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 Many biologists now argue that the tree concept is obsolete and needs to be discarded,” and as scientists quoted in the article said, “We have no evidence at all that the tree of life is a reality” or the tree is being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.

Secularism Saves, Religion Destroys?

There's a common falsehood that is popular among many atheists and secular speakers out there that secularism is the answer to a harmonious civilization whereas religion inevitably leads to extremism, holy wars, murder and oppression (even hatred) in the name of god and kingdom. Such thinking is entirely inaccurate, as are other beliefs that tend to go along with such an idea.

Secularism is by no means any better than mainstream (or otherwise) religious or spiritual belief systems that exist throughout the world. Somehow these atheists and secularists have gotten it in their heads that secularism and atheism are NOT belief systems akin or comparable to religion. This is absurd because secularism and atheism are very much belief systems that shape an individual's life and viewpoint of the universe, the world, mankind, and the individual within it all. So to pretend that there's a gross difference between secularism and religion is to wear very thick blinders. Both are philosophical ideologies at their core and how they effect a person stems directly from that foundation. Secularism is humanism, a "religion" based on the idea that naturalism is all there is and mankind is an accident of nature and little more than a highly evolved animal. Secularism also wishes to eliminate religion from places of education, public discussion, government (and other authority), even entertainment. For a group that loves to preach about tolerance and diversity, they are actually quite intolerant to ideas that do not jive with their own.

Much is said these days in secular circles about religious extremism. The biggest culprit of religiously motivated or inspired terrorism is found within certain sects of Islam, and this has been true for more than two decades now. However non-religious (or vaguely spiritual) people see this and pin the terrorist (or ticking time bomb) on ALL organized religion. They'll point to historic tragedies such as the Crusades and the Inquisition, both taking place during cultures heavily dominated and invested in either Roman Catholic Christianity or Islam. Clearly religion and belief in god is a great inspiration of horror and evil in the world, right? And so non-religion, such as secular atheism or humanism, must then be the salvation of mankind and the end of human on human violence!... Such a belief or statement could not be more wrong.

The problem of extremism or ideologically motivated violence is by no means restricted to religion. It broaches all kinds of belief systems, all stripes of political bents and ALL viewpoints. Christians can easily understand this because we understand that the broken human condition that causes all of this is sin, which permeates and infects EVERYONE no matter who they are. Sin is like a poison. Left unchecked, it is catastrophically destructive and cruel. Secularism and atheism do not even believe in the existence of sin, believing that morality is in large part a social construct and little else. So who is better prepared to address the corrupted human soul? The ones who reject the existence of both soul and sin, or the ones that know it for what it is?

Is secularism the answer to moderating and regulating religion to prevent catastrophic violence between human beings? No. At best it's no better than religion in this matter. However, it might actually be even worse, because it holds no solid moral foundation or absolute truth. The atheist likes to point to tragedies in history connected (loosely or closely) to religion, things like the Crusades and Inquisition. In the secularist mindset, theocracy (government and power held by organized religion) is inherently corrupt or easily corrupted, mere steps from extremist evil. Yes, those particular horrors of history were awful, but religion is by no means the only factor for such occurrences. Neither is theocracies, or political conservatism. Most wars are not religiously inspired or motivated, merely using religion as an excuse for the real reasons for the war, such as greed and power.

Secularism and atheism have a human death count in the multiple hundreds of millions in just the last 100 years alone. The crusades and inquisitions were centuries ago and killed far fewer people on the whole. The inquisitions for instance may have killed a few thousand in all. Secular communism, however, is a very modern social and governmental construct, and it's slaughtered hundreds of millions in far shorter a time period than all religions combined for all of history. Stalin and communist Russia, communist China, and Germany's Hitler and the Nazis in World War 2 were all heavily influenced and inspired by humanism, secularism and naturalistic Darwinism (evolution). In this way you could almost say that communism is the secular version of a theocracy. Germany was the breadbasket of Darwinist thought and evolution inspired eugenics were the heart and soul of much of the Nazi mentality. They rounded up Jews, people of colour, and the physically and mentally disabled for death because they were considered inferior humans, a detriment to the betterment of more highly evolved mankind. These people were relegated to a sub-human status, and murdered and brutalized because of it. Communist Russia and China killed hundreds of millions in the name of preserving their government control and destroying all opposition and alternate belief systems, especially against Christianity. These were and are heavily atheistic and secular driven belief systems and mentalities that dominate in these large scale modern death camps. Secularism and atheism is in no way harmony and innocence. It's hands are as bloody or worse than mankind's biggest and longest lasting religions, and it's happening today right along side Islamic terrorism. The only difference is that it's institutionalized and government sanctioned. The only difference is that all this genocide is done in the name of man and at the cost and eradication of freedom (freedom that Christianity has been a strong supporter and creator of the world over).


The Real Problem

The problem is not religion, or even politics. The problem is mankind's heart in general. The problem is our eagerness and easily corruptible fallen sinful nature. Secularism and atheism don't even have a "higher power" to answer to or provide them direction, instruction, correction or meaning. To them, we're evolved animals, a cosmic accident of chemistry and physics.

True Christianity is based upon salvation, mercy, love, repentance, and compassion. Jesus Christ came and died on the cross when the Jews wanted him to rise up and become a holy warrior king and save them from the Romans. He refused. He came to save our lost souls, to show us a better way, to lead us back to God through love and mercy. The value of a human life and compassionate love are two monumental core tenets in Christianity. Yes, Christians or people who have claimed to be Christian or do things in the name of God have done terrible things in the past and even the present. But so have secularists, humanists, atheists and Darwinists. Examples of this are the Columbine school shooting in the USA (the two young men considered themselves to be cleansing society of religion and being an instrument of natural selection, one even wore a shirt that said exactly that as he shot his fellow classmates dead) and the murder spree a couple years ago in Norway where an avowed evolutionist shot dead 100 teenagers and government workers in the name of attacking Islam and the tolerance of it. The problem is NOT religion. The problem is strong over the top ideology combined with a lack of loving merciful compassion and the heartfelt knowledge that every life is exquisitely valuable.

Secularism is not salvation for the ills of society. It could be better described as oblivious unintended suicide. To eliminate the God given value of human life, of the soul, and to reduce us all to cosmic accidents and lucky-to-have evolved and survived animals in an entirely cold and callous universe is to beg for the de-humanization of all mankind. Human history both ancient and modern paints us a large scale picture of the evil and cruelty that mankind is capable of. Atheism and humanist secularism are at best no better than religions when it comes to these large scale sins. It's because the problem is not religion, or God, or faith, holy scripture, or even politics. The problem is mankind's ability to twist and warp any and all ideologies and philosophies into dark and destructive tendencies for fortune, fame and power. The problem is sin, something we are all guilty of to one extent or another.

Thankfully there's a means of redemption, forgiveness and salvation found through the death and resurrection of Jesus Christ. We are all His and He loves each and every one of us. That's a heck of a lot more positive and inspiring than, "We're stuff that stars burped out and that chemistry and physics accidentally patched together into complex animals." In Christianity there's a true possible solution. There's an understanding of the existence and potential of evil and wrong in all of us. Compassion, love, and deeply valuing all human life is the only cure. Those principles go hand in hand with salvation through Jesus Christ.


UPDATE

Added links to a few articles giving more detail and information on the topic.

Whitewashing Darwinism's Ongoing Moral Legacy  (EvolutionNews, Darwinism's influence taboo to discuss)

Slouching Toward Columbine: Darwin’s Tree of Death  (http://blog.beliefnet.com)

James J. Lee, Hostage-taker and Darwinist  (EvolutionNews, Discovery Channel shooting in Maryland, plus a summary of other similar incidents)

From Darwin to Hitler: Evolutionary Ethics, Eugenics, and Racism in Germany  (Amazon.com)

GENETICS: All Creatures From Noah's Ark?

Evolutionist Argument:  You believe that all animal life on earth died out in a giant global flood except for a male and female of each “kind” that were saved on a big boat. Now, a few thousand years later, you believe that ALL living creatures came from those few that were saved on Noah’s Ark… Seriously? All dogs, all cats, all reptiles, all bugs, EVERYTHING, from one large floating zoo? Crazy!

Animals Entering the Ark – from the movie Evan Almighty.

Any Evolutionist or atheist that makes such an argument as the one written above has made a monumental mistake of judgement and logic. Noah’s ark has no problem explaining how life survived the flood and became as it is today, while Evolutionists have a massively worse problem trying to explain ALL forms of life (all plants, birds, bugs, reptiles, mammals, bacteria, etc.).

