Evolution - The Assumptions Dominate

Assume Everything

As I've been debating some atheists online and reading up on a lot of the evolutionary studies and data supposedly promoting a number of Neo-Darwinisms core beliefs, I've come to a frustrating realization. The assumptions or beliefs dominate the interpretation of the data. This is something I've known for a long time, but now I'm really seeing it clearly. I'll show you what I mean.


Similarity And Common Ancestry

The idea of common ancestry is based upon the belief/assumption that similarity equals common ancestry except when it's extremely obvious that it doesn't. This means that whenever a characteristic of a living organism is similar to another organism, the immediate assumption is that this similarity exists because both organisms descended from the same ancestral "parent" somewhere in the distant past. But similarity does NOT automatically mean common descent!

Trying to point this out to an evolutionist is almost impossible, however, because they are so heavily bound by this belief that they can't even consider that it isn't absolutely true. The assumption or belief dominates their interpretation of the data so that all similarities immediately mean common ancestry, except in the cases where it's extremely obvious that it can't possibly be explained by that (this is called convergence, when two greatly separated organisms come up with the same characteristics independently).

Similarity, at it's core, just means that the characteristics are similar. That's it! They're SIMILAR! It's the extrapolation and the assumption that interprets and converts this hard data into the story of common ancestry. This belief often completely ignores what has been proven to be naturally possible by physics, chemistry, and genetic mutation, because they believe it so strongly that it overrides the evidences that say, "This can't actually be the best explanation for this."

The assumption dominates the interpretation of the data. Similarity almost always equals common ancestry, no matter what the natural processes of biology say about this being a valid hypothesis or belief.


Gene Duplication

Gene duplication is another prime example of the assumption dominating the interpretation.

Gene duplication is currently the "best" explanation for how new genetic data and functions arise in living organisms over time. You see, scientists for a long time have seriously struggled with the realization that there is far too much complex genetic instructions in living organisms to have simply arisen by small point mutations. Point mutations (single "letter" mutations in a gene) simply cannot create such large scale changes and sets of new novel data without being considered harmful garbage and culled by natural selection. So evolutionists have latched onto "Gene Duplication" as the explanation for the huge size of the genetic library in organisms, and use it as the explanation for how new functionality can arise over time. It basically saves Evolutionism from the obvious limitations of nature "coming up" with new genes and genetic data.

But since this idea has taken off, now EVERYTHING is considered a duplication event! That gene looks a lot like that gene. That means that one of them was accidentally duplicated, mutated, and became imbedded in the genome adding new unique functionality... This means that now similarity ALSO means (assumed) its a result of gene duplication. But this doesn't just stop at highly similar whole genes. This is also taken on the miniscule level of segments of genes. These two pieces of a gene are similar, and so they're a "partial gene duplication". So up and down the analysis of entire genomes, scientists are matching similar chunks of genetic code and declaring them to be examples of gene duplication. Why? Because they're similar, and they have to have an explanation for how all this additional genetic data came about.

However, just like with the argument of similarity equaling common ancestry, this is entirely an interpretation based upon an assumption, that similarity in the genetic code represents an instance of gene duplication. But it only works that way so long as you believe it to be the reality, because once again similarity is assumed to mean something that it doesn't have to mean. These people must build an evolutionary structure to all of life and so these two fundamental beliefs (one old and one new) dominate the entire interpretation of the existing data. The believed "story" explanation takes precedence over all else.


Final Thoughts

Similarity does not automatically mean common ancestry or gene duplication. There are many equally plausible explanations for similarity, none of which point to Evolutionism.

For example, the letter A is similar to the letter H in a number of ways. The shape of the letter, the fact that it uses straight lines, the fact that both are letters in the English alphabet, etc. However this does not automatically mean that we must assume that A beget (is the parent or grandparent of) H. The similarity between them does not mean common ancestry from A to H.  It's simply similarity and that's all.

The same can be pointed to with regards to computer programming code. Computer code uses the exact same core functions and systems to accomplish everything from your web browser to the latest high tech 3D computer/console game. It's all using the exact same kinds of computer code. But because the code is similar (using the same things like variables, IF...THEN statements, and LOOPS), it doesn't mean that your web browser automatically and naturally (without any intelligent involvement at all) gave birth to the game Call of Duty. Or that simple duplication of code from your web browser is the prime explanation for the fact that the code between both programs is essentially quite similar when all is said and done. Similarity does NOT mean common ancestry and does NOT mean a duplication event.

