Saturday, August 14, 2010

Quote of the Day: "What Were All These Genes Doing Prior To The Advent Of Sponge?"

Darwinism goes all squishy on Sponges:

“It means there was an elaborate machinery in place that already had some function. What I want to know now is what were all these genes doing prior to the advent of sponge.” -- Charles Marshall, director of the University of California Museum of Paleontology in Berkeley.

Good question!  Wait a minute. This guy is probably a Creationist. In which case, stupid question!

They probably were just another "fluke bordering on the miraculous" waiting to arise.

Tune of "Blackbird":

Soggy sponges in the dead of night
Take those unformed wings and learn to fly
All your life you were only waiting for this moment to arise

Soggy sponges in the dead of night
Take these unformed eyes and learn to see
All your life you were only waiting for those genes to be set free

Sponges fly, sponges fly
Into the light of the dark black night.


P@J said...

you recognize, of course, that he was not asking that question rhetorically, but is actually researching where the genes came from.

If you read the paper, it is pretty clear that we know very well where they came from (read up on the introduction of mitochondrial DNA to eukaryotes before you go there), his research will be on which specific mitochondrial lines provided the source to modern sponges.

Note I said "Modern sponges". The genetic make up of Precambrian sponges was no doubt quite different, but as DNA is not very well preserved over 600 Million Years... indirect methods will need to be used.

Irony: this is an actual demonstration of how simple and undirected the process was that caused mutlicellualr life to form from a mass of single-cellular life. This is one of those supposed "missing links" that creationists think are still missing. This research is proof of the process of evolution, and you somehow read it as being in opposition to "darwinism".

Joe said...

I'm confused. Is P@J saying that modern sponges (d)evolved from humans?

RkBall said...

No. This is a missing link that we didn't even know was missing -- which makes the both of us lousy creationists!

Here's what this means:

We are a lot like sponges, a lot of your friends are probably sponges, and when you take a sponge bath, it is a meeting of minds. A wet sponge -- 97.86% water; humans 97.86% water -- coincidence??!!

Ever seen a picture of a human brain -- sponge-like, eh? Humans are basically just sponges who grew arms, legs, eyes, etc. One cell at a time.™

We are not special. If we have rights, sponges have rights. One of the consumer rights of sponges is not to get soaked.

Plus the secret life of sponges proves once and for all that goddiddindoit -- which means no eternal life for any of us -- yeah!

P@J said...


In case you are actually confused, we and modern sponges shared a common ancestor.

This common ancestor was much more like a sponge in morphology that it was like us. However, it is most likely that it was more similar to us genetically, as the genetics of sponges are really, really complicated, and change at a much higher rate than those of most Eumetazoans (and given niegh 600 millions years to adapt, their genetics have likely adapted more than ours have)

And Ball, this does not prove that God did not do it, it just proves that it can happen without the need for supernatural guidance. Lack of evidence is not evidence of lack.

P@J said...

Oh, and Joe, there is no such thing a "devolution". In the history of evolution, life forms evolved into more complex forms at the same rate that they evolved into less complex forms. For every variant that gained a protein sequence, an adaptation, a skill, or a feature, one lost the same things. This is why we find humans (main adapted advantages being opposable digits and complex cerebrum) are not as good at breathing sea water as a sea cucumber is, and why humans are somewhere in the middle of the pack when it comes to size of the genetic code.

This is the main complaint that most Christians have with evolution and genetics: it pretty much proves we are not “special”, but are just part of the web of life. Ball’s bad jokes notwithstanding.

Joe said...

So then you are saying that DNA has nothing to do with the form of the creature? If the DNA of the ancient sponge is 'quite different' than the DNA of the modern sponge why do they look so similar? Are you saying there is some other guiding force that over rides the genetic code of the DNA?

P@J said...

Joe, DNA is not a blueprint.

A sea cucumber and a cucumber have very different DNA, but they look alike.

Actually I am not going to go on. Just the fact you asked that question demonstrated the impossibility of having a meaningful intelligent discussion on the subject. It gives me a headache thinking down to this level. Read a book. Preferably one written this century.

RkBall said...

"Joe, DNA is not a blueprint."

Did Joe say it was?

By not a blueprint do you mean that DNA does not provide a sketch for the external appearance of something -- hence, sea cucumber vs. cucumber?

Isn't "blueprint" just a metaphor like molecular clock?

BTW, I've ordered a molecular clock from The Science Store. I hear it takes a licking, and keeps on ticking. I think because it has self-repair mechanisms built-in!

Joe said...

So what you are saying P@J is that ancient sponges weren't actually sponges? They didn't work like the modern sponge does? If so how did they function? If they functioned in very different ways than the modern sponge functions doesn't that take away from the Darwinist posit that sponges being such simple multi-celled creatures evolved before more complex multi-celled creatures? You Darwinists are so confusing changing your story when you realize you just boxed yourself in.

