Thursday, May 15, 2014

Evolution Professor: Orphans Not a Problem for Evolution

Fact Checking the Evolutionists

In my previous post I discussed Joel Velasco’s claim, in his recent debate with Paul Nelson, that biological designs fall into a nested hierarchy. Velasco is by no means alone in making this bizarre claim. It is not controversial that it is not true, yet evolutionists routinely insist that, as Richard Dawkins once put it, genes across a range of species fall into a “perfect hierarchy, a perfect family tree.” If, like many, your first question is “what are they thinking?” then go to the [1:33:21] mark in the Nelson-Velasco debate where for the final few minutes of his response segment, Velasco sheds light on the closing of the evolutionary mind.

Nelson had brought up the problem of ORFans—genes that are unique to a particular species. They contradict common ancestry’s nested hierarchy model and when they were first discovered evolutionists figured they would go away as more genomes were decoded. But that didn’t happen. We now have an explosion of genomic data and, yes, more and more ORFans have been discovered.

Velasco addressed this problem with several arguments. First, Velasco reassured the audience that there isn’t much to be concerned with here because “Every other puzzle we’ve ever encountered in the last 150 years has made us even more certain of a fact that we already knew, that we’re all related.” In other words, evolution has a track record we can rely on.

Unfortunately that too is not true. In fact practically every major prediction of evolution has failed. For example, one of those puzzles was the finding of long stretches of identical, unconstrained DNA in otherwise distant species. Such a finding, an evolutionist had told me years earlier, would falsify evolution, period. His point was that evolution was falsifiable. That was yet another false claim. The finding of identical, unconstrained DNA did not so much as put a dent in the evolutionist’s certainty (and yes, he is still believes in evolution).

When their expectations turn out to be false, evolutionists respond by adding more epicycles to their theory that the species arose spontaneously from chance events. But that doesn’t mean the science has confirmed evolution as Velasco suggests. True, evolutionists have remained steadfast in their certainty, but that says more about evolutionists than about the empirical science.

In fact Velasco’s appeal here to “all that other evidence” (my paraphrase) is typical. Yes, you can raise minor issues around the edges that have not yet been resolved, but we’ve got this mountain of rock solid, compelling, overwhelming evidence proving evolution beyond any reasonable doubt.

This is yet another form of theory protectionism. It shifts attention away from a theoretical failure, appealing to a mythical, non existent, list of proof texts. Aside from the problem that no such set of compelling evidence exists, it is irrelevant. The question in hand is how evidence X (in this case unique genes) bears on the theory, regardless of the other evidence.

Velasco’s next argument was to suggest that this ORFan problem was really nothing more than a semantic misunderstanding—a confusion of terms. Because these are unique genes, ORFans also go by the name of “orphans.” It is, according to Velasco, nothing more than a clever homophone that creationists have surreptitiously exploited to confuse people. As Velasco explained: “first of all, it’s important to understand, Paul says, ‘Oh these are genes without any ancestors.’ Well, no. It’s like, ‘Oh the name implies it.’ Well, this is one of these cases of scientists, sort of, thinking it sounds cool and, sort of, just playing into the hands of creationists.”

Sorry but this has nothing to do with creationists. And no, there is no such confusion of terms. The play on words is not misleading. Do these genes have ancestors? Velasco’s response (“Well, no”) is a misrepresentation of the empirical science. Of course we don’t find ancestors. That’s why evolutionists were surprised, and that’s why they figured the problem would go away as more genomes were decoded. But that too was false and we cannot now just assert “Well, no.”

But Velasco continued with his denial of the empirical evidence: “So the things that we label ORFAN genes, don’t necessarily actually have no relatives. They’re actually just open reading frames that, right now, you can’t get significant homology.” (Note that Velasco here means “identity” not “homology.” Homology either is or is not. Like pregnancy, you can’t be a little bit homologous.) Velasco’s argument here is guilty of what he just finished criticizing the creationists of—confusing the terms. He says there is no problem here because, after all, these data are really just open reading frames for which, right now, there is no “significant homology.”

Huh? That’s the point. Velasco can spin the terms, but that doesn’t change the evidence. That these are open reading frames without similarities is what evolutionists did not expect. It doesn’t fit the theory.

Velasco’s next argument was to give a misleading example of ORFans arising from distantly related species: “First of all, lots of it is just the lack of information. Right. So you sequence this bacteria species which is very distantly related from other bacteria, and it has this gene that you don’t recognize any of its relatives. Why? Well it might have shared a common ancestor a billion years ago, with anything else you’ve discovered. So, it could have changed a lot in that time.”

