"You are so steeped in your own dogma you see nothing around you and live in a total fantasy world you made up.
You have one life to live and you will spend it defending your fantasy world. That is sad."
As 2MAR$ posted:
Why Evolution is Right
The "Too Complex Argument"
Why is it logical to trust science?
Contributed by Ryan Serio
Evolution denial is the faith-based conspiracy of choice for our time. Information from all fields of science unanimously point to evolution being factual, but many people refuse to accept this. In the past, people believed that the Earth was the center of the universe, and despite objective data suggesting otherwise, it took very long for this geocentric paradigm to be overturned. The ridicule from angry biblical literalists on those accepting scientific data pointing away from commonly held beliefs continues to this day. Acceptance of evolution is viewed with hostility and contumacious rebellion by those who refuse to open their eyes and challenge their pre-established beliefs that organisms were created as "kinds" with humans separate and above the animal kingdom. This ignorance must cease. Just as the fact of heliocentrism became accepted over time, so will evolution. But people living now should not have to live with the persecution from angry Creationists who ignorantly try to make reality conform to their irrational beliefs.
This article is for anyone who wants to know exactly why evolution is a fact, whether you accept it and want to know more about it or whether you don’t know enough to make an informed opinion. It is organized so that some of the more common arguments against evolution are presented and then systematically refuted with factual information obtained from scientific data. I have confidence that those seeking answers will find them below.
IDists will often present a fallacy of bifurcation, or false dilemma, stating that either evolution or creation is true and a person cannot be a theist if one accepts evolution. Please note that this is completely untrue, and some of the most prominent evolutionary biologists and molecular geneticists in the world are actually theists. So this article is not intended to be an attack on religion but rather to provide clarification of scientific knowledge.
Argument#1: A scientific theory is still just a theory. When you believe in a theory, it becomes dogma.
Response:Unlike the layman’s idea of a theory, a scientific theory is far from a hair-brained idea. A scientific theory is a set of hypotheses corroborated by a large amount of data that explains the workings of a particular aspect of reality. It is based on solid facts, and connected through mechanisms to explain why the empirical data leads to a specific phenomenon. If one piece of evidence against the hypotheses forming the basis of the theory emerges that conflicts with an aspect of the theory itself, then the entire theory would be falsified and discredited. So obviously the theories that have withstood the test of time are all on a very solid foundation. Despite constant scrutiny from fellow scientists, there has been absolutely no evidence to overturn them. Theories are theories BECAUSE all of the factual evidence points in that one specific direction.
Dogma and science are mutually exclusive. There cannot be dogma in science by definition. Science is constantly looking to uncover information about the universe we live in, and even the most solid theories are never considered complete. There is always more to add on as new information is received. Sometimes this will fine-tune the understanding we have; other times it will revolutionize how we perceive it and lead us into a completely different direction. This does not undermine the previous knowledge but expands on it in a more sophisticated manner, which gives us greater depth in knowledge. If a theory was ever considered complete, then and only then would it be considered dogmatic. It would be at that same point where science would end and faith/belief would take over. Just because humans who practice science often have dogmatic views on certain aspects of life doesn’t equate to science itself being dogmatic. Where science exists and is being practiced, dogma is necessarily absent.
Science does not prove anything true, but science CAN prove things to be false. The purpose of an experiment with a specific hypothesis in mind is never to prove that hypothesis correct. In contrast, the hypothesis that the original hypothesis is false (null hypothesis) is what must be shown to be false. As data is accumulated which points in one direction favorable to a hypothesis, the null hypothesis becomes increasingly more invalid to the point where its relevance becomes highly insignificant. It is at this point when you could say that data favors the hypothesis. When an enormous amount of data supports a hypothesis, then you could assimilate data together from a set of related hypothesis and formulate a theory. However, if later evidence points away from the correctness of the theory and negates even one aspect, the theory may be overturned. Most of the time, much of the theory is still valid but certain deviating points are either partially or completely replaced. Science is objective, NOT subjective, and can never be dogmatic because it is always self-transcending itself as new data becomes assimilated.
Evolution is both a fact and a theory. Evolution by means of natural selection is called the theory of evolution, but data from many fields of science conclusively show that evolution occurs regardless of how complete the theory of evolution may be.
