Protein structures and intelligent design

Originally posted by mattison0922

Originally posted by soficrow
Okay - this isn't really on topic, and I just scanned only the first post.

BUT - the examples in the first post all fit with what might be described as "fractal design."

Sofi, your example escapes me. I can't for the life of me come up with a way that a biological rotary motor can be considered a fractal. Can please elaborate? Thanks.

Okay. I could be full of it on this one - but - I scanned the bits about jaws and hinges, then ball and sockets - both organic, biological. Relevant background to me is that inventors seem usually to copy from life, and simply translate into non-living mechanical.

Anyway - the jaw and hinges/ball and socket examples made me think of faces and joints - and fractals. ...There is a hypothesis that complex organisms like animals really are just composites of microbes - again, fractals - what happens/forms in the minute particular are reflected in the macro.

...Not a 'position' I can defend. Just a leap. And that's how I got there, more or less.

Originally posted by soficrow
Okay. I could be full of it on this one - but - I scanned the bits about jaws and hinges, then ball and sockets - both organic, biological. Relevant background to me is that inventors seem usually to copy from life, and simply translate into non-living mechanical.

Anyway - the jaw and hinges/ball and socket examples made me think of faces and joints - and fractals. ...There is a hypothesis that complex organisms like animals really are just composites of microbes - again, fractals - what happens/forms in the minute particular are reflected in the macro.

...Not a 'position' I can defend. Just a leap. And that's how I got there, more or less.

Sofi, thanks for the clarification. I understand your point. I think your argument is reasonable, but it is not really in conflict with IDT. IDT doesn't have a problem with the idea of 'common descent,' which is what I think you were going for with the fractals thing. In essence, multicellular organisms are in fact large collections of single cells. Whether or not it's appropriate to call the single cells that make up a multicellular organism as being 'single celled organisms' is debatable, but not really germane to the topic at hand either way.

So the fractal analogy is somewhat reasonable right down the the level of single cell. Below this level is where the 'fractal equation' breaks down. In essence this is why IDT has come about. Thus far, there is not a reasonable naturlistic law, phenomena, theory, or otherwise that can account for the formation of the first fractal.

Now I am going to comment on something I don't really know much about, But in essence isn't the fractal argument and argument from an ID perspective? Certainly the fractal is a repeat of some mathematical expression, that continues from the 'micro' to 'macro' scales, but the ultimate source of that fractal equation is based on an intelligent source, ie; the individual that derived or input or whatever is done with equation. So while the fractal is in fact a repeated pattern, is it not derived from sort sort of intelligence, or is it a consequence of some mathematical law?

What follows is almost pure drivel, written while hurried, tired, distracted, etc. I considered deleting it - but decided to let it stand as evidence of my own humanity.

Originally posted by mattison0922

Sofi, thanks for the clarification. I understand your point. I think your argument is reasonable, but it is not really in conflict with IDT. IDT doesn't have a problem with the idea of 'common descent,' which is what I think you were going for with the fractals thing.

Nope. Again - sorry, but I didn't read the thread. Just scanned the first half post. The fractals concept jumped out at me - so I spewed without thinking further.

So the fractal analogy is somewhat reasonable right down the the level of single cell. Below this level is where the 'fractal equation' breaks down.

Are you sure? (I don't know, but it seems the info above may suggest otherwise.)

In essence this is why IDT has come about. Thus far, there is not a reasonable naturlistic law, phenomena, theory, or otherwise that can account for the formation of the first fractal.

That may be. On the surface, I have no problem with accepting the notion of an "over intelligence" - described as a God, or as an evolved cohesion, or any of several other descriptions.

Now I am going to comment on something I don't really know much about, But in essence isn't the fractal argument and argument from an ID perspective?

It may be - seemed obvious to me. Maybe you can develop it?

Certainly the fractal is a repeat of some mathematical expression, that continues from the 'micro' to 'macro' scales, but the ultimate source of that fractal equation is based on an intelligent source, ie; the individual that derived or input or whatever is done with equation. So while the fractal is in fact a repeated pattern, is it not derived from sort sort of intelligence, or is it a consequence of some mathematical law?

Maybe the original fractal IS God - but if so, who created her?

I don't mean to be disrespectful. I love this sort of discussion - but just can't do it right now. ...In any event, if the fractal thing works for you, use it.

And BTW - if an intelligence is responsible for the first fractal, then offering to postulate a mathematical law as an opposing argument does not work IMO.

'Nite.

Originally posted by soficrow
Are you sure? (I don't know, but it seems the info above may suggest otherwise.)

Am I sure? Hell no. But that's not the point, I don't see anything in Rren's post that would describe any complex systems as having arisen via a 'fractal' like process. I am certainly willing to listen (read) though.

That may be. On the surface, I have no problem with accepting the notion of an "over intelligence" - described as a God, or as an evolved cohesion, or any of several other descriptions.

Okay... I read your "On the surface" as I have no problem... accepting... God but.... What's the 'but?' In essence, the 'but' is what this thread is about.

For example, I don't think it's unreasonable to describe some biological systems as being co-opted from existing biological systems, BUT that doesn't explain the origin of biological complexity in general.

Maybe the original fractal IS God - but if so, who created her?

Ahhh yes... the old 'Who designed the designer' argument... an argument that is distinctly outside of the realm of science, and is thus outside of the realm of IDT.

But on a philosophical note, you can think of it like this: If science is at all reliable the universe arose out of a singularity, commonly referred to as the 'Big Bang.' The 'Big Bang' represents T=0, ie: the 'Big Bang' is the beginning of space-time. Space-Time, being the product of the Big Bang, didn't exist prior to the 'Big Bang,' hence time is really only a product of the creation of the extant universe, and has existed the same amount of time as the Big Bang. The 'Creator' of the Big Bang, is thus not subject to time, and therefore does not necessarily have a 'beginning.'

