I’m honestly surprised by how fast I drew this considering how good it looks for a spur-of-the-moment sketch. I threw on the different biotechnology fields rather randomly, I tried to have some logic to it such as specific fields stemming from from others but it was something I could always change, but no one seemed to have any problem with it and I was pleased to see that many others liked it too, so much in fact it was voted as that years design for the back of the shirt.

The design was digitized and when the shirt was printed it looked like this:

For my first ever printed shirt I was very pleased with the outcome, I also got to design the shirt for the following year also, but more about that in a later post.

When I was about sixteen, I remember laying in my backyard. It was early summer in Florida, and the heat was that balmy sort of pleasantness where you can enjoy it as long as you don’t move. Drowsiness took over that afternoon as I spread my hair out over a blanket and let the sunlight sink into my skin. A humid, warm wind caressed my arms and legs, and I remember staring deeply into the grass next to my face. I studied each blade of grass, watched the ants hauling one piece of sand at a time, saw a dragonfly land before it took off for the cherry tree, and I marveled.

Not for the first time, I remember thinking that the world was a miraculous place. Grass and tress can grow– it always seemed beyond me that living things have the ability to reproduce, to heal, to extend further into their piece of the universe. I wondered at the near-impossible intricacies that defined every moment, every breath. How rich and wide and wonderful the world was.

What always accompanied these thoughts was a bone-deep awareness of God’s handiwork. How can anyone think this is anything less than created? That a blade of grass or the color of my eyes is all because  of chance?

I grew up believing in literal six-day young earth creationism. I’ve read every book they published on the subject, and spent two years in college regularly reading the new issues of Ex Nihilo (it’s been renamed as Journal of Creation). I fervently defended it any time I had the opportunity. To me, the “theory of macro-evolution,” as I always referred to it, made no sense. I had also been told by nearly everyone in my life that theistic evolution was a completely untenable point of view– if you believe in God, and you believe that God created things, it’s nonsensical to not accept the events of Genesis. Why do you need neo-Darwinian evolution if you believe in God? I had been taught that evolution was an intellectual outgrowing of atheism– if you don’t believe in God, well, you still need an explanation for how the world got here– hence The Theory.

For me, personally, I think I emotionally needed creationism. I was frequently and intensely overcome by awe when I viewed nature, and I somehow needed for it to be orderly and precise. In order for my universe to make sense, creationism was the only answer I had access to. I grew up being told to take the Bible supremely literally, to always assume that its statements were always completely fact-oriented. I heard arguments that the first chapter of Geneses was mythic poetry, and I was harshly commanded to ignore that lie. The Bible is not a myth, it is not a fairy tale, and everything about our faith depends on a literal interpretation of the first three chapters. If we can accept that these are not literal, what else in the Bible are we going to accept as non-literal? Not believing in creationism was a slippery slope that could only end in atheism and, horrendously, moral relativism.

~~~~~~~~~~~~~~~~~~~~

When I was in graduate school, I abruptly encountered an impasse. At this point in my life, I had grown used to re-examining many of my deeply held and most cherished beliefs. But, I hadn’t gone anywhere near evaluating the validity of young earth creationism. It had been such an integral part of my faith system for as long as I could remember believing in God, and, at that moment, it seemed superfluous. Honestly, to me, it still is.

But what brought me to this place, what wrenched me from a staunchly-defended position to one of ambivalence, was a single scientific study. In all my previous internet forays, I had made an odd friend of sorts. We were each other’s opposition on a variety of forums, but we somehow formed a respectful bond. He sent me a study that linked endogenous retroviruses and common ancestry. I read it, and the evidence was powerfully compelling.

So, I did what any good creationist would do– I found a geneticist that works with Answers in Genesis, and I wrote him a letter. I included a link to the study and asked him to provide a counter-argument.

The reply I received was complete and utter  BULL SHIT.

I cannot express that firmly enough. My letter had been articulate and had indicated that I had a passing, non-scholarly familiarity with biochemistry and genetics. His reply was dismissive, anti-intellectual, belittling, and insulting. He reacted childishly and implied that if I could accept any peer-reviewed study as “evidence for evolution,” that obviously I wasn’t educated in creationism enough, and he directed me to the AiG page on genetics. Which did not address my question at all.

I was so far beyond frustrated. And I decided that I wasn’t going to bother anymore. I wrote my friend back, told him what had happened, and that I would, eventually, re-think some things. Not right then– right then I was putting together a paper on Frankenstein, the birth of chemistry, and how scientific philosophy affects literature. I asked him a few questions about galvanism and moved on with my life.

