Tuesday, 9 December 2014

Tokyo Ghoul





Just thought I should share this awesome anime music video(AMV). I started watching Tokyo Ghoul last month and now Im hooked.



There's just something about the pure psychoticness of it.....

On Transitional Fossils & Imperfect Design

Note: I am a novice in many of the established sciences I often advocate for. if one wants a more comprehensive assessment, please visit some of the established sites, such as Understanding Evolution or Talk Origins. I will attempt to give my own view of the information contained in these sciences, while linking interested readers to more.

 When we talk about evolution spanning many millions of years, the sheer number of organisms living and dying, we simply cannot observe these changes in real time. Thats why we need to indirectly infer these changes by studying the fossils themselves to construct a detailed view of its evolutionary history.

This is the first hiccup that creationists will always attack. So we cant observe macro-evolution? Then doesnt it rely on faith to believe in it?

This is heavily mistaken on several levels.

 You see, if we only rely on direct observations (the philosophy known as empiricism), we would miss out on a whole new level of science. As a matter of fact, valence bond theory, molecular orbital theory (something Im much more familiar with) and even Einstein's theory of relativity were vindicated by indirect inferences!

Did you think we could observe gravity actually bending time? Or actually see the electron shells of atoms? Of course not. However, these scientific theories explained a lot of what we could observe. The process of science doesnt rely on empiricism alone, but also rationalism. We make rational inferences and formulate theories based on available evidence, then find further evidence to test them.

Let us turn back to Darwin's Theory of Evolution. Nevermind that there have been observed instances of speciation before, or that it was found that bacteria had evolved the capability to digest nylon (note that nylon is a synthetic polymer invented in the 1930s). Nevermind the evolution of antifreeze proteins in Arctic and Antarctic fish. Lets look at transitional fossils.

So, what is a transitional fossil? A transitional fossil is simply a fossil organism which has features intermediate of its ancestor and progeny. Often, paleontologists group fossils with particularly striking intermediate features under the term "transitional fossils". In fact, there are a huge number of them!

It could even be argued that all fossils are transitional (this is not entirely true, rather "intermediate" more accurately describes the situation). Mainly because life, as a whole is in a constant state of flux. Speciation events continuously occur.

No other analogue of common ancestry comes closer when we look at the evolution of languages. Consider the Spanish and Italian languages. Did you know that they actually share common ancestry with Latin? Over time, they were adopted and modified by their respective cultures until they are completely distinct languages from each other. Then look at the Mandarin language:



From http://www.omniglot.com/chinese/evolution.htm
This is going off on a tangent, but note how Chinese characters slowly evolved from simple sketches of the objects they were supposed to represent? (All the characters are arguably transitional forms).

I would now like to address a fellow blogger (and someone I respect) who wrote recently that transitional fossils probably don't exist here. Hopefully I can fairly represent his argument by picking his main points. So he writes:

Logically we have to qualify what a transitional is. I defined it as a species between designs. For example an ape, whether extinct or extant is designed to be arboreal, and thereby dwell in trees, but a human is a bipedal designed to walk uprightly on two legs. So to transition you need to go through many imperfect stages in between the two states of being.

Logically, just now think, given there are millions of species on earth, how many organisms should look anatomically CLUMSY, because they are transitioning, in an 'imperfect stage' between what they were and what they're becoming?
 
This point in particular, was what inspired to write this post. So he asks, if evolution were true shouldn't we expect to see hundreds of awkward, transitioning organisms in the animal kingdom?

Further down, he concludes:

 I expect to see 'transitionals' everywhere, if evolution is so prevailent in nature. I see none. Furthermore I see that every species is a whole design, viable, with all of the tools needed to do it's job, perfect for it's specific job.

I feel that to address his points we need to consider several factors. First of all, a transitional form does not "need" to imperfect. Its unfair to imagine a "real" transitional form to be some awkward, mutated, crocoduckian abomination.  While it is true there are often fitness "trade-offs" when a species is evolving towards a particular trait, this does not accurately portray the situation.
I ll summarize a few points.

1. First, when design proponents argue that "everything is well-designed" one would point out this is not necessarily so.

Look at the flying squirrel. It is not capable of true, powered flight like birds or bats are, and could be considered "inferior" tp them. It has a much cruder design for its "wings" (the patagium) yet it soars gracefully through the trees by gliding.

Its even possible that the flying squirrel is a "transitional" precursor to true winged squirrels in the future. Who knows?

 I will try to illustrate this further by pointing out a very famous transitional fossil of the evolution of birds from flying dinosaurs.

Consider Archaeopteryx.

Image courtesy of Livescience here
(Again slightly off-topic).
I am continuously saddened when creationists constantly accuse scientists of deceiving the masses. It seems their only purpose is to slander evolution and accuse evolutionary biologists of being deceitful, capricious liars.

Even worse is when you realise that creationists cant even agree on whether Archaeopteryx is a dinosaur or a bird. You have one site which implies that fraudulent scientists have claimed Archaeopteryx is a bird (later revising the hoax to a dinosaur).

Then you have Jonathan Sarfati correcting them and claiming that Archaeopteryx is indeed a bird and NOT a hoax. Really.....(at least Sarfati has the integrity to prevent the promulgation of lies though....)

Enough of that, lets ignore the debate entirely and focus on Archaeopteryx itself. If it was a genuine bird, then it wouldnt have been a very good one.

First, Archaeopteryx has asymmetrical flight feathers. Second, it does NOT have a sturdy breastbone. It would have been an inferior flyer compared to modern day birds.

There are also subtle, tell-tale signs that it is distinctly reptilian. First, its "beak" (if it can even be considered a beak) has teeth. It also has a long, bony tail. If we saw Archaeopteryx, it would probably be a freak.

Then consider the giant panda, which feeds on bamboo. As a matter of fact, it seems largely maladapted to its environment. It has a carnivorous digestive system and lacks the ruminant gut most herbivores have to properly digest cellulose. Thats why it has to consumer prodigious amounts of bamboo to survive!

 By the way, there are actually a lot of "freaks" in the animal kingdom even today. (See these freaks and  these giant animals). Oh, check out this fish with transparent blood and  this worm-like amphibian too.

