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Author Topic:   Converting raw energy into biological energy
molbiogirl
Member (Idle past 751 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 196 of 314 (419839)
09-05-2007 1:00 AM
Reply to: Message 192 by Rob
09-04-2007 11:53 PM


Behe's Balderdash II
In fact, if we disolved in water (using the formal chemical names) ribose-5-phosphate, glutamine, asparic acid, glycine, N10-formylTHF, carbon dioxide, and energy packets of ATP and GTP- all the small molecules that are used by the cell to build AMP- and let them sit for a long time (say, a thousand or a million years) we would not get any AMP.

Wow.

You don't read anything I post, do you? C'mon. Admit it.

Prebiotic Formation of ADP and ATP from AMP, Calcium Phosphates and Cyanate in Aqueous Solution Origins of Life and Evolution of Biospheres Vol. 29, No. 5

Because we do not know what the conditions were. We only theorize based upon limited data.

The data is hardly limited, Rob. Grow a pair and dip into pubmed sometime.

And lab techs manufacturing evidence is hardly objective...

I don't mind doing additional research on pF1. Expect the cites tomorrow.

Or that they do not look anything like life as we know it. In fact, theyre not even alive...

I repeat. Behe said "the molecules of life" are easy to make.

Are you now disagreeing with Behe?


This message is a reply to:
 Message 192 by Rob, posted 09-04-2007 11:53 PM Rob has responded

Replies to this message:
 Message 197 by Rob, posted 09-05-2007 1:20 AM molbiogirl has responded
 Message 199 by Rob, posted 09-05-2007 2:08 AM molbiogirl has responded

Rob 
Suspended Member (Idle past 3958 days)
Posts: 2297
Joined: 06-01-2006


Message 197 of 314 (419843)
09-05-2007 1:20 AM
Reply to: Message 196 by molbiogirl
09-05-2007 1:00 AM


Slow down girl...
molbiogirl:
You don't read anything I post, do you? C'mon. Admit it.

Prebiotic Formation of ADP and ATP from AMP, Calcium Phosphates and Cyanate in Aqueous Solution Origins of Life and Evolution of Biospheres Vol. 29, No. 5

Yeah yeah yeah... yipe yipe yipe!

So give me some more details about this bit:

Prebiotic Formation of ADP and ATP from AMP, Calcium Phosphates and Cyanate in Aqueous Solution Origins of Life and Evolution of Biospheres Vol. 29, No. 5

What does it say about it? Is it a model? has it been done?

For all I know they are reporting a failure. I get zilch, zero, and nada, when doing a web search for your bit...

Show me baby!


This message is a reply to:
 Message 196 by molbiogirl, posted 09-05-2007 1:00 AM molbiogirl has responded

Replies to this message:
 Message 204 by molbiogirl, posted 09-05-2007 2:45 AM Rob has responded

  
Rob 
Suspended Member (Idle past 3958 days)
Posts: 2297
Joined: 06-01-2006


Message 198 of 314 (419844)
09-05-2007 1:40 AM
Reply to: Message 191 by Doddy
09-04-2007 7:31 PM


I spoke too soon...
Let's take a step back here...

Rob writes:
No unwhole parts will do... just as my truck won't self assemble if I put all of the thousands of parts in the garage and wait. I need a mechanic. And my truck is crude and primitive technology compared to these systems

Doddy: This analogy falls over, because macroscopic systems don't compare with microscopic ones. Your truck parts won't be floating around your garage, bumping into one another, but biological molecules will. If the truck parts that are fit together bump into one another, they won't usually stick without a bolt or rivet to stick them, but biological molecules fit together because of their intrinsic properties. No truck part has electrostatics and van der Waal forces to worry about, as those are tiny forces, but very real on the scale of biological molecules. In most ways, the truck is much harder to build than a biological system. In part, this is why I get so fed up with the IDists calling flagella 'outboard motors' and so forth, because an outboard motor is way harder to see self-assemble.

Ok the truck is a bad analogy. I agree as I conceded in my last response. But hold on...

You're assuming the existence of the parts to begin with. That is not what the evidence shows.