Argument#2: There could have been two separate creation events: one ending with the extinction of the dinosaurs and the second beginning with the creation of man.
Response: To understand why this is not plausible, it would be beneficial to understand faunal succession, or the changing of fossils through time. Faunal succession confirmed evolution as factual in the early 1800s, predating Darwin’s theory of evolution by natural selection by over 40 years. The geologists who championed evolution through faunal succession were both devout Christians and started as biblical literalists before altering their views based on their findings. One, Georges Cuvier, was actually trying to disprove evolution through the fossil record when he made his discoveries.
The geology of faunal succession began in 1795 when an ordinary working man, Will Smith, noticed patterns in the rocks he was observing and was able to correlate different fossils with different rock strata. Over time, it was observed that the older the rocks were, the older and more primitive the fossils that were found. Basically, the rocks from different ages had distinct and consistent patterns. This led to the science of biostratigraphy, which is a very helpful tool used today for the detection of oil-containing regions. It was soon determined that based on the fossil record in differently aged rocks, there must have been a total of 27 Creation events in the history of Earth to account for the vast array of changes through time. This gave support to Lamarck’s idea of evolution and set the stage for later studies by Darwin and Mendel to further advance the science of evolution through important biological discoveries.
Aside from faunal succession, it is also known that birds definitively evolved from dinosaurs. Many dinosaurs have been discovered with fossilized feathers, showing a key biological transition between genuses. In addition, experiments with gene expression show that if bird DNA is extracted and injected into mice, the mice grow dinosaur-like teeth (Prothero 2007) Birds do not have teeth, but still have the same genes as their dinosaur ancestors. These genes are suppressed in birds, but can be reexpressed when introduced into a mammalian genome.
Argument#3: DNA is irreducibly complex and must have been created.
Response: DNA cannot be irreducibly complex for two major reasons. One, it has come into existence by evolution from more primitive nucleic acids. DNA is a highly specialized, highly organized, passive molecule without the ability to function without something else acting upon it. However, there are other nucleic acids similar to DNA which can act on their own accord and catalyze their own activity. They are called ribozymes and are RNA molecules. Instead of having a double stranded helix, RNA is a single stranded polymer. Its only base that differs from DNA is uracil, and it is no surprise that RNA formed first, considering another base, cytosine, deaminates into uracil which can greatly distort the reading of genetic information in producing protein products. When DNA evolved, natural selection avoided this problem by using a methylated uracil, called thymidine, as the base instead of normal uracil. Now some Creationists have argued that it would not be possible for cytosine to form under prebiotic conditions, so therefore the RNA world hypothesis is wrong. However, if they knew about actual evolution they would see that this idea actually strengthens the theory. If cytosine and uracil are incompatible in the storage of genetic information for gene transmission, then this would be a relatively recent combination which would evolve around the time DNA first arrived. Cytosine is a purine, and a number of other purines could have easily preceded it in RNA that would be capable of transmitting genetic information with high stability. Just as natural selection picked thymidine to replace uracil, so could early ribonucleotides have used a different base than cytosine. To believe that RNA existed in its current condition billions of years ago would be wrong–RNA is a ribonucleotide, and many different components can be used, with natural selection then guiding the process of which component allow the function to be carried out the most efficiently over time.
RNA is also able to catalyze its own metabolism, giving it a great advantage over the more specialized DNA molecule, which is dependent on protein catalysis for its function. The folding of RNA greatly resembles that of proteins, and makes it much more thermodynamically stable than DNA, with its low entropy double helix. This could have facilitated catalysis of macromolecules before the more specialized DNA molecules evolved as the principal carriers of genetic information. Some enzymes, such as RNase and certain components of ribosomes, are still entirely composed of RNA instead of proteins. When the majority of RNAs catalytic abilities were taken over by specialized enzymatic proteins, a novel nucleic acid like DNA could then evolve with enhanced ability to store genetic information in exchange for the loss of catalytic function.
