of cleanup (>$5 billion) could take a sizable chunk out of BPs annual profit (~$22 billion).




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