Since DNA must change over the eons the DNA of a creature first evolved must have changed as well except the creature first evolved is still amongst us and if the creature is still amongst us then did its DNA actually change? If its DNA did change then why does it still look and act the same way as the creature that first evolved? Its all so confusing.

P@J said...

Joe implied the same thing that you imply: that DNA provides some sort of “sketch” of external appearance. This is a profound misunderstanding of genetics. In fact, we have had this discussion once, Ball, regarding the difference between genetic encoding and gene expression. Gene expression varies widely based on environment.

This is why now, 20 years after the human genome project began, we still can’t find a gene that causes blue eyes (for example).

It is much better to think of DNA as a recipe. For the purposes of allegory: Imagine you want to make a loaf of bread. If you use blueprints, reverse engineer from photos, or a rough sketch, you could make a masonry brick or a meatloaf, and it would look pretty close to a piece of bread. If you follow a recipe, you will end up wit ha loaf of bread (although you may end up with a meatloaf if you use a meatloaf recipe). That is much more how DNA works.

Let’s further suppose that somehow we find some preserved DNA from some long-extinct animal. What we cannot do it look at the DNA and say “this will form a 6-legged animal with 4 eyes and a furry blue carapace that eats funguses”. That information is simply not encoded in the DNA. What we may do is find sequences in the DNA that match what we know as mammal, insect, or reptile, annelid, whatever, and make reasoned summaries about the animal: e.g. it was a reptile, closely related to crocodiles, but likely more ancient.

Joe said...

"What we cannot do it look at the DNA and say “this will form a 6-legged animal with 4 eyes and a furry blue carapace that eats funguses"

Isn't the plural of fungus fungi?

Spelling aside. So what you are saying is if you could take the DNA of say a mammoth and implant it in the living egg of an elephant to create a viable zygote and you let that zygote develop until birth you would have no idea what the resultant animal would be? Are you saying that if said experiment were to be successful you might wind up with a tyrannosaurus rex or maybe a star nosed shrew?

P@J said...

No, Joe. That is not what I am saying. I said nothing like it. What I am saying is that if you found some random DNA lying around frozen in ice or something, you would have no way of knowing if it was mammoth DNA, unless you compared it to known mammoth DNA. If you compared it to the DNA of star-nosed shrews, Tyrannosaurus Rex (wherever you got that DNA from) and a modern elephant, you may be able to conclude that the common lineage of the mammoth was closer to the elephant that it was to the shrew, and the shrew closer than the saurischian, but you wouldn’t be able to identify a “long trunk” gene or a “long tusk” gene or a “long hair” gene, or a “eats grass” gene and determine the animal’s morphology or behavior from that.

Joe said...

Well there P@J it would seem that you now have what they call a conundrum. Either the DNA determines the shape and function of the creature or it doesn't. I have no interest in looking at a strand and determining what the resultant creature must look like. It wasn't in my mind when I first posted on this topic. What I am saying is that a specific DNA code gives you a very specific creature and that if you alter that DNA so that it is "quite different" then it is very very very unlikely you would have a creature that would look and function the same as an older version of the same kind of animal. If you take an ancient sponge and give it a "quite different" DNA you probably wouldn't have a sponge.

P@J said...

My only conundrum, Joe, is trying to explain 150 years of incredible research performed by some of the greatest minds in science to someone lacking a High School education in Biology.

Specific DNA sequences play a role in determining the shape and function of a creature, but so does the environment in which the sequence is expressed. Remember, every cell in your body contains the same DNA sequences, so why do brain cells not develop in the liver? Because of the environment in which those cells form. Extend this out to the entire complex life form to the hundreds of different cell types in the body, and you see how significant environment is.

A good explanatory example is thalidomide. Children born affected by thalidomide were genetically no different than those born without the influence of Thalidomide, but they were morphologically very different. This is because in the womb, when it came time for limb-bud development and the appropriate gene sequences (IGF-1, FGF-2) were “turned on”, the thalidomide messed up the environmental factors (likely by restricting angiogenesis by alphaV-betaIII integrin dimer, but that is only the most plausable theory, there are others). This led to disfigurement of the limbs. If we were to find a DNA sample of a thalidomide victim, there would be no genetic evidence of how their morphology differed during development, yet it was the action of DNA (in an artificially modified environment) that caused their disfigurement. Same DNA, very different morphology result.

Back to sponges, you are simply wrong, and the paper that started this whole exchange demonstrates one of the many ways you are wrong. Your “common sense” idea of how DNA, genetic change, and body morphology varies wildly from the actual facts of the matter. Sponges are not like us, they do not have limbs or organs, therefore they can tolerate a significant amount of DNA change and remain essentially sponge-like.