Another reason why DNA (or RNA, for that matter) could not be irreducibly complex is that it is a molecule with 3 chemical components. How can a molecule be irreducible when it gets reduced to three separate chemicals composed of different arrangements of atoms? Nucleic acids consist of a simple 5 carbon sugar, a nitrogen containing purine or pyrimidine, and a phosphate group. The nitrogenous base chemically reacts with the sugar to generate an N-glycosidic bond, while the phosphate group readily forms a phosphodiester bond with the other end of the sugar. The negative charge of the phosphate allows for ionic bonding with positively charged ions, and the first nucleic acids could have reacted with a plethera of minerals in nature. This is conducive to polymerization by allowing the negatively charged molecules to line up side by side. Once in the proximity, the energy rich nucleophilic phosphate group of a nucleotide di or triphosphate attacks the energy deficient electrophilic hydroxyl group on the neighboring sugar to drive the elongation reaction forward so a long chain of nucleic acid can readily form and ligate naturally.
Argument#4:We cannot determine how closely related different species are just by looking at their DNA.
Response:Side by side comparison of DNA between different species shows us exactly how closely related each species is to the other. Take the following sequences from the globin gene of various apes for example:
Gorilla: CCCTTCCAACCAGGCC
Chimp: CCCTTCCAACCGATTA
Human: ATAAACCAACCGATTA
As you can see, the last 5 bases were mutated as we went from the gorilla gene to the chimp gene. Humans also retained this mutation, showing common ancestry, plus acquired another mutation (ATAAA) which shows that gorillas are our more distant relatives and that we diverged from a common ancestor with chimps more recently than with gorillas. If you were to go even further back, you will see the same patterns with orangutans having sequences more similar to gorillas than to chimps, and so forth the further we trace back our evolutionary history. This is the genetic basis for the construction of cladograms showing branch points of divergence between related species.
Analyzing the genomes of extinct species is more difficult due to the degradation of genetic material, but it can still be done fairly accurately. DNA is simple to work with because of its properties and stable for up to 10,000 years. Once denatured and unwound from its double helix, if you apply proper conditions, DNA will reanneal in the same way it was before, since bases will pair up with their opposites (G with C, A with T). DNA fragments from fossils can be analyzed due to this property upon amplification. Single stands of degraded DNA can be cooled to allow for hybridization with small primers of matching bases. Using heat-stable Taq polymerase and a random assortment of deoxynucleotides for construction, elongation of the chain occurs exactly as it was before to generate a new template of double-stranded DNA. This template is then denatured again to start the process over and generate additional copies of DNA in an exponential manner for a highly convenient analysis. Using this technique, we can determine DNA sequences from fossils that are thousands of years old for comparison with those of organisms alive today or with other extinct, fossilized species.
Argument#5:If chimps and humans were related, they would have the same amount of chromosomes. If they really fused together in human evolution, then where is the second centromere and what became of the additional telomeres?
Response: There was a break in chromosomes 2A and 2B of our direct ancestors. Then they rotated 180 degrees and fused together to form the human chromosome 2. We know this because of the tandem array of nucleotides present in telomeres TTAGGG, which was cut off at the fusion point in each of the 2 fused chromosomes after the 4th nucleotide, creating a TTAG break on one end and a GATT break on the other, which were each paired with their respective bases at the fusion site. Only one centromere was required, so the other became functionally inert with mutations over time, and the fused telomeres also lost their activity because of their positional change to the middle of the chromosome and also became junk DNA alongside the rest of dead viruses and repeats in the genome. Only the ends remained as telomeres based on their location. Ends of chromosomes are regulated by lysine methylation of surrounding histones, particularly at K27, which recruits transcriptionally silencing PcG proteins located in the proximity to help maintain their function as telomeres. When inversions occur, regions that were formerly telomeres lose their epigenetic regulation and get incorporated with junk DNA subject to mutations.
Argument#6: If there was nothing but bacteria for 2 billion years, then evolution couldn’t have all of a sudden sped up so that humans appeared just a billion years after the first multi-celled organisms.
Response: The early atmosphere was very hostile, and organisms had to use whatever they could for energy sources. Some of the first bacteria to evolve used sulfur sources to generate energy in a manner similar to photosynthesis. When light began being harnessed as an energy source by the first photosynthetic organisms in the generation of sugar for nutrition, a byproduct was molecular oxygen.