How's that for some philosophical hand-waving

And BTW - if an intelligence is responsible for the first fractal, then offering to postulate a mathematical law as an opposing argument does not work IMO.

Hmmm... perhaps you've missed my point, or perhaps due to my own ignorance the point was not well stated. Your statement is correct; if life was a fractal, then reducing it to a mathematical law would in fact negate hypotheses taken from the IDist perspective. My point was more akin to if life was based on some fractal equation, then the origin of the equation/formula itself must have had an intelligent source.

Of course, please keep in mind, I know pretty much nothing about fractals other than the basics.

'Nite.

Originally posted by Zipdot
Hoo boy... There's a lot to talk about here... I don't know where to begin.

Yeah i take the 'drunk boxer' approach to the debate. Keep throwing hay-makers....and hope that, eventually, I land one.

I liked the idea of "irreducible complexity" the first time around, when it was predicted by evolution supporter Hermann J. Muller in 1939 and called "interlocking complexity." (Source)

I noticed that mattison already dealt with the actual specifics here so i won't, but if you "liked the idea" then what exactly is your problem here? What's the theory, based on natural selection, that accounts for this "intelocking complexity" to your satisfaction? If your arguing that the "idea" of irreducible complexity has been evidential for quite some time and yet there still is no reasonable naturalistic explaination......well thanks and welcome to our side, we need all the help we can get. Although i realize you're parroting somebody else here, i think your confusing irreducible complexity with specified complexity. (Read this page and maybe check out one of the books they recommend)

We're currently exploring the possible step by step evolution of complex biochemical pathways. It's a work in progress. However, we're not ready to throw our hands up and say "Ya got me. It must be DESIGNED that way. Yeah," and then wipe our sweatty brows.

WOW...this is getting rediculous.. well atleast you've re-worked the "GOD did it" BS. Of course, "Ya got me. It must be designed" is still BS and missing the point, but *shrug* atleast you've managed to get some lipstick on that pig. Oh and as far as, "We're currently exploring the possible step by step evolution of complex biochemical pathways" you do know who is doing that work, yes Zip? The same guys you opponents - would label pseudoscientists, would have ridiculed for not accepting YOUR metaphysical pre-suppositions, would like to see have all their funding cut, etc., etc., etc., ad nauseum psssst...it's the ID theorists...irreducible complexity and specified complexity (your interlocking complexity) are very real, emperically based and experimentally evidential observations. We can just give up though...cause you guys are working on it....riiiight

It may appear that evolutionary theory "breaks down" in microbiological examination, but I believe that what we're really seeing is a simple lag period between discovery and explanation.

You're basing your "beliefs" on what exactly Zip? Natural selection is inadequate to account for the origin of biological complexity, simple as that...it does break down, not maybe..it does period. Just as physics break down at the singularity so does naturalism at the abiogenesis event. I realize that's a punch in the gut to your world-view but, and no offense, that's too bad - your pre-suppositions are irrelevant, or atleast they're trumped by the evidence. You may think - you may believe - but until you can back that up with something substantial, it's just opinion and not science(notice where all the psuedoscience is coming from yet?). These protein structures are machines not "machine-like"...if we cracked open a rock and found cogs, levers, wheels, motors, oars, operating instructions (DNA) at infinitum..well, we would say that rock is a designed mechanism or machine and rightfully so. If we saw this level of design in a signal from space we would deduce design, and rightfully so. But because we crack open a cell and see design, well we have to disregard it...why you may ask? Because of evidence? No? Established scientific laws and/or principals? No. But because it doesn't fit in with the meta-physical pre-supposition..now that's good science.

As an FSME, I am attempting a campaign for cohesiveness, which I think has largely been achieved. More and more, in our forum, we are seeing concessions and willingness to accept alternative ideas.

Gets easier when the people actually know what the alternative idea is. It's amazing how many people can form an opinion based soley on rebuttal information (these guys always seem to be the most vocal too ironically). But i learn something new every day so i ain't complaining...too much. I like you regardless of your position on ID and have already voiced my support for your biological theory of everything, known as Creationtelligentignerlution(ism)...so my objectivity is without question. If ya'll would just admit that i'm right and you're wrong this would be alot easier...after all, not to brag, but i got a very solid 'B' in high-school biology honors....iow resistance really is futile.

Originally posted by soficrow
Okay - this isn't really on topic, and I just scanned only the first post.

BUT - the examples in the first post all fit with what might be described as "fractal design."

Soficrow here's some info you may be interested in, from ISCID (International Society for Complexity Information and Design)

burgeoning field of research in DNA science involves attempts to understand the self- assembly capabilities of complex biological molecules such as proteins and DNA by producing synthetic molecules that form periodic or aperiodic crystals, thereby demonstrating the propensity for such synthetic molecules to bind together in predictable ways. Recently, such experiments have been combined with prefatory computer simulations to produce more complex fractal aperiodic crystals based on synthetic molecules, and although the results are interesting, it is noteworthy that the self-assembling biological molecules being so 'modeled' are assumed to have evolved by Darwinian mechanisms - despite the probabilistic prohibitions of such a process occurring - and that little reference is made to the likelihood of complex self assembly capabilities arising by such mechanisms ...(more)