Of course, just because they arent particulary well designed doesnt mean that they are simple. (More on that later).

2. How does one know that modern species aren't transitional forms?

The fish-tetrapod transition occurred in the distant past, during the Devonian, but why not we look at some modern species of amphibious fish that can give us vital clues of how the transition might have occurred?

Consider the mudskipper.

Image courtesy of NatGeo

 
It is truly a fish adapted to live on land. It uses its pectoral fins to walk on land. It can propel itself forward by flexing its muscles.

It breathes air through its skin and pharynx (but only when its wet). It can store water in its gill chambers as extra oxygen supply. Its entirely possible that fish like these are precursors to new species of amphibians in the distant future wouldnt it?


3. Exaptation and Jury-Rigged Design
So what is exaptation? It simply means a shift in function of a trait during the evolution of a particular species. What happens is that a trait originally used for one purpose is eventually adapted for another.

In the aforementioned example, I glossed over briefly, the evolution of birds from theropod dinosaurs. Why would theropods possess feathers, one might ask? Well, feathers might have originally kept theropods warm. They might also served to increase running speed when hunting prey.


This is a re-constructed skeleton of a "terror bird". Note how similar its anatomy is to dinosaurs. Image is from Wikipedia
These designs, are then in essence, "jury-rigged" and co-opted from prior forms, often with very subtle weaknesses. (See some at Talk Origins here).

I ll lay out some more evidence for imperfect design, particularly in the cellular respiratory and photosynthetic processes. Its very likely they evolved from putative metabolic processes.

The RubisCO enzyme is crucial in the carbon fixation process (for photosynthesis) as it catalyzes the carboxylation of RuBP. But one major problem with this enzyme is that it cannot differentiate between carbon dioxide and oxygen. So if there is a significant amount of oxygen, the activity of this enzyme is severely affected.

Above all, we have even succeeded in creating variants of RubisCO which are more effective than the ones in nature that does not have this weakness!

Even the cellular aerobic respiratory process (in combination of glycolysis, the Kreb's cycle and the electron transport chain) are only about 34.5% efficient. That means they only succeed in metabolizing about 34.5% of the energy from glucose. Would you consider this effective?

4.   Punctuated Equilibrium 

I wont go into too much into this. But first theorized by Stephen Jay Gould, it posits that species are often at an equilibrium, at a local fitness peak (I alluded to this in my previous post). Only when drastic changes in environment or ecology occur, then selective pressures favour rapid evolution of certain traits.

This probably means that many of the organisms we see today are at the top of a local "peak" and hence are optimized to the environment they are in, thanks to millions of years of evolution.

Conclusion

 Nature is very complex, and it would be surprising if it wasnt.  But just because nature trumps human design doesnt then necessitate a better designer for it.

This is simply because of our limited understanding and ingenuity, such that we require to draw inspiration from what we can observe. Consider modern designs as compared to primitive ones. The former is clearly much more complex than the latter. But it doesn't necessarily mean people today are much smarter than people in the past, it just means we have much more information and build upon the successes of our forebears.

 The laws of physics are very complex, does that require a designer too?

I suppose for Christians (and other adherents of monotheistic religions) they would say: yes.

But that is a discussion for another time.

Thursday, 4 December 2014

Some stuff

Ah, its been a while since I posted, but just finished exams, so expect posting frequency to rise until sometime in January.

I might delve deeper into philosophical stuff this time round though. There's some stuff I wanna discuss....

Tuesday, 23 September 2014

Must read posts, 23/9/2014

Its been a while since I last posted, but these are must-reads.

Happy Jason Lisle day! Diogene's  huge smackdown of YEC astrophysicist Jason Lisle's solution to the "distant starlight problem". The anisotropy synchrony convention simply doesnt work anymore.

Smoking Gun evidence of an ancient Earth : GPS data confirms radiometric dating. Naturalis Historia shows how multiple independent methods of dating can form concordance.

By Grace Alone : This is very different from my regular recommendations, but worth a read more than anything else.....

Friday, 15 August 2014

Evaluating ID

   One thing I noticed is that, it is far easier to attack ideas than to defend them. Often its because defending is in response to an attack, which the defender needs time to think through, carefully deduce the opponents argument, point out flaws and do his or her own research to rebut the attacker. So, I will play a little game, if you may, engaging in back-and-forth arguments for and against design, throwing in some specific examples. This is going to be a long post though, composed over several days.

A note though: I am only familiar with general arguments for ID. If anyone knows more refined points, please inform me and I will take them into consideration.

So what is the concept for intelligent design? At the Intelligent Design homepage, it states "
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection

  In the recent years, the Discovery Institute has come under fire for being religiously motivated, but I ll move past that and take a closer look at their arguments. Coming from a physics/engineering background, I can see how design can be appealing, regularly dealing with concrete, specific answers. And although non-religious, I lean towards the Rare Earth Hypothesis that Earth-like planets are a special and unique occurrence.

One of the key features of DI's theory is that the designer is not identified. In other words, you could replace the designer with anyone (God, aliens, the Matrix etc) and the theory remains just as valid.

The first problem immediately becomes apparent. You see, the Discovery Institute doesnt just insist biological systems are designed, even the Earth was designed to accommodate complex, intelligent life. (Check out their documentary the Privileged Planet for example.) What is the problem with this?

It immediately points to the exclusion of certain designers (sorry Cthulhu, you couldn't have created Earth) and very strongly towards God. Their article rebutting the idea of panspermia (life from other planets) heavily implies this. Do they have a religious agenda? Actually it couldnt be less obvious that they are religiously motivated.

 However, ID lends support to deism, which is a philosophical, not religious position. Fair enough, lets focus on biological systems first, since arguments for/against fine-tuning of the Universe are wandering into the realm of the un-falsifiable.


