Front Loading Doesn’t Help ID

Forgive the lack of posting, I’ve been having a rough time of late.  However, I am once more inspired, so here we go.

A few friends and myself are both discussing things with a creationist and helping another person with their own creationist issues.  Once again, it is obvious to anyone who even compares the sides to this discussion that ID is totally vacuous.  The creationists are totally unknowledgeable about science; the process, the data, the analysis, and the facts.  It is most depressing that someone who can’t even construct valid sentences thinks that they can successfully argue against people with Ph.D.s in the field (and me).

Today, a discussion of ‘front-loading’ came up and I’d like to add some material so, if you are caught out by a creationist, then you have a response that they cannot deal with on the issue of front-loading.

What is front-loading.  Well, it’s not formally defined anywhere that I care to look (i.e. biology texts, peer-reviewed literature, etc.) and the creationists I have asked are nearly as bad at answering questions as Rick Perry.

But here’s what I understand.  Front-loading is the method by which all the possible future phenotypes have been inserted into the genome and only await ‘activation’.  This was done by the designer since (according to creationists), evolution can’t do it.

Most creationists rarely use this argument.  It really is a poor argument and most creationists will avoid it like the plague because it is so poor.  Except in one case, then it is very common.

That case is in regards to evolutionary or genetic algorithms.  The claim is that the programmer inserted the answer into the code.  This is plainly ridiculous since the main purpose of industrial use of genetic algorithms is to do things that humans can’t.

Look closely at the examples and notice that, in every case (and every case that I am aware of) genetic algorithms outperform human results.  In at least one case, humans still don’t even understand how the evolved system works.  If no one can figure out how it works, then it’s not likely to be front-loaded is it?

But why couldn’t alleles be front-loaded into a genome and then be ‘turned on’ in the future.  Well, there are a couple of reasons and the first is a real doozy.

Jonathan Wells has written a new book about ‘junk DNA’.  The creationist belief is that science was once wrong about what ‘junk DNA‘ is, then science is wrong about everything else.  Of course, it was scientists that discovered functions for some non-coding DNA, not creationists.  Further, the earliest mention I can find of any creationist argument for a function for some non-coding DNA was 1994 or 1995 and that was Michael Behe.  Of course, Stephen J. Gould said the same thing in 1977 (or thereabouts).

Anyway, the problem is that creationists who want to argue for front-loading have to talk about how that squares with all that non-coding DNA.  Consider HLA-A.  The human population has some 673 alleles for HLA-A.  Now, you, as a person, can only have two alleles.  One from your mom and one from your dad.  Yet, creationists would have us believe that those other 671 alleles are present in your genome… must be present in your genome because of front-loading.

No mutation can create new alleles that are functional, according to creationists (well some of them).  So, all 673 alleles must have been front-loaded into the human genome at the time of ‘creation’.  It gets even worse when you consider that all the genes with more than 10 alleles (Noah, his wife, and the three daughters in law… assuming that they were all heterozygous… which for technical reasons is unlikely) must also have been front-loaded into the genome.

But what’s worse for the creationist is that, back to the ‘mutations cannot add information or produce functional proteins’, the method for ‘activating’ these front-loaded alleles must have been… gasp… mutation.  Whoops.

Think about that a second.  According to creationists, you personally have all 673 alleles for HLA-A in your genome.  Only two are activated, because that’s all you can have (where the other 671 alleles are is open to whimsical speculation).  There are ways to tell genes to deactivate one allele and activate another allele.  But this is all (with the exception of epigenetics) done by changing the genome.

How do you get cancer?  Because the genetic instructions for a cell changed.  Instead of doing whatever its supposed to do, the cell has changed to just making copies of itself.  Heck, cancer is a fantastic argument against front-loading in and of itself.  According to creationists, you have every form of cancer that ever has been and ever will be, in your genome, right now.