Before talking about the significance of oxygen, it is important to know what energy is. Energy is the capacity to do work. Many chemical reactions occur spontaneously, but many others cannot happen without an input of energy to overcome thermodynamic barriers. The ability to overcome the obstacles to allow a reaction to proceed spontaneously after energy input is measured by what is called "free energy" and is a property of temperature, excess heat, and entropy (disorder). It is a physical property quantified in units of kilojoules/mol and related to equilibrium, meaning the tendency for reactions to proceed either forwards or in reverse about equally. Reactions that have positive free energy cannot yield products from reactants without the input of energy. Energy in biology usually comes from nucleotide triphosphates such as ATP. The breaking of bonds of phosphate molecules yields an extremely negative free energy, so when ATP is coupled to a nonspontaneous reaction, the overall free energy becomes lowered and the reaction can proceed to yield products in the presence of ATP. So where does this highly energetic ATP come from?–Some ATP can be generated from processes that require no oxygen, such as glycolysis, but very little is produced. One glycolytic cycle yields only 2 molecules of ATP to provide energy for cellular reactions.
Once oxygen became incorporated into the environment by photosynthetic organisms, energy began to be used in ways it could never before. Some bacteria evolved electron transport chains which allowed for oxidative respiration, efficiently using molecular oxygen to chemically generate a large number of ATP molecules to facilitate a number of energy-utilizing cellular reactions. These bacteria were very small, and for protection they took refuge inside larger archaebacteria that had never evolved mechanims for utilizing oxygen for energy production. The trade-off allowed these bacteria to coexist peacefully, and is described as endosymbiosis. Over the course of many, many generations, the two bacteria evolved into the functional unit of life–the eukaryotic cell. Nuclei evolved to contain genetic information and membrane bound organelles emerged for specific purposes, compared to older prokaryotic cells which did not contain these features. The oxygen-utilizing bacteria evolved into the powerhouse of cells–the mitochondria, and it still to this day contains its circular bacterial DNA and genes inside it. Additional functions of the mitochondria developed, including beta-oxidation of fat once large multicellular organisms evolved. So with the introduction of the mitochondria which utilized oxygen to generate ATP at a fast rate, there was more energy being provided than ever before. Whereas glycolysis yields just 2 molecules of ATP, one round of beta oxidation of a single fatty acid yields 106! It is no surprise that evolution rapidly accelerated after the introduction of a critical amount of oxygen to the atmosphere.
Argument#7: It would take 10^67 repetitions of the entire history of the universe to randomly create all possible proteins just once. The amount of proteins in existence are only a fraction of the possibilities. Therefore, proteins are intelligently designed.
Response: There are many thermodynamic constraints which prevent every single plausible protein from being formed. Biology is based on chemistry, which is limited by the laws of physics.
Proteins are the end products of gene translation and are the active molecules in cells as far as function. They are composed of chains of their building blocks, the amino acids. There are 20 amino acids, which break down to more specific groups based on their functional R groups. The organization of aa’s in 3D space leads to the secondary structure of protein domains, which then become arranged into tertiary structures by weak, noncovalent interactions like electrostatic salt bridges, vanderwaal’s forces between dipoles and hydrophobic interactions. You have the small, compact, achiral glycine often present in secondary turns. Then there are the bulky proline rings that prevent helical configurations. Then you have the branched chain amino acids (leucine, isoleucine and valine) which are strongly hydrophobic and methionine, phenylalanine, tryptophan and alanine which also have hydrophobic R groups aiding in membrane binding and hydrophobic noncovalent interactions. Other R groups are acidic (Aspartate and glutamate) or basic (histidine, lysine, and arginine) which give them high solubility in aqueous environment as well as allow electrostatic interactions such as the binding of Lys and Arg to negatively charged PO4 groups in DNA. Finally you have the polar, uncharged amino acids like serine, cysteine, threonine, tyrosine, asparagine and glutamine, which aid in additional processes such as phosphorylation of OH groups of Tyr, Ser and Thr in cell signaling, the formation of N-glycosidic bonds from the amide portions of asparagine, and the formation of tightly bound disulfide bridges between cysteine residues.