First, let me offer credit to intelligent design. There exists other scientific fields that do attempt to detect the presence of deliberate tinkering. Richard Deem of godandscience.org, aside from criticising the general push of ID, has an interesting list of points:

  1. Archaeology: Is that rock formation natural or due to intelligent design?
  2. Anthropology: Do sharp, pointed rocks occur naturally or are they designed by intelligent beings?
  3. Forensics: Intelligent cause of death or natural circumstances?
  4. SETI: Are those radio signals natural or caused by intelligent beings?
This is actually quite a good argument. We look for signs, "motifs" if you may, that indicates a particular biological system is designed. However, the first difference one would notice between ID and these other scientific fields is this: we know what features to look for, because we know that natural processes cannot produce certain features, where-else


Take the study of stone tools by archaeologists and anthropologists. How would one know if a stone was designed, or simply occurring in nature? Of course, arrow-heads would be a dead giveaway - shapes like that dont occur naturally, written records and observations of arrow-making further back this up. For more obscure, primitive artifacts, we look for systematic flaking i.e. a stone with numerous flake scars is unlikely to have been the result of natural breakage. Natural rocks may have flake scars, but its unlikely they would have so many. See here for more.

This same principle (to me at least) cannot applied to intelligent design. This is because:
a) We do not know the mechanisms the un-identified designer could have used;
b) Our minds may be too primitive to comprehend design, if life was indeed designed.
(In fact some primitive tribes thought cameras could steal your soul. What if we are tribesmen, gazing upon some vastly incomprehensible design?)

Lets go a little into details and revisit William Paley's famous watchmaker analogy. He says that, if we find a watch in the field, we can easily discern that it had a designer.  This argument, while compelling, does not work upon closer inspection. First of all, we know a watch is designed because watches dont simply appear as random products of nature. We can even observe them being designed and manufactured!



Is this beautfiul snowflake intelligently designed?



 Well, a counter-rebuttal would be you could say we dont see apes evolve into man either, so how can we know evolution occurred either? I will discuss this further detail in the near future, but we will get to the basics by giving an evolutionary counter-example to the "common design, common designer" argument. It means that common designs that function effectively are re-used by the designer because it works.

In evolutionary theory, two similar biological structures (anatomical or genomic) can be homologous or analogous. The former means that two particular organisms inherited the structure from a common ancestor(common descent theory), while the latter implies the process of convergent evolution i.e. two unrelated organisms gaining a very similar biological structure.

What happens is that organisms with homologous  structures slowly attain morphological differences over time, while organisms with analogous structures actually grow more to resemble each other.

One important point is organisms with homologous structures often bear remarkable similarities in genome sequence. In contrast, organisms that arrived at a trait via convergent evolution bear little or no resemblance in genome sequence to each other. A good example would be bats and birds, which diverged all the way back from the age of dinosaurs.

How does this challenge ID? Well I now take "common design, common designer" to its extreme conclusion via reductio ad absurdum. If birds and bats had a common designer implementing a common design for flight into of their wings then wouldnt it follow that they have anatomical and genetic similarities as well? They don't!




You can see from this picture that bats and birds have different anatomical structures for their wings. Notably bats have the mammalian "five finger" structure. Well you could then say "this is an example of the Designer exerting creative power", but how are we even going to test that?


   I ll illustrate this again by a not-completely original example of convergent evolution, first posted at the evolution blog the Panda's Thumb here, by a former YEC.

The Arctic cod and Antarctic nothothenioid are notable in possessing anti-freeze proteins to prevent their blood from coagulating. But the unique thing about them is that their protein structures do not resemble each other. Each evolved their traits independently! If you are interested, please read the original research paper, first published in PNAS here for more information. (Also note that the nothothenioid antifreeze protein is very similar structurally to fibrinogen - a protein involved in blood clotting).


Evolutionary theory produces a unique feature known as a fitness landscape. Taking one particular environmental condition, there are several ways evolution by natural selection can act to produce a population with an average phenotype which is well adapted to its present condition. This is represented by the local "peaks" A, B and C. However if an organism is at the top of a local maxima, say A, it will have to experience a decrease in fitness before being able to climb the highest peak B. (this is a very layman explanation of a complex science, so apologies).


There's more than one way to adapt


Lets look further at more of the points the Discovery Institute makes.


Another fundamental concept of a scientific theory is that it must be:

a) produce testable hypotheses
b) falsifiable


The IDEA center has a good intro to the testability of ID.

The Short Answer: Yes. Intelligent design theory predicts: 1) that we will find specified complexity in biology. One special easily detectable form of specified complexity is irreducible complexity. We can test design by trying to reverse engineer biological structures to determine if there is an "irreducible core." Intelligent design also makes other predictions, such as 2) rapid appearance of complexity in the fossil record, 3) re-usage of similar parts in different organisms, and 4) function for biological structures. Each of these predictions may be tested--and have been confirmed through testing!

I will be taking a look at them, from 1 to 4. I have already challenged point 3 and will briefly skim through the others.



1) We will find specified complexity in biology. The problem is specified complexity needs to be defined more specifically so to speak. Proteins, although generally complex and carry out specific tasks, are actually less specific than people like to think. Lets look at enzymes, proteins meant to catalyze chemical reactions. Although hundreds of amino acids long, the only real important parts are at the active site which consists of only several amino acids. THOSE are the complex specified parts. Want proof? Go on wikipedia and look up the range of protein structures. Note how many "protein folds" are re-used for different proteins (particularly the alpha helix and beta pleated sheets).

 Ah, irreducible complexity. This is actually  a very interesting point, because oftentimes evolution that increases complexity proceeds by stepwise transitions until a complex organ/organelle is formed. The logic goes: if an ancestral component protein or anatomical structure is removed, then the whole system would cease functioning, then prior steps would have no function and would be useless according to evolutionary theory.

On the Uncommon Descent blog you can see the icon for ID - the bacterial flagellum. In fact, they should actively testing for its irreducible complexity! Take apart the bacterial flagellum by deleting part by part. See if the flagellum still functions. Experiment on other biological systems too.