~~~~~~~~~~~~~~~~~~~

Last Saturday, I was walking through the woods that line the Chesapeake Bay. At first my walk was energetic and brisk, but when I reached a deeper part of the woods where the houses disappear and all you can hear are the gentle lap of waves, I slowed down. I paid attention. I listened to the multi-layered symphony my footsteps caused. The gentle, gritty, sliding crunch of sand, the muted crack of pine cones and twigs, the crinkle-snapping of leaves, and the plush, muted compression of pine needles. Sunlight bounded off of barely-cresting waves, the wind murmured back and forth between the treeline and the shoreline. I stopped and closed my eyes. I heard the birdsong, felt the wind, absorbed the sun.

And as I listened, I felt a newness . . . a dawn, of sorts.

I don’t need literal six-day young earth creationism to be overwhelmed by the beauty and majesty of nature. I don’t need it for my world to make sense. I don’t need it in order to believe in balance, or provision.

For me, I can look at the artistry of Genesis and see the beauty and power of myth. I find it comforting, actually, that my religion began by deeply rooting itself in myth. That I have a creation story that emphasizes order instead of chaos, where the creation of the world was intentional instead of happenstance. I have a creation myth where the creator-god looks on the physical splendor of what he’s made at calls it morally perfect and absolutely beautiful.

]]> http://athoughtfulchristian.wordpress.com/2013/03/17/unpackaging-evolution/ Mon, 18 Mar 2013 04:41:50 +0000 Robert Van de Water http://athoughtfulchristian.wordpress.com/2013/03/17/unpackaging-evolution/ http://musingsofscience.wordpress.com/2012/12/24/the-happening-of-evolution/ Mon, 24 Dec 2012 12:08:26 +0000 Francis Smallwood http://musingsofscience.wordpress.com/2012/12/24/the-happening-of-evolution/ Is evolution a fact? In the previous post, we noted that a ‘fact’ in science is not apodictic, but always provisional—it may always be confounded by a new discovery.  Following Ruse’s proposition, we considered the three-fold division of evolution into (1) its happening, (2) its paths and (3) its mechanism. If each of these (admittedly interdependent to differing extents) elements can be satisfactorily established, then, yes, we may declare evolution a fact beyond reasonable doubt.

Darwin’s Theory

Darwin presented his theory of evolution as ‘one long argument,’[1] not in a dense, unwieldy tome solely within the purview of the cognoscenti, but in a work of popular science, which could be followed by the lay reader. In this work, the Origin of Species, Darwin sought to marshal evidence from a variety of disciplines in order to establish a Whewellian consilience of inductions: his theory of evolution explicating the evidence; the evidence, in turn, pointing to his theory.

The idea [of a consilience] is that somehow, if a hypothesis is true—tells us about the real world—then various facts or other claims follow from it, and will keep doing so. And there is a kind of feedback process here. As the hypothesis leads to new information, so its derivations themselves confer a kind of probability upon the hypothesis.[2]

It would help to briefly consider what Darwin’s theory actually was. According to Darwin, species were not immutable, but were the product of a gradual process of evolution, the primal (though not sole) cause of which was natural selection. Today, his theory is commonly referred to as ‘evolution by natural selection’; Darwin referred to his theory as ‘descent with modification’. Philosopher of biology Elliott Sober has argued that these characterisations do not accurately convey the essence of Darwin’s theory suggesting that Darwin’s theory be referred to as ‘common ancestry plus natural selection.’[3] This characterisation acknowledges the relative indepdendence of each of the two ideas, an independence which can be appreciated historically, for whilst Darwin did much to convince the scientific community of the first idea, he failed to convince even some of his closest ‘disciples’ of the second.[4] Nevertheless, the thesis of common ancestry is absolutely integral to Darwin’s theory. If common ancestry can be demonstrated, then species cannot be immutable and one is forced to propose a mechanism to account for the process.