The evidence shows that the biological parts are manufactured. Proteins are not formed by chance.

First, they are coded in the DNA, they are then transcribed from an RNA replica of the particular DNA sequence for that protein (so the RNA is itself transcribed). Then the amino acid chain assembled within the Ribosome is shaped into the proper three dimensional structure, and it is then transported to the area it is needed.

And they have to be put together in the proper sequence. Electric motors for example (like the bacterial flagellum) are built in sequence as the genes are expressed. There's a lot more going on here than parts from nowhere floating around in an accidental surfactant bubble and just 'coming together under me'.

Let's take a look at the flagellum for a moment just as an example:

Minnich on the question: ‘What is the most remarkable aspect of the bacterial flagellum?’

“The most amazing aspect of the bacterial flagellum to me is… (actually I can’t limit it to one aspect). You have the motor itself, very sophisticated; Howard Berg at Harvard (I’ve heard him speak several times) has labeled it ‘the most efficient machine in the universe’; the fact that it runs (normally in E. Coli) at 17,000 rmp. Two gears, forward and reverse, water cooled, proton motive force, it’s hardwired to a signal transduction system and has short term memory… That’s fascinating!

But then when you step back and look at the genetics in terms of the program, the blueprint to build this system, you find another layer of complexity. In the genes it’s not enough to have the fifty genes required; we find that they are also fired (or expressed) in a given sequence. And that there are checks and balances, so if there is a problem in assembly; that information feeds back at the genetic level and shuts down expression. There are gate keepers. There is communication molecularly at a distance (and a significant distance). So you build a scaffold on the end of this thing that is protruding from the cell, and it’s feeding back and saying, ‘ok, we have enough of that sub-unit, now send the next sub-unit.’

We don’t understand how this works yet. But it’s fascinating! It’s something that I could spend the rest of my life studying it’s so intriguing in terms of how this system works.”

(Scott A. Minnich Ph.D., Associate Professor of Microbiology at the University of Idaho. He was an assistant professor at Tulane University, and did postdoctoral research with Austin Newton at Princeton University and Arthur Aronson at Purdue University.

Minnich’s research interests are temperature regulation of Y. enterocolita gene expression and coordinate reciprocal expression of flagellar and virulence genes. He is widely published in technical journals, including the ‘Journal of Bacteriology’, ‘Molecular Microbiology’, ‘Proceedings of the National Academy of Sciences’, and the ‘Journal of Microbiological Methods’.)

Doddy:

While I will concede that for anything to be called an organism, it must be separated from the environment by a membrane, the actual membrane is pretty simple. Phospholipids, like all surfactants, form layers, even bilayers, at certain concentrations in solution. They self-assemble. Likewise, a protein with many hydrophobic amino acids like glycine or leucine on one end will attach to the membrane. That sort of stuff is easy to stumble upon by accident, and what we see in living things today is just the evolved version of those accidents.

If it's so easy, then why the appearent obstacles in this aritcle? http://news.yahoo.com/s/ap/20070820/ap_on_sc/artificial_life

"Bedau figures there are three major hurdles to creating synthetic life:

• A container, or membrane, for the cell to keep bad molecules out, allow good ones, and the ability to multiply.

• A genetic system that controls the functions of the cell, enabling it to reproduce and mutate in response to environmental changes.

• A metabolism that extracts raw materials from the environment as food and then changes it into energy."

Oh I see, it must also be able to multiply... I wonder what trigers that cascade?

Edited by Rob, : No reason given.

Edited by Rob, : No reason given.


This message is a reply to:
 Message 191 by Doddy, posted 09-04-2007 7:31 PM Doddy has not yet responded

  
Rob 
Suspended Member (Idle past 3958 days)
Posts: 2297
Joined: 06-01-2006


Message 199 of 314 (419850)
09-05-2007 2:08 AM
Reply to: Message 196 by molbiogirl
09-05-2007 1:00 AM


Re: Behe's Balderdash II
molbiogirl from post 98:
Prebiotic Formation of ADP and ATP from AMP, Calcium Phosphates and Cyanate in Aqueous Solution Origins of Life and Evolution of Biospