Did God create the various forms of life on earth, or did they arise gradually through natural evolutionary processes--the majority view among Western scientists?[1] Without a time machine one can't demonstrate divine creation any more than a family tree of microbes evolving into fish, clams, and trilobites. So strict observational science can't help us.
A forensic approach is more suitable. Here, evidence can be defined as "what's expected under one view", but "very surprising under a competing view." As an example, suppose Fictitious Fred was killed in his home by three gunshots to the back of his head. The following evidence soon emerges:
A matching gun was found in the garage of Hypothetical Harry, an acquaintance of Fred.
Footprints matching Harry's shoes were found at the crime scene.
Harry's car was seen parked at Fred's house at time of the crime.
Harry is well known for his bouts of anger.
Fred had recently returned from an extended vacation in the Bahamas, despite owing Harry a large sum of money.
Given this evidence it would be expected that Harry really did commit the crime, but very surprising if he did not. Therefore this data acts as evidence of Harry's guilt.
Likewise we can infer design or evolution through evidence. Designs created by intelligent minds are put together differently than those assembled through a process of mutation and natural selection (evolution). This article explores three patterns we find in living things that are expected under design, but are opposite what an evolutionary process would create.
Design and evolution have opposite expectations about whether the DNA of complex organisms will be mostly functional or mostly unused junk. The next three paragraphs are optional reading for those who do not have any background in biology. After that the main point will be discussed.
All living things are made of cells. Each cell has one one or more strings of DNA (chromosomes) with instructions for how and when to assemble their parts. Along a string of DNA are four types of molecules that form a four-letter code for storing information. Humans have about 37 trillion cells,[2] and most of these cells have the same 3 billion "letters" of DNA required to make a human. Additionally, in mammals there are usually two copies of each chromosome. Other mammals have similar amounts of DNA.[3] Generally, simpler organisms have less DNA than those more complex[4], but there are some notable outliers.[5]
But the DNA does not stay exactly the same from one generation to the next. A mutation is a change to DNA. Examples include one DNA letter changing to another, or groups of letters being duplicated, going missing, or written backward. Evolutionary theory proposes that all mammals (and all life) descended from a common ancestor, and that over billions of years, these mutations created the differences between humans, elephants, tomato plants, e coli bacteria, and every other organism.
Organisms with more DNA and more cell divisions between generations have more mutations. Humans have about 100 mutations per generation.[6] Since humans and other orders and families (groups) of mammals have billions of differences in their DNA[7], other mammals would also need to mutate at around the same rate in order to account for this many differences in the time available.[8]
Now for the main point: Having about 100 mutations every generation creates a problem for evolutionary theory. Most mutations that have any effect on an organism are harmful.[9] If all DNA were functional, humans (and other mammals) would receive about 100 harmful mutations per generation. This would cause all offspring to be less fit than their parents, and natural selection could at best only ensure the least-damaged survive. Each generation would have more harmful mutations than the prior, and the population as a whole would gradually degrade until it went extinct.[10, 14] If such an evolutionary process cannot even preserve the information in DNA, it certainly could not have created it.
However if most DNA is not used, then most of the 100 mutations would not be harmful and this problem could be averted. And indeed, for over four decades evolutionary biologists proposed that only about 1-6% of human/mammal DNA performed any function, and the rest junk DNA.[11-14]
In recent years, new research has seriously challenged this low estimate. At least 85% of human DNA is read and transcribed (copied) into RNA[15], a similar molecule used for both transmitting information and performing functions of its own. Yet some have still argued most DNA is unused junk, suggesting cells only transcribe all this DNA by mistake and that these RNA transcripts aren't actually used.[16] The data suggests otherwise:
These RNA transcripts loop and bind to themselves in complex 3D structures[17], which requires specific information. For example, the diagram below shows how complementary A-U and C-G RNA "letters" pair. They could not do this if their sequence was random.
Cells create these RNA transcripts in precise and specific patterns depending on their cell type and the stage of human development. Disruptions in these patterns correlate with disease.[18] This is not expected if these RNA transcripts are only created accidentally and randomly.
In the human brain, we've seen that 80% of RNA transcripts are taken to specific locations in their cells, depending on the type of transcript.[19] Why would cells do this for random junk transcripts?
When these RNA transcripts are mutated, they usually affect development or cause disease. The function of most are still unknown, but a large enough subset have been tested that it's statistically safe to assume the rest are mostly functional.[18]
This is not to say that every DNA or RNA letter is important, or something would be degraded if changed. But we can confidently say far more than 1-6% of DNA is functional.
Continuing our theme of expected vs unexpected: the prior four points are expected if the majority of DNA is functional, but unexpected if it is mostly junk. Moreso, if living things are designed we should expect as much DNA as possible to be functional[20-21], apart from what has become broken by mutation. But in an evolutionary view, mammals having large amounts of functional DNA is very unexpected and cannot be explained. Therefore having large amounts of functional DNA is evidence for design.
Can genes be used to group organisms into family trees, to determine what evolved from what? Design and evolution have opposite expectations here as well.
A gene is a section of DNA that performs a specific function. If all life on earth is related and evolved from a common ancestor, we should be able to build a family tree of species by comparing their genes.
On the other hand, a good engineer can take and reuse parts from one design to the next as needed. This is not to expect a completely random distribution of functional parts. For example, an iPhone and an Android phone are much more similar to one another than either is to a desktop computer or a car. But the iPhone also shares code with Mac OS X, and Android uses code from Linux--two unrelated computer operating systems. The phones have different family histories depending on which components are compared.
Researchers have also noticed the lack of a family tree among the animals they study. NewScientist reports:
[Michael] Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes [worms]. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts - also known as tunicates - are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. "Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another," Syvanen says. "We've just annihilated the tree of life. It's not a tree any more, it's a different topology [shape] entirely."[23]
A 2012 evolution textbook also states:
since embracing Darwin’s tree-like representation of evolution and pondering over the universal Tree of Life, the field has moved on... the Tree of Life turns out to be more like a 'forest'[24]
This is clearly not the family tree predicted by evolutionary theory.
Proponents of evolutionary theory have gone from citing trees as evidence of common descent to now attempting to explain why a tree can't be found. Three explanations are proposed, but each is problematic:
Convergent evolution--two species happened to evolve the same genes the same way. But with the high mutation rates described above, long term evolution should not be possible at all. Evolving the same genes twice is even more improbable.[25]
Horizontal gene transfer--a virus takes a gene from one organism and insert it into another. Before realizing that genes did not form clear family trees, biologists used to think horizontal gene transfer was impossible in animals and never occurred. It seems suspect that viruses are now proposed (without evidence[26]) to be providing up to half of the genes in organisms such as sea squirts.
Incomplete lineage sorting--if one species split into several others at the same time, then no distinct family tree could be found by comparing genes. That's certainly true. But this explanation fails because nobody thinks fish, birds, and mammals all split from a common ancestor at the same time. Or perhaps the common ancestor had more genes, but each species lost a different set of genes. But this fails when additional species are compared, since by chance unrelated species would need to have lost the same genes. And if evolution is primarily a reductive process, that is more consistent with design than it is evolutionary theory.
Evolutionary explanations fail to account for a lack of a tree, but the distribution of genes in organisms is similar to how we distribute components in our own designs. Therefore this too is evidence for design.
Given the data on so many harmful mutations accumulating with each generation, one might wonder why we or any complex animals still exist at all. Thus the title of this section. First, all mammals have two or more copies of each chromosome. If a gene on one chromosome becomes broken, a working copy on the other will usually still suffice. But the redundancy (fail-safe backups) goes beyond that.
In our most reliable systems we use two, three, or more components doing the same job together in case one of the others fail. We build the backup systems in different ways (different software, different CPU, different manufacturers, different teams building them) so that each will have different strengths and weaknesses.[27-28]
Likewise in our own DNA we've often found that two or three genes must be broken before any problems are noticeable.[29-30] And like our own designs, biological backup systems are built in different ways, rather than just being copies of existing genes.[31]
We've already discussed how since evolution cannot even maintain genes in complex organisms, it could not have created them. But these backup systems are even more problematic for evolution. If an organism has one of its backups broken by a mutation, it will still produce just as many offspring, and therefore natural selection would not weed out those with broken backup systems. This is not to say that redundancy halts the multi-generational accumulation of harmful mutations, only that harmful effects go unnoticed until more genes are disabled.
Additionally, if evolution were to create backup systems we should expect it to do so by copying existing genes, a process which can occur in a single mutation. Creating a unique gene from scratch is immensely more difficult.[25] But there they are.
So we return to our theme of expectations and evidence one last time. Genetic redundancy matches our own designs, but is the opposite of what evolution would create. Therefore it too is positive evidence that we and other organisms were designed.
So who or what is the designer of living things? God? Aliens? Do we live in a simulation? Over the last several decades we have discovered much evidence that physics itself appears to be designed. If this were not so stars and planets could not exist, nor could atoms even combine together to create matter.[32-33] Aliens could not design the universe that in turn allows them to exist, and any beings who created our universe as a simulation would first need their own universe designed to allow for their own existence. This requires that a mind itself be the first thing that exists, creating everything else. A mind creating the universe is the definition of God.