Using DNA configured abstract Wang tiles in xgrow simulation software with the kinetic tile assembly model, researchers Paul Rothemind et. al have attempted to begin to gain an insight into the principles behind the rules for biochemical self assembly by generating Sierpinski Triangles with DNA binding rules computationally, and producing amazing rezults in-vitro with fractal crystal grow guided by the simulated tile configurations. This fascinating work incorporates some astonishing observations and conclusions (with actual Sierpinski Triangle fractal patterns produced in crystals in- vitro) but may demonstrate some of the hallmark problems with using in-silica simulations to draw conclusions about biochemical/biological systems, in that CSI is assumed to be the product of chance based evolution, and the methodology and experimental-simulative procedures involve the induction and imposition of externally imputed rules and parameters for cellular automata in order to obtain desired results, which are then reflected in-vitro...(more)

I realize that isn't exactly what you and Matt are talking about...but close enough to be helpfull i hope. Also you may want to read this discussion with Carlos Puente who holds a PhD in Hydrology from MIT.

www.iscid.org...

benito (Mar 25, 2004 9:18:59 PM)
i read your book Treasures and i am amazed at the complexity and order inherent in the patterns. Unlike the monsters of the Mandelbrot set, the natural patterns of those of order and suggest an underlying design. What do you think underpins the order and complexity of such design: is there a Design in the designs we see?
carlos puente (Mar 25, 2004 9:22:46 PM)
Thanks benito, the object one gets via these ideas certainly evoke those in the Mandelbrot set, but these ones turn out not be fractal, for if one looks inside at increased resolutions one would not find additional structure. The objects are indeed mathematical designs, for once a trail of iterations is set one always finds them. The order one sees is rather lovely and at the same time mysterious for it depends in a non trivial manner on the actual iterations.

J. Nelse (Mar 25, 2004 9:31:39 PM)
Dr. Puente, how does your research relate to Intelligent Design, if at all?
carlos puente (Mar 25, 2004 9:35:38 PM)
Thanks J. Nelse, well, this research is not classical intelligent design research as practiced by others at ISCID, but certainly the objects that one encounters inside the bell are indeed designs, and the relevance to nature of some of them, i.e., ice crystals and biochemical rosettes, clearly show an intelligent way to think about them. That there is aconnection between the binary expansion of pi and the rosette structure of DNA inside the bell, certainly makes one wonder how is it that such is there.

As Matt said fractals, so far as i'm aware, are a pro-ID argument implying (requiring?) an intelligent agent, somewhat similar to what an algorithm is/does.....but this stuff is so far over my head it may as well be written in Sanskrit . If you're a mathematician the link (ISCID) i gave you should cover some of the areas your interested in, or look up some of William Dembski's stuff (he's a mathematician/ID theorist) on chaos and information theory, which delves into fractals if i remember correctly.


.....or......

Originally posted by mattison0922
My point was more akin to if life was based on some fractal equation, then the origin of the equation/formula itself must have had an intelligent source.

Of course, please keep in mind, I know pretty much nothing about fractals other than the basics.

What he said...

Thanks for the links Rren - great stuff. Much appreciated.

Again, I should apologise to you and mattison at least. I do not have the time or resources to contribute fully or responsibly to this discussion. I know very little about "Intelligent Design" or the related debate, and can't take the time to educate myself right now.

That said, I have no doubt whatsoever that living organisms adapt, change, and evolve. Virtually every bit of research I do on disease - and I do a lot - supports that conclusion. With respect to microbes, plants, humans, and other animals.

IMO - if any natural process can definitively prove the existence of Intelligence Design - evolution does. Living beings are designed to respond to environmental change, adapt to it, and evolve at a genetic level when environmental change proves permanent. Moreover, adaptation and evolution seems to occur inter-dependently, via the various parts of the system inter-relating to balance the whole, in harmony. The process is elegant - and at least apparently, it's intelligent.

Also IMO - The question of teaching ID and evolution is not an either-or prospect. Evolution is a mechanical/scientific process - the scientific study of evolution answers the questions "What?" "Where?" "When?" and "How?" ...On the other hand, Intelligent Design addresses the questions "Who?" and "Why?"

I see Intelligent Design as a legitimate - and perhaps necessary - supplement to scientific study, IF it is taught by the Socratic method. Approached properly, ID might help preserve young peoples' essential intuitive respect for life - and to help them always to appreciate life in its full complexity, as a mystery, and beautiful.


.

One of the debates put up on the site suggest that robots who create more sophisticated robots cannot represent biological evolution. I can agree, but I do think they can represent evolution itself. They then make the arguement that a designer was needed to hand the robots the materials and program them initially and therefore does not represent evolution but intelligent design. Wrong. Evolution does not hinge on the belief of a creator or the non belief of a creator, but whether or not life is capable of evolving. I think what they are trying to get at is a link between creative control of life and a god, and evolution and the big bang. Blahness.

I have also never heard of a link between Adam's lifespan and the great debate. Maybe they are confused as to what they are saying or are they providing an arguement for both sides?

www.reasons.org...

I am also unsure of the article "Virus Argument No Longer Immune to Challenge". Why does this genetic drift occur? If they cannot answer this, how can they make a claim as to whether or not it involves any link to evolution or not? I am not even sure if the article makes the claim at all.

Originally posted by Frosty
They then make the arguement that a designer was needed to... program them initially and therefore does not represent evolution but intelligent design. Wrong.

So.... a designer WASN'T required to build and program the initial robots?
Please clarify.

Evolution does not hinge on the belief of a creator or the non belief of a creator, but whether or not life is capable of evolving.

Okay... but this thread isn't about evolution, it's about ID. Besides, IDT is an origins theory, and doesn't necessarily stand in opposition to the idea of extant live 'evolving' by any traditional definition.

I have also never heard of a link between Adam's lifespan and the great debate. Maybe they are confused as to what they are saying or are they providing an arguement for both sides?

What does Adam's lifespan have to do with IDT?

www.reasons.org...

'Reasons' is an Old Earth Creationist site, not an ID site.