Sober and Orzack note that ‘the best evidence of common ancestry comes from neutral or even deleterious features.’[5] As Gould frankly puts it, ‘ideal design is a lousy argument for evolution.’[6] According to an evolutionary hypothesis, adaptation is the result of natural selection. But if adaptation is perfect, then an evolutionary hypothesis becomes less likely, as perfect adaptation is more suggestive of intelligent design. If, on the other hand, adaptation is not perfect, or if there are non-adaptive or maladaptive traits, then a hypothesis of intelligent design becomes less likely and an evolutionary hypothesis more likely. As Stephen Jay Gould writes, ‘you cannot demonstrate evolution with perfection because perfection need not have a history.’[7] However, ‘if organisms have a history, then ancestral stages should leave remnants behind.’[8] History is revealed by ‘the useless, the odd, the peculiar, [and] the incongruous’.[9] Natural selection effaces the marks of history. This is what makes evolutionary convergence (the evolution of similar features in independent lineages) such a nuisance for phylogeneticists. Is the feature shared by two groups homologous (due to common ancestry), in which case a close phylogenetic relationship is inferred? or is it due to convergence, in which case it would be a mistake to infer a close phylogenetic relationship?[10] Thus, ‘The more a trait’s distribution can be explained solely on the basis of natural selection, the less evidence the trait will provide for shared ancestry.’[11] One must look, then, to those non-adaptive or maladaptive traits in order to prove the happening of evolution.

Morphology

Homology provides perhaps the most striking confirmation of evolution. Darwin was convinced that the exquisite adaptations which pervade the living world were the result of natural selection ‘daily and hourly scrutinising, throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good’,[12] yet natural selection can only work with what is to hand. An intelligent designer could presumably fashion a novel structure of whatever materials required, but such a luxury is denied to selection. Selection can only modify existing structures, making do with whatever is to hand, as it were: ‘the parts may change to almost any extent in form and size, and yet they always remain connected together in the same order.’[13] Homologies are testament to common ancestry. Unlike convergences, ‘Entities are homologous if, in principle, they can be traced back to a single genealogical precursor.’[14]

Several homologous vertebrate forelimbs

Looking within our own subphylum, the vertebrate forelimb presents a striking example of homology. If you take a look at the diagram above, you can see that the limbs of humans, dogs, whales and birds are all variations on a common theme. One can see the humerus, the radius and ulna of the lower arm, as well as the digits (reduced to three in birds). Whilst the limb in each species is adapted for a particular function, it is apparent that the isomorphisms are due to the inheritance of the structure from an ancestor common to all four species. Homologies such as these only make sense in the light of evolution, and that is what makes them such good pieces of evidence. As Darwin wrote, uttering a common refrain throughout the Origin, ‘On the ordinary view of the independent creation of each being, we can only say that so it is; – that it has so pleased the Creator to construct each animal and plant.’[15]

Biogeography

Just as only ‘descent with modification’ can adequately explain homology, so can only evolution adequately explain the other classes of facts Darwin considered. To take a second example used by Darwin we look to biogeography; a subject to which he devoted two chapters in the Origin. This area provided perhaps the most cogent proof of evolution; both Alfred Russel Wallace and Joseph Hooker came to accept evolution on account of the geographical distribution of species. Biogeography was also cenral in Darwin’s conversion to and discovery of evolution. Richardson writes that ‘Ultimately, biogeography offered the only sufficiently elaborated body of knowledge on the relationship of species to their environment, and to changes in that environment, that could constitute a valid test case for Darwin’s developing theoretical speculations on transmutation and his search for an efficient cause of change.’[16] Why should it be that, despite highly similar environmental conditions prevailing in regions of distant continents the species that one finds there invariably bear close resemblance to the species of that area and not of the distant area?

