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. “It would literally be chaos if there wasnt order.”

    Unless what was percieved as order was actually matrices of probablilty. Predicitable with a high degree of certainly is not the same as order, Bron. It appears to be order. The nature of the universe is to fall into disarry. That’s what entropy is: the reduction of order within systems. To quote Homer SImpson speaking to Lisa upon her building a perpetual motion machine, “We obey the Laws of Thermodynamics is this house, young lady!”

  2. Dredd:

    the world does have order to it or we would not be able to figure it out. Science depends on order for its existence, if there was no order it would be impossible to come to any conclusions. Everything would be up in the air, we couldnt write a simple equation like F = ma. The acceleration of gravity would be constantly changing and would render the product useless even though the equation itself would still be valid. But we wouldnt necessarily know the equation is valid. It would literally be chaos if there wasnt order.

    Sure there are uncertainties but those usually are made clear with additional knowledge.

  3. Maybe I think a sandwich is food because a sandwich is food, Dredd.

    sandwich \ˈsan(d)-ˌwich, ˈsam-; dialect ˈsaŋ-\, n.,

    1a : two or more slices of bread or a split roll having a filling in between b : one slice of bread covered with food

    It’s not my fault you have to make up defintions to words to complete your fantasy, have problems integrating the Law of Identity or that you like to dryhump the Pathetic and composition fallacies to rationalize your pet theory you use to give you a sense of order in a world where order is the exception. What’s really impressive about your whole speil on this issue is that you don’t even realize that last bit is what you are doing: conflating improperly understood science into a substitute for religion. One of the very foibles of humanity you were so recently bitching about.

    Really, do please keep prattling on. I think it’s hysterically funny. The more you do it, the funnier it gets.

  4. Gene H. 1, April 10, 2012 at 3:10 pm

    ….

    You’ve already demonstrated copiously elsewhere you don’t know what I mean when I say utilitarian pragmatist
    =================================
    The thingy “utilitarian pragmatist” is someone who thinks “sandwich” means the food from grandpa’s dictionary kitchen, McTell News, made by the god of all machines, Black & Decker.

    Your are so clade baby, do McTell.

  5. Bron,

    You’ve already demonstrated copiously elsewhere you don’t know what I mean when I say utilitarian pragmatist. Firstly, in specific, I’m a weak rule utilitarian. Strong rule utilitarianism is an absolutist system and suffers from the same crippling defects any absolutist system does. “From what I can gather about Utilitarian Pragmatism, the rock is what you would use to drive the nail. It works and is available to the largest number of people.” The number of people has less to do with weak rule utilitarian pragmatism than you think. WRUP (it’s easier to type) is less value system than a problem solving methodology. Weak rule utilitarianism states that rules should be framed and formulated on previous examples that benefit society, although allows that it is possible under specific circumstances to do what produces the greatest happiness and/or promotes the greater good by breaking the rule (which, by the way, is much how jurisprudence works in practice). In that sense, greater value to all does concern others as a judgement, but it’s not always a value judgement – often it is quantifiable. Especially when you apply pragmatist tradition of evaluating truth in the light of logic, experimentation, and skeptical rational inquiry (much like the scientific method). For example, not that you’ve ever noticed, but my argument for universal health care insurance is not just nested on egalitariansim or humanism, rather it has at its core a pragmatic and logical business case for adopting such a system based upon systemic efficiencies gained through maximizing the size of the risk pool, eliminating paperwork and the associated costs, etc. To the contrary, “[y]ou use different tools for different jobs because not all jobs or tools are created equal” is the very essence of utilitarian pragmatism. Factoring others into the equation comes from also being an egalitarian and a humanist, more so than the utilitarian pragmatism. Just as I am not an absolutist, philosophically I am more than one thing. Philosophy is, after all, just another tool. Different tools for different jobs.

  6. The Toxins of Power blog has a series focusing more closely on parts of molecular machines:

    Writing in the journal PLoS Pathogens, the team from Queen Mary’s School of Biological and Chemical Sciences show how they studied the molecular machine known as the ‘type II bacterial secretion system’, which is responsible for delivering potent toxins from bacteria such as enterotoxigenic E. coli and Vibrio cholerae into an infected individual.

    Professor Richard Pickersgill, who led the research, said: “Bacterial secretion systems deliver disease causing toxins into host tissue. If we can understand how these machines work, then we can work out how it they might be stopped.”

    (Do Molecular Machines Deliver Toxins of Power?).

  7. Additions to grandpa’s dictionary:

    “Many cellular processes are carried out by molecular ‘machines’ — assemblies of multiple differentiated proteins that physically interact to execute biological functions … Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.” (Evolution of increased complexity in a molecular machine, Nature, 2012).

    “The most complex molecular machines are found within cells.” (Molecular Machine).