A caveat though. Just because a system is irreducibly complex, doesn't mean it couldn't have evolved. Do you know why?

  a) Mutations could act upon existing genes, deleting and removing parts of a system. If the parts that have been deleted or pseudogenized only carry out secondary, unimportant functions then the system would still be working. Hence an "irreducibly complex" core - that has lost certain original working parts, but losing more would render the system unusable. A good analogy would be how natural arches form - underlying rocks are eroded until the arch is left. The arch is now irreducibly complex!

b) Exaptation - this is a very important part of evolutionary theory that intelligent design proponents overlook when criticising evolution. What happems is that a prior anatomical structure / gene is co-opted to perform a different function. A cogent example is the fish-tetrapod transition. For a transitional form like Tiktaalik, it is able to use its fins for walking on land as well as swimming in water.


2) Rapid appearance of complexity in the fossil record This is probably referring to the Cambrian explosion. I lack the credentials to properly analyze it, but remember  The Cambrian explosion shows a trend of increasing complexity, although a relatively rapid one. Please read this very detailed critique of Darwin's Doubt here to understand the nuts and bolts.

One more note about it is that the Cambrian seas were actually very volatile because oxygen levels were constantly fluctuating, resulting in several extinction events that wiped out many genera. Well maybe the Designer didnt mind watching many newly designed species bite the dust after all......


4) Function for biological structures - Well most biological structures already have a function but i think people are jumping to conclusions by proclaiming it intelligently designed. The problem is there are huge swathes of non-coding DNA in the genome. A general trend of biological complexity goes like this - the larger the fraction of non-coding DNA, the more complex the organism. Take the human genome, which appears as mostly junk. Yes, some of these non-coding DNA have important functions but others don't, and may even be harmful. (See retrotransposons - jumping genes that copy their sequences all over the human genome. Really).


 Conclusion

For now ID appears too much to be a philosophical than a scientific one. It needs a greater testability and predictive quality before it can be considered science. Funny enough I don't really mind if they actually do find genuine evidence for design (and its implications) but who knows? Next up I will discuss falsifiability of evolution and intelligent design, as well as more points listed on the IDEA centre.

Friday, 11 July 2014

Dark Souls: Epic Narration





This. By far one of the best lore videos for Dark Souls. The writing and flow is just superb.

Once done be sure to listen to this awesome soundtrack  of Artorias, the Abysswalker.




Thursday, 10 July 2014

Prologue

Note: This is merely a first draft, so excuse its potential sloppiness. With that, hopefully I can get this project off to a good start.

She worked in the Old Baths.  The olive green pools were always filled with patrons from all across Semerium during the day; men and women of high blood and birth. The smell of rancid sweat and fragrant oils coalesced to form a sweet, sickly smell. Great flues blew palls of steam from the houses into the cool spring air. It was such a strange scene, an eerie juxtaposition of chaos and peace, rowdy shouts and mirthful laughter and the clatter of glass breaking interspersed with moments of quiet contemplation. The floors were polished marble, fickle and slippery. Flickering candles cast dancing shadows of leering dragons from the walls. Mocking. Judging. You will never be a dragon. Pity you, hatchling. Their brass heads snorted billowing steam from lead conduits, hidden from view, that ran along their length. But cold. Why was it always so cold. The steam that rolled over her body felt like tenebrous wisps of smoke, devoid of the warmth of life. Conniving eyes seemed to pierce her thoughts everywhere she went.

It was always the same. Their names changed, but their purpose was the same. Only men and women of status, noble as they were, could waste their lives on such debauched pleasantries. The rest, all the other good for nothings, starved and died like the dogs on the wharves.

When she was free of her duties in the depths of the night, she would make her way to the top floor and just gaze balefully at the city beyond, spread out like a sprawling canvas. The shingles from a thousand roofs reflected the starlight from above, twinkling with a playful gaze. To the south, the Styrox River fed into the Bay of Many, along with it dozens of ships bound east. In the distance, the silhouette of Mawgar Palace loomed above the surrounding buildings, casting its eternal shadow into the gloom. She remembered how when she first came here, years ago, she gazed in wonder at the bright and gaudy decorations, a riot of colour and senses, exotic dancers from foreign lands.

But it was all a fa├žade now. She had grown up. Places, like people, had a habit of lying to you. She had learnt this, step by painful step.

She missed home. She missed it so much.

                                          ***************************************

Obeying wasn't that hard. So easy to remember. You just have to do what Lady Rishe says. Obey our patrons like a good girl. Serve them tea. Scrub them. Rub their bodies with fragrant oils. Let them touch you. Undress you if they please.

She would slowly get used to it, she told herself. People who were dead inside forget slights against them so easily. The first time she voiced her opinion, grand lady Rishe had struck her till she bled all over.  Back to being a good girl then. Forget their gazes. Turn your heart to lightening our guests.

She approached the East wing, a small pot of scented oil under one arm and creamy silk towels  under the other. The smallest bath-house, reserved for the wealthy among the wealthy. Her guests were in the Warm Bath, and she had to prepare for their massage.

Three highborn men sat in the pool of green water at the centre of the room, sharing a jest amongst themselves. She recognized the lead man, a plump man of forty with a handlebar moustache as Cretar Cromm, cousin of the viceroy. She averted her gaze away from them and glanced upward. A mosaic of armoured figures at war with each other covered the entire ceiling. She set her towels down, next to the pool.

"Come here, girl."

 She looked at him. His clean shaven face bore an enigmatic nature, with slanted brows and a curved jaw. His slit like mouth was twisted in a nearly imperceptible leer. His cheeks were dull grey, as if carved of dying flesh. His  deep-set blue eyes watched her as a lion watches its prey.

"More warm water for you, my lord?"

"Fine lady, what could warm me more than the comfort of your touch? Join me."

"My lord, I would love nothing more than to comfort you for your stay, and what better way than an anointment of the sacred oils to ease you?" she forced a smile, noticing that the other two men had fallen silent. "Please come to the antechamber once you are finished, my lord."

"Oh, no, we wont be needing that." He began smiling in return. "Put the pot down and sit here. I command it, fine woman."

 There was no way she could disobey the command of an honored guest. She couldn't. Lady Rishe would strike her again.

She stepped into the pool and sat beside him, still smiling.

He drew closer to her and began stroking her hair, ever so gently. "What's your name, girl?"