If we look to the islands off the American shore, however much they may differ in geological structure, the inhabitants, though they may be all peculiar species, are essentially American…We see in these facts some deep organic bond, prevailing throughout space and time, over the same areas of land and water, and independent of their physical conditions.[17]

What could account for the similarity between neighbouring species if the environmental conditions appeared to be irrelevant? If one Australian species would have been just as well adapted to the environment of an American species, why should the two species be so dissimilar yet bear such peculiar affinities to the species of their homeland? ‘This bond, on my theory,’ wrote Darwin, ‘is simply inheritance, that cause which alone, as far as we positively know, produces organisms quite like, or, as we see in the case of varieties nearly like each other.’[18] It is migration that is responsible for the similarities between mainland and offshore species, and it is restrictions to migration which are responsible for the differences between species inhabiting identical environments on opposite sides of the globe. At the close of the second chapter on biogeography, Darwin writes, ‘I think all the grand leading facts of geographical distribution are explicable on the theory of migration…, together with subsequent modification and the multiplication of new forms.’[19]

Geographical distribution of Galápagos tortoises

Embryology

In a letter to Joseph Hooker, Darwin referred to the section on embryology as his ‘pet bit’[20] of the Origin. Darwin had written that ‘certain organs in the individual, which when mature become widely different and serve for different purposes, are in the embryo exactly alike.’[21]If one looks at, say, the early embryo of a human and the early embryo of a fish the two embryos are remarkably similar; even though the two go on to develop into very different organisms. And the early stages of the human embryo resemble the adult forms of ancestral forms. Darwin goes on to write that ‘The embryos, also, of distinct animals within the same class are often strikingly similar: a better proof of this cannot be given, than a circumstance mentioned by Agassiz, namely, that having forgotten to ticket the embryo of some vertebrate animal, he cannot now tell whether it be that of a mammal, bird, or reptile.’[22] As evolution proceeds, newer developmental instructions are layered on top of more ancient instructions, forming a kind of developmental palimpsest.

We cannot, for instance, suppose that in the embryos of the vertebrata the peculiar loop-like course of the arteries near the branchial slits are related to similar conditions,—in the young mammal which is nourished in the womb of its mother, in the egg of the bird which is hatched in a nest, and in the spawn of a frog under water. We have no more reason to believe in such a relation, than we have to believe that the same bones in the hand of a man, wing of a bat, and fin of a porpoise, are related to similar conditions of life… In two groups of animal, however much they may at present differ from each other in structure and habits, if they pass through the same or similar embryonic stages, we may feel assured that they have both descended from the same or nearly similar parents, and are therefore in that degree closely related. Thus, community in embryonic structure reveals community of descent.[23]

Molecular Genetics

Homology, biogeography and embryology provided three lines of evidence which Darwin wove into his consilience. A fourth line of evidence which was not available for Darwin but which provides eloquent confirmation of the happening of evolution comes from molecular biology. It is a striking fact that all organisms share the same genetic material. Not only do all organisms share the same genetic material, they also share the same genetic code. This is an instance of a ‘universal homology’.[24] A triplet code is written in the four-letter nucleotide alphabet of DNA codes for an amino acid (the constituent building block of a protein or polypeptide). For example, the triplet code GGC (guanine·guanine·cytosine) codes for the amino acid glycine. With a triplet code composed of four letters, there are 4³ possible triplets to code for only 20 amino acids (as well as punctuation marks), so that there is a great deal of redundancy in the code, so that, for example, GGG (guanine·guanine·guanine) also codes for glycine. As Sober notes,

As long as there are multiple codes that each would work, a shared code is evidence for common ancestry. And the more such codes there are, the stronger the evidence that the near-universality of the code provides for common ancestry. This point holds even if the shared code we observe in the life around us turns out to be optimal.[25]

It is not inconceivable that different groups of organisms should have different codes, and for this reason the universality of the code (with its minor variants) testifies to the happening of evolution. The most satsisfying explanation for the universality of the code is descent with modification.

~

The pieces of evidence presented here have provided confirmation of the first element of evolution: its happening. Only if descent with modification—that is, evolution—has occurred can we satisfactorily account for the facts before us. The theory of evolution wields extraordinary explanatory power, accounting for a plethora of otherwise disparate facts. The happening of evolution can be known without knowing the causal mechanisms responsible. In the next post, I shall consider the second element of the theory of evolution: its paths.

