Religion, Science

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. Dr. Robert Sapolsky, a world renowned brain scientist, says this about certain microbes he is furiously studying in his laboratory:

    On a certain level, this is a [microbe] that knows more about the neurobiology of anxiety and fear than 25,000 neuroscientists standing on each other’s shoulders…

    (Hypothesis: Microbes Generate Toxins of Power). Wow … “knows”???

  2. Basic simple machines found in microbial dynamics:

    Lever: A lever is a simple machine. A lever is a board or bar that rests on a turning point. This turning point is called the fulcrum. An object that a lever moves is called the load. The closer the object is to the fulcrum, the easier it is to move. (a hammer can be used as a lever to pull out a nail.)

    Inclined Plane: An inclined plane is a simple machine. It is a flat surface that is higher on one end. You can use this machine to move an object to a lower or higher place. Inclined planes make the work of moving things easier. You would need less energy and force to move objects with an inclined plane.

    Wheel and Axle: The wheel and axle is another simple machine. The axle is a rod that goes through the wheel. This lets the wheel turn. It is easy to move things from place to place with wheels and axles.

    Screw: A screw is a simple machine that is made from another simple machine. It is actually an inclined plane that winds around itself. A screw has ridges and is not smooth like a nail. Some screws are used to lower and raise things. They are also used to hold objects together.

    Wedge: A wedge is a simple machine used to push two objects apart. A wedge is made up of two inclined planes. These planes meet and form a sharp edge. This edge can split things apart.

    Pulley: This simple machine is made up of a wheel and a rope. The rope fits on the groove of the wheel. One part of the rope is attached to the load. When you pull on one side of the pulley, the wheel turns and the load will move. Pulleys let you move loads up, down, or sideways. Pulleys are good for moving objects to hard to reach places. It also makes the work of moving heavy loads a lot easier.

    (Simple Machines). Machines do not have to have moving parts.

    Atoms and complex molecules, and combinations thereof, have complex moving parts (e.g. neutrons, electrons, and protons). They capture photons of many power ranges, from infrared up to ultraviolet and beyond.

    Microbes contain conglomerates that are made into simple machines, them beyond to pumps and motors.

    Some of them can do photosynthesis, which is absorbing a photon by having an electron move to a higher orbit. Kinda like a simple battery. Then the photon in some cases is emitted to cause glowing in the dark. Like in “red tides”.

    Pumps are made from molecules. One thing they do is to take material from inside a microbe then, after using a wedge type simple machine to cause a breach in a target, then pump material into the target, which could be another cell.

  3. Scientists are going bonkers if some commenters are to be believed, because they are using the terms machine, machinery, and the like, to describe things going on in living organisms:

    “A unique biochemical machinery (Fig. 1) is present in envelope membranes …” (p. 715)

    “In plastids cpDNA exists as large protein-DNA complexes called nucleoids, which are associated with the translation machinery.” (p. 715).

    “The characterization of putative constituents involved in the envelope-import machinery is presently the most active field in envelope research.” (p. 716)

    “Finally, the evolution of the envelope-import machinery during plastid development remains to be elucidated.” (p. 716)

    “As the only common membrane structure among plastids, envelope membranes contain the machinery for the assembly of plastid-specific glycerolipids, i.e. from the fatty acids, glycerol, and polar head groups (Gal for galactolipids, sulfoquinovose for SL, and glycerol for PG; Fig. 2).” (p. 717)

    “Therefore, enzymes involved in chlorophyll synthesis and degradation are present in the same membrane but at different stages of plastid differentiation, thus demonstrating the transformation of the envelope biochemical machinery during plastid interconversions.” (p. 720)

    “The purpose of this short overview is to present the complexity of the plastid envelope biochemical machinery and its importance in cell metabolism, especially as a major site in plant cells for membrane biogenesis.” (p. 720)

    “The complexity of the envelope biochemical machinery is further demonstrated by two-dimensional gel electrophoresis analyses of envelope proteins (Fig. 5).” (p. 720)

    “Furthermore, of the several cDNAs encoding envelope proteins that may have been obtained (for instance analysis of the envelope import machinery continuously generates such cDNAs), only a few of them correspond to proteins with known functions, and most of them do not have homologs in other organisms.” (p. 720)

    (The Biochemical Machinery of Plastid Envelope Membranes, emphasis added). Somebody better call home and make sure the venerable copy of the Uber Alles Dictionary is intact.

  4. Bron 1, May 18, 2012 at 9:44 am

    Dredd:

    those same academicians extol the benefits and virtues of a controlled economy even though it doesnt work in reality.