This is not at all representative of the ORFan data. In fact, we find ORFans not only between neighboring species, but between different variants of the same species. By raising this example of “very distantly related” species, Velasco trivializes the ORFan problem and misrepresents the science.

Velasco next continued along this line, arguing that the ORFan problem is nothing more than a gap in our knowledge. For the more we know about a species, the more the ORFan problem goes away. And which species do we know the most about? Ourselves of course. And we have no ORFans: “Well what about humans, we know a lot about humans. How many orphan genes are in humans? What do you think? Zero.”

Again this is a misrepresentation of the science. First, our overall knowledge of a species is irrelevant. ORFans come from genomic data, period. One could know nothing at all about a species except its genome and nonetheless be perfectly accurate in knowing its ORFans.

Second, dozens of unique genes have been found in the human genome. And that could be just the tip of the iceberg for, as Nelson adroitly pointed out, early work on the human genome downplayed long stretches of unique human DNA because it didn’t fit the theory of evolution.

Next Velasco argued that while new ORFans are discovered with each new genome that is decoded, the trend is slowing and is suggestive that in the long run relatives for these ORFans will be found: “In fact if you trend the absolute number going up, as opposed to the percentage of orphan genes in organisms, that number is going down.”

But so what? This is what one would expect if unique genes were common. Velasco seems to concede some uncertainty here, but in typical fashion concludes triumphantly: “I can make some bets though. I think in 50 years this will not be seen as a problem, in fact it’s not seen as a problem now.”

So there you have it. One failed defense after another resulting in complete and utter victory. Not only are ORFans not at all likely to be a problem 50 years from now, in fact they are not even a problem now. As usual, evolutionists lose every battle but always win the war. I guess the species really do fall into a nested hierarchy after all.

32 comments:

  1. For unguided evolution eukaryotes are a problem.

    Just sayin'...

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    1. This article makes claims with no citations... Cant be trusted.

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    2. This article makes claims with no citations... Cant be trusted.

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  2. In the following video, Jeffrey Tomkins PhD. states that 7% of human genes are unique:

    The Myth of 98% Genetic Similarity between Humans and Chimps - Jeffrey Tomkins PhD. - video
    https://vimeo.com/95287522

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    1. Would this be the same Jeffrey Tomkins who is associated with the Institute of Creation Research?

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  3. When a subset of the theory-relevant data (genes, sequences, etc) is consistent with a hypothesis while other theory-relevant data (other genes, sequences, etc) is inconsistent with it, neither set of data can be said to be evidence for the hypothesis. A hypothesis has no plausibility if it is neither self-evident nor supported by inductive evidence.

    The only sense in which you can say the hypothesis of naturalistic UCA (regardless of what the actual tree history is) is plausible is in the sense that you can say it is one of only 2 hypotheses that are not virtually completely arbitrary. But that sense is worthless insomuch as it gives us no clue which, if either, of the 2 are true.

    On the other hand, there is non-empirical (not empirical, i.e., in the sense that empirical, natural science would consider it) , historical inductive evidence for one of those hypotheses while there is zero inductive evidence for the other.

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  4. The overwhelming amount of evidence that collaborates biological Darwinism doesn't magically disappear in the face of specific lines of evidence that are inconclusive. They simply tell us nothing one way or the other.

    To suggest otherwise is to suggest that we know nothing without an exhaustive explanation. However, if theories start out as conjecture and grow more accurate via criticism, this would be a unreasonable expectation.

    All theories are incomplete and contain errors to some degree. But, by all means, please provide a theory that doesn't fit that description.

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    1. Example: take gravitational theory and quantum mechanics - of which the latter is is the most successful predictive theory to date.

      We know that at least one contains errors to some degree and both are incomplete because we lack a working theory of quantum gravity.

      Can we rule out that some designer decides to pull on objects according to their mass, but chooses otherwise at the small scale? No, we cannot.

      So, where is the objection by intelligent design proponents? Why isn't this a misrepresentation of science?

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    2. Scott, there isn't any evidence that collaborates Darwinian biology- oops there is disease and deformities, but that is it

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    3. Absolutely no evidence? You do realize, that is completely untenable, right?

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    4. Scott: We know that at least one contains errors to some degree and both are incomplete because we lack a working theory of quantum gravity.