Many other fields of study are detailed, for example,  29+ Evidences for Macroevolution.  This article and others on that website contain many compelling arguments worthy of notice.

This evidence, however good, represents just a relative few pixels in the whole high definition screen of life origins.  The individual pixel arguments, yes, could be argued as fact and are presented as such.  But the whole extrapolation, and that is what it is, that we can trace our origins back to sea worms and the like – this part is not fact.  This part of it is unprovable – it is extrapolated from the existing pixel-like evidences.

The high definition image of life origins cannot be revealed from the limited number of existing pixel arguments, however bright they may be.

Excerpt:

The theory of evolution states that the species arose spontaneously, one from another via a pattern of common descent. This means the species should form an evolutionary tree, where species that share a recent common ancestor, such as two frog species, are highly similar, and species that share a distant common ancestor, such as humans and squids, are very different. But the species do not form such an evolutionary tree pattern. In fact this expectation has been violated so many times it is difficult to keep track. These violations are not rare or occasional anomalies, they are the rule. Entire volumes have been written on them. Many examples are the repeated designs found in what, according to evolution, must be very distant species. Such evolutionary convergence is biology’s version of lightning striking twice. To explain this evolutionists must say that random mutations just happened to hit upon the same detailed, intricate design at different times, in different parts of the world, in different ecological niches, and so forth. The idea that the most complex designs we know of would spontaneously arise by themselves is, itself, not scientifically motivated and a real stretch of the imagination. But for the same intricate designs to arise independently by chance is even more of a stretch. That is why evolutionist’s claim this week that they have found evidence for convergent evolution was so intriguing.

[...]Though evolutionists sometimes deny biological convergence, it is a scientific fact. And a paper from this week added yet another example:

In mammals, hearing is dependent on three canonical processing stages: (i) an eardrum collecting sound, (ii) a middle ear impedance converter, and (iii) a cochlear frequency analyzer. Here, we show that some insects, such as rainforest katydids, possess equivalent biophysical mechanisms for auditory processing. Although katydid ears are among the smallest in all organisms, these ears perform the crucial stage of air-to-liquid impedance conversion and signal amplification, with the use of a distinct tympanal lever system. Further along the chain of hearing, spectral sound analysis is achieved through dispersive wave propagation across a fluid substrate, as in the mammalian cochlea. Thus, two phylogenetically remote organisms, katydids and mammals, have evolved a series of convergent solutions to common biophysical problems, despite their reliance on very different morphological substrates.

It is another curious example of biological convergence, so rather than attempt to deny the undeniable, evolutionists now claim it as another confirmation of evolution.

I’m a software engineer, and we re-use components all the time for different programs that have no “common ancestor”. E.g. – I can develop my String function library and use it in my web application and my Eclipse IDE plug-in, and those two Java programs have no common ancestry, but they do have a common designer. So you find the same bits in two different programs because I am the developer of both programs.

Previously, I blogged about another example of convergence reported by Science Daily. One of the predictions of intelligent design theory is that examples of convergence, which is really just re-use of common code by the designer, will be everywhere in nature. And that predictions just keeps getting confirmed as science marches forward, and the primitive religion of naturalism retreats.

Excerpt:

Darwin’s tree of life might be visible in DNA, if DNA didn’t conspire to scramble the signal.

Mysterious Jonathan writing at Uncommon Descent.

Here’s his thesis:

Recently on this blog, I have been exploring and examining some of the genomic arguments for common descent. As I have been documenting in recent weeks, while the case for common ancestry — on the face of it — looks mightily strong, closer inspection reveals that the arguments don’t, in fact, stand up under more rigorous scrutiny. In the vast majority of instances, the corroborative data is very carefully cherry picked from the pertinent data set, and the non-congruent evidence is discarded or ignored.

And here’s a snippet:

One popular argument for common descent is the case from the discipline of biogeography — that is, the study of the geographical and historical distribution of species in relation to one another. The argument is based largely around the observation that species are related in accordance with their geographical proximity with respect to one another.