Those of us that believe in Noah’s Ark believe that Noah, with the help of God, managed to collect and care for a male and female of every KIND of creature on the ark. Though we might not know what exactly constitutes a “kind” in every situation, we do know that if you only had to take one male and one female dog onto the Ark, and if you took them on as cubs, they’d be able to generate all the varied dog species we have today, given a cycle of many generations and natural breeding. As dogs spread all over the world, natural selection easily explains how the dog population can change into all different kinds of dogs over time, especially if they all originated from a pair of dogs with an immensely more diverse set of genetics. Such a situation is completely plausible, realistic, and adheres perfectly to our scientific understanding of how genetics and breeding works. But note that all dogs are still dogs, all cats are still cats, all monkeys are still monkeys, and all people are still people. No where does any of these surviving creatures “evolve” into different kinds of creature.

So we, as Bible believing Christians, have no problem explaining all kinds of living creatures today because we simply state that they have ALWAYS existed (since God’s Creation of Earth). Sure, they’ve changed and become much more diverse over many years, but they truly have all descended from one male and one female of their kind.

 

The Biblical Story of Noah’s Ark Fits The Science of Genetics

Biology and genetics are an incredible complex and wondrous field of science, but Neo Darwinism (evolution from molecules to single celled organism to all life on earth) actually goes in the opposite direction that science tells us it should, and does. The story of Noah’s Ark, however, and all living creatures that exist today since that time (about 4000 years ago), fit perfectly into the scientific understanding of genetics.

The Bible says that God created everything in a perfect condition, like a book without a single misprint or flaw. That being said, from the time of Creation to the Flood, is estimated to have been around 2000 years. 

Since we’re playing in the realm of genetics and reproduction here, what would happen if you had two dogs (a male and female) that contained the entire “dog” genetic library within their genes? The genes of those dogs would contain ALL the genetic possibilities and variability that God had “programmed” into them. Over time with each successive generation, new species of dogs would arise as different variations of those genes became dominant and/or lost. Mankind, throughout its existence, has bred all kinds of species for all types of different creatures (horses, dogs, livestock, chickens, cats, sheep, etc.). That’s all done through selective breeding, which is something Evolutionists AND Creationists completely agree on. It’s a proven well documented and heavily verified science. Dogs over time breed different kinds of dogs. That same principle works across all other forms of life on our planet both in the past and today.

 

Neo Darwinism Is In WAY More Trouble Than Noah’s Ark

What if we compare the Creationist explanation of modern day life to the Darwinist explanation? Not surprisingly, you find that the Darwinist is in WAY more trouble trying to explain the existence of all life (not just air breathing life) than Creationists are.

The argument against Noah’s Ark that exists at the start of this blog post states that believing all present day dogs (or any other kind of creature) descended from a common biological ancestor, is preposterous… But that’s exactly what Darwinists believe!!! That ALL living things on earth of ALL kinds (not just air breathing creatures) descended from common ancestors. Not just all dogs from dogs, but ALL things (plants, bugs, bacteria, mammals, fish, etc.) from a specific limited set of ancestor life forms! Mammals all evolved from the same thing, according to Darwinists. Cats, dogs, monkeys, bears, deer, gophers, rabbits, horses, cows, elephants and even humans! We ALL supposedly descend from the SAME common ancestors…

Tell me now. WHO is the crazy one? If all dogs cannot have descended from a single pair of dogs, then all mammals could most definitely not have “evolved” from a couple “almost mammals”, and absolutely NOT from a single celled organism, which itself evolved from a pile of chemical goo, so the Evolutionist believes.

An example of the Evolutionary “Tree of Life”. All life from a single celled organism. But they still can’t explain where that “single celled organism” came from.

 The Evolution Of Life Runs Backwards

Neo Darwinism (the modern theory of evolution) actually claims that life runs in the OPPOSITE direction from what history and science tells us it does. 

Genetics shows us that a small group of creatures have to be very similar genetically in order to breed together. Even many different species of dogs, or horses, or cats, or whatever else of the same kind, cannot properly breed with their own kind because over time their genes have become too different to properly and successfully “pair up”. Why? Because the genetic library (DNA) is finite, limited, and it digresses (falls apart and shrinks) over time. It does NOT expand or grow and develop brand new sets of genetic information and advancement. This is why if you take twelve similar dogs and breed them over and over and over again (performing no intelligent natural selection of your own, simply letting them breed on their own) you’ll eventually end up with a pile of very genetically weak and sickly dogs.