There's truth to the saying, "a true believer needs no evidence, a true skeptic will accept no evidence." But we should strive to be neither and instead do our best to follow the evidence wherever it leads.
There is merit in citing those who disagree to support one's point. Except for #9, 10, 20, and 28, all sources below are either hostile to the idea that life is designed, or have not made their position known.
Whitman, Larry. "Many Scientists see God's hand in evolution." Washington Times. 1997.
Bianconi et. al. "An estimation of the number of cells in the human body." Annals of Human Biology. 2013.
Gregory, T. Ryan. "Animal Genome Size Database." Accessed Jan, 2017
Lui, Guosheng et. al. "A meta-analysis of the genomic and transcriptomic composition of complex life." Cell Cycle. 2013. See figure 2B.
Crick, Francis and Leslie Orgel. "Selfish DNA: The Ultimate Parasite." Nature. 1980. Crick and Orgel state, "We also have to account for the vast amount of DNA found in certain species, such as lilies and salamanders, which may amount to as much as 20 times that found in the human genome."
Moral, Larry. "Human mutation rates - what's the right number?" Sandwalk. 2015.
Meader et. al. "Massive turnover of functional sequence in human and other mammalian genomes." Genome Res. 2010.
Figure 2 shows that the various mammals listed share about 100 to 280 million letters of DNA, indicating the other 2.7 to 3 billion letters are different.
Based on the assumption of common ancestry, evolutionary biologists often count the DNA differences to estimate how long ago a would-be common ancestor would have lived. TimeTree.org can be used to lookup estimates of these times. If a lower mutation rate is proposed, ancestors would become much older than a 4.6 billion year old earth, which is clearly problematic.
Wolf-Ekkehard Lönnig. "Some Further Research on Dollo's Law." Ornamental Biotechnology. 2009. Lönnig describes how despite "literally billions of induced mutations... all the important mutation breeding programs have come to an end in the Western World instead of eliciting a revolution in plant breeding" because almost nothing useful came from those many mutations.
Gibson et. al. "Can Purifying Natural Selection Preserve Biological Information?" World Scientific. 2011.
This simulation used a population size of 10,000 and 10 harmful mutations per generation. Under a wide range of realistic and even overly-generous parameters, fitness decreased until the population went extinct.
King, Lester and Thomas Jukes. "Non-Darwinian Evolution." Science. 1969. Page 794, top of third column. The authors state: "Either 99 percent of mammalian DNA is not true genetic material, in the sense that it is not capable of transmitting mutational changes, which affect the phenotype, or 40,000 genes is a gross underestimate of the total gene number... it is clear that there cannot be many more than 40,000 genes."
Ohno, Susumu. "So much 'Junk' in our Genome." Brookhaven Symposia in Biology. 1972; Ohno states: "at the most, only 6% of our DNA base sequences is utilized as genes." By "genes" Ohno does not necessarily only protein coding exons, but rather any functional region of DNA, as the term was used the time.
Graur, Dan. "How to Assemble a Human Genome." 2013; Dan Graur is an evolutionary biologist and leading proponent of the "Junk DNA" view. On slide 5 Graur states "If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome."
Moran, Larry. "A creationist tries to understand genetic load." Sandwalk. 2014.
Moran states: "If the deleterious mutation rate is too high, the species will go extinct... It should be no more than 1 or 2 deleterious [harmful] mutations per generation"
Hangauer et. al. "Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs." PLOS Genetics, 2013.
The authors expect their 85.2% estimate to increase: "we observe an increase in genomic coverage at each lower read threshold implying that even more read depth may reveal yet higher genomic coverage"
Moran, Larry. "Junk & Jonathan: Part 6—Chapter 3." Sandwalk. 2011.
Moran writes: "We also expect that a lot more of the genome will be transcribed on rare occasions just because of spurious (accidental) transcription initiation."
"New Insight Into the Human Genome through the Lens of Evolution." Garvin Institute. 2013. The article explains: "the nucleic acids that make up RNA connect to each other in very specific ways, which force RNA molecules to twist and loop into a variety of complicated 3D structures."
Mattick, John S. "The extent of functionality in the human genome." The HUGO Journal. 2013.
Mattick writes: "the vast majority of the mammalian genome is differentially transcribed in precise cell-specific patterns to produce large numbers of intergenic, interlacing, antisense and intronic non-protein-coding RNAs, which show dynamic regulation in embryonal development, tissue differentiation and disease with even regions superficially described as ‘gene deserts’ expressing specific transcripts in particular cells... where tested, these noncoding RNAs usually show evidence of biological function in different developmental and disease contexts, with, by our estimate, hundreds of validated cases already published and many more en route, which is a big enough subset to draw broader conclusions about the likely functionality of the rest."
Mattick, John. "Video Q&A: Non-coding RNAs and eukaryotic evolution - a personal view." BMC Biol. 2010.
Mattick writes: "in 80% of the cases where we had sufficient resolution to tell, these RNAs are trafficked to specific subcellular locations."
Dembski, William. "Science and Design." First Things. 1998.
Long before junk DNA was disproved, Dembski predicted: "On an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function."
Miller, Kenneth. "Life's Grand Design." Technology Review. 1994; Miller is a biologist and an outspoken critic of intelligent design. Long before junk DNA was disproved, he predicted: "If the DNA of a human being or any other organism resembled a carefully constructed computer program, with neatly arranged and logically structured modules each written to fulfill a specific function, the evidence of intelligent design would be overwhelming."
Howe et. al. "The zebrafish reference genome sequence and its relationship to the human genome." Nature. 2013.
Lawton, Graham. "Why Darwin was wrong about the tree of life." New Scientist. 2009.
Anisimova, Maria. "Evolutionary Genomics. Statistical and Computational Methods, Volume 2." Methods in Molecular Biology. 2012.
Sauer, Robert T. "Functionally acceptable substitutions in two alpha-helical regions of lambda repressor." Proteins. 1990. Saur estimates that only "about one in 10^63" sequences of amino acids will form a specific protein fold.
For example see "Lateral transfer of tetrahymanol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen." Biol Direct. 2012. Horizontal gene transfer was assumed to explain mysterious genes shared between unrelated organisms, but the authors were unable to "find any traces of putative LGT vectors such as transposable elements in the flanking regions of the STC genes in the genomes from the ciliates Tetrahymena and Paramecium", and they admittedly know of "no distantly-related STC homologue encoded in any mitochondrial genome characterized to date," meaning that "there is no evidence linking [the] findings to endosymbiotic gene transfer from the mitochondrial (or plastid) ancestor and no other reason to think these organelles are relevant to this case of gene transfer." Likewise the paper reporting discordance in sea squirts did not mention any signs of horizontal gene transfer.
Holzmann, Gerald J. "Mars Code." Communications of the ACM. 2014. The article describes the redundancy used on the Mars Curiosity rover: "Every precaution was taken to optimize the chances of success, and not just in the development of the software. Critical hardware components were duplicated, including the rover's main CPU ... Running the same landing software on two CPUs in parallel offers little protection against software defects. Two different versions of the entry-descent-and-landing code were therefore developed, with the version running on the backup CPU a simplified version of the primary version running on the main CPU. In the case where the main CPU would have unexpectedly failed during the landing sequence, the backup CPU was programmed to take control and continue the sequence following the simplified procedure."
Walter Bright, a former Boeing engineer, describes how redundancy is used to increase airline safety.
Kellis et. al. "Defining functional DNA elements in the human genome." PNAS. 2012. The authors explain: "Loss-of-function tests can also be buffered by functional redundancy, such that double or triple disruptions are required for a phenotypic consequence."
Noble, Dennis. "Problems with Neo-Darwinism." 2013. At 16:27 Noble explains: "Simply by knocking genes out we don't necessarily reveal function, because the network may buffer what is happening. So you may need to do two knockouts or even three before you finally get through to the phenotype. ... If one network doesn't succeed in producing a component necessary to the functioning of the cell and the organism, then another network is used instead. So most knockouts and mutations are buffered by the network."
Wagner, Andreas. "Robustness against mutations in genetic networks of yeast." Nature Genetics.
Collins, Robert. "Why a Fine-Tuned Universe?" Science+Religion Today. 2008.
Agrawal et. al. "The anthropic principle and the mass scale of the Standard Model." Physical Review. 1998. This paper outlines just one of the examples of fine tuning. The authors explain: "We estimate that for v/v0 >= 5 there will be no stable nuclei, as the mass excess of the neutron is greater than the nuclear binding energy. For v/v0 <= 5 a variety of nuclei will continue to exist, with fewer and fewer stable isotopes surviving as v/v0 increases... As v decreases from v0, the neutron becomes stable, then mn = mp, followed eventually by a region where the proton is unstable to decay p → n + e+ + νe [proton decays into neutron, positrion, and electron neutrion]" In simple terms, v is any given mass of the Higgs, and v0 is the mass it has in our universe. So if it's much larger, then the nuclei of atoms won't stick together and there will be no molecules. If it's too small, protons decay into neutrons and then there are no atoms. Either way there can't be any life at all.