And here is the problem – this is dynamite:

So, when the biogeographical data does not accord with the predictions and expectations made by common descent, one always has ‘oceanic dispersal’ as an ad hoc fudge factor — including the rather remarkable claim that Monkeys made it across the Atlantic from Africa to South America! As Casey Luskin notes here, molecular studies claim that the South American monkeys diverged from the African monkeys around 35 million years ago. But Africa became an isolated island continent around 80 million years ago!

Apparently, monkeys rode on the back of the Flying Spaghetti Monster from Africa to South America.

I actually thought that the evidence for common descent was fairly good, because Behe accepts it and he is not a Darwinist. I didn’t like it, but facts are facts. But I’m glad that Jonathan is shedding some light on this issue. I would like to be able to argue against it, if the evidence is there.

In evolutionary biology, convergent evolution is the process whereby organisms not closely related (not monophyletic), independently evolve similar traits as a result of having to adapt to similar environments or ecological niches.

It is the opposite of divergent evolution, where related species evolve different traits.

On a molecular level, this can happen due to random mutation unrelated to adaptive changes; see long branch attraction. In cultural evolution, convergent evolution is the development of similar cultural adaptations to similar environmental conditions by different peoples with different ancestral cultures. An example of convergent evolution is the similar nature of the flight/wings of insects, birds, pterosaurs, and bats.

All four serve the same function and are similar in structure, but each evolved independently.

Jonathan Wells explains the problem that convergence poses for naturalistic evolution:

Human designers reuse designs that work well. Life forms also reuse certain structures (the camera eye, for example, appears in humans and octopuses). How well does this evidence support Darwinian evolution? Does it support intelligent design more strongly?

Evolutionary biologists attribute similar biological structures to either common descent or convergence. Structures are said to result from convergence if they evolved independently from distinct lines of organisms. Darwinian explanations of convergence strain credulity because they must account for how trial-and-error tinkering (natural selection acting on random variations) could produce strikingly similar structures in widely different organisms and environments. It’s one thing for evolution to explain similarity by common descent—the same structure is then just carried along in different lineages. It’s another to explain it as the result of blind tinkering that happened to hit on the same structure multiple times. Design proponents attribute such similar structures to common design (just as an engineer may use the same parts in different machines). If human designers frequently reuse successful designs, the designer of nature can surely do the same.

I’m a software engineer, and we re-use components all the time for different programs that have no “common ancestor”. E.g. – I can dump develop my String function library and use it in my web application and my Eclipse IDE plug-in, and those two Java programs have nothing in common. So you find the same bits in two different programs because I am the developer of both programs. But the two programs don’t extend from a common program that was used for some other purpose – they have no “common ancestor” program.

Now with that in mind, take a look at this post from Evolution News.

Excerpt:

two new studies in the January 26th issue of Current Biology, a Cell Press publication, show that bats’ and whales’ remarkable ability and the high-frequency hearing it depends on are shared at a much deeper level than anyone would have anticipated — all the way down to the molecular level

Just as I noted that convergent genetic evolution was said to be “surprising” under neo-Darwinian thinking, this article reports, “The discovery represents an unprecedented example of adaptive sequence convergence between two highly divergent groups and suggests that such convergence at the sequence level might be more common than scientists had suspected.”

The typical Darwinist tack is to call similar structures “superficially similar”. I.e. – the appearance (phenotypes) are similar, but at the genotype (code) level, there is nothing in common. They have to say that because there is no common ancestor who shares the structure, so the biological information CANNOT be similar. A naturalistic theory can’t accommodate similarities at the genetic level unless there is a shared common ancestor who has those instructions. But guess what? When you actually take a closer look at the evidence… the biological information IS similar between bats and whales – AND THEY DON’T SHARE A COMMON ANCESTOR. So it exactly like the software design scenario, where the designer has put the same bits into two programs that were developed independently and don’t extend from a common program.

The Science Daily article explains more:

“The natural world is full of examples of species that have evolved similar characteristics independently, such as the tusks of elephants and walruses,” said Stephen Rossiter of the University of London, an author on one of the studies. “However, it is generally assumed that most of these so-called convergent traits have arisen by different genes or different mutations. Our study shows that a complex trait — echolocation — has in fact evolved by identical genetic changes in bats and dolphins.”