A couple years ago I visited a zoo and one of the scientists there briefly mentioned that there are so few cheetahs left in the wild now that they will never again be a strong vibrant species. Why is this? Because the genetic library of the world’s living cheetahs has shrunk so much over time that they can no longer produce an adequate supply of genetically healthy offspring. Their genetics are handicapped, forever, because there’s not enough genetic variability between them all anymore. This very same principle works within the population of mankind. Lock a set of people onto an island and don’t allow anyone from outside to join their population, and within a short number of generations you’ll end up with a very genetically weak and damaged population group. The babies that survive birth will be overflowing with tons of genetic defects resulting in all manner of physical and mental handicaps because their DNA is so polluted with copied and duplicated errors. This is why we can’t marry and have babies with our siblings, and why we shouldn’t even make babies with cousins. Because the genetic flaws in our own DNA are going to be very similar to a lot of the same genetic flaws in our near relatives, resulting in children born with genetics that ONLY contain the errors and have no alternate set of genes without the errors to make up for the genetic damage.

This is scientific fact! Genetics and DNA is a library of variability, but over time that library becomes polluted with countless copying errors that degenerate that library, making it inferior and weak. To combat this major problem, mankind even has laws in place to prevent people from marrying and having children with near relatives. Look at all the diseases and handicaps both physical and mental that exist throughout our population today. A good number of these (most of them, actually) have a genetic origin. They are caused by weak error-riddled DNA. Mankind’s population and genetic library is massive, yet it’s still so heavily damaged that we’re producing tons and tons of genetically damaged children. Copy errors in the genetic code are HARMFUL, NOT beneficial, like evolutionists so badly want to believe. Science shows us that the exact opposite of Neo Darwinism happens to DNA over time. It degrades and loses information. It does NOT gain it.

Creationists have NO problem explaining why this happens. We believe that God created a perfect genome, a perfect set of DNA for all life on earth (a perfect set of dog DNA, a perfect set of Turtle DNA, a perfect set of Human DNA, etc.) and that when mankind sinned and brought corruption into the world, that perfect world began to break down. So instead of a perfectly preserved genome existing in all kinds of life all over the planet, life is now running on borrowed time with a genetic library that is gradually falling apart collecting more and more copy errors with each new generation. There still exists a vast quantity of genetic variability in life and that variability results in all the different appearances and structures of life all around us today, but change within the DNA of life over time is degrading that DNA, NOT improving it, like Evolutionists believe. The funny thing is that Evolutionists know this and admit this, because it’s hard and proven science, but they blindly and wishfully believe that these laws of entropy don’t apply when it comes to their theory of Evolution, because it CAN’T have applied for their beliefs to have worked, or happened.

Non-Life Into Life

Making matters even worse for Neo Darwinists is that they still can’t explain how life actually began. They’ve been trying ever since Darwin first put forth his theories about the origins of life on earth, but they’ve never been able to make non-life become alive, despite our massive and impressive amounts of technology and scientific understanding. The problem is that life doesn’t just happen. It doesn’t appear out of no where. The only way to make life is to make it with more life. You can’t build life from the ground up no matter how hard you try. The “basics” of life are way too complex and intricate for that to ever work randomly or naturally. But Evolutionists believe that this must have happened at least once eons ago in the past because we’re surrounded by life today, despite the fact that science shows us this is impossible.

You cannot take all the basic components of a computer broken down into their simplest molecules, toss them into a box, mix it up and have a fully functional computer appear by random out of the mess. It’s impossible. The EXACT same problem exists when trying to explain life today. Evolutionists try to get around this by calling the molecules that make up life “organic”, but that simply means that the set of molecules they’re looking at are what life is made of. I can say the same sort of thing about the molecules that make up a computer (these are “computer molecules”), but it still won’t change the fact that mixing them together at random won’t ever produce a functional computer.

Life is very special, very complex, and even our vast intelligence and modern technology combined with our scientific understanding can’t do half of what life does constantly all around us every day. Life is no accident of nature. Life is an intentional creation, intelligently designed and supernaturally strung together and jolted into existence by Almighty God.

Conclusion

Evolutionists say that ALL life came from a single celled organism and a pile of mixed up chemical goo… And to them, this is realistic and plausible, despite science significantly showing otherwise.

Don’t ever let an Evolutionist tell you that all animals coming from Noah’s Ark is ridiculous, when they themselves argue that all life, period, came from non-life, by accident. That makes it pretty obvious which of the two parties in this debate have to have monumental amounts of blind faith. The Bible believing Christian’s understanding of the world and life matches perfectly with what science tells us about it, however the Neo Darwinist believes in the exact opposite of what science shows us in order to believe that all life evolved from non-life. Christianity has no problem with the real and observable scientific facts of genetics. Evolution does.

All air breathing creatures today came from all the creatures saved on Noah’s ark.