I am also unsure of the article "Virus Argument No Longer Immune to Challenge". Why does this genetic drift occur?

Your question is vague and not well stated. Genetic Drift occurs as result of alteration of allelic frequencies in reproductively isolated populations as a result of natural selection. What's your issue?

Originally posted by mattison0922So.... a designer WASN'T required to build and program the initial robots?
Please clarify.

A designer was needed to create the robots. That what I said.

Originally posted by mattison0922Okay... but this thread isn't about evolution, it's about ID. Besides, IDT is an origins theory, and doesn't necessarily stand in opposition to the idea of extant live 'evolving' by any traditional definition.

Of course not, but I am putting into question the integrity/accuracy of the information of the site given be the OP.

Originally posted by mattison0922What does Adam's lifespan have to do with IDT?

I have no idea, I read the article and did not understand it, maybe you should give a it a go.

Originally posted by mattison0922'Reasons' is an Old Earth Creationist site, not an ID site.

C'mon, ID is just PC slang for 'creationist'.

Originally posted by mattison0922Your question is vague and not well stated. Genetic Drift occurs as result of alteration of allelic frequencies in reproductively isolated populations as a result of natural selection. What's your issue?

No it doesn't, that is what the genetic drift is, but why does it happen they were unable to clarify, so they simply say it debunks evolution?

Originally posted by mattison0922What does Adam's lifespan have to do with IDT?

Originally posted by Frosty
I have no idea, I read the article and did not understand it, maybe you should give a it a go.

I just read through Virus Argument No Longer Immune to Challenge again, and I don't see anything about Adam. Irrespective of where you got this information, it's irrelevant to ID, as Adam is irrelevant to IDT.

Originally posted by mattison0922'Reasons' is an Old Earth Creationist site, not an ID site.

Originally posted by Frosty
C'mon, ID is just PC slang for 'creationist'.

Okay... You're right

Originally posted by mattison0922Your question is vague and not well stated. Genetic Drift occurs as result of alteration of allelic frequencies in reproductively isolated populations as a result of natural selection. What's your issue?

Originally posted by Frosty
No it doesn't, that is what the genetic drift is, but why does it happen they were unable to clarify, so they simply say it debunks evolution?

Not sure what your beef is but did you not read the statement:

Instead, modeling studies show that the drug-resistant strains are already present when drug therapy begins. They do not emerge after drug therapy is initiated. In other words, pre-existing strains of RNA viruses happen to be insensitive to specific antiviral drugs, and these continue to live while the drug-sensitive strains die off.

Allelic variation exists. End of story. Allelic variation exists, and allelic frequencies shift as a result of selective pressure. I don't see how it could be anymore clear than this.

The point is that drugs, and selective pressure in general, don't induce genetic change, they exploit pre-existing genetic change. This is true in the case of antibiotic resistance in general. What's so difficult to grasp here?

Originally posted by mattison0922
Allelic variation exists. End of story. Allelic variation exists, and allelic frequencies shift as a result of selective pressure. I don't see how it could be anymore clear than this.

The point is that drugs, and selective pressure in general, don't induce genetic change, they exploit pre-existing genetic change. This is true in the case of antibiotic resistance in general. What's so difficult to grasp here?

I like to use analogies in concepts and processes. How about this one...*clears throat*

Boggle! Anyone ever play this game? Surely you've seen the box if not:

Here's how it's done. There is an encased cube with dice that have letters instead of numbers printed on them. A player shakes up the cube and tries to write down as many words they can form with the letters that face up.



What words do you see here? Imagine these words are exhibited traits. We don't "see" the alleles, rather the "words" that they spell. There will never be an @ to show up. Nor a # or a ? or a %. Why not? Well @, #, ?, or % were never printed on the dice placed inside the cube. DNA is made of up 4 nitrogenous bases - Adenine, Thymine, Guanine, and Cytosine (Urasil in RNA). There will never be 5 bases, nor 3 (does not work either since they need matching pairs). Those are the letters printed on the dice whether we like it or not. It's true that with the length of the DNA strands, that means a LOT of combinations, but can't ame a @ # ? % show up on those dice.

Hey teach, how'd I do?

[edit on 6-12-2005 by saint4God]

I'm not assuming this is directed towards me, but....

Originally posted by saint4God
Hey teach, how'd I do?

Originally posted by saint4God
What words do you see here? Imagine these words are exhibited traits. We don't "see" the alleles, rather the "words" that they spell. There will never be an @ to show up. Nor a # or a ? or a %. Why not? Well @, #, ?, or % were never printed on the dice placed inside the cube. DNA is made of up 4 nitrogenous bases - Adenine, Thymine, Guanine, and Cytosine (Urasil in RNA). There will never be 5 bases, nor 3 (does not work either since they need matching pairs). Those are the letters printed on the dice whether we like it or not. It's true that with the length of the DNA strands, that means a LOT of combinations, but can't ame a @ # ? % show up on those dice.

Your basic statement here is correct.... though not exactly the analogy I was going for.

Let me try again:

Take the following sentence:

"I am sensitive to antibiotics."

Let's say that this sentence represents the Protein encoded by the gene that renders a bacteria sensitive to a drug. This protein is why the bug gets killed by antibiotics. Now small changes can occur within this protein where the sentence (protein) still makes sense (functions), but is changed somewhat, very little, or perhaps not at all.

For example:

"I am very senstive to antibiotics."

"I am somewhat senstive to antibiotics."

"I am extremely senstive to antibiotics."

"I AM senstive to antibiotics."

So in these examples the meaning has changed slightly or not at all.

Take the example:

"I am not senstive to antibiotics."

Please note there is more than one route to this end, though different changes are required.

ie: "I am resistant to antibiotics."