Now obviously these two examples cannot reproduce on their own like a living organism can, however the points still stand. The only time the assumptions listed above stand is when they are used upon living organisms because it's assumed (again, another assumption) that reproduction and time can solve anything. It can't. All of this is a dramatic example of very creative reaching for explanations that circumvent the plausible reality.

They are so bound and determined to explain all of this by way of materialistic reproduction that they completely reject and ignore the possibility of common design (common programming) by an intelligent designer. The more in depth you go into all of this, the more you see that nature has some extreme limitations and barriers that simply can't be ignored, yet they are, by way of these two dominant assumptions (common ancestry and gene duplication). Intelligent Design as an explanation, however, is NOT handicapped by the need for these assumptions and interpreted explanations because it isn't required that all life accidentally just happened. Intelligent Design says that this is all intelligently designed, at least from the start, that the programming is similar not because of common ancestry or gene duplication but because of a common programming language being used and a common "programmer" having written all the code.

The Crumbling "Tree Of Life"

I've been debating another atheist online the past few days about the topic of the "evolutionary tree of life" (or "phylgenic trees"). Evolutionism assumes that all life evolved from common ancestors and that most similarity between organisms is because of this common ancestry. However the classic "tree of life" is falling apart as science has descended into analyzing genes and DNA. The stories they thought they had figured out, with a tidy tree of branching organisms from the beginning of life until now, is looking vastly different when you study the genes rather than the physical (morphological) structures and features. This really isn't that surprising to people who believe that everything did NOT evolve from common ancestors. However it's seriously shaking up the Neo-Darwin community as it sets fire to one of the core tenets/beliefs. The following is one of my responses to the atheist I've been debating. The topic is about how the "tree of life" is having some very serious problems recently. The other point I've been making is that the reason for these problems is that the "tree of life" is based on an assumption first with the data and information then placed upon that tree by scientists in order to make it all fit their presumptions. It's a case of, "This is how we believe it is, so this is how we'll make it look."


EvolutionNews.org (May 12 2009):  A Primer on the Tree of Life (by Casey Luskin)

http://www.discovery.org/a/10651

"“Ever since Darwin the tree has been the unifying principle for understanding the history of life on Earth,” but because “different genes told contradictory evolutionary stories,” the notion of a tree of life is now quickly becoming a vision of the past — as the article stated “today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded,” and as scientists quoted in the article said, “We have no evidence at all that the tree of life is a reality” or the tree is being “annihilated.”"

ScienceDaily (Sep. 23, 2011): Evolutionary Tree of Life for Mammals Greatly Improved
http://www.sciencedaily.com/releases/2011/09/110922141907.htm

This article does not discuss the major contradictions between molecular genetic analysis and morphological versions of the "tree of life" (which is one area where a great amount of conflict is arising), however it does give a good example of one of my other points, the fact that all these "trees" are generated with a substantial amount of human direction. The algorithms and systems are purposefully programmed and organized in such a way as to include, exclude, connect and disconnect things based on a set of pre-input criteria and adjustments. Essentially it's a case of telling the program, "This is how you must handle all this data and these are the bounds within which you will work and connect the dots." When you get down to it, the program is told what the scientists already believe, and must simply figure out the little in-betweens and unknowns based on the greater whole that's already assumed.

To quote from the article...

"To date divergence times on their phylogeny of mammalian families, Springer and colleagues used a "relaxed molecular clock." This kind of molecular clock allows for the use of multiple rates of evolution instead of using one rate of evolution that governs all branches of the Tree of Life. They also used age estimates for numerous fossil mammals to calibrate their time tree.

"We need to have calibrations to input into the analysis so that we know, for example, that elephants and their nearest relatives have been separate from each other since at least the end of the Paleocene -- more than 55 million years ago," Springer said. "We were able to put together a diverse assemblage of fossil calibrations from different parts of the mammalian tree, and we used it in conjunction with molecular information to assemble the most robust time tree based on sequenced data that has been developed to date.""

 There's a massive amount of calibration done on these "trees" in order to make them "turn out right". Otherwise they'd turn out VERY wrong. Garbage in, garbage out. In this instance, the scientists included a lot of known fossils and dates, "relaxed" the molecular clocks (mutation rates, etc.) to allow a vast amount of variability in mutation rates so that the mutation analysis and predictions would NOT end up outside the KNOWN bounds. This is basically building the tree themselves and telling the program to fill in the gaps based on the pre-constructed tree, and allow the program to use whatever mutation rate it needs to in order to achieve the results the scientists/programmers want. Wow.