"Ranili, sir," she lied. "My lord, this is not appropriate-"

 "A fitting name," he whispered into her ear, while running his hand under her robe. "Let me show you the grace a lord is capable of bestowing upon good, obedient subjects, especially girls your age.
She stiffened. Don't fight back. Show dis-interest.

His lips began caressing her neck and shoulder. He rubbed his nose on her ear and smelt her "So sweet. Like ambrosia.........that's what I name you. Ambrosia, nectar of the gods."

 She pushed away from him, gently "My lord, please, there are things I must do-"

"Shhhh, child, " he hushed. "You are such a beauty, girl," he moved his other arm against the side of her neck, pushing her back against the pool.

"Exarch Jormen, this is neither the time nor the place," said the third man.

Jormen. That was his name. She made a mental note. You will be the first

Jormen shot his companion a stiffening look "This is a place of pleasure. Tis a shame if the girls are not part of it, are they?"

"As you will, my lord."

 His hand reached below.

Tears were now brimming in her eyes. "Stop it." She was no longer reacting mindfully but began struggling against his advances. But he was strong. Too strong.

"Stop squirming, girl." He breathed. "Be good, and your lord will reward you," he ripped her dress. She screamed.

He grabbed her hair and smashed her head on the side, stunning her. Then he spun her around and wrapped his arm around her neck.

By the gods, no. She fought back as hard as she could, ramming her elbows to his side to no avail. He pushed her face down on the side of the pool and brought his face next to hers. His hot breath felt like that of a demon.
She felt his cold tongue slide up her cheek and bit back a scream. 

"Exarch. Primador Yakov requests your presence immediately." A man stood at the entrance.

Slowly, ever so slowly, his grip released. She coughed and dragged herself out of the pool.

"Would you be so kind as to pass my deferential apologies to the Primador? This house is most uncatering to my tastes, to much misfortune. We will meet in my solar."

She grabbed her flowery robe on her way out and stifled her tears.

This was a place for a proper girl, Lady Rishe always chided. Fight the cold, do as you are told, and you wont be sold.

Good girl, she told herself, good girl and she fell to her knees in great sobs. The pain in her heart twisted, like a knife edge.

 Escape. I must escape. 


Note: The prologue is meant to be a little perturbing and meant to show what kind of world our protagonist lives in. I welcome any criticism you may have as I am new at this. NEEDS MORE EDITING

Tuesday, 8 July 2014

Historical Perceptions of the Age of the Earth

 This might be an ongoing series, depending on my inclination.


  Before evolution, the first dangerous idea, was of course deep time. Espoused by geologist James Hutton and further developed by Charles Lyell, they claim it was this heretical thought that gave Darwin the springboard to formulate his theory of evolution by natural selection. What's ironic is that, the earliest discoverers of deep time were actually opposed to evolution.



William "Strata" Smith
First, a little background if you may. The field of geology was expanding enormously throughout the 18th and 19th centuries. People were digging up fossils of extinct animals that, at the time, were utterly bizzare and alien. The public was being wowed by tales of monsters, from the skulls of noble mammoths found in the frozen wastes to  demonic plesiosaurs which were purportedly agents of Satan. Enter William "Strata" Smith, the father of English geology. He observed that, while working on railways, how well sorted fossils were from one layer to another, hence earning him his namesake.  Using this fact alone, he went on to plot the first geological map of entire Britain. A very remarkable feat indeed, especially considering he worked alone without any modern equipment.
What he never realized was that his valiant efforts would change the perceptions of the world we live in forever.
 Geologists began pondering the observations from the fossil record. What did this mean? When did these creatures live? If they were brought aboard Noah's Ark, why have none survived to this day? Most importantly, why were they so well sorted, from layer to layer? How could Noah's flood sort the fossils with such precision?

Bear in mind the notion of a global flood had already taken a beating almost a century ago, during the exploration of the Americas. Naturalists (many whom were also members of the clergy) struggled to explain a) the enormous diversity of animal life, particularly in the Amazon basin b) the origin of native Americans.
A particularly salient (and mildly amusing) question posed by Sir Thomas Browne was in this quote:

"How America abounded with Beasts of prey and noxious Animals, yet contained not in that necessary Creature, a Horse, is very strange"

In which he ponders why, if native American Indians were descendants of Noah who dispersed at Babel, why did they decide to bring rattlesnakes, but forgot the horses? Another pressing problem was that Genesis only described the creation of one land, so to speak. Yet enormous continents existed that were completely separated from the rest of Europe.


But I digress. As you can see, the idea of a global flood and a young clockwork Earth was being increasingly challenged by the fossil record. Remember, this was long before James Hutton's ideas became popular and Charles Lyell first published his book, the Principles of Geology.

Jean-Baptiste Lamarck
Then in 1809, heresy! Jean-Baptiste Lamarck, French war veteran turned naturalist, published his book Philosophie Zoologique, in which he proposed that organisms slowly evolved over time. His foundation for the mechanism by which the change occurred was the theory of inherited traits, which postulated that organisms changed over time with "use or disuse" of their innate organs and passed down these traits to their offspring. He was way off the mark, but his theory actually has some basis in reality.

Lamarckism went against everything the Christian church taught, so enter brilliant distinguished scientist, Georges Cuvier, founder of modern anatomy. A man of wanton erudition, he had already come to realize a vast number of species in the fossil record were extinct. He noted the degree to which fossils were sorted according to strata, and was the first to recognize that elephant fossils found near Paris were distinct from living elephants we see today, or even the skulls of Siberian mammoths, and hence categorized them under a distinct species, the mastodon. He was the first to identify fossils found in South America belonged to a giant sloth, now known as Megatherium. And hence, he came up with the theory of catastrophism. Earth, he argued, had underwent a series of divine creations, succeeded by catastrophes which resulted in extinction events. The global flood, occurring about 4000-5000 years ago, was simply the most recent of them, he argued. In doing so, he utterly dismissed evolution and affirmed the theory of divine creation.

Cuvier's ideas were monumental. It helped found the modern field of palaeontology and formulate the idea of extinction events.