  8. “I’m a utilitarian pragmatist. You use different tools for different jobs because not all jobs or tools are created equal.”

    I am not sure how that makes you a utilitarian pragmatist? If you need to drive a nail you can use a hammer, a rock, a piece of steel, a nail gun, any hard object which you can grasp. The most effective is a nail gun under certain conditions, then a hammer. But a rock will do in a pinch.

    From what I can gather about Utilitarian Pragmatism, the rock is what you would use to drive the nail. It works and is available to the largest number of people. A Rational Capitalist would use a nail gun or a hammer.

    Thus the house would get built and the greater good would be served even though your focus is not on the greater good but maximizing your profit in the construction of the house.

    I have a friend, a great man, who is a builder and is retired and now builds homes to sell for charity, he takes the profits from the homes he builds. The more money he makes, the more he can give to charity. The market will only bear so much so if he wants to make more money he has to improve his construction methods. He cant be a Utilitarian Pragmatist even though he is donating all of the profits to charity, he has to be focused on continuous improvement and pinch every penny he can from the process. Which means doing the work faster which reduces the wages earned by labor. Not very utilitarian.

    I know one thing, I wouldnt admit I was a Utilitarian Pragmatist. That is like saying “I dont know shit from shinola and want everyone else to be in the same boat.”

    “To give you an example: if a building were threatened with collapse and you declared that the crumbling foundation has to be rebuilt, a pragmatist would answer that your solution is too abstract, extreme, unprovable, and that immediate priority must be given to the need of putting ornaments on the balcony railings, because it would make the tenants feel better.

    There was a time when a man would not utter arguments of this sort, for fear of being rightly considered a fool. Today, Pragmatism has not merely given him permission to do it and liberated him from the necessity of thought, but has elevated his mental default into an intellectual virtue, has given him the right to dismiss thinkers (or construction engineers) as naive, and has endowed him with that typically modern quality: the arrogance of the concrete-bound, who takes pride in not seeing the forest fire, or the forest, or the trees, while he is studying one inch of bark on a rotted tree stump.”

    Are you sure you are a “Utilitarian Pragmatist”?

  9. Oh, I am sorry. My father died when I was young so I sort of understand. I imagine having an absent father was harder than having a dead one.

  10. Bron,

    You seem to think I haven’t read Rand, but unfortunately I have. That’s where the criticisms of both her premises and her conclusions come from. You also mistake the nature of the above criticism. The primary criticism of Rand is her faulty premises that lead to faulty conclusions. Rand herself wasn’t a binary thinker, but she was an absolutist. Her absolutism is in part rooted in her outcome determinism which was in turn rooted in her mental illness and the conditions under which she grew up. Her work appeals to binary thinkers because her ultimate conclusions are absolutist. Binary thinking and absolutism are two different things. You are a binary thinker. That is how you think. What you think is in absolutes. Her conclusions – no matter that she recognizes the reality of complexity – are absolutist. This is why her work appeals to you. It grants certainty and in absolute terms. It’s the same reason most religions (but not all) appeal to people.

    I know you understand Newtonian physics. If you understood quantum mechanics better, you’d know that absolute certainty is an illusion. Everything (and I do mean everything) exists in matrix of probablilites.

    Also, my attack on Dredd wasn’t Randian at all and any similarity was because of the derivative nature of parts of her work. My attack on Dredd was Aristotlian.

    “The only difference is that you arent a total capitalist and think the government can do more than it should.” Not correct. I think the government can do more than it does, should by the terms of the Constitution, and doesn’t because it has been coopted by oligarchs/plutocrats instead of looking out for the best interests of all citizens. And of course I’m not a “total capitalist”. I’m not an absolutist. I’m a utilitarian pragmatist. You use different tools for different jobs because not all jobs or tools are created equal.

    “As far as your dad goes, he raised you didnt he? So how bad can he be?”

    Actually, no, he didn’t. I was raised by my mother and grandparents. When I was a child, my dad was largely absent.

  11. Gene H:

    one more thing, when it comes to individual rights I am pretty closely aligned to your way of thinking. Are you a binary thinker too?

    I do admire your intelligence, yes I do. That is sincere and not mockery.

    As far as your dad goes, he raised you didnt he? So how bad can he be?

    No matter how hard we try to shake, there is always some of our parents dust under our shoes.

  12. Gene H:

    “It could be this but it could be that so we have to take the facts and figure out if this action is right or wrong in relation to the circumstances”.

    Something like this statement is what you are saying?

    “There are, of course, complex issues in which both sides are right in some respects and wrong in others — and it is here that the “package deal” of pronouncing both sides “gray” is least permissible. It is in such issues that the most rigorous precision of moral judgment is required to identify and evaluate the various aspects involved — which can be done only by unscrambling the mixed elements of “black” and “white.””