Nature (27 June 2012): Phylogeny: Rewriting evolution
http://www.nature.com/news/phylogeny-rewriting-evolution-1.10885

"Yet, says Peterson, the tree is all wrong."

""I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree," he says. The technique "just changes everything about our understanding of mammal evolution"."

This is a very recent example of how analyzing different parts of genomes and DNA return drastically different results in evolutionary relationships, something that should NOT be so all over the map for progressive step-wise evolution if it were true. Trying to extrapolate a gene backwards or forwards along the same kinds of understanding and lines as a "tree of life" results in dramatically different outcomes depending on the gene or genes included or analyzed, as if each gene has a completely different evolutionary history from the other, yet all these genes are supposed to be interconnected along ancestral reproductive lines and mutation.


Trends In Ecology And Evolution (June 2009): Gene tree discordance, phylogenetic inference and the multispecies coalescent
http://www.sciencedirect.com/science/article/pii/S0169534709000846

"Many of the first studies to examine the conflicting signal of different genes have found considerable discordance across gene trees: studies of hominids, pines, cichlids, finches, grasshoppers and fruit flies have all detected genealogical discordance so widespread that no single tree topology predominates."

 Telegraph.co.uk (January 2009): Charles Darwin's tree of life is 'wrong and misleading', claim scientists
http://www.telegraph.co.uk/science/4312355/Charles-Darwins-tree-of-life-is-wrong-and-misleading-claim-scientists.html 

"Dr Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, said: "For a long time the holy grail was to build a tree of life. We have no evidence at all that the tree of life is a reality."

"" More fundamentally recent research suggests the evolution of animals and plants isn't exactly tree-like either.Dr Dupré said: "There are problems even in that little corner." Having uprooted the tree of unicellular life biologists are now taking their axes to the remaining branches.Dr Bapteste said: "If you don't have a tree of life what does it mean for evolutionary biology. At first it's very scary -- but in the past couple of years people have begun to free their minds."

 Both he and co-researcher Dr Ford Doolittle stressed that downgrading the tree of life doesn't mean the theory of evolution is wrong just that evolution is not as tidy as we would like to believe."

 EvolutionNews.org (January 2011): Common Design in Bat and Whale Echolocation Genes?
http://www.evolutionnews.org/2011/01/common_design_in_bat_and_whale042291.html


On top of all this is the very serious issue of convergence, especially genetic convergence where identical or near identical genes appear in very disconnected lineages and have arisen entirely independent, yet are so shockingly similar even at the molecular level. As more and more genomes are being sequenced, species very distantly separated on the typical "tree of life" are showing some shocking genetic similarities in the convergent features they have independently evolved. These things cannot be explained adequately by common ancestry because of the rarity and sudden appearance of them, however there they are, as if entire chunks of functional DNA from one distant species were copied and pasted into a completely different organism separated by many millions of years of evolution. This is NOT what Neo-Darwinism expects to find or can explain. Neo-Darwinism requires slow gradual mutation (changes) of existing genes over large quantities of time in a generally stepwise fashion. But whole systems and structures of function are appearing out of nowhere and they just don't line up along a neat evolutionary path. This is not at all a problem for the Intelligent Design community as we don't assume first that all life is traceable back to common ancestors from beginning to end. However this is catastrophic for Neo-Darwinism because it relies so heavily on this belief that all things evolved from common ancestors way way back.

Debate Fog Into Empty Victory (Intelligent Design vs Neo-Darwinism)

Here's a lesson in the political-style writing and speech that can often get in the way of good solid debate between Intelligent Design advocates and those who support Neo-Darwin Evolution.

The past couple of weeks I've been reading blog posts and write ups about a heated discussion/debate between supporters of Intelligent Design and Neo-Darwinist Evolution with regards to a newly published book "Science And Human Origins". The book is by Intelligent Design scientists and discusses all sorts of scientific studies, data and evidence that shows that the major questions about whether or not humans actually evolved from apes is still full of giant holes and doubts. However, when reading these blog posts, though the Intelligent Design supporters have made a number of good points, there's one particular point that they're making a big deal about that though valid, isn't nearly as big of a deal as they believe or say it is.

To see the latest post from ID supporters (and one of the authors of the book), and related articles, check out this link (at Evolution News).

Both sides of the debate are shouting their victory over the other, each claiming to have trounced their competition in the origins debate, but the reality is that neither side has done so as strongly as they believe (or want others to believe).