Now, here is an example that makes sense, but changes the meaning of the sentence. Though qualitatively the change is no different than those above.

So... in ANY given population of bugs, examples of each sentence (gene) will exist. In the presence of selective pressure, only two examples from above would survive, thus shifting the allelic frequency.

The analogy is not perfect, single mutations are more likely in the case of antibiotic resistance, and large regions don't generally change at once, but perhaps it's a better description than before.

The universe that we inhabit has particular qualities-- qualities of space, of motion, of matter, of velocity, of mass, of volume. Things interact with each other in relatively predictable ways because of the nature of the universe. Matter can only be arranged in particular ways, it interacts with other matter in particular ways, it moves in particular ways as a result of the application of particular forces, and so on.

The human concept of "intelligence" is inextricably bound to our perceptions of the universe and the ways in which its component parts exist and interact. The more accurate one's perceptions are of the nature of the universe, and the more accurately one can define, explain, analyze and predict how some particular part of the universe will exist or act or interact, the more "intelligent" one is perceived as being.

Therefore, the true nature of the universe is really the thing against which human intelligence is measured, and it's therefore axiomatic that we should see, in the "design" of the universe, "intelligence." The laws of physics dictate that the structure of the universe cannot be, in the purest sense, random-- its component parts and the ways in which those parts interact with each other are limited by the nature of our reality. Any arrangement of any disparate parts that we might conceive that is actually practical and/or useful is practical and/or useful only insofar as it functions effectively within the parameters of reality as we know it, and that same reality as we know it limits the possible combinations of disparate parts that can arise outside of our control in the same manner and according to the same rules.

The fact that our designs-- the results of our intelligence-- might mirror, or be mirrored by, designs that arise from some other source, or by some other method, within the universe, only demonstrates that that which is most effective is, again axiomatically, similar to that which is most effective. Anything that we might discover in the universe that is highly efficient and well-adapted to the true nature of reality as we know it can't help but be similar to that which we might design by application of our intelligence, since our standard of intelligence is measured by how well it corresponds with reality as we know it.

So-- since the perceptive and analytical ability that we humans refer to as intelligence is measured by how well it corresponds with the reality of our universe, any design that we might come across that is not our own, but that does correspond well with the reality of our universe, well strike us as "intelligent." A creator is not necessary.

Thanks Mattison . That helps me out. I pretty much consider myself a layperson these days...who happens to be able to level with my doctor a little better as to why I'm sick . Actually it has come in quite handy. I've managed to not get severely sick for a good couple years, thank God. *goes back to working on a home-cloning system*

My new position as a molecular plant pathologist has introduced me to an astonishing method of infectivity. An Oomycete (fungus-like organism, but not a true fungus) named Haptoglossa mirabilis infects its host rotifer cells via a miniature cannon called a ‘gun cell’ As the image below suggests, gun cell is an appropriate description based on physical appearance and mechanism.

www.uoguelph.ca..." target='_blank' class='tabOff'/>

Please note the following structures:
1. muzzle
2. reinforced bore
4. ‘Plug’
5. Projectile Chamber
6. Projectile
12. Nucleus

The basic mechanism of action is described below.

1. When a rotifer or nematode touches the tip of the gun cell it fires.

2. The projectile is shot through the muzzle of the gun cell.

3. The projectile blows a hole through the animal's epidermis.

4. The fungus everts a hypodermic-like syringe through the hole into the animal's body. The protoplasm and nucelus of the fungus are pumped throught the hypodermis using the osmotic power of the swollen basal part of the gun cell.

5. The soft tip of the hypodermic swells up to form a spore-like structure (sporidium).

6. The animal, reacting to the injection winces and swims off and the now mature sporidium breaks off and is released into the body cavity of the host nematode or rotifer.

7. Feeding on the host's nutrientas, the sporidium enlarges rapidly and to form a single-celled thallus that may completely fill the body cavity of the host.

8. The host dies and the parasite produces exit tubes to the exterior through which the zoospores escape.

Note: The entire process from # 1 - #8 takes place in about 1/10th sec.

A micrograph of Gun Cells is shown below.

www.uoguelph.ca..." target='_blank' class='tabOff'/>

A few more comments from researcher George Barron about the mechanism of action:

The head of the harpoon is laminated. This means that it is compressible. As it is pushed up the barrel of the gun it will fit tightly and prevent leakage to maintain maximum muzzle velocity. As it emerges from the muzzle it pierces the cuticle of the nematode. At the head emerges it will 'decompress' and make a hole wider than the width of the bore. This will facilitate penetration by the everting tubular "hypodermic".

The gun cell is anchored to the substratum by a mucilaginous glue. It also has a swollen base. When the base is anchored the business end of the gun cell is then tilted upwards at an angle of about 30 degrees which is very suitable for contact with the nematodes and rotifers that graze bacteria in the vicinity of the cell.

The basal vacuole is the power pack for the cell. It is at high Osmotic Pressure. When the gun cell is released the pressure up front is removed and water flows in rapidly through the semipermeable membrane surrounding the vacuole. This squeezes the protoplasm and nucleus, like toothpaste, through the tubular hypodermic. The Haptoglossa gun cell is only about 15 microns long.

Now… the question: Is this an IC system? It’s certainly not homologous to any system I am familiar with, which means pretty much nothing. But there is surprisingly little information about the genetics of such a system.

Rather than debate whether or not this system is IC, which seems to get us nowhere, perhaps this could be a ‘research project’ for some of us who are interested in this topic.