    You are just so precious when you agree with Ayn Rand. I have been reading what you have been saying lately and when I just keep quiet and dont argue with you, it is amazing how closely your thinking resembles Rand’s. The only difference is that you arent a total capitalist and think the government can do more than it should. The other stuff you are pretty close.

    Your denunciation of Dredd is almost pure Randian in nature. I would not have been so hard on Dredd, he is entitled to his opinion wrong or right. Dredd is not going to overturn the concept of Darwinian evolution on this blog with his ideas of intelligent “machines”.

    You really should read Rand, you and she have a lot more in common than you might think.

  13. Bron,

    “You can talk about binary thinking all you like but most of life is black and white. The shades of grey come in when people try to nuance something in opposition to the principles.”

    No. Grey comes in because the nature of reality is analog, not digital. Very few principles are absolute and the ones that are are all scientific principles. Social principles like the definition of good and evil are based in socially defined values and they are relative. You simply think most of life is black and white because you’re incapable of dealing with the reality that it isn’t. Black and thinking is a a form of absolutism combined with denial. You don’t deal well with complexity or with conflict – your primary response to conflict is aggression. It’s not your fault. It’s like color blindness. Just because you can’t see the color red doesn’t mean it doesn’t exist. The same goes for the grey in discussing ethics . . . and justice for that matter.

    You also display a remarkable lack of understanding of how mitigation works at law. It’s not a binary decision at all. Not all mitigation is equal. Not all circumstances are equal. If it was and if mitigation was a binary choice, there would be no need for argument beyond presentation of evidence. Pure black is as rare as pure white. They exist, surely, but they are the extreme ends of a bell curve. You pay lip service to mitigating circumstance, but it is apparent you don’t really understand them. If ethics were all absolutes, there would be no mitigation.

    “Value judgements are based on an individuals morality. By saying there is grey means you can ignore having to make a value judgement. In my mind grey is the lack of morality; ‘it could be this but it could also be that, who knows what is right or wrong’.”

    Your mind is wrong. Grey isn’t the lack of morality. It’s the recognition that morality or ethics is relative to a situation and therefor more complex than absolutes allow for. “[I]t could be this but it could also be that, who knows what is right or wrong” is an oversimplification and a retreat to epistomological nonsense. It answers nothing, but offers the ethical equivalent of throwing up your hands. Just because something is not plainly good or evil does not mean you cannot figure out where along the spectrum that thing lies. “It could be this but it could be that so we have to take the facts and figure out if this action is right or wrong in relation to the circumstances” is a far more complex question to answer, but a question that stands to yeild a far more just outcome than black and white thinking. Your way of thinking is lazy. Recent studies show that low-effort thought promotes political conservatism. Combined with a brain not well equipped to deal with complexity or confronation and you get a recipe for retreating to absolutism.

    Like someone with color blindness, you are sensory and sense processing impaired. Unlike someone with color blindness, you haven’t learned to live with or compensate for your limitation. My father is actually quite a bit like you, Bron. He’s short on empathy and his proclivity is to be an ethical absolutist. The real difference is that he knows he’s (as he calls it) “empathy impaired” and he tries to work around it. You, on the other hand, think it’s the rest of the world that is out of whack so you want to force it into your absolute boxes when absolutes are the exception not the norm.. The rest of the world is analog in which data is represented by continuously variable physical quantities and qualities. It’s not 1 or 0, but somewhere in between. To insist that it conform to your socially defined little boxes perfectly is also a recipe for disappointment. Whether you can overcome this disadvantage is part choice and part physiologically delimited ability. You constantly put forth ideas and get (insert reaction here) whenever someone finds fault with it or criticizes your lack of empathy and/or humanity, yet you keep on keepin’ on, when instead you should be questioning your underlying operational principles in the light of constant and consistent opposition. But you can’t do that. Change is a threat and brings conflict and you don’t handle threats or conflict well.

    It’s okay though. We, the non-disabled in this regard, understand. There is an upside though. All men are created equal, but not all men are equally created. While such thinking is a disability in something like law or sociology, it probably serves you well in engineering.

  14. Gene H:

    I understand why you dont like her. But she most certainly did try and make sure she knew what the nature of a thing was and what aspects of a thing were part of its nature and what were results from that nature.

    You can talk about binary thinking all you like but most of life is black and white. The shades of grey come in when people try to nuance something in opposition to the principles. Are there mitigating circumstances? I would say yes but that isnt the same thing. If you kill someone they are dead, black or white, zero or one. Figuring out the motivation is then left to a court of law.

    The mitigating circumstance is still a zero or a one, self defense or not self defense, not self defense then manslaughter, and so forth until a just sentence is found based on the facts of the case.