Chromosome 2: Apes and Humans

One of the key points of this particular piece of the debate is connected to chromosome 2 in humans. Chromosome 2 looks a lot like a pair of chromosomes found in apes that may have fused together in humans. Evolutionists surmise that if we really did evolve from apes, then a long time ago we too had two distinct chromosomes just like apes but that somewhere along the long timeline of very ancient pre-history these chromosomes joined together in humans but not apes.

There are many issues here, but one of the big points that both sides actually agree on is that in the grand scheme of things, this possible fusion event doesn't actually prove that humans came from apes, because humans could have originally had the two chromosomes separate just like apes, with the fusion happening relatively recently in the human genetic past. In other words, it's quite plausible that both humans (fully human) and apes (fully ape) had these highly similar chromosomes as two seperate chromosomes and that in recent human history, only in humans, they combined. That means there's no direct connection between the fusion event and supposed evolution from apes. The key point from the evolutionist is that the similarity in this particular chromosome to two chromosomes in apes indicates common ancestry. The Intelligent Design advocate says that this similarity simply means similar functional genetic code that works as intended, as designed by an Intelligent Creator, and that humans did not evolve from monkeys but that they were made as two unique kinds of living organism. So in the end, the fusion event doesn't really mean a whole lot, though it's interesting to study. Yet even while the evolutionist admits that the apparent fusion of chromosomes doesn't have to mean we came from apes, they still argue that it's good evidence for this belief.


"Victory" In Misdirection

Unfortunately both sides are arguing that they've defeated their opponents in the argument based on the idea of misdirection (clouding the real debate), while they themselves are actually throwing up misdirection themselves! It's a case of the pot calling the kettle black. They're BOTH misdirecting readers and BOTH accusing the other of doing it in order to try and win a point.

The Intelligent Design side of the argument has made a number of good points, some of which have tied directly to the fact that the evolutionists have focused on just the issue of chromosome 2. "Science And Human Origins" is a big book with multiple chapters, each addressing different areas of science and data that show just how weak the evidence for human-ape common ancestry is. Chromosome 2 is only a couple paragraphs in the big book, but it's where a couple evolutionists have focused. Remarkably, the evolutionists admitted that they had not read the book itself, had not even read the chapter in question, and would NOT be reading it because they knew (believe) it would be garbage anyway. Win for the Intelligent Design group here! The evolution scientist won't even READ the detailed debate points and all the scientific articles cited by the Intelligent Design writers!

But as great of a point as this revelation is in favor of the Intelligent Design group, they then take the ball and run with it well beyond the winning goal. They started crowing about how the evolutionists haven't read their points (which is valid), and that to make matters even worse, the evolutionist refuses to even enter the arena of the greater debate itself. The evolutionist has focused on a couple paragraphs in a book he hasn't even read, and that's all. Win for Intelligent Design!... Yes, true, but also no. Let me explain.

This is misdirection on the part of the Intelligent Design writers. It's a good point, but to make such a big deal out of it is to warp it into being more than it is. The evolutionist has decided to focus on the issue of Chromosome 2 and not bother with the rest. He's focusing on Chromosome 2 specifically. Not reading the book in question is a dumb move and it certainly hurts his case, but focusing only on Chromosome 2 instead of all the rest as well is NOT an explosive victory for Intelligent Design scientists like they claim it is. A person can adequately debate or dispute a particular point without having to address all connected or related points (which can be a huge enormous undertaking)


Not A Nail In The Coffin

So the Intelligent Design scientists are saying, "We win because you're not addressing all the other information in the book, only focusing on Chromosome 2." While the evolutionist basically sits there and says, "I never meant to address the whole book at large, only this specific point about Chromosome 2. But because you're trying to drag me into discussion of all the other stuff, you're clouding the issues I'm bringing up." These quotes are not actual quotes, they're just paraphrases of the general points being made.

The evolution scientists are ALSO guilty of misdirection in that they've argued that the points made against common ancestry from the direction of Chromosome 2 indicates that the whole rest of the book must be garbage (a book they haven't read). They disagree about some interpretations of the scientific data regarding Chromosome 2, and by connection, ALL the points made by the Intelligent Design group must be wrong as well. That's their cloud of fog hanging over the debate.

So BOTH sides are arguing largely from one standpoint (ID the greater whole and evolution the one specific point), and both claiming victory over the other because the opposing side is trying to drag the other side "over the line" they've drawn in the sand like an old fashioned tug of war. BOTH sides cloud the debate, and then both sides accuse the other of doing exactly that, and by connection claiming victory over the other. Oi!