We could look up sequences, etc, and perform alignments, look for potential homologous genes, etc. In short, we could attempt to support or reject a hypothesis of IC based on circumstantial evidence, ie: gene homologies and other techniques that don’t require us to be in a lab. Most of the resources to perform this type of analysis are freely available on the internet… could be fun and informative. All are welcome to participate, but it’d be nice if we could get some ATS authorities from both sides of the argument in on the fun. Members that come to mind: Rren, Zipdot, Nygdan, Byrd, FatherLukeDuke, etc., though it is understood that mods are especially busy and may not have time to participate in such a project. Feedback?

Originally posted by mattison0922
My new position as a molecular plant pathologist

Is that anything like a janitor calling himself a sanitation engineer? C'mon Matt fess up. You're just cleaning the beakers and getting coffee for the "real scientists"......

An Oomycete (fungus-like organism, but not a true fungus) named Haptoglossa mirabilis infects its host rotifer cells via a miniature cannon called a ‘gun cell’ As the image below suggests, gun cell is an appropriate description based on physical appearance and mechanism.

Found another site with pics taken from Chapter 15 of Dr. Barron's "The Nematode-Destroying Fungi" that may be usefull: www.mycolog.com...

The basic mechanism of action is described below.

....snip....

Note: The entire process from # 1 - #8 takes place in about 1/10th sec.

Pretty amazing. But when we normally talk about an IRC(ie., designed) molecular machine it's usefull, or serves a positve function in the cell, no? What i mean is that this 'gun cell' seems like a bad thing, so why would you design one...does that make any sense? Does it perform a neccesarry job or does it only have a negative impact on its host cell? I'm still reading on this, so these questions may be stupid and/or irrelevant. I get so lost in the jargon when i read ID material sometimes, that it takes me awhile to get a decent grasp of the basics (ie., what's relevant and what's not). I'll reread some of the more technical stuff 10 times before i even comprehend the basics of an issue.....this looks like it's gonna be one of those.

Now… the question: Is this an IC system? It’s certainly not homologous to any system I am familiar with, which means pretty much nothing. But there is surprisingly little information about the genetics of such a system.

I've been thinking about what IC means quite a bit lately. Normally IDists concern themselves with what components are part of the "IC core"...ie., couldn't have been "built" or evolved via a series of small steps. But, do we not also have to try and identify what system handled this function prior to the component in question being built via an evolutionary process? Know what i mean? What component did the bacterial flagellum's job prior to its "creation" via evolution, or the ATP, cilium, gun cell, etc., etc.? Forget about the IC argument that the "component parts" are not functional seperate from the "whole" (therefore invisible to natural selection)...but what happens if we remove "the whole"? Is that a seperate question or just a different way to say/ask the same thing?

We could look up sequences, etc, and perform alignments, look for potential homologous genes, etc. In short, we could attempt to support or reject a hypothesis of IC based on circumstantial evidence, ie: gene homologies and other techniques that don’t require us to be in a lab. Most of the resources to perform this type of analysis are freely available on the internet… could be fun and informative. All are welcome to participate, but it’d be nice if we could get some ATS authorities from both sides of the argument in on the fun. Members that come to mind: Rren, Zipdot, Nygdan, Byrd, FatherLukeDuke, etc., though it is understood that mods are especially busy and may not have time to participate in such a project. Feedback?

Well i'll help wherever i can, but i don't know what help i'd be in "performing alignments, looking for homologous genes, etc". Mostly cause i have no idea what you're talking about. I don't know Zip's educational background ], but i'm sure Byrd and Nygdan could be helpfull, if they had the time or inclination, You said, " techniques that don’t require us to be in a lab" and "resources ... are freely available on the internet" so if us layman can help, tell/show me what i can do and i'm in.

Ok i'm back to the books...where's the best place to start in your opinion? Is there any point in getting Dr. Barron's book? I assume from what i've seen so far that it's intended for scientists and not layman....i'm still trying to understand the captions from the pics in the page i linked.

[edit on 11-12-2005 by Rren]

Originally posted by Rren
Is that anything like a janitor calling himself a sanitation engineer? C'mon Matt fess up. You're just cleaning the beakers and getting coffee for the "real scientists"......

Given the amount that I know about oomycetes, and plant pathology in general... that sounds about right.

Found another site with pics taken from Chapter 15 of Dr. Barron's "The Nematode-Destroying Fungi" that may be usefull: www.mycolog.com...

I saw this as well, and I wasn't sure what to make of it, so I didn't post it.

Pretty amazing. But when we normally talk about an IRC(ie., designed) molecular machine it's usefull, or serves a positve function in the cell, no? What i mean is that this 'gun cell' seems like a bad thing, so why would you design one...does that make any sense?

Sure, it absolutely makes sense. But isn't 'positive' a relative term? Positive for which organism, host or parasite? It's obviously not in the best interest of a nematode or rotifer to be shot with what effectively amounts to be a poisoned harpoon, but it must be advantageous for the Haptoglossa. It seems like it's just a part of it's life cycle.

Does it perform a neccesarry job or does it only have a negative impact on its host cell?

I see your point, but is the burden of proof on the benefit to host or the parasite? I am certainly no expert in host parasite relationships, but I would imagine there is a fine balance between allowing your host to live long enough to permit the parasite at least one full life cycle.

I'm still reading on this, so these questions may be stupid and/or irrelevant. I get so lost in the jargon when i read ID material sometimes, that it takes me awhile to get a decent grasp of the basics (ie., what's relevant and what's not). I'll reread some of the more technical stuff 10 times before i even comprehend the basics of an issue.....this looks like it's gonna be one of those.

I hear that... and there are no stupid questions.

I've been thinking about what IC means quite a bit lately. Normally IDists concern themselves with what components are part of the "IC core"...ie., couldn't have been "built" or evolved via a series of small steps. But, do we not also have to try and identify what system handled this function prior to the component in question being built via an evolutionary process?