    Value judgements are based on an individuals morality. By saying there is grey means you can ignore having to make a value judgement. In my mind grey is the lack of morality; “it could be this but it could also be that, who knows what is right or wrong”.

  15. You’ve mistaken me for someone interested in further enabling your fantasy, Dredd. As I said, enjoy your delusions. I sure do. I think they’re hilarious.

  16. Up-thread, I supplied a definition of an intelligent computer terminal from a dictionary that struggled to shed some light on the subject.

    An “intelligent computer terminal” … “knows” how to do many things, including scientific endeavors. Science methodology.

    Those software / hardware thing-a-ma-jigs (computers) can also be “taught”, etc., to do religion if you want to teach them to.

    Robo-pastor. I can assure you that “Turing machines” can be set up such that most folks would not know whether they were talking to a “flesh and blood” entity or a computer.

    I worked on a software project for Motorola once upon a time.

    They hired me as the exclusive developer for software to be the brain of a computer that would monitor, instruct, program (or whatever your old dictionaries would call it) two prime computers. It was a trinity of hardware and software fused into one 24/7 entity.

    One of those two prime computers communicated directly with satellites, the other prime was a backup to prime one, but was kept live and a mirror of the first, so it could take over without a hiccup should the need arise for any reason.

    The computer I programmed monitored both of the other two, but I had no knowledge of the internals of the other two, except via the manual that specified the “language” for communication with the other two.

    Of course the language was the same for both, however, the interaction with the live prime-1 varied in subject matter compared with the backup prime-2.

    These three computers were all placed in “a sandwich” of electronics that was put inside a hardened box, then distributed in various locations around the city’s surrounding freeway system (there were about 20 of the boxes).

    The communications system on-board, for that day and age, was quite up to date. There were 8 very fast asynchronous serial ports and one network port (802.2) for each prime, and one dial-up telephone communication port for the monitor.

    The async ports attached to “probes” into the prime’s internals, so as to monitor their internals.

    The network port shared communication among the computers.

    The dial-up was modem based, so that office communication (human to machine) could be facilitated over telephone lines.

    I could use a modem, as could those using the system afterwards, to contact the non-prime, the monitor, to find out what was going on with the prime computers, program them, upload new software to them, etc.

    Of course the operating system of the computer I programmed to monitor and control the primes was a multi-threaded multitasking operating system of good sophistication.

    There was no word in any dictionary at the time that would define much of any of that operation in any way that would give a real clue of what was going on to others.

    I had to do it all, for security and other reasons, in other words, I was the only software engineer who was the architect and developer (engineer) for the monitoring computer software system (I did not work on the prime computer OS or applications).

    A “smart terminal” or “intelligent terminal” is one way of explaining what the monitor was doing. It was certainly doing what no single individual human could even hope to do.

    Intelligence, knowledge, science, and religion have always been very elastic words that stretch to embrace new things that arise.

    Microbes are orders of magnitude more able than such computer / software configurations, and when they network together, which they certainly do, the capacity grows by orders of magnitude beyond those computer systems.

    In general, the weakness in any computer system is the intelligent, sentient, humans who program them, not the software or hardware (although there are exceptions to that generalization.)

  17. Bron,

    If you don’t recognize that Objectivism is an exercise in outcome determinism and poor rationalization by now, I’m not sure how I can help. Rand took a valid (and scientific) principle, combined it with totally erroneous biology, psychology and sociology and used the whole lot to justify/rationalize her own greed and selfishness (which have nothing to do with valid measurable scientific biology, psychology and sociology – one data point is not a trend). Her own greed and selfishness that are a direct result of 1) her proclivity (she was demonstrably a a diagnosable socipath by both DSM and WHO criteria) and 2) her deprived environment – both materially and ethically – growing up (which excerbated her proclivity). Science points to the fact that evolution is driven by competition and cooperation and that both are (probably equally) important mechanisms in determining the survival of a gene line. Her theories are pure competition. All black and white and no gray. The reality is gray. She was operating from flawed and incomplete premises to reach a conclusion she wanted because she determined that selfishness and greed were good to start with simply because she was already greedy and selfish. A=A works if you properly understand A to begin with. This is why Marcus Aureilius was so forceful in admonishing that importance of asking “of each and every thing what is it in itself.” Rand didn’t do this. Her assertions about human nature are wrong because they are based on her as the sole sample space and she was a broken person psychologically and ethically speaking. Her psuedo-philosophy for that very reason appeals to other broken people or those prone to binary thinking to begin with (which as we are discovering is a physiological difference). Rand was really operating off of A=x but I’m going to say x means what I want it to in order to feel good about myself instead of what the evidence indicates.

  18. I am not sure how you can misuse the law of identity. I need help with that statement.

Comments are closed.