  Lamarck soon fell out of favour. In fact, after Lamarck died, penniless, Cuvier wrote a eulogy to him. Although at first glance, it seems to be honouring Lamarck's contributions to natural history, Stephen Jay Gould noted that Cuvier was subtly denigrating Lamarck.


The Cenozoic Age of Mammals. Image from
 http://www.peabodystore.com/images/posters/mammalposter.jpg


However, Cuvier's ideas on species' fixity and repeated catastrophes opened the idea that the Earth was far older than 6000 years, contrary the Ussher-Lightfoot chronology. Many theologians still struggled with this issue and eventually came up with the "gap" theory which  explained there was a vast period of time which separated the events of Genesis 1 and Genesis 2. That way, a global flood and a young age of Man's existence was still tenable. Nevertheless, even this idea would be challenged in the future.

Conclusion: As you can see, even the most ardent opponents of evolution advocated an ancient Earth. The innate sorting, the striking differences in anatomy of fossils were vital in proving that our Earth is far older than the official date of creation. Joel Duff of the Natural Historian has an excellent series on 19th century scientists as well.

See them here:

The Earth on Show

William Buckland Grappling With Deep Time

Kirkdale Cave Hyena Den: A Challenge to a Young Earth

Mary Anning: Plesiosaurs, Pterosaurs and the Age of Reptiles

Highly recommended!


Next up: the geology of James Hutton and Charles Lyell, and the Reverend William Buckland's admission of error.




Saturday, 5 July 2014

Something else....

I have been thinking intensely over the past few months.

Bear with me for a moment. You see plot lines for stories constantly weave through my head, like a restless maelstrom demanding placation. One plotline in particular, struck me in the solar plexus and held me for months. So much so that it is demanding to be written, as much a failure it may become in the future.

I can see the characters, the men and women in the play,  giving the breath of life to the world I designed, how they look like, how they behave, their hopes and dreams and fears. I just cant, for the life of me, remember their names and the places they reside in.

Perhaps, if I can finally muster the strength, I will periodically post drafts of my ongoing project to this blog.

A few hints.

Its going to be a fantasy series with interspersed with "high" and "low" elements so to speak. I will try to focus on several characters, maye a false protagonist or two. I drew some inspiration from "A Song of Ice and Fire" as well as some other novels I ve read. Even Dark Souls may come into play.
Ultimately though, the plot came to my mind while I was in a massive bout of depression last year, so one would expect lots of tragedy. I sure hope my characters can survive through it.

Either way, I hope to continually post updates here, time to time alongside my science blogposts.
Hope you all enjoy!

Bio Geo (part 2)

If you have the time (or money), please visit these awesome places!

Part 1 of this series is here.

Mount Roraima

Image courtesy of http://masspictures.net/mount-roraima-venezuelabrazilguyana/



South America has no shortage of wonders (see the Cano Cristales River in Colombia or the Salar de Uyuni in Bolivia) but for now lets look at its sprawling mesas.  A sight to behold indeed. The image on the left is a helicopter photo of Mount Roraima, the highest tepui (isolated table mountain) in South America. Part of a chain of table mountains known as the Pakairama chain, which stretches across 3 nations: Brazil, Venezuela and Guyana. 

The tepui are the remains of an ancient, Pre-Cambrian plateau, once part of the super-continent known as Gondwanaland, uplifted by tectonic activity and slowly eroded over untold eons, leaving these spectacular vistas of roiling clouds and waterfalls higher than anywhere else on Earth. 

 As you can see, the table mountains are isolated landforms, meaning of course, species that resemble no other can thrive in these geographically unique places. As my previous post pointed out, geographical isolation of small, isolated locales of a sample population leads to peripatric speciation. Lets take a closer look at Mount Roraima. 


Young Heliamphora nutans, red pitcher plants endemic
to South American mesas
This is just one of several species of pitcher plants on Roraima.  Most of the plateau is bare sandstone, and rainfall continuously washes soil off the edges of its sheer 400m high cliff edges.

What does that mean? Well, because of the nutrient-poor ground, many of the plants have taken on carnivorous traits. Pitcher plants abound on top of this massive table mountain.

Image courtesy of National Geographic video here
   

 Also pictured : the Roraima bush toad. I wont spoil too much, but just watch the linked video here to see how it escapes a  hungry tarantula. Just a few of the unique species on Roraima.

In truth though, the plateau isnt as isolated as one would like to think: species from the plains below have occasionally been found on top. Even endemic species have been estimated to diverge from the ancestral population only a few million years ago, which is far younger than the age of the plateau itself.

Why would this be? My hypothesis is that birds may occasionally capture prey from the lowlands and bring them to nesting grounds on the cliff surface. The living species are escaped specimens. Perhaps, but there doesnt seem to be conclusive proof. Furthermore, there is actually a steep ramp to one side.

A caveat for aspiring visitors though: its not easy to get to the top, although thankfully, you dont need to scale the sheer cliff face with rope. There is a track on one side of the cliff face to the top.
See more info here.

Socotra Island

This might seem like trees from another planet, but they are actually from an island on Earth.
Behold, the dragon's blood tree, its scientific name which is dracaena cinnabari, found nowhere else in the world but Socotra. So called because of the crimson sap harvested from their trunks, prized during the Middle ages, the unique, crown shape is a form of adaptation mechanism for survival in dry climate - the crown shape provides an "umbrella" to reduce water loss in the hot and dry climate.

What is unique about Socotra is that it is not a volcanic island. Located in the Indian Ocean, closest to Somalia, but under Yemeni jurisdiction, tectonic activity detached it from mainland Africa during the aforementioned Pliocene, from about 2.6 - 5 million years ago. What researchers believe is that this species went extinct on the mainland but the island's relative isolation prevented it from being out-competed or driven to extinction by fundamental shifts in climate. In fact, almost a third of all flora and fauna on Socotra Island is found nowhere else on Earth!




 Another unique species found nowhere else on Earth is this cucumber tree, Dendrosicyos socotranus, related to the cucumbers we eat. (Note that another species of tree, the Averrhoa bilimbi is also known as cucumber tree but is in no way related to the agricultural ground cucumber.)

Just a few of the unique species here. As for endemic birds, I ll let pictures and attached links tell you all you need to know. Read this for starters.


