The Evolutionary Gorilla In The Room

-Submitted by David Drumm (Nal), Guest Blogger

One common tactic in the creationist’s war against evolution is to falsify evolution by demonstrating a counterexample. If such a counterexample existed, it would indeed spell the demise of evolution. The Precambrian Rabbit would be such a counterexample. After failing to find even one counterexample, some creationists have given up trying to falsify evolution and now seek to disabuse evolution by claiming it is not falsifiable. Other creationists, unable to falsify evolution, get all metaphysical and point out that the principle of falsifiability is not falsifiable.A recent paper in the journal Nature, Insights into hominid evolution from the gorilla genome sequence, after sequencing the western lowland gorilla genome, it was found that “in 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other.”

Creationists pounced, noting that depending on which DNA fragment is used for analysis, humans are more closely related to gorillas than to chimpanzees. Although this was termed “Bad News” for evolution, it would have been worse news for probability theory. While the genomes of humans and chimpanzees show a mean genetic difference of 1.37%, and a 1.75% difference between humans and gorillas, the key word is “mean.” These probabilities do not imply that there is a uniform genetic difference across all genes. Of the tens of thousands of genes, some are more similar and some are less similar. On average, humans are more closely related to chimpanzees than to gorillas.

On the genetic path from our Most Common Recent Ancestor (MCRA) to humans and gorillas, different genes mutated at different times. Although cladograms, like the one below for Humans, Chimpanzees, Gorillas, and Orangutans, show a single branch to each species, this does not imply that all the genetics differences occurred simultaneously. One would have to be a creationist to believe that all the mutations occurred simultaneously.

One would also expect to find that certain DNA fragments would more similar between humans and orangutans. This is exactly what was found in this report, based on a complete orangutan genome, published in Genome Research, in which the authors said that “in about 0.5% of our genome, we are closer related to orangutans than we are to chimpanzees.”

Even the well-funded BioLogos, a group dedicated to trying to accommodate Christianity and science, sees the errancy of these arguments:

This is exactly what one expects from the species tree: humans and chimps are much more likely to have gene trees in common, since they more recently shared a common ancestral population (around 4-5 million years ago). Humans and orangutans, on the other hand, haven’t shared a common ancestral population in about 10 million years or more, meaning that it is much less likely for any given human allele to more closely match an orangutan allele.

Creationists are engaged in a desperate, but lucrative, attempt to pull a Precambrian Rabbit out of their hat. This attempt is particularly pathetic.

H/T: Pharyngula, John Wakeley (pdf), Pharyngula.

 

238 thoughts on “The Evolutionary Gorilla In The Room”

  1. Dredd, natural processes at work at the molecular or cellular level are not “science” any more than a quartz crystal sticking out of a dirt bank refracting light rays are science. Speaking as a terminal degree scientist, I posit that science is the systematic observation, quantification and use of these natural phenomena.

  2. 1) “It suggests that algae knew about quantum mechanics nearly two billion years before humans,” says Scholes.”

    Algae didn’t and doesn’t know jack shit, Dredd. It’s not conscious. Algae utilized quantum mechanics. So what? Quantum mechanics is a natural process. A simple plant utilizing a natural process. Who’d have thunk it? However, you reading that and deriving that algae literally knew about quantum mechanics and was using QM in some deliberate conscious manner? That’s as stupid as believing the Bible is the literal word of God or that the moon is made of cheese. Just because you read something, Dredd, it doesn’t mean you understand it. Speaking of which . . .

    2) Microbial symbiosis does not change DNAs role in evolution. It modifies the inputs. DNA still tells cells what to be.

    3) “Various non-life machines like prions, phages, and viruses can also be symbiont to humans and other species to help them survive”

    You need to learn what a metaphor is, Dredd. Prions, phages, and viruses are not literally machines. Again, if you use the term machine in this context literally, you are again demonstrating your ignorance about biology and what role prions, phages, and viruses play in biology. They are an intermediate step between non-organic interactive compounds and prokaryotic life and they remain interactive with prokaryotic life because they share common chemistry, but they are not really machines. No one built them. They arose from the process of abiogenesis. If you think they are really machines? You are arguing for Intelligent Design because for them to be purposefully designed and built would require conscious intelligent intervention. There was no conscious intervention in abiogenesis.

    Tools are built by conscious beings. Machines are complex/compound tools. The only conscious beings we know of are complex prokaryotic life. Prions, phages, and viruses are not complex prokaryotic life, but rather the intermediate stage between inorganic chemistry and life. Bacteria is simple prokaryotic life. Humans and other animals are complex prokaryotic life. Simple prokaryotic life is the intermediate step to complex prokaryotic life. Therefore, machines do not come before either simple or complex prokaryotic life. Your statement that machines came before microbes fails as a matter of logic and proof. Q.E.D.

    Reading, comprehension and proper integration of knowledge into a wider knowledge base are not the same thing. You’ve demonstrated that you can read. You have not demonstrated that you comprehend properly or integrate well.

    Now that your alleged “proof” is disposed of (largely because you didn’t understand it in proper context), how about you stop moving the goal posts and answer the following question:

    Which is older in human history as a sociological phenomena, religion or science?

    Let’s see if you can go wrong in such a dazzling way again. You know what W.C. Fields used to say? “If you can’t dazzle them with brilliance, baffle them with bullshit.” I’ll have to say one doesn’t get to see dazzling bullshit such as your above argument in favor of your ridiculous statements every day, but it certainly wasn’t baffling as to how you reached your erroneous conclusions. You’re reading but not understanding what you read.

    Try harder.

  3. The Evolutionary Gorilla in the room has no chance of continuing to exist, nor do humans for that matter, unless a non-living machine like entity, collectively called a virus, had not injected genetic material into our ancestors long ago:

    Various non-life machines like prions, phages, and viruses can also be symbiont to humans and other species to help them survive:

    If not for a virus, none of us would ever be born.

    In 2000, a team of Boston scientists discovered a peculiar gene in the human genome. It encoded a protein made only by cells in the placenta. They called it syncytin.

    What made syncytin peculiar was that it was not a human gene. It bore all the hallmarks of a gene from a virus.

    Viruses have insinuated themselves into the genome of our ancestors for hundreds of millions of years.

    It turned out that syncytin was not unique to humans. Chimpanzees had the same virus gene at the same spot in their genome. So did gorillas. So did monkeys. What’s more, the gene was strikingly similar from one species to the next.

    (Discover). While that may complicate things, in the sense that it is more controversial to contemplate non-live machines doing things critical for living things, nevertheless, it emphasizes the importance of microbes and even smaller entities in terms of what we need for survival on this planet.

    (… Machines or Organisms?). Primates like the gorilla, or humans, can not continue as a species without the help of a tiny microscopic entity that intervened millions of years ago.

  4. The old dogma of random DNA mutation as the “driving force” of evolution is disfavored.

    The more up-to-date research calls for consideration of microbial genetics as the underlying substantial consideration:

    SYMBIOGENESIS

    Symbiogenesis is a theory of evolution. It argues that symbiosis is a primary force of evolution, because acquisition and accumulation of random mutations or genetic drift are not sufficient to explain how new inherited variations occur. According to this theory, new cell organelles, new bodies, new organs and new species arise from symbiosis, in which independent organisms merge to form composites. This challenges some standard textbook ideas of how evolutionary change occurs. To some degree, Darwin emphasized competition as the primary driving process of evolution, symbiogenesis emphasizes that co-operation can also be important to the process of evolution.

    In the late 20th century, Lynn Margulis claimed that microorganisms are one of the major evolutionary forces in the origin of species, endosymbiosis of bacteria being responsible for the creation of complex forms of life.

    Margulis’ theory of symbiogenesis

    Margulis emphasizes that bacteria and other microorganisms actively participated in shaping the Earth, and helped create conditions suitable for life (e.g., almost all eukaryotes require oxygen, and only developed after cyanobacteria have produced enough atmospheric oxygen). She also argues that these microorganisms still maintain current conditions and that they constitute a major component in Earth biomass.

    She showed that free-living bacteria and other microorganisms tend to merge with larger life forms, seasonally and occasionally, or permanently, perhaps under stress conditions. In the now generally accepted endosymbiotic theory, Margulis demonstrated that current plant cells resulted from the merging of separate ancestors, the chloroplast evolving from endosymbiotic cyanobacteria (autotrophic prokaryotes). A more recent additional hypothesis for the origin of some algal and plant cells is the fusion of Thermoplasma (sulfur reduction, fermentation), Spirochaeta (motility), alpha-proteobacteria (oxygen respiration) and Synechococcus cyanobacteria (photosynthesis).

    Margulis claims that most of the DNA found in the cytoplasm of animal, plant, fungal and protist cells originated as genes of bacteria that became organelles, rather than from genetic drift or mutation.

    Along these lines Margulis has argued that bacteria have the ability to exchange genes very easily and quickly, even between different species, by conjugation or through plasmids. For these reasons, the genetic material of bacteria is much more versatile than that of the eukaryote (see Primary nutritional groups for more on the extent of bacterial ability in terms of nutrition). Margulis claims that versatility is the process which enabled life to evolve so quickly, as bacteria were able to adapt to initial conditions of environment and to new changes by other bacteria.

    (emphasis added, see Dr. Lynn Margulis link up-thread).

  5. Why DNA of mammals must be reconsidered:

    How do species originate?

    Lynn Margulis presents an answer to the one enduring mystery of evolution that Charles Darwin could never solve: the source of the inherited variation that gives rise to new species.

    These researchers argue that random mutation, long believed (but never demonstrated) to be the main source of genetic variation, is of only marginal importance. Much more significant is the acquisition of new genomes by symbiotic merger.

    The result of thirty years of delving into a vast, mostly arcane literature, this is the first attempt to go beyond – and reveal the severe limitations of – the dogmatic thinking that has dominated evolutionary biology for almost three generations. Lynn Margulis, whom E.O. Wilson called “one of the most successful synthetic thinkers in modern biology,” presents a comprehensive and scientifically supported theory that directly challenges the assumptions we hold about the diversity of the living world.

    ….

    Lynn Margulis, Distinguished University Professor in the Department of Geosciences, University of Massachusetts, Amherst, is a member of the National Academy of Sciences and the Russian Academy of Natural Science. She received a National Medal of Science from President Clinton in 2000.

    Her books include What is Life?, What is Sex?, Slanted Truths (all co-authored with Dorian Sagan) and Symbiotic Planet.

    (Dr. Lynn Margulis).

  6. Some evolution based research points out that scientific capabilities are two billion years older than humans:

    A team of University of Toronto chemists have made a major contribution to the emerging field of quantum biology, observing quantum mechanics at work in photosynthesis in marine algae.

    “There’s been a lot of excitement and speculation that nature may be using quantum mechanical practices,” says chemistry professor Greg Scholes, lead author of a new study published in Nature. “Our latest experiments show that normally functioning biological systems have the capacity to use quantum mechanics in order to optimize a process as essential to their survival as photosynthesis.” … It also raises some other potentially fascinating questions, such as, have these organisms developed quantum-mechanical strategies for light-harvesting to gain an evolutionary advantage? It suggests that algae knew about quantum mechanics nearly two billion years before humans,” says Scholes.

    (The Tiniest Scientists Are Very Old, emphasis added). The microbes that chose humans as a symbiont species had been around billions of years prior to mammals, so one wonders how they took part in genetic events across species.

    Nal’s focus on human DNA captures some “finger prints” and “foot prints” that could be part of that trail.

    Up-thread I show that microbes communicate with each other, and with “purely human” cells as symbiont members of the human species, as they perform various “human functions”, including brain development.

    Microbial science is very ancient, yet very up to date as well.

  7. raff,

    Don’t forget the calzone. 😉

    And beer. Sweet, sweet beer. (drool)

  8. pete,

    A good call. A lot of the protoscience that led to modern science is rooted in what would eventually become medicine, especially in the Chinese tradition. But using something because you know it has value and understanding why it has value in a systematic, codifiable, verifiable rationale way are not the same thing. Rae’s ointment (that’s a great movie, one of me and my dad’s favorites) would have likely been found (as OS alluded to earlier) by accident or trial and error. Any causation attributed to its usefulness by primitive societies lacking formal science would have likely been mystical or simply accepted as being part of nature. Modern science is in many ways a systematic search for rational causation in complex systems. The systematics of that approach, the scientific method, is what differentiates modern science from its predecessors. The method is one of the most useful tools ever created in that it is both a tool for organized interrogation/investigation and verification/falsification. One need only compare the value of the knowledge gained through alchemy versus the value of the knowledge gained through modern chemistry to see the value of the scientific method and the difference between protoscience and science. Also, shamanic practices and early religions were likely contributors to primitive medicines too. The guys testing all those mushrooms to see which ones made you see the gods were likely a lot of the same guys who found other useful naturally occurring products as well. Or ended up dead or horribly ill – the error part of trial and error in those days. 😀

  9. i’d say medicine was one of the firsts. it’s hard to draw on walls and sing around the campfire when your head hurts.

    i recall in the movie “quest for fire” rae dawn chong had a soothing remedy for burns.

  10. Gene,

    I was going to bring mathematics into the musician mix but I was afraid you’d give me a math problem and I’d have to skulk away in shame carrying my “we musicians came first” theory in an animal skin rug.

  11. Blouise,

    I’m pretty sure the development of language, the development of music and in third tangent, mathematics, were conjoined. Although they may have developed at different rates, their interrelationship is undeniable.

  12. Gentlemen,

    Before they could do any of that, they could hum/sing. We musicians were way ahead of you scientists and linguist and tool makers.

  13. Gene, no real argument, but I also posit that drawing came long before writing.

  14. OS,

    I will stipulate that tools are the forerunners of science in the same way counting is the forerunner to mathematics, however, I do think writing is what made science a formalized (and more efficacious) endeavor.

  15. Gene, we have no way to prove anything one way or the other, but I am convinced science began the way all things scientific happen, by observation, trial and error. Probably language developed concurrently, since it would be necessary for Ogg to explain to Ugg, just how to get that nut open with a rock. My guess also is that some of the first implements were probably weapons. Human beings being what they are of course. We do know that some primates have created tools, the forerunners of science.

  16. Gene, two Sergeants were talking about their Second Lieutenant, fresh from OCS. Someone walking past heard one of them refer to him as, “a wedge.” Curious, the person asked what was meant by that. The Sergeant replied, “The wedge is the simplest tool.”

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