    It is all tied together, old ideas never lose their luster to stupid people whether in biology or economics, they cannot afford the energy to think. Dont rock that boat.
    ==================================================
    I try to avoid the rocking of the boat by quoting authorities. My research leads me to conclude that I am, at least, on track:

    Quorum sensing is the regulation of gene expression in response to fluctuations in cell-population density. Quorum sensing bacteria produce and release chemical signal molecules called autoinducers that increase in concentration as a function of cell density. The detection of a minimal threshold stimulatory concentration of an autoinducer leads to an alteration in gene expression. Gram-positive and Gram-negative bacteria use quorum sensing communication circuits to regulate a diverse array of physiological activities. These processes include symbiosis, virulence, competence, conjugation, antibiotic production, motility, sporulation, and biofilm formation. In general, Gram-negative bacteria use acylated homoserine lactones as autoinducers, and Gram-positive bacteria use processed oligo-peptides to communicate. Recent advances in the field indicate that cell-cell communication via autoinducers occurs both within and between bacterial species. Furthermore, there is mounting data suggesting that bacterial autoinducers elicit specific responses from host organisms. Although the nature of the chemical signals, the signal relay mechanisms, and the target genes controlled by bacterial quorum sensing systems differ, in every case the ability to communicate with one another allows bacteria to coordinate the gene expression, and therefore the behavior, of the entire community. Presumably, this process bestows upon bacteria some of the qualities of higher organisms. The evolution of quorum sensing systems in bacteria could, therefore, have been one of the early steps in the development of multicellularity.

    (Microbial Hermeneutics). Those who dispute the authorities should come up with other authorities with differing research conclusions, otherwise their opinion is just that.

    Later Bron.

  5. Dredd:

    those same academicians extol the benefits and virtues of a controlled economy even though it doesnt work in reality.

    It is all tied together, old ideas never lose their luster to stupid people whether in biology or economics, they cannot afford the energy to think. Dont rock that boat.

  6. The oldest dictionary is a great conversation piece, but it does not define anything modern science is interested in, especially molecular machines:

    This means of evolving complex molecular machines—duplication followed by specialization—had been proposed previously, but it was difficult to generate this sort of direct, biological test of the model. The ability to resurrect ancient proteins has changed that, and I expect we’ll be hearing more about how evolution has assembled these machines.

    (How did molecular machines evolve?). The great machine age first happened ~14 billion years ago, ~10 billion years before the Earth happened along.

    That is also much earlier than organic microbes (composed of molecular machines) came on the scene.

    Old school Darwinists try to figure everything out by asking how this or that human part evolved, as if that was the origin of what is essential, forgetting to focus on the ~14 billion years that preceded humanity.

    That is like trying to figure a person’s entire life by examining the last two seconds.

    It is obviously not a very successful technique.

  7. The snobbery of establishment science has hit the big time:

    Creativity enhances life. It enables the great thinkers, artists, and leaders of our world to continually push forward new concepts, new forms of expression and new ways to improve every facet of our existence. The creative impulse is of particular importance to scientific research. Without it, the same obstacles, ailments, and solutions would occur repeatedly because no one stepped back and reflected to gain a new perspective.

    Unfortunately, in the academic world—where much of today’s scientific innovation takes place—researchers are encouraged to maintain the status quo and not “rock the boat.” This mentality is pervasive, affecting all aspects of scientific research from idea generation to funding to the training of the next generation of scientists.

    (The Scientist). The dogma loving, status quo grasping, insecure types that fear losing grandpa’s dictionary, just can’t muster enough curiosity to go where no scientist has gone before.

    There will never be a cure for grandpa bushie’s dictionary usage that way.

    It ain’t “word” til grandpa’s dictionary says it is word by crackie.

  8. “Sex is the only thing that is more complicated that science or religion,”

    Really.

    That’s almost as ridiculous as saying microbe practice science or religion. Sex is a fundamental drive in all non-asexually reproducing organisms. Sex may seem complicated in humans but that’s only because most humans are idiots when it comes to sex due to cultural (usually religious) influences. In the majority of the animal kingdom, it’s no more complicated than breathing or eating. You find an attractive viable mate, you rub against each other, you make offspring. Sex, unlike science and religion, isn’t a human created cultural institution.

    However, if you want to create straw men Dredd, you need to do better than pointing to epigenetics. I’ve already said that evolution is more complicated than simple natural selection and that both environment and symbiosis play a role. Mutation is the driver of evolution no matter what causes the mutations. Evolution is not natural selection. Natural selection is a mechanic of evolution, but I never said it was the only one and unlike you I haven’t tried to “mystify” the role of bacteria and viruses in the process into something mystical and pseudo-religious. If you’re now trying to imply my understanding of evolution is simplistic in defense of your pet idea, you’d be wrong.

    However, that has nothing to do with your fantasies about microbial life having cultural institutions simply because they exhibit primitive behaviors. Your original assertions are still ridiculous on their face.

  9. In my post up-thread, beginning with the statement “Those scientists who do not know what to look for won’t find it”, quotes a noted scientist had the gall to say:

    The social behaviours of microorganisms include sex …

    Sex is the only thing that is more complicated that science or religion, so I must sound the alarm the Brits are coming, the Brits are coming:

    What if Darwin’s theory of evolution – or, at least, Darwin’s theory of evolution as most of us learned it at school and believe we understand it – is, in crucial respects, not entirely accurate?

    Such talk, naturally, is liable to drive evolutionary biologists into a rage, or, in the case of Richard Dawkins, into even more of a rage than usual.

    (Why everything you’ve been told about evolution is wrong). Someone needs to send them a copy of The Holy Dictionary, a.k.a. “U No Whut I mean Verne”, straight away.

  10. Those scientists who do not know what to look for won’t find it, but those who do have already found it:

    Sociobiology has come a long way. We now have a solid base of evolutionary theory supported by a myriad of empirical tests. It is perhaps less appreciated, however, that first discussions of social behaviour and evolution in Darwin’s day drew upon single-celled organisms. Since then, microbes have received short shrift and their full spectrum of sociality has only recently come to light … Like any society, however, microbes face conflict, and most groups will involve instances of both cooperation and competition among their members. And like any society, microbial conflicts are mediated by three key processes: constraints on rebellion, coercion that enforces compliance, and kinship whereby cells direct altruistic aid toward clone-mates … The idea of sociality in the mere microbe can be met with a raised eyebrow and a smirk. Nevertheless, for as long as there has been evolutionary biology, and indeed sociology, microbes have featured in descriptions of social life … The social behaviours of microorganisms include sex … there can be no doubt that microbial communities are shaped by the individual struggles that face all organisms, but there is room for some romanticism too. For with any struggle comes the benefit of alliances, familial or otherwise, that invest in a shared common good. Some microbes will even die for the cause, rupturing to secrete a toxin can be simultaneously altruistic to those that are immune and spiteful to those that are not. In applying terms like altruism to microbes, though, we are met with something of a paradox. As Spencer realized long ago, the individual microorganism seems destined to be both selfish and altruistic because, in its eagerness to divide, it faces the ultimate metaphysical sacrifice: a loss of self.

    (Social behaviour in microorganisms; Social behaviour: genes, ecology and evolution. Editors: T. Szekely, A. J. Moore, J. Komdeur. Cambridge University Press, by Kevin R. Foster, Harvard University). People argue about who made the first automobile:

    “Exactly who invented the automobile is a matter of opinion.”

    (Who invented the automobile?). There is little wonder, then, that something billions of years older will generate opinions too.

    Determining which opinion is “the correct one” by alleging it is the one held by the person with the biggest fangs, is quite devolved.

  11. The expert whose genetic makeup renders him a “successful psychopath” and a sociopath, is a good example of the folly of eugenics type thinking:

    Epigenetics is just one of many disciplines supercharged by the Human Genome Project. Another is proteomics, which focuses on the structure and function of proteins within an organism. It shows us more clearly how our genes and proteins coexist and interact with the genes and proteins of the trillions of microbes each of us hosts. Indeed, our bodies contain ten times more microbial cells than human cells. Human microbiomics studies the approximately three million microbial genes in the human body, a genetic load so massive it is almost nonsensical to talk about “our” bodies at all. The food we eat, the drugs we consume, our emotional and social environments, or whether we get vaccinated (“vaccinomics,” of course) — all these factors affect how our genes are expressed. Each action sets in motion a Rubik’s cube of metabolic variables we have only begun to comprehend.

    As medical science struggles to apply these new discoveries to society’s benefit, human genome research, now unstoppable, continues to evolve. Ironically, though, this initiative to tailor health care to the individual genome — the touchstone of the Human Genome Project and personalized medicine — increasingly reveals that our genes, and we as individuals, do not function in isolation from other life forms and the environments we all inhabit. Whatever secrets genes contain, our book of life and that of a microbe remain written in the same language.

    (One Man’s Junk Gene Is Another Man’s Treasure Gene?). Listen cats, watch out for those junk yard dogs.

  12. Again, the fallacy of simple cause.

    Thinking evolutionary biology is solely responsible for values is a gross oversimplification. But then again, from simple minds come simple thoughts like trying to inject mysticism into science and making prime facie ridiculous assertions like microbes practice religion and science. You could sell your midi-chlorian fantasy to George, but I’m sure that he’s already got it copyrighted too.

  15. Each gorilla to her own beliefs and facts:

    … But many philosophers in the second half of the 20th century really seemed to think that they were laying the foundations for science by laying down the conceptual (necessary) truths. I asked one: show me one example where 20th century conceptual analysis laid a foundational plank for any empirical science — any empirical science. No answer.

    …

    If I want to know where values come from, I will go to evolutionary biology …
    …

    Theorizing is of course essential to make progress in understanding, but theorizing in the absence of knowing available relevant facts is not very productive.
    …
    My current interest is in moral values, and to address where values come from … many sciences are relevant; evolutionary biology …

    (Casual-Machines, 3 AM). Altruism in microbes is a value study of evolutionary biology:

    Altruism is a well understood topic in evolutionary biology; the theoretical ideas explained above have been extensively analysed, empirically confirmed, and are widely accepted. Nonetheless, there are a number of conceptual ambiguities surrounding altruism and related concepts in the literature; some of these are purely semantic, others are more substantive …

    (Biological Altruism, Stanford). If only these scientists knew H gene formal logic they would stop wasting their time trying to find the origin of values using evolutionary biology, because the H gene formal logic, fused and combined with grandpa’s dictionary, says so.

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