Conclusion

As one can see, biogeography provides evidence for evolution via the process of natural selection. This post is a little sketchy on the details, nevertheless I will provide more info in the future.
Enjoy!



Socotra golden-winged grosbeak







 

Socotra warbler



Monday, 23 June 2014

"Observational Science" and the Bible

Introduction, or why am I writing this?

As a science enthusiast, I am increasingly frustrated when creationists say science can be clearly demarcated into "two types of science": observational and historical science. Why? Because its clearly an arbitrary reason for business tycoons like Ken Ham to partition science into two types, so that his True Christian brethren can be excused for rejecting findings in evolutionary biology, geology, paleontology, astronomy and archaeology. I will focus on refuting this false dichotomy in the near future, but for now lets turn to observational science, which Ken Ham calls the "good, Christian kind"  and the Bible.

First, a little background. Lets say I am quite familiar with this line of argumentation, having been exposed to it. I had been in intense spiritual and emotional pain after recently leaving another religion when a good friend of mine invited me to a church he was attending. Long story short, I got into trouble with the local pastor over matters like evolution and millions of years. It was a very depressing experience, to say the least, and made my inclination to spirituality suffer again. Nevermind.

What I am here to discuss here is, basically, during the infamous debate, Ken Ham's asserted that observational science confirms the Bible. Unfortunately this is only true via deliberate cherry-picking.


So let's play Ken Ham's game. Most slides are taken from the debate directly.

1. An intelligence produced life
No evidence. Why is that? Ken Ham makes this assertion without backing it up. No intelligence has ever communicated with us and proclaimed that He produced the life we say. Of course, if pressed, Ken Ham will retreat to the Bible, but how does he know the Bible is this intelligent agent's method of communicating with him? The same can be said of any other religious text. I am also willing to bet God never directly said to him "Yes I made you!"

In fact, life could have very well been produced by an unconscious supernatural force and the prediction would be just as valid. Or its possible, well, abiogenesis occurred.

2. Animals only producing after their kind
Untenable and unfalsifiable. The Bible never delineates the extent of what a kind is. So Ken Ham must resort to the ultimate flawed, fallible creature, Man, to arbitrarily define the Biblical Kind.



 Of course, they are forced to adopt Linnaean taxonomy (another arbitrary man-made invention) to justify the Biblical kind. In this case, each "kind" corresponds to the Linnaean family hierarchy. Sounds good in theory right?

Take a look at the Elephant Kind. Note something unique, where-else Cat Kind and Dog Kind have their Latin names "Felidae" and "Canidae" respectively, the Elephant Kind has "Order Proboscidea". Why that extra word tacked on?

They have just committed a violation of their own definition of kind and the Linnaean taxonomy it sprung from: an order is above a family in hierarchy. In fact, Order Proboscidea comprises a huge extent of extinct mammals, marked by their inheritance of a proboscis, an "elephant trunk" so to speak. Only one family of Order Proboscidae survives to this day though; the Elephantidae family. The reason is they had to include the mastodon, which belonged to an entire different "family" under this order because mastodon fossils have been found in supposed "post-Flood deposits". Bear in mind that the mastodon has 4 tusks.

Another very serious problem is this. Entire Linnaean families often require hundreds of thousands of years to achieve the enormous diversity of species within them. But for Ken Ham, all this diversity had to be attained within four thousand years. In this case, a few hundred "kinds" of mammals from the Ark have to produce nearly 10,000  living species within 4000 years. I ll illustrate this by example.

At about 41 minutes into the debate, he draws a quote from this article  regarding dog diversity:

"We provide several lines of evidence supporting a single origin for dogs, and disfavoring alternative models in which dog lineages arise separately from geographically distinct wolf populations (Figures 4-5, Table S10)."
And backs it up with this picture:

The whole paper is available on arXiv here.
I do not know why Ken Ham used this paper at all for the origin of dogs.  I'm not sure whether to laugh or cry, after reading the paper. Do you know why?







This is the actual picture:

Image from http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004016















What Ken Ham did was, in essence, invert this graph so that we were unable to see the evolutionary timescale of speciation necessary to produce all the ancestral species of modern dogs . You can see the golden jackal (dingo) diverge almost four hundred thousand years ago, then the other ancestral dogs from a time period of 12-15,000 years ago, during a genetic bottleneck that reduced the wolf population from 2000-25000 individuals. No, not 7 pairs!

What saddens me is how deceitful this is. This is an example of Ken Ham's deliberate mis-representation of data to support his view. And to support his hypothetical hyper-evolution, the mutation rate must be sped up three-fold for the other species and almost a hundred times for the golden jackal. This speciation rate is far too quick! Where are the transitional forms? Why dont we see such rapid speciation today? Why dont we see rapid speciation among humans too?

3. Evidence confirming a global flood

Self-refuting. By Ken Ham's own standards, a global flood that occurred in the past would fall under the realm of historical science and based on unprovable assumptions. The only retort Ken Ham can provide is the extremely poor mantra that he asks the children who visit his museum to repeat: billions of dead things buried all over the earth. Of course, having animals living and dying over hundreds of millions of years explains things just as well, if not better, but I ll let that slide for now.  There's a more pressing issue.

From Genesis 6 (KJV):
 And it came to pass, when men began to multiply on the face of the earth, and daughters were born unto them,2 That the sons of God saw the daughters of men that they were fair; and they took them wives of all which they chose.3 And the LORD said, My spirit shall not always strive with man, for that he also is flesh: yet his days shall be an hundred and twenty years.4 There were giants in the earth in those days; and also after that, when the sons of God came in unto the daughters of men, and they bare children to them, the same became mighty men which were of old, men of renown.5 And GOD saw that the wickedness of man was great in the earth, and that every imagination of the thoughts of his heart was only evil continually.6 And it repented the LORD that he had made man on the earth, and it grieved him at his heart.7 And the LORD said, I will destroy man whom I have created from the face of the earth; both man, and beast, and the creeping thing, and the fowls of the air; for it repenteth me that I have made them.8 But Noah found grace in the eyes of the LORD.

What can we infer from this passage? 
a. Man had multiplied over the face of the earth
b. sons of God came down and had children with the daughters of man, bearing giants, who were men of renown. 
The rest you should know: God sent the flood to destroy everything, except Noah and his family, plus seven pairs of each clean kind and a pair of unclean ones on the Ark.
Then where are the human fossils? Up to this date not a single one has been found in the vast majority of sedimentary rock. Not even fossils of modern animals, such as domestic dogs and cows, have been found in supposed Flood Deposits. Furthermore, we should expect to find half-giants buried in the rock, but we dont. Even sadder is that creationists have committed fraud to back up the idea humans lived with dinosaurs, see Malachite Man and Paluxy.
Lastly, there are thousands of salt mines all over the world. How can a global flood explain this?     
4. Evidence confirming One Race
This is probably the only prediction that the Bible got right. The assertion is that humans had a single origin (Noah-Babel) so there is only one race of man, so to speak. The homo sapien.  However, what is problematic is when you consider the existence of other species of humans, such as Neanderthal and Homo Habilis

The current AiG stance is that they were post-flood humans that went extinct rapidly, despite many archaeological sites, buried in several layers, where they used to live. Can they be considered part of the race of man? 

5. Evidence confirming the Tower of Babel
Where are the remains of this purported tower? Seriously no Ron Wyatt tricks! This tower was supposed to be enormous in size, and was in the city of Babel. Yet we havent found evidence of its existence!!! 
 I presume what they mean is, the single origin of all languages around the world. This has some basis in reality, except the place of origin is in Africa. From the linked Dailymail article:
Dr Atkinson, of Auckland University, has now come up with fascinating evidence for a single African origin of language.In a paper published today in Science, he counted the number of distinct sounds, or phonemes, used in 504 languages from around the world and charted them on a map.The number of sounds varies hugely from language to language. English, for instance has around 46 sounds, some languages in South America have fewer than 15, while the San bushmen of South Africa use a staggering 200.Dr Atkinson found that the number of distinct sounds in a language tends to increase the closer it is to sub-Saharan Africa.He argues that these differences reflect the patterns of migration of our ancestors when they left Africa 70,000 years ago.Languages change as they are handed down from generation to generation. In a large population, languages are likely to be relatively stable - simply because there are more people to remember what previous generations did, he says.But in a smaller population - such as a splinter group that sets off to find a new home elsewhere - there are more chances that languages will change quickly and that sounds will be lost from generation to generation.
Either way the YEC is presented with a dilemma. To accept this model, he or she will have to agree that humanity's place of origin was from Africa, not the Middle East. To reject it, then its possible languages could have risen spontaneously from different geographic locales. So which is it?  

6. Evidence confirming a Young Universe  

Ken Ham did not present a single point in favor of this during the entire debate. Unfortunately, all the evidence points to an ancient Universe. From the massive levels of impact cratering across the Moon, Mars, Mercury, the Galilean moons Callisto and Ganymede, the Saturnian moon Tethys, (read my previous posts) to the fact that the Milky Way is 40000-50000 light years across. Their winding up of spiral galaxies and comets have been refuted here and here. Besides, a young Universe is on a very different level than a young Earth - spacetime must be dilating by a magnitude of millions to make galaxies appear billions of light years away. Is this the result of a deceitful God?  

Going off on a tangent, I find their dismissal of the Oort Cloud amusing. They have never seen or heard their God, but suddenly when it comes to an undetectable source of long-period comets, they dismiss it and claim the "evolutionists" are making shit up. Read up a brief discussion of the Oort Cloud here. See a more detailed refutation here

What about this.....
Being Answers in Genesis, it makes sense the entire focus of the text would be in Genesis. Let me pull up this part from here:

Genesis 30:31-43

New International Version (NIV)
31 “What shall I give you?” he asked.“Don’t give me anything,” Jacob replied. “But if you will do this one thing for me, I will go on tending your flocks and watching over them: 32 Let me go through all your flocks today and remove from them every speckled or spotted sheep, every dark-colored lamb and every spotted or speckled goat. They will be my wages. 33 And my honesty will testify for me in the future, whenever you check on the wages you have paid me. Any goat in my possession that is not speckled or spotted, or any lamb that is not dark-colored, will be considered stolen.34 “Agreed,” said Laban. “Let it be as you have said.” 35 That same day he removed all the male goats that were streaked or spotted, and all the speckled or spotted female goats (all that had white on them) and all the dark-colored lambs, and he placed them in the care of his sons. 36 Then he put a three-day journey between himself and Jacob, while Jacob continued to tend the rest of Laban’s flocks.37 Jacob, however, took fresh-cut branches from poplar, almond and plane trees and made white stripes on them by peeling the bark and exposing the white inner wood of the branches. 38 Then he placed the peeled branches in all the watering troughs, so that they would be directly in front of the flocks when they came to drink. When the flocks were in heat and came to drink, 39 they mated in front of the branches. And they bore young that were streaked or speckled or spotted. 40 Jacob set apart the young of the flock by themselves, but made the rest face the streaked and dark-colored animals that belonged to Laban. Thus he made separate flocks for himself and did not put them with Laban’s animals. 41 Whenever the stronger females were in heat, Jacob would place the branches in the troughs in front of the animals so they would mate near the branches, 42 but if the animals were weak, he would not place them there. So the weak animals went to Laban and the strong ones to Jacob. 43 In this way the man grew exceedingly prosperous and came to own large flocks, and female and male servants, and camels and donkeys.




After someone asked me to read this, I cannot help but feel troubled. This shows a) apparently breeding goats in front of striped branches produces striped goats??!!! b) what does this show you about Jacob's integrity to Laban???

Conclusion

One of the greatest obstacles to me converting to the Christian faith is this. Apparently I am supposed to abandon most of my pre-existing acceptance of mainstream scientific views on the age of the Earth and the evolution of man. As someone who has spent years reading science articles and whatnot I find this so hard. Very very painful in fact. I hope that in time Christians will come to realize that there isnt a conspiracy by evil secularists to undermine the Biblical authority just scientists reporting honestly on the data they gathered.