Joe said...

Well Praise the Lord and pass the ammunition DNA doesn't matter any more! Great news indeed! I am thinking of sending my pet mouse to the plains of Africa so it can reach its true potential as an elephant! I must admit though a few years ago I tried a similar experiment with my pet gold fish. I turned it loose on the prairies of southern Alberta hoping it would morph into a prong horned antelope. I guess I was a bit too optimistic because all it did was turn into a worm. Well at least worm food. I guess I will just have to read more books. (sigh)

RkBall said...

"Joe implied the same thing that you imply: that DNA provides some sort of “sketch” of external appearance."

I wasn't implying it. I was just trying to understand the point you were getting at -- because all kinds of science articles etc. associate DNA with the blueprint metaphor.

I think most people understand the metaphor blueprint, to mean a set of instructions to produce something -- like, e.g., a blueprint for economic renewal, a blueprint for the spread of democracy. I don't think most people think of it in the crude literalist sense you seemed to be doing.

RkBall said...

Blueprint: any exact or detailed plan or outline

2. To lay a plan for.

2. plan or guide: a plan of action or a guide to doing something
"His administration's policies became a blueprint for those that followed."

Joe said...

I don't think that 'blue print' is exactly the right word to describe the function of DNA. A blue print is a piece of paper with lines drawn by one person that are interpreted by someone else to construct something something that is not part of one person or the other.

DNA is completely different. It is much closer to the hard drive on a computer with an integral software package that can not be separated from the hardware. If you alter the hardware you alter the software. If you alter the software you alter the hardware. The software's function is to build the hardware and the hardware's function is to pass on the software.

Like any well designed program there are redundancies built in so minor errors don't ruin the project but at the same time a 'quite different' software will of necessity build a 'quite different' hardware. Now it is possible to observe changes in the hardware that occur when the environment changes but should the environment change back the hardware changes become undone.

None of which is sufficient to adopt the atheist/antitheist position that pure 'natural' forces will produce... For one thing there can be no pure 'natural' forces secondly a wise Designer would have built in an adaptive feature into His creation. By wise Designer I mean One who is able to build all that we see and don't see excepting of course Him.

P@J said...

Joe, you have nothing to contribute to this discussion. I tried.

Rick, here are two good articles that explain how the DNA can be both the source of all reproduced information required for human development, yet not have any direct control of morphology.

This one is a slightly sketchy analogy, but close to reality.

This one a little sharper in tone, but may answer many of the questions you have about genetic information (written by a biologist anf computer programmer)

RkBall said...

PJ -- you like the recipe metaphor -- I found this. Plus, I scratched around and came up with a post on the whole blueprint metaphor thing. Of course, I could not resist appending the usual Creator-affirming insights to the end of it.

Blueprints and Recipes: Gendered Metaphors for Genetic Medicine
by CM Condit - 2001 - Cited by 4 - Related articles
(1992) contends that the blueprint metaphor is the “predominant metaphor for genes andDNA fragments” (p. 1470), while Barbara Katz Rothman (1998) identi- ...

RkBall said...

Joe -- I think your software analogy is spot-on. As a former programmer, as soon as I hear about something being switched on and off, I'm thinking programming.

What is beautiful is the way the Creator "hides" from the skeptics -- there is no way of knowing whether the switches turn on and off by accident, or at the Creator's direction.

But, as they say, the proof of the pudding [recipe] is in its eating.

Where there's pudding, there's a recipe. Where there's a recipe, there's a recipe-maker. And, where there's pudding, there's a cook.

RkBall said...

"I don't recall writing small segments of self-modifying, recursive code and sprinkling them throughout my program…or perhaps more accurately, writing software that was one-third auto-loading noise maker and sprinkling a few words of functional code among them."

PZ's words sound out-dated, and, I would say, getting outdateder by the day. While hugely junk would fit nicely with the mindless darwinian narrative, I doubt its going to fit the evidence as it unfolds. But, neo-darwinism is infinitely elastic; the facts on the ground may shift, but the philosophical foundation -- no god, no design, no intelligence -- remains the fixed, immovable constant -- regardless of what the unfolding evidence will indicate.

Joe said...

Well P@J the fault lies on your side. The difficulty is your logic which glibly says 'quite different DNA' while admitting we don't have any DNA to compare. The to try to say that a cucumber and a sea cucumber look the same. Well maybe on a dark night if you were drunk enough they would look alike. The FACT is we don't have the DNA for comparison so the best we can do is infer that the DNA is quite different based on Darwin's theory or we could infer that because the two creatures look the same and function the same they would have very similar DNA. Without supporting evidence both views are equal in value. Anything beyond that is speculation or shall I say determining a pattern where no pattern exists.

"... nothing intellectually compelling or challenging.. bald assertions coupled to superstition... woefully pathetic"