Which leads us to a very interesting possibility.  We should look for them.  Creationists will say that ‘cancers are mistakes’, but in reality cancers are extremely well evolved for their environment.  Unfortunately, they still tend to kill the host.  But, we don’t have to do that.  We could, instead, look for all 673 HLA-A alleles.  If we don’t find them, then that’s a shot against front-loading.

Oh wait, someone did that.  Did they find 673 alleles in the genome?

Nope.

Nail in the coffin of front-loading.

But wait, the creationist says.  I’m OK with ‘microevolution’.  It’s only macroevolution that is front-loaded.

Which makes absolutely no sense.  This is the classic example of the creationist shoveling shit in the hopes to hide his statements without thinking about what he is saying.

The creationist, using this argument, is actually arguing that macroevolution DOES happen.  It’s just controlled by genes that are already present in the organism.  But go ahead, ask the creationist is macroevolution happens and you will get a vehement “NO!”

In that case, what’s the point in having macroevolutionary changes front-loaded?  The creationist must either accept that macroevolution happens or accept that front-loading does not.

There is one final piece and it’s pretty technical and we don’t have the answers yet, but I suspect that we will soon enough.

Consider the dog (Canis familaris).  What the creationist is saying with the front-loading argument is that the ancestral dog had every gene and allele to make every single dog from the toy dachshund to the Bull Mastiff.

This should be readily easy to test too.  We just need DNA sequencing data from many dog breeds.  We also need to know what the ancestral species of all domestic dogs is.  And then we need the gene sequence from that species.

Then all we have to do is find all those alleles and genes from the dogs in the wolves.  If they are there, in their entirety and without any changes, then front-loading is supported.  If they are not there, in their entirety, then front-loading is refuted.

Curiously, no creationist scientists seem to be working on this (or anything else for that matter), while scientists from dozens of disciplines are actively involved in this area of research.

Anyone want to place a bet on which hypothesis will be supported and which refuted?

BTW: A common attack from creationists on this topic is to quote Dr. Elaine A. Ostrander.

One of the most interesting questions still to understand … is why did the wolf keep locked in its genome everything that was necessary to make a Pekingese to a Great Dane.

Of course, anyone with a lick of sense would realize that she is not saying that every single allele needed to make a toy poodle, and a beagle, and a Great Dane, and a mastiff, and a whippet, and a  (everything else) is actually present in the wolf.

Instead, the genetic diversity that evolution can act on is present.  For example, it would be exceedingly difficult to breed a great variety of breeds of cheetah, even in 15,000 years because the genetic diversity in the cheetah population is very, very low.  Dangerously low in fact.

Wolves, on the other hand, much like humans have a great genetic diversity.  Evolution has a great deal of raw material to work with.  That and selection pressures that are caused by the breeding of dogs by humans results in rapid divergence of the species we call dogs.

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13 Responses to Front Loading Doesn’t Help ID

  1. Eugen says:

    Ogre

    “Of course, it was scientists that discovered functions for some non-coding DNA, not creationists.”
    I would make rough guess that half of scientists working in DNA research are religious.

    Regardless of whether cell is designed or evolved, it appears to be an automated bio chemical nano system. Would you agree with that?

  2. OgreMkV says:

    I think I can agree with that.

  3. Eugen says:

    That’s fair Ogre.
    I’m not a biologist so I have nothing to lose. Here we go:

    What we need is a crazy idea. Does anyone have a crazy idea?
    Niels Bohr

    1.Cell probably needs the whole DNA otherwise it wouldn’t spend tremendous operational and energy resources to copy it during the cell division. What could be the purpose for non coding (“junk”) DNA?

    2. Scientists recently discovered the DNA fills volume inside a nucleus resembling the shape of Peano or Hilbert curve. This shape provides for well organized repetitive structure instead of chaotic tangle.

    3. DNA Skittle visualization tool ( free download) clearly shows repetitive patterns interchanging with seemingly random distribution of nucleotides in non-coding DNA. Also, interference and modulation type patterns are visible.

    4. One dimensional string could be periodically marked (repetitive patterns from (3)) for bending and formation of two dimensional matrix (like a QR code). Next it is possible to layer (stack) multiple two dimensional data matrices to fill volume which is suggested by the shape of Peano or Hilbert curve from (2).

    5. Combining previous three points it is possible to envision a form of three dimensional chemical data storage system as a purpose for non-coding DNA.

    6. 3D chemical data storage would have enormous capacity and inherent information redundancy. For ex. smaller important 3D section could be repeated in layers imprinted radially away from original. Also we could imagine some form of chem-holographic storage.

    Possible purpose for data storage system could be storage of: meta data, cell tissue position, cell type, number of divisions or some general control.

    http://www.wired.com/wiredscience/2009/10/fractal-genome/

  4. OgreMkV says:

    The only issue I have is with point 1.

    There is are two important points here. The first is that just because a DNA sequence is non-coding does not mean it is non-functional. There are at least 6 known functions of non-coding DNA (http://en.wikipedia.org/wiki/Non-coding_DNA).

    The second point is that, unlike data storage systems, DNA doesn’t have a Trim command. There is no way to delete things that don’t work anymore. So mistakes, junk, snippets of old viruses that didn’t work right, all that stuff is in our genome… and there it will remain.

    However, further mutation can occur to those DNA sequences that actually don’t do anything without harm to the organism. So, there is a ready source of material for modification.

    You make an interesting point. However it doesn’t point to a designer.

  5. Eugen says:

    Direct evidence it is not , a clue maybe. This is more of a geek talk.

    Yes 1. should be corrected. I read about functions being found for non coding dna. If you play with DNA Skittle it shows many weird patterns, some looking like amplitude modulation at different intervals. It looks like most of non coding DNA is involved in this pattern forming. It has to be important, it’s not just some messy jumble of nucleotides. There are some virus leftovers and what not – maybe like old Windows OS installation.

    http://dnaskittle.com/

  6. OgreMkV says:

    Here’s the problem though. There is an equally valid explanation for the phenomenon that is actually a better explanation than ID. That is that the system evolved.

    The human brain is wired to find patterns, even in things were no pattern exists.

    I don’t know and haven’t studied the subject, but I’d be willing to bet that not only does the system you describe appear to be higher level information storage (emphasis on the ‘appear’), but that it is also energetically less difficult to form.

    When you look at chemistry, you should really consider chemical reasons for the systems, shapes, etc first.

    Do you know that there is actually a very, very good reason for life on Earth to have l-amino acids and D-sugars? It has to do with the chemistry and energy involved.

    Basically, we have a theoretical explanation for how it works. A designer is a) an unnecessary complication* and b) has never been found to actually exist.

    * By this I mean, ‘who designed the designer’ for one. And if the first designer didn’t need a designer, then why do we? Among other questions.

  7. Eugen says:

    “When you look at chemistry, you should really consider chemical reasons for the systems, shapes, etc first.”
    Yes,I agree and yes humans can recognize patterns anywhere. This 3D chem-storage idea is maybe due to too much science fiction in my youth. I’m probably bigger geek than you after all. Nevertheless, little bug keeps bugging me.

    “.. l-amino acids and D-sugars?”
    I heard about it but I wasn’t aware of energy requirement.Links handy?

    “A designer is a) an unnecessary complication*…”
    I think Dawkins is promoting that idea. BTW why didn’t he debate Craig in UK when he had chance recently? That would be debate of the century. Did Dawking get “cold feet”?

  8. OgreMkV says:

    Eugen, seriously. Have you read work by Craig? The man is nuts. If you support him, then I think we’re done here.

    The reason Dawkins doesn’t debate is very simple. That would lend an air of legitimacy to someone who has done nothing to deserve it. Why won’t Craig debate anyone in a forum with written arguments? Is he chicken?

    No, he’s not chicken, he’s a good debater. Debating has very little to do with the quality of arguments. It’s more akin to selling used cars. On the other hand, in a written debate with no time or space limits, every single argument can be dissected at length and Craig (indeed no creationist) wants that to happen.

    The D- and L- thing: First, I have it slightly backwards, there is a slight energy difference. However, the main point is that chemically speaking you must have sugars of one handedness and amino-acids of the other handedness. Otherwise biochemistry won’t work. You might be interested in Quack ans Stohner 2003 (a or b) for more info. No links because I’m getting it from Luisi’s The Emergence of Life.

    And believe me, very, very few people are bigger geeks than I am :)

  9. Eugen says:

    Just quick one, it’s getting late.

    My friend,you don’t understand.. Try to beat this. I played melodica in grade 6. Melodica!

    http://en.wikipedia.org/wiki/Melodica

    About Craig-Dawkins tomorrow.

  10. OgreMkV says:

    OH… a band geek. No, I can’t beat that.

    A friend and I did design an alternate biochemistry (carbon cycle) based on ketones when we you in high school.

    Craig-Dawkins would be like me-Dawkins debate. It would be awesome on my resume… not so cool on Dawkins. Maybe if Craig had actual evidence for his beliefs… well, then he’d write them up in a peer-reviewed journal and there still wouldn’t be a debate.

  11. Eugen says:

    Sometimes I think of good old geek days.

    First of all if biologist wants to play philosophy he should expect to be invited to philosopher’s wasp nest to get stung.
    I was skipping news about Craig’s UK tour because all these debates sound the same to me. If I can afford two hours, one to watch would be Dawkins – Craig. Than I heard Dawkins came up with an excuse, some story of genocide in the Bible (I’m not familiar with that story). Why would he care about Bible genocide story?
    Isn’t Bible just a fairy tale for him?
    Maybe this is blasphemy but parts of the Bible definitely sound like fairy tale even to me. I can imagine an atheist considering the whole Bible as a fairy tale. So why use a fairy tale as an excuse when that event didn’t even happen?
    What Dawkins should have done is just ignore Craig’s invitation instead of fairy tale excuse.

  12. OgreMkV says:

    Well, here’s the deal. You see people like Craig (and, honestly, you) are not taking an unbiased look at this. Really, what do you think would have happened if Dawkins ignored in the invitation to debate. You already asked if he was scared when he turned it down, what would you have said if he had ignored the invite? What would Craig have said?

    Yes, the Bible is a fairy tale. I don’t see anyone standing up to debate the modern worshipers of the Greek gods (http://www.guardian.co.uk/world/2007/feb/01/religion.uk).

    You see, even though you are trying, you still have the blinders on about your religion. You’re doing a good job, but you are still basing everything around it.

    Then again Craig wasn’t just talking about a Biblical genocide story. He approved of it (and if I recall correctly, thinks it should happen today). That’s a pretty big difference.

    I’m not going to put words in Dawkins mouth, but my take on it is that religion is not only a fairy tale, but it is actively dangerous in our society. Yes, the religious do some good works. They also do some horrible things based on their religion. In the balance, i believe (and I’m sure Dawkins does to) that the negative aspects of religion far outweigh the positives.

    Here try this; http://stephenlaw.blogspot.com/2011/11/superior-audio-recording-of-my-debate.html

  13. Eugen says:

    “..you still have the blinders on about your religion..”
    Probably. I try to stick to science; religion must be sneaking in from sub conscience.

    I still think it would be better to ignore invitation. Most people would forget it quickly. By using excuse Dawkins did, it appears he accepts Bible story as true and he just disagrees with the action of genocide and whoever supports it. If Bible is “Hansel and Gretel” than genocide didn’t happen the same way fattening of Hansel by the witch. Why even mention a fairy tale.

    This has nothing to do with me believing or not believing in God; it’s just simple logic.
    As for Craig’s style, I noticed he overwhelms opposing debater with massive amounts of philosophy. Some opposing debaters don’t handle it well, stumble and look lost that way. That’s how good orator wins audience. Harris and Hitchens handled it well, they are philosophers.
    Thanks for links. I’ll check them later.

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