      J: If the LNC is valid for determining certain impossibilities (and you say you've adopted it), one of the sets of equations can't be "TRUE" at the level of generalization we seek inductively. In the meanwhile, both sets of equations have UTILITY! What you and yours can't get through your head, seemingly, is that "having utility" and being "overwhelmingly evident" are EASILY distinguishable by sane people.

      As I've said over and over, the debate here is about what there is inductive EVIDENCE for, not what has utility or not. Although the hypothesis of UCA doesn't seem to have any more utility than SA, in the first place. A theist-SA'ist of the kind that explains the reality of moral obligation, warranted belief, etc by benevolent ID can agree with that adaptive descent is bifurcated and still think the earth is too young, etc for UCA to have occurred naturally with any plausible probability. IOW, such an SA'ist already posits a benevolent, competent designer for other explanations and then merely posits that said designer designed the SEPARATE ancestors of some SA scenario that doesn't require as many SEEMINGLY serendipitous mutations, etc.

      As I've said and explained before, ID explanations are much easier to do than naturalistic ones.

      Indeed, one can't even explain the validity of our inference to "unobserved" event regularities of any kind apart from teleological explanation. This is why an a-teleological metaphysics can never amount to anything but a set of utterly bald pontifications. Personal credulity is the only "criteria" in such a methodology since nothing seemingly HUMAN about belief formation is assumed to have validity per se.

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  5. CH: That these are open reading frames without similarities is what evolutionists did not expect. It doesn’t fit the theory.

    The problem with this sort of argument is that expectations are not always falsifications. We can expect details about a theory to be one way, but find that the details are different while not being incompatible with the underlying explanation.

    For example, If I had hypothetically never seen or expected to see an El Camino, this wouldn't falsify a theory that posited a self-powered, four wheel vehicle.

    Of course, if you think there is or can be no underlying explanation, then you're left with mere predictions. The same could be said if you're an instrumentalist in respect to biological evolution.

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  6. Epicycles...
    Like Ptolemaic Astronomy.
    A theory that doesn't match reality, yet the "experts" declare it to be so.
    "We can tweak it, so it's true."

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  7. Cornelius Hunter: In my previous post I discussed Joel Velasco’s claim, in his recent debate with Paul Nelson, that biological designs fall into a nested hierarchy. Velasco is by no means alone in making this bizarre claim.

    Orphan genes don't undermine the overall nested hierarchy.

    Orphans can apparently arise de novo out of noncoding DNA, which harbors many sequences in a transition stage known as protogenes. These protogenes are then tested for functions, but over generational time scales. There's also some evidence that the generation of orphan genes is due to lineage specific adaptation.

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    1. Do the protogenes have any function now? If not, how can they be tested? Is some sort of teleology involved?

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    2. natschuster: Do the protogenes have any function now? If not, how can they be tested?

      Protogenes don't form genes. That's why they're called protogenes. They may be fragments of old genes or mis-copies of existing genes. They can then be shuffled and tested by evolution.

      natschuster: Is some sort of teleology involved?

      The process is posited to be natural mechanisms. It's something like the immune system which mixes and matches different components randomly, but the components are those that have worked in the past.

      Carvunis et al., Proto-genes and de novo gene birth, Nature 2012.

      A common misperception is to think of the genome as a static entity. Rather, it is constantly in flux with elements being combined and copied.

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    3. So there is totally a random process, that somehow just hits upon a lucky combination. Then does he organism turn them on? How does the organism know how and when to turn them on?

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    4. natschuster: So there is totally a random process, that somehow just hits upon a lucky combination.

      It's not "totally random" because it starts with parts known to work in other situations, just like the immune system works by combining parts known to have worked before.

      natschuster: Then does he organism turn them on? How does the organism know how and when to turn them on?

      There's some evidence that the generation of orphan genes is due to lineage specific adaptation, or in recently split lineages.

      See Wissler et al., Mechanisms and Dynamics of Orphan Gene Emergence in Insect Genomes, Genome Biology and Evolution 2013.

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    5. There isn't any evidence that unguided evolution can produce anything, let alone a gene.

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    6. Were the orphan genes always turned on? If they weren't when did it happen?

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    7. natschuster: Were the orphan genes always turned on? If they weren't when did it happen?

      As we said, genomes are not static, but dynamic. There's a lot of shuffling that occurs. De novo generation seems to be more common in recent splits, especially in taxa that involve rapid speciation.

