Friday, May 10, 2013

Andyjones Replies

Andyjones has responded to my post on failing to educate him about science. His response is: Failure to Educate? Failure to Persuade. I'm reposting his entire response ....
Larry Moran replied to my latest post with an admission of failure. He thinks he has failed to educate, but I think rather he is confusing the word ‘persuade’ with the word ‘educate’.

He thinks I am rationalising junk DNA with a pile of ‘what-ifs’. But the fact is that most of my ‘what-ifs’ are already known to have some basis in reality. I am not denying any obvious reality. Indeed, the basic machinery of life looks like design, far more than when Paley was around. Yes, there could also be a great deal of junk. That’s why I have said a number of times that ID is not committed to the idea that there is no junk.

Yet, from my point of view, I see a whole pile of Darwinian/post-Darwinian materialists who have only partly explored the genome, working from an assumption that the genome was not designed, and thus are jumping the gun on the evidence. For example, Larry still seems to think that pseudogenes are of themselves ‘solid evidence’ of broken genes despite the fact that we know that at least some pseudogenes influence the rate of translation of real genes by competing with them; a simple design reason why there should be ‘false genes’ = pseudogenes. Who has explored the rest of them?

From his emotive response to my perfectly valid, albeit speculative suggestions (though they were not plucked out of the air either), I don’t trust this guy to think clearly and calmly about the possibility of design. That’s the real problem.
This is all very frustrating. Why do IDiots who have no serious training in biochemistry and molecular biology think they know more than the experts?

And why do they refuse to learn when we attempt to educate them?


  1. We all know Andyjones' problem. He is an IT professional who thinks he is a scientist because he has a spool of ethernet cable. Certain IT professionals think they're smarter than the world's scientists because they controls their department's administrator password. We call those people Intelligent Design proponents. A dog could be an IT professional if it knew administrator password.

    Much of the Intelligent Design cult can be explained as the narcissistic egomania induced by the power-trip people get when they learn to write code. Writing code is not really difficult-- no actual thought is involved. 13-year-olds on dope can write code.

    Perhaps ancient Babylonia was like this, shortly after the invention of writing, with raging egomaniac assholes who think they're geniuses because they could put one hieroglyphic after another.

    1. " A dog could be an IT professional"
      Whod've thought, Diogenes is a cynic....

    2. I'm sorry if I seem hard on IT professionals.

      However, the IDiots bring it on themselves, because they constantly, constantly invoke their incredible genius (they can write code-- and not just in Basic!) as proof they're right about intelligent design.

      They don't need to know no stinkin' biology-- they've heard about this here DNA, and they know it's the same thing as the computer code that they're the *only* experts at writing. Because they can write code, that means they know that life is too complex to be the result of blind chance. (In fact most physicists and molecular biologists can write code, and I imagine geneticists and others-- but they don't invoke that as an argument from authority-- only IDers brag about 'I can write code, so I understand how complex functional things are').

    3. When I did my doctorate one had to demonstrate competence in two foreign languages. Mine were German and Fortan. :)

    4. Dio writes,
      "I'm sorry if I seem hard on IT professionals."

      Darn it, I was getting ready to accuse you of 'scurrilous lies'.

    5. Not only is FORTRAN not a human language, it's not even a programming language. It's BASIC with a while loop.

    6. No while loops in FORTRAN, at least the last version I worked with, FORTRAN 66.

      It does have the 3 way arithmetic IF statement and the computed GOTO statement, for those occasions when normal GOTOs and IF statements just won't suffice in making your code suitably cryptic.

    7. Christ you must've written code on stone tablets with a chisel.

    8. Clay tablets with a reed.

      The short drying time help focus one's thoughts.

  2. UGGGGH.

    Andyjones sez: For example, Larry still seems to think that pseudogenes are of themselves ‘solid evidence’ of broken genes despite the fact that we know that at least some pseudogenes influence the rate of translation of real genes by competing with them; a simple design reason why there should be ‘false genes’ = pseudogenes.

    Andy, Andy. Larry was very, very clear about the low abundance of many transcripts, right? Was that not clear? How could that not be clear?

    Let's go over it again, genius. You think pseudogenes have function because in an entire living cell, perhaps they've got ONE RNA transcipt, one-- and you think that ONE RNA transcript interferes with or regulates the translation of the real gene from which the pseudogene was duplicated.

    Riiiight. Except the the real gene from which the pseudogene was duplicated might have enormously more abundant RNA transcripts-- say 100,000 x as abundant. How could one pseudogene transcript "regulate" 100,000 real gene transcripts? Is one RNA transcript per cell of a pseudogene a mechanism of regulation important enough to make 3 billion nucleotides functional, or make man superior to monkey or give humans a soul?

    The last question is quite serious: if you think all those pseudogenes contribute to the fitness/adaptation/complexity/superiority of the host [that's you], thus making you superior to, say, the marbled lungfish [which has 40 x more DNA than humans] or an amoeba [which has 100 x more DNA than humans], than wouldn't your same mechanism make the marbled lungfish and the amoeba hyper-ultra-complex?

    By your IDiot hypothesis, the marbled lungfish and the amoeba should be so complex they should have time machines and a colony on Arcturus by now.

    1. And again we ask: why are there differences in the sizes of genomes of different onion species LARGER than the entire human genome?

      And once more: If the average human baby has ~130 more mutations than its parents and ~260 more than its grandparents etc., and if all mutations are "CATASTROPHIC" as ID proponents always insisted they are, and if all DNA is functional like Intelligent Design requires, then why don't all babies die?

    2. then why don't all babies die?

      Well there's a simple answer to that, we've only been around for 6,000 years or so and some of those generations were 900 years long.

    3. then why don't all babies die?


    4. Dammit, we will be rumbled!

      M. Lungfish

    5. But wait: if there are mutations that don't affect the organism, and if in fact most mutations don't affect the organism, isn't that an argument for junk DNA? If almost all DNA is functional, most mutations should have effects.

    6. The purpose of junk DNA, then, is to provide a vast number of targets in which mutations can occur without causing any effect, thereby sparing the functional DNA from the harmful effects of mutations. And the Designer, in his infinite wisdom, did that deliberately.

      Checkmate, atheists!

    7. Mutations come in all shapes and forms, and indeed junk DNA (jDNA) protects against some types of mutations, such insertion mutagenesis, which in humans can lead to insertional oncogenic transformation (

      For whatever reason, however, this is a difficult hypothesis to understand. But there are other well documented theories, such as the ‘nucleo-skeletal hypothesis’ proposed by Thomas Cavalier-Smith, and the ‘nucleotypic hypothesis’ proposed by Michael Bennett and developed by Ryan Gregory, which propose that *all* jDNA has a biological role.

      For mysterious reasons, the bloggers here at Sandwalk, including Ryan Gregory, pretend that these theories, which have been discussed in dozens of articles and books, do not exist. Even more enigmatic is the fact that the people referred as ID-ots, who preach a biological role for jDNA, do not bring these theories into discussion. Aren’t they aware of these theories?

    8. @Claudiu,

      I'm guessing you did not read the bladderwort genome paper, then. (see below). There appears to be a plant that gets along fine in the absence of all of this protection (despite the presence of a few hundred TEs, where some appear active).

  3. "Why do IDiots who have no serious training in biochemistry and molecular biology think they know more than the experts?"

    Be grateful that you don't live in the United States. Everyone here knows that those-there professors have only "book learnin'" and none of that COMMON SENSE!

    Seriously. I've had students complain that I counted (x + y)^2 = x^2 +y^2 as wrong.(*)

    (*) we weren't working in fields of characteristic 2.


  4. You see, you think you are trying to educate him about science. He thinks you are trying to persuade him to lose his religion.

    I just don't get how a computer programmer like him can cling so tightly to the intelligent design hypothesis. Sexual reproduction is entirely in opposition to the idea that life is designed. As a professional programmer myself, I would be utterly horrified to have my product randomize itself so regularly. If life was designed, we would reproduce asexually so that the offspring could be guaranteed to have the same ideal characteristics of the parent.

    1. Good points.

      Of course, to IDiots, there is no such thing as true randomness. To them, sexual recombination isn't really random. That's because they don't just believe in "intelligent design", they believe in a supernatural destiny. They believe they're the direct and intended products of an incomprehensible mind that can engineer the future at it's will.