The reason why there are not more proteins from these building blocks is simple chemistry. It is the reactions with the R groups of amino acids that give proteins their unique properties. Those that become functional in specific ways become selected while others fail to be passed on because they are either inactive or deleterious. What works is conserved, ie, passed down from generation to generation and often from species to species. When a new combination is formed by mutation that gives the organism a protein with a new function that help it adapt and survive better than the wild type protein then that eventually gets selected and so on and so forth, leading to greater and greater complexity throughout evolution. So we don’t see every random combination of proteins. It is a guided process through natural selection.
Argument#8: Fossil dating is inaccurate and depends on belief of how old you think it is. You cannot experiment with something from the past so it is belief and not real science.
Response: Fossil dating has nothing to do with belief. It is based on techniques of carbon and radiometric dating. Carbon dating is very accurate and can date material tens of thousands of years old. Thanks to new techniques involving isochron dating of glacial varve sediments, we can accurately calibrate C14/C12 atmospheric ratios as far back as 45,000 years.
So how do we get estimates of millions and billions of years for other fossils? Do the "evolutionists" pull it out of their ass as ignorant Creationists suggest? Well, sorta (don’t quotemine that). It has been explained by the story of cow manure popularized by 20th century scientist George Gamow. Say a rancher let out all his cows to pastures before he collected them and locked them into different corrals for each pasture. He can find the dates he locked them into the corrals by looking at their shit. By measuring the total amounts of shit in each corral and dividing that by the shit produced by the corresponding herd, he can predict the dates with precision. The shit represents the lead produced by decaying uranium and the locking up of the cows in their corral symbolizes the formation of radioactive deposits in solidified rocks. By measuring the amount of lead isotopes in igneous rocks in the immediate vicinity of fossilization, geologists can use precise mathematical techniques using the known half-lives of those isotopes to find the age of the rocks and thus the age of the fossil in millions and billions of years.
Transitional fossils have been discovered and dated very accurately to give us a timeline of when macroevolutionary divergences occurred. Then DNA analysis gives us the sequences of DNA that changed to provide the mutations needed for phylogenic divergence of these organisms. Since development of transitional species occurs over a long period of time through the accumulation of small changes, the idea of a "missing link" is fallacious. Even so, paleontogists have discovered fossils that could be considered such missing links such as the "fishibian", Tiktaalik, which represents the transition of animals from the aquatic environment to land, one of the biggest evolutionary leaps in history.
Argument#9: The failure of genetic reductionism to explain why genes are in an on/off state and affected by proteins and other environmental factors imply that they are designed.
Response: By sequencing the genomes of animals alive within the past 10,000 years, we can analyze and compare what is known as "fossil DNA" with other unrelated species that have diverged hundreds of millions of years ago. Similarly to how we compare the genomes of a certain family, such as primates, side by side to look for departures where evolution generated new mutations to be carried on to future descendents in the pedigree, we can combine that information with the fossil dating techniques to get an accurate depiction of when certain species diverged and acquired novel mutations. Two examples where this strategy are particularly effective are duplication mutations and fossils of viruses that live in our cells.
A clear example of duplication showing the effects of evolution is that of the globin gene. We can trace this back to plant ancestors, which contained 4 exons. 800 million years ago, 2 exons fused and this mutation was passed down up until the evolution of primitive fish. A duplication then occurred 500 million years ago on the same chromosome of later fish and early amphibians and both copies remained functional. A rearrangement mutation brought them to separate chromosomes and further duplication ensued. Some copies developed mutations that gave them new functions while others suffered debilitating mutations in key regions which made them inactive, nonfunctional pseudo genes. Comparative analysis between different genomes of organisms has enabled us to precisely track the history of other gene mutations in this same way throughout time.
Fossil viruses are common in the genomes of all living organisms. Only 1.5% of DNA encodes for proteins in humans but 8.3% of our DNA is the remnants of primitive infections from viruses that infected sex chromosomes in sperm and egg cells. Over time, mutations in key regions prevented the viruses from replicating and they died out amidst the genomes of the organisms they once infected. Comparing our genome with the genomes of other primates give us definitive confirmation of their close relatedness. Most of the viruses are found in the exact same location with the exact same mutations. This shows that the viruses infected our primate ancestors but died out before humans evolved. Some of the dead viruses were actually used to advance the process of evolution as well. Before introduction of the syncytin virus in early amniotic tetra pods, all vertebrates laid eggs. The syncytin virus was incorporated into the part of the genome that formed the first placenta due to its cell fusion properties. Without it, mammals would still be inefficiently laying eggs. This process occurred after the divergence of mammals and reptiles from synapsids, so reptiles, dinosaurs and birds followed a separate evolutionary line free from syncytin viral infection and lay eggs to this day.
Argument#11: The similarities in genetics have nothing to do with evolution and have everything to do with God’s blueprint, as he uses the same building blocks to create different kinds.
Response: We can accurately trace the evolution of genetic mutations throughout evolution from one species to another. We know at what point certain divergences began based on analysis of specific genes and the proteins they encode. Mutations occurred prior to divergence in every case, and remained throughout speciation. Then, at certain stages, additional mutations occurred that have produced duplications and pseudo genes, as those duplications became mutated and functionally inert. Every once in awhile, the duplications mutated in a way that gave them a new function, which dramatically increased divergence rates. We can track primate evolution back to the Pangea super continent and an extinct species known as Pergatorium. New World monkeys then evolved and inhabited what became South America. Then Old World monkeys showed up on the African continent and they were followed by orangutans, gorillas and chimps and humans.
The further we trace back our lineage, the closer our genomes are with our closer relatives. This is not only true of genes but also transposons as well. The Alu repeat sequence, which is the most common repeat in the human genome, first began with our primate ancestors and continued until humans had evolved before they became inactive. The process began with our ape ancestors and ended with human beings. There is no way to design two separate species in that way without evolution occurring leading to the formation of separate lineages, including humans. It is just not possible.
We know what genes have duplicated throughout evolution, when these duplications arose, what happened to these genes after divergence of different primate species, what mutations led to different amino acids translated, and how specific proteins evolved from the time our ancestors were Old World monkey including the exact sequences that were mutated and at what specific point on an evolutionary scale. There is no way any sensible adult could deny macro evolution with this information available!
Argument#12: Evolution proceeds from life that was generated spontaneously, but all life comes from life.
Response: This idea is a form of Creationism known as "spontaneous generation". Spontaneous generation has nothing to do with evolution. When it was confirmed by Pasteur over 150 years ago that life could not be spontaneously generated from nonlife, it was hotly protested by theists. Theists believed that God infused life into inorganic material because of its plasticity, a notion that was later rejected by Pasteur’s experiments and Darwin’s findings on evolution. When Pasteur disproved this hypothesis, this set the stage for modern theories of abiogenesis. Pasteur provided a deathblow to that idea and modern Creationists then had to refine their god of the gaps approach to just ONE Creation event. The censuring of spontaneous generation supports evolution, and shows that there could only be life emerging once on a single planet with evolution taking its course following abiogenesis. The universality of the genetic code since divergence from the original common ancestor supports this.
People who vituperate spontaneous generation are not debunking evolution OR abiogenesis but Creationism!!! Abiogenesis was accepted as a result of the dismissal of spontaneous generation, and later confirmed by chemical evolution, which showed that the first life form was a thermophile Archaea (ancestor of bacteria) that was able to use inorganic sulfur in the reducing atmosphere of hot springs.
Spontaneous generation is basically the emergence of life from non-life at different points in time. The general rule is that life can only come from life. There was a point when life had to start though. That is abiogenesis. It could only happen once per hospitable planet because once life emerges, other organic matter will then be used for nutrition well before it can pass the critical stage of development from which life can emerge. There was an article recently about how a ribozyme was created in a lab from inorganic material and began to self-replicate under those conditions. This is basically how it is believed that the first life forms emerged. If a molecule containing genetic information such as a ribonucleotide can 1) replicate, and 2) catalyze its own metabolism, then you have the basis for natural selection and complexity will increase as a result in due time. For example, if any naturally formed ribozymes evolved a lipid membrane to contain their catalysis then they would have a large selective advantage over the promiscuous ribozymes and would be the basis for the first cells. RNA, which contains genetic information, can self-replicate and autocatalyze, as shown by the data being accrued in reproducible experiments with RNA. It carries functions of both proteins and DNA that enables natural selection to act upon it. |