[...]“We were surprised by the strength of support for convergence between these two groups of mammals and, related to this, by the sheer number of convergent changes in the coding DNA that we found,” Rossiter said.

Read the whole thing at Evolution News. This is quality work by Casey Luskin.

Here’s the case for common descent:

UCA is now supported by a wealth of evidence from many independent sources, including: (1) the agreement between phylogeny and biogeography; (2) the correspondence between phylogeny and the palaeontological record; (3) the existence of numerous predicted transitional fossils; (4) the hierarchical classification of morphological characteristics; (5) the marked similarities of biological structures with different functions (that is, homologies); and (6) the congruence of morphological and molecular phylogenies.

(Douglas L. Theobald, “A formal test of the theory of universal common ancestry,” Nature, Vol. 465:219-222 (May 13, 2010).)

And here’s a response to each of those points:

• (1) Phylogeny and biogeography don’t always agree.
• (2) Phylogeny and paleontology don’t always agree.
• (3) Transitional fossils are often missing (or the “predicted” transitional fossils fall apart on closer inspection).
• (4) Hierarchical classifications often fail.
• (5) “Homologous” structures often have different developmental pathways or different structures often have “homologous” developmental pathways.
• (6) Morphological and molecular phylogenies are often incongruent.

Before I read this post, I only knew about 3, 4, 5 and 6.

I thought that I would post this because I haven’t said much about common descent before. I’m against it.

despite their apparent simplicity, understanding viruses has been one of biology’s greatest challenges since the beginnings of the molecular revolution. the traits that we have discovered to be ubiquitous among viruses are relatively straightforward. generally, a virus consists of a single piece of naked DNA, encapsulated in some sort of protein-based coat. viruses cannot be considered cells because they contain none of the internal machinery necessary for growth or self-replication. instead, many viruses replicate by inserting their DNA into the cells of a host. this invading DNA is able to co-opt the host cell’s own replication proteins, and turn the host into a small factory for new viruses.

many but not all of the viruses that cause human disease use this strategy, and they often do so with alarming efficiency. another common viral replication strategy is to insert DNA into a host, and integrate that DNA into the hosts own DNA. viruses that employ this strategy are effectively choosing symbiosis inside a host, and replicate themselves in step with the host cell’s own cycle.

it may seem strange that some viruses act aggressively- invading, replicating and moving on once they have plundered all the resources available, while others choose a life of harmless symbiosis within their host. how can we come up with a general definition for all viruses if this is the case? shouldn’t we classify these critters as two unique types – neither truly alive perhaps, but fundamentally different in their non-living existence?

to answer this question, one must think carefully not about what viruses are doing but why. in both cases, a fragment of DNA is simply trying to replicate itself in the most effective way possible. for some, this means integrating itself into an organism, and reproducing in concert with the organisms own generations. for others, it means rape, kill, pillage and burn. viruses  are the ultimate narcissists- no ambitions for complex structure or function,, simply a raw, unabashed need for self-propagation.

if existence driven entirely by the need to replicate and produce more of oneself what it means to be a virus, i don’t think it’s a far stretch of the imagination to draw parallels with organisms that we officially classify as “alive”. with simple single-celled life, the similarity is easy to see. unicellular bacteria are essentially DNA vessels, but with extra compartments for the tools and machinery required to replicate. some single-celled bacteria do reproduce sexually and, in exchanging DNA, produce offspring that are not genetic clones. nevertheless, the idea is essentially still simple propagation of genes, but given one more level of complexity in that the replication process is self-sufficient.

but how much similarity can there possibly be between a complex, multi-cellular organism, and a single replicating strand of DNA? try thinking of a complex organism, like a cat, horse, or even human, as a nation of cells. each cell is an individual citizen, and each citizen has a specialized job that he must perform as an effective member of the community. if too many citizens dissent, or get lazy, and choose not to perform their allocated jobs, the community falls apart. and what do these citizens, many of whom look and act very different, and would certainly never be caught getting coffee or drinks together, all have in common? dependency on each other for replication.

a human being is orders of magnitude more complex than a virus, and I am not trying to diminish that complexity, or even to claim that it can be reduced to aggregate of cells driven by a simple process. but the common purpose of genes, in everything from their rawest form that do not even consider living, to the most complex organism evolution has produced, speaks to the ancestry we all share.