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    8. But genes are sometimes turned off. Non-coding DNA is turned off. I'm asking if the pre-cursers to the ORPHAN gene were on or off. If they were turned off, then how were they turned on when they became ORPHANS.

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    9. natschuster: I'm asking if the pre-cursers to the ORPHAN gene were on or off.

      Some orphans are the result of duplication, insertion, rearrangement, and point
      mutation. However, genes may also evolve de novo from non-genic DNA. Much of the genome is already transcribed, and non-genic regions may become translated by the acquisition of an open reading frame through mutations.

      Most of these translates are non-functional or sometimes toxic. If toxic, they would be purged by natural selection. But occasionally they may have a beneficial effect. At that point, they are subject to selection, and may become longer and more complex.

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    10. So they get turned on by accident?

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    11. natschuster: So they get turned on by accident?

      Mutations are random with respect to fitness, however, the non-genic regions are not random.

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  8. This reads like another instance of the inflatable strawman. Pick an interesting problem in the field and inflate it - blow it up out of all proportion - into yet another fatal blow to the heart of evolution. Just like irreduceable complexity, except that the theory seems to have survived that challenge as well.

    Orphan or ORFan genes, in simple terms, are sequences which have no known - sress known - homologues in other species. Given that, as yet, we are far from having a complete 'readout' of the genomes of all other extant species, that should not be surprising. Nor should the fact that homologues have eventually been found for what were previously thought to be orphans. And, as Zachriel points out, it is quite possible to conjecture how orphans might have emerged de novo in non-coding regions of DNA.

    Of course, if you like analogies - and we know that Paleyists have a great fondness for them - then perhaps orphans are aptly named. Perhaps, they should be envisaged as the the Oliver Twists of the genomic world. First discovered, lost, friendless and alone, they are gradually found, through the twists and turns of a Dickensian plot, to have family connections and an ancestry and, once reunited, all live happily ever after.

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    1. Ian:

      This reads like another instance of the inflatable strawman. Pick an interesting problem in the field and inflate it - blow it up out of all proportion - into yet another fatal blow to the heart of evolution.

      Well ironically you just created a strawman. Unfortunately it is typical. When evolution's predictions fail, then just contrive overstated criticism, blowing it up "out of all proportion," so you can knock it down.

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    2. So you're not claiming that ORFans are a fatal blow to the theory of evolution?

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    3. Correct Ian. Just as retrograde motion is not a fatal blow to geocentrism and ships disappearing over the horizon are not a fatal blow to the flat earth theory.

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    4. What theory of evolution? Darwin had one but he didn't know of genes.

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  9. Cornelius Hunter Correct Ian. Just as retrograde motion is not a fatal blow to geocentrism and ships disappearing over the horizon are not a fatal blow to the flat earth theory.

    Ah, so now the theory of evolution is like the flat Earth theory and orphan genes are like the ships that disappear below the horizon?

    Okay, the way ships disappeared below the horizon could not be explained in terms of a flat Earth but it could if you assumed a round Earth. In other words, the observation led almost inevitably towards the better explanation. So if orphan genes are like the ships disappearing below the horizon, what better explanation are they leading us towards? Or is this just another shaky analogy?

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  10. This gives the appearance to me of that age-old approach that says, "You are not afforded the same privileges as me."

    In the 1970s we were led to believe that the overwhelming majority of the genomic content was in fact "junk". This was jumped upon by the naturalistic crowd as evidence against a designer.

    Yet there were those small voices who made the prediction that in fact what was seen as junk was merely attributed that due to the fact that we did not understand non-gene (classical gene) coding function. Such an approach where the pro-designer would say "it gives this appearance but that is only because we do not yet know the function of it" was mocked and looked down upon.

    Yet this is the same approach that naturalism turns to. ORFan/orphan genes are not well understood within the evolutionary theory therefore it is attributed to the case of "unknown" mechanism of evolution however there is "confidence" that in 50 years time it will be known.

    Fair enough, there is unknown aspects and indeed we cannot know every mechanism in nature for sure (despite what we as scientists pretend). However the same argument must be afforded to other observations. I.e. just because something looks like junk DNA does not mean that it is. Just because something looks like common descent does not mean it is.

    E.g. mutational hotspot regions, pseudogene undiscovered function (more and more pseudogenes are turning out to be regulatory elements of DNA, or tissue/environment-specific expression, etc.). Yet whenever someone posits such an explanation for these observations that deviates from the most evolutionary-supportive argument, there is laughing, ridicule and mocking. As the evidence above points out - unjustifiably so.

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