      One wonders how they square their "divine foresight" with quantum physics. Simply put, they can't. Supernaturalists have to reject quantum physics at bottom.

  5. Despite his mention of extrapolating from evidence, it seems Andy missed the point about it still constituting ad-hoc rationalizations and post-facto reasoning that isn't in proportion.

    Yes, some very few "pseudogenes" have been found to be functional. But the ratio are in three to four orders of magnitude. Thinking that therefore the rest, or the majority of the rest, therefore also are, is an irrational extrapolation. The reasoning is entirely ad-hoc.

    Yes, there could be actual functional regulation done on the basis of "weakly binding" regulatory elements. Again, the number has to be extremely low compared to the amount of "normal" regulation. Again, the extrapolation is not in proportion, there is no justification for seriously considering that there'd be SO MUCH "spurious regulation" (for lack of a better term).

    Yes, there could still have been some functional DNA in mice megabase deletions, but it would still be an irrational (as in our of proportion) extrapolation to think the entirety or even the majority of the deleted sections were functional regions.

    Andy simply doesn't get how WEAK the "evidence" for functional junk is. He takes the tiny bits we have of functions having been discovered in "junk" regions and then seemingly extrapolates this over (at least) the majority of the rest. He thinks this constitutes extrapolating from "the evidence", but the proportion is untenable on the evidence.

    I think the only interesting thing to note here is that Andy apparently is okay with *some* junk, as long as (he ad-hocs) "the designer" could have thought of some obscure use for the rest.

    1. I though it had been rather positively in Kitzmiller vs Dover demonstrated that ID is nothing more than creationism repackaged. So why does anyone waste time trying to convince religious zealots of anything outside those zealots' tiny little vision of God? And just how does their outright lying to accomplish their goals jive with their religious faith? Isn't bearing false witness one of the Ten Commandments?

      I know lots of people of faith who believe in evolution, so what is it with these people?

    2. Look at the Discovery Institute website, that will tell you what you need to know. They are religious and are politically conservative. A generally toxic combination that has so perverted the concept of Jesus that you might as well imagine Yosemite Sam up on the cross.

    3. sez srm: "…you might as well imagine Yosemite Sam up on the cross."
      Naah, iIt's Bugs Bunny on the cross. Yosemite Sam is playing the role of "Gethsemane Sam—the rootin'est, tootin'est, shootin'est Legionnaire this side o' the Eu-phra-tes River!"

  6. You know, I'm politically conservative and still believe in evolution, and although I consider myself agnostic (while strongly suspecting the atheists are right) almost all of my friends are both Christians and conservative, and yet every one of them believes in evolution as well.

    Slapping labels on people is seldom useful. Yes, the ID proponents are hard to fathom, but calling them names isn't helpful.

    1. I disagree. Insulting and ridiculing them at every opportunity (while still rigorously debunking their claims) is a necessary countermeasure to one of their chief tactics, which is to give the uninformed the impression that there is genuine scientific controversy over the status of the truth of evolutionary theory, and that creationists are serious and competent scientists touting a controversial but reasonable alternative. True, insulting them does leave them the option of claiming that they are victtims of a conspiracy against their views. However, that is a much weaker position from which to argue.

      Respect is not a given. It must be earned. IDiots and other creationists have not earned it.

    2. If we treat them as colleagues, and pretend as if their arguments are within the bounds of ordinary, real scientific controversies, they'll use that to claim they're real scientists and there really is a scientific controversy.

      We have to make it clear that their arguments are below the lower limit of what's acceptable in scientific arguments-- below in terms of factual accuracy (they constantly make things up), and use of induction and the scientific method.

      In real scientific controversies, it is not acceptable to make things up, and when caught, to make up some more things.

      So if we don't call them 'IDiots'-- OK, then how do we convey the fact that their claims are based on 'facts' they made up wholecloth?

      If you have a better way than that to get across to John Q. Public that their arguments are below the lower limit of what's standard in real scientific controversies, I'd like to know what way you would suggest.



    1. Thanks twt!

      The original paper is open access (Nature (2013) doi:10.1038/nature12132)