It's like both teams are playing with different sets of rules and neither one will compromise or agree to work in the same realm and so neither side can ultimately hold any kind of solid victory over the other. It means that many of the GOOD points and jabs are lost in the air amidst the fog. Essentially it's a case of both sides claiming the exact same victory podium based on the concept of debate itself, rather than the points within that debate. That's an empty win.

Evolution: King of Contradictory, Inconsistent Logic

I read an interesting little blog article today about the fact that the famous "evolutionary tree of life" so often found in biology text books doesn't really exist in nature and that even modern scientists are finally starting to admit this. The idea of the "biological tree of life" is that you can map similarities between living organisms and fossils into a branching "tree" of evolutionary progress and/or dead ends. It's the idea of common ancestry, everything is connected way back in the past and has branched off from the same ancient common ancestors. The responses to the blog post I read were quite fascinating and are a great example of an astounding flaw in evolutionist apologetics thinking.

Blog Post this article is related to: The Evolutionary Tree Failed But Evolutionists Still Insist Evolution is a Fact

When Creationists or people that believe in Intelligent Design (and not Darwinistic evolution or all-encompassing common ancestry) point this major failure of Darwinism out (the classic "tree of life"), a common response by pro-evolutionists is to argue that clearly evolution is much more complex and variable than was assumed. The "tree of life" is much more like a "very tangled bush" instead, but they still argue that there's enough of a "core tree-like structure" to life that the proof of common ancestry IS there.

The problems of so many instances of life supposedly being along the same branch (due to apparent similarity), and then the genetic studies on these organisms revealing vast differences between them far beyond what should exist when compared against the famous "tree of life", is a nasty punch to Neo-Darwinism. The same is true for organisms that are highly separated on the "biological tree of life" but turn out to have vast genetic similarities despite being physically very different. It boggles the mind and destroys the tidy concept of the biological tree of life (which was always an entirely assumption-based (instead of fact-based) belief anyway). The evolutionists, however, continue to argue that there's still enough "good and accurate structure" to the "tree of life" model that it's a mathematically valid and very probable reality.

But this is a classic case of contradictory logic. As I've debated with some atheists and evolutionists online over the last half year or so, I've found that this kind of "stance-jumping" is extremely common among them. They'll argue one point in defense of evolution and then completely disregard that exact same logical point at another. It's, "win in any way you can, even if we constantly disobey our own previously stated logical and factual stances." There's very little consistency in their position. They contradict themselves all over the place.

Case in point...

Mathematical statistics and probability are used to defend the crumbling "biological and historical tree of life". They say that there's enough mathematical probability and similarity in the structure of the tree to still be considered a valid belief/fact. However when the math does NOT support evolution at all, they say math, statistics and probability has nothing to do with it, or is not relevant. Why? Because they only like the math when it agrees with them.

The probability of life arising from non-living molecules is astronomically impossible. The probability is trillions of times beyond what's mathematically possible, let alone actually plausible. It is absolutely impossible for a simple protein to form in nature except by way of life building it on purpose. The odds for just ONE such simple Protein forming in nature is 1 in a trillion trillion trillion trillion trillion trillion (etc.). It's simply not mathematically possible. In fact, there isn't even enough matter and energy (probabilistic resources) in the entire universe to get anywhere close to giving this equation a chance. And yet these scientists claim that this exact event (a protein forming with no help from life or intelligence) happened MANY times.

But the math just doesn't work! The entire universe has no way of producing a single protein without life intentionally building it from an already existing blue print. When such things are pointed out to evolutionists and scientists, they shrug it off and say that, "Clearly life happened, since life is here, so the odds and statistics don't really matter." This is a VERY common argument by evolutionists and atheists.

Note the completely contradictory statement and stance compared to their arguments regarding math, statistics and probability when it comes to the biological tree of life. It's completely illogical to consider "the math" to be a valid proof or evidence defending your stance (belief) in one related instance but to ignore it completely with regards to another aspect of your worldview (beliefs). There's no consistency of stance and position there, which throws your entire structure of supposed logical reasoning out the window.

Either probability, statistics and math ARE a valid proof of something's reality (in this case, Darwinistic Evolution) or they are not. You can't have it both ways, as the evolutionists clearly desire.
 

For more on the numerous problems with the "evolutionary tree of life" check out this 5 part entry at EvolutionNews.com. A Primer on the Tree of Life