Anyhoo…

First, this argument is based upon a fundamental misunderstanding of primate genetics: Humans do have more genetic variation than do apes, NOT more defects.

Here’s a little secret, from me to you — Everybody is a mutant, and even identical twins have slight genetic variations between them. Most mutations, contrary to popular belief, are simply useless, not necessarily harmful, happening because of extremely minor errors in DNA replication in the cell so inconsequential that the majority have no effect on the survivability of the organism.

Generally speaking, there are some harmful mutations, and these are selected against, but some benefit the organism if selection criteria in its environment are favorable, and these enhance its ability to perpetuate those same traits by out-producing its competitors in successful offspring, which then, if conditions remain favorable, themselves produce offspring, and so on. Hence natural selection.

Yes, the old cliché of evolution being summed up as the tautology “the survival of the fittest & the fittest are those who survive” is a classic straw man misrepresentation, oversimplified to the point of falsity. Evolution really has more to do with differential reproductive success than it does with any simple and direct survival fitness of the individual organism.

Second, this argument completely ignores what is known about population genetics. It ignores the fact that over time and with favorable circumstances, populations can and will increase, increasing the number of individuals and thus the number of chances for variation in the gene-pool by simple genetic drift.

And given the chance, these variations will happen. We know they will, because they have.

For humans, the major factors for this have been advances in medicine, agriculture and other applications of science and technology which favor the growth and maintenance of large populations in those nations with access to them.

Humans have, at least H. sapiens, started out about 100,000 or so years ago with a relatively sparse population growing to the billions now on Earth over time. The great apes, on the other hand have never had these factors involved at any point in their prehistory, even at the known height of their population. Thus they have never been very numerous compared with humans, except in early prehistory when there were only several thousand Homo sapiens in existence. Thus do modern apes have fewer variations in their genomes in comparison with humans.

This is no real mystery at all, and certainly doesn’t call into question the fact of human descent alongside modern apes from a presumably ape-like common ancestor. While the details of human evolution have yet to be completely filled in, they will be added, and it is one of the most evidently well-supported ideas in science. And no…there is no plausible evidence that we were bio-engineered by aliens. Fnord.

Provine makes clear what follows from the truth of evolution: no free will, no objective standard of good and evil, no life after death, no meaning in life. Johnson argues that the Cambrian explosion disproves Darwinian evolution, and the only reason why Darwinian evolution is widely-accepted is because materialism is pre-supposed.

If materialism is pre-supposed, then only atheistic answers to the origins question are allowed, so naturally Darwinism wins – it has to win once you make a philosophical assumption that matter is all there is. (An assumption contradicted by the big bang theory, which requires the creation of all matter from nothing.

Here’s a summary of the debate:

Debate before an audience between two professors on the naturalistic vs. the theistic way of understanding human existence.

William Provine, Professor of Evolutionary Biology at Cornell University, cites evidence supporting neo-Darwinian theory and argues that microevolutionary processes account for the origin of all life. He asserts that modern evolutionary theory is incompatible with belief in God; that there are no absolute moral and ethical laws; that free will does not exist; and that human character is merely a result of heredity and environment.

Phillip Johnson, Professor of Law at the University of California in Berkeley, agrees that modern neo-Darwinian theory is atheistic and scientific; however, as a general theory it is a philosophical dogma that is inconsistent with the evidence.

Provine and Johnson debate basic questions: Do we owe our existence to a creator? Can the blind watchmaker of natural selection take the place of God? Moderator is Timothy Jackson, Dept. of Religious Studies, Stanford University.

And here’s a couple of clips from the opening. (H/T Uncommon Descent via ECM)

The rest are  linked here.

This is very much worth watching, especially for atheists who typically are not aware that evolution rests on a philsophical assumption that is assumed, and that contradicts astrophysics. That has to stop. And the best way to stop it is by calling it out into the open using debates like this one.

For those of you behind a firewall, here are text excerpts.

And don’t forget about my recent post about the role of pre-suppositions like the pre-supposition of naturalism in historical Jesus research. The post contains debates where this is actually discussed as well.