But there's really no way to know this is there, unless the organism has redundancy in it's method of reproduction. Then it might be reasonable to assume that one system evolved while the other maintained. But from what I've read so far, and this is admittedly not much, it seems like the gun cell is just a natural part of the life cycle of this particular organism. Now... evolutionarily speaking, one would assume that the parasite was likely free-living initially, and evolved this mechanism of reproduction. ID is not limited to that. If this mechanism is the product of NS, then there should be evidence of it, ie: co-option of components from other systems, etc.

What component did the bacterial flagellum's job prior to its "creation" via evolution, or the ATP, cilium, gun cell, etc., etc.?

Well, isn't this the assumption? That there was not a prior function for ATP synthase for example. It's part of one of the most fundamental energy production pathways in biology. The flagellum is seemingly just as ancient. The point is if there is evidence that these proteins were harvested and changed from other systems there should be evidence of it.

The searching for gene homolgies, etc. is this evidence of which I speak.

Forget about the IC argument that the "component parts" are not functional seperate from the "whole" (therefore invisible to natural selection)...but what happens if we remove "the whole"? Is that a seperate question or just a different way to say/ask the same thing?

I know what happens if you remove ATP synthase, you get cells that don't grow for &%$@. I've made lots of mutations to this system. I can't say about the gun cells yet.

Gotta cut this short, my wife want's me to take her to dinner. More later.




[edit on 11-12-2005 by mattison0922]

Originally posted by Rren
Forget about the IC argument that the "component parts" are not functional seperate from the "whole" (therefore invisible to natural selection)...but what happens if we remove "the whole"? Is that a seperate question or just a different way to say/ask the same thing?

In my own mind, I see both as being valid questions, ie: the c subunit of ATP Synthase is part of the IC core of that protein, but the ATP synthase is also part of a larger energy conversion core within mitochondrial/thylakoid, and some plasma membranes.

Well i'll help wherever i can, but i don't know what help i'd be in "performing alignments, looking for homologous genes, etc". Mostly cause i have no idea what you're talking about.

...[deletia] You said, " techniques that don’t require us to be in a lab" and "resources ... are freely available on the internet" so if us layman can help, tell/show me what i can do and i'm in.

There is a decent description of sequence alignment here, but breifly: sequence alignments compare the sequences of nucleic acids and proteins, comparing their similarity in an effort to determine relatedness. A gene where 900 out of 1000 nucleotides are the same is said to be 90% homologous. It is noteworthy that the degree of homology between a protein and a gene are related but not necessarily the same. Due to the redundancy of the genetic code a gene that is 90% homologous at the DNA level, could be more like 97% homologous at the protein level. Their exist a variety of freeware programs capable of doing this. Simply seach and download a seqence from NCBI, perform a BLAST (Basic Local Alignment Search Tool), and voila, you're given a bunch of genes and their degree of relatedness. Then you can perform more complex manipulations, if desired or necessary... pretty cool actually.

Ok i'm back to the books...where's the best place to start in your opinion? Is there any point in getting Dr. Barron's book? I assume from what i've seen so far that it's intended for scientists and not layman....i'm still trying to understand the captions from the pics in the page i linked.

Well, I am currently trying to obtain whatever primary literature I can on this subject. Unfortunately, I am like 4 hrs from the main campus where all the libraries are, so I can't really get anything that's not downloadable without going through ILL. Not that ILL is a big deal, but honestly the .pdf has pretty much ruined me from ever really wanting to go the library again, or put up with a hassle greater than logging into library's website and clicking 'print.'

If I were you, I wouldn't get his book... maybe if I saw it for cheap in used book store or something, but I can imagine there'd be much in there interesting to you. I will probably purchase some other related texts. If I can get that on Amazon, I might buy it though. His books are definitely written for scientists who have a direct interest in the field.

I did email Barron last night to see if he could forward me some reprints of his stuff. He hasn't gotten back to me yet, but hopefully he will.

Originally posted by mattison0922

I have no idea, I read the article and did not understand it, maybe you should give a it a go.
I just read through Virus Argument No Longer Immune to Challenge again, and I don't see anything about Adam. Irrespective of where you got this information, it's irrelevant to ID, as Adam is irrelevant to IDT.

Yes, and what is your point?

Originally posted by mattison0922
Okay... You're right

Thank you.

Originally posted by mattison0922Your question is vague and not well stated. Genetic Drift occurs as result of alteration of allelic frequencies in reproductively isolated populations as a result of natural selection. What's your issue?

Originally posted by Frosty
No it doesn't, that is what the genetic drift is, but why does it happen they were unable to clarify, so they simply say it debunks evolution?

Not sure what your beef is but did you not read the statement:

Instead, modeling studies show that the drug-resistant strains are already present when drug therapy begins. They do not emerge after drug therapy is initiated. In other words, pre-existing strains of RNA viruses happen to be insensitive to specific antiviral drugs, and these continue to live while the drug-sensitive strains die off.

Allelic variation exists. End of story. Allelic variation exists, and allelic frequencies shift as a result of selective pressure. I don't see how it could be anymore clear than this.

The point is that drugs, and selective pressure in general, don't induce genetic change, they exploit pre-existing genetic change. This is true in the case of antibiotic resistance in general. What's so difficult to grasp here?

How do you know that drugs do not induce genetic drift? You read one article that says HIV has genetic variations even before drug administration and now all genetic variations occur free of drugs and selective pressure?


It still would not answer why it happens.

Saying it's 'pre-existing' does not change the subject. Why is it 'pre-existing'? God? LOL! That's what the site is trying to make a conection with.

My theory is that is pre-existing do to millions of years of evolutions in which life of all kind has undergone environmental changes. Now whether you belive in that or not, I still think it sound better than 'It god fault'.

Originally posted by Rren
The information below is from an old-earth creationist web-site which I highly recommend(believers and non). These men are real scientists, not the pseudo types that are often seen in the creationist set, and IMO they present a logical and scientific approach to intelligent design that both the believer and non believer can appreciate.Reasons To Believe



Protein Structures Reveal Even More Evidence for Design
By Fazale (Fuz) R. Rana, Ph.D.IN FULL HERE

Recent structural characterization of three proteins, RNA polymerase II, thioredoxin reductase (from E. coli), and chloroplast F1-F0 ATPase, provides exciting additional evidence for Design at the subcellular level.1, 2, 3 These three proteins possess, as part of their architectural make-up, components that are literally machine parts. These new discoveries add to the growing list of molecular motors (enzyme assemblies responsible for cellular movement) and other enzyme systems that are direct analogs to man-made devices

Chains with jaws and hinges:

RNA polymerase II has remarkable machine-like character.9 RNA polymerase II subunits form a channel that houses the chain-like DNA template. “Jaws” help grip the DNA template holding it in place during RNA synthesis. The newly formed RNA chain locks into place a hinge clamp as it exits the RNA polymerase II channel. A funnel-like pore delivers the small subunit molecules to the RNA polymerase II channel. Then the small subunit molecules in the channel are added to the growing end of the RNA chain.

Ball and socket joint:

In a similar vein, structural characterization at 3.0 Å resolution reveals that thioredoxin reductase function is built around a ball and socket joint.10 This enzyme, isolated from the bacterium E. coli, assists in the transfer of electrons between molecules. During the catalytic cycle, the enzyme undergoes a conformational rearrangement that involves the 67° rotation of one of its domains around a clearly defined swivel surface.

Rotary motors:

Finally, recent image analysis by a team from Germany and Switzerland using atomic force microscopy has revealed structural information about chloroplast F1-F0 ATPase. On the basis of this work, we can now add this enzyme to the growing list of ATPase enzymes that are rotary motors.11 As with the other rotary motor ATPases, chloroplast ATPase has a rotor, stator, and turbine.

The watchmaker Arguement, originally from William Paley in 18th century, basically says: as a watch needs a maker, so nature does also.

Skeptics have long argued that nature and a watch are sufficiently dissimilar so that the conclusion drawn from the Watchmaker argument is unsound.
The discovery of enzymes with domains that are direct analogs to man-made devices addresses this concern, because of the striking similarity between the machine parts of these enzymes and man-made devices. Furthermore, as the list of enzymes with machine parts grows, the conclusion of the Watchmaker analogy grows even more certain. Experts in inductive thinking will point out that the more objects taking part in an analogy, the more sound the conclusion arrived at through analogical reasoning.

Seems interesting, that these very small, things have such "designed qualities"......A question: Are these seemingly designed mechanisms believed to have been apart of the original forms of life soon after abiogenesis, and how is this explained in evolutionary theory.










[edit on 25-4-2005 by Rren]

I'm not even going to read the entire thread, just reply to this first post...

First off, I didn't bother reading that whole website. They're not true scientist's in my eye's. My reasoning is these so called scientist's are trying to justify the existence of god by trying to find fault's in current scientific theories.

This is wrong, oh and that's wrong to, this is how we think it really is because it fit's with our view of god.

I do find this as a strange thing for a so called scientific look at ID/Creationism...

# 7

* A study of gypsy moth parasites demonstrates that the creation of a diverse array of specialized parasites indeed is consistent with an all-powerful, all-wise, and all-loving Creator.

So, simply because gypsy moth's have parasite's that are specialized to the gypsy moth, that in itself is scientific validation for proof of god?

Can sumone please explain that furthur to me? Does anyone see the lack of common sense there?

# 5

* New insights into the physics of the Moon’s origin establish more evidence for Earth’s supernatural design so that it can support life.

So, because we came to exist on a planet with a moon and evolved/adapted to the physic's of such a planetary relationship that in itself is furthur scientific validation for proof of god?

These people are just simply amazing .... *ly stupid.


# 4

* Is human evolution a fact? Evidence continues to mount against any genetic link between ancient modern humans and Neanderthals. This undercuts some young-earth creation models for human origins, as well as the evolutionary multi-regional hypothesis.

Ok, this one here HAS to be a joke! First off, no one said evolution was a FACT. It is well known to be a theory and is taught to our children as a THEORY. Secondly ... genetic link between neanderthals and human's? The word DUH suddenly pop's up in my head, not sure why... You figure it out.

I'd also like to point out the other human like ancestor's of man that ALL lived at the same time as man, we didn't co-exist with just neanderthal's guy's.

# 1

* Multiple independent confirmations of dark energy bolster the most spectacular evidence for the supernatural design of the universe for life.

My favorite ... First, dark matter/energy HAS NOT been confirmed. Second, dark matter/energy might not actually exist. WE DON'T KNOW. It's pure theory/speculation. So... who's confirming this in such a way that give's this so called spectacular evidence of god?

As for the whole DNA bit (motors n such) posted in this thread ... Do you expect DNA or anything to find a more difficult mode of operation? Just because DNA resemble's motor's n such doesn't imply anyone intelligent creating them. The universe has been around for billion's of year's. Who's to say the actual building blocks that started life on this planet actually STARTED on this planet. The universe is a VERY HUGE place where we see the building blocks of life EVERYWHERE. So in that light, DNA had a veeeery long time to find the best possible mode of operating.

I don't claim to know it all, I don't claim to have all your answer's. But if religous people are gunna claim to have it, please... put sum damn thought behind it. If god really did create us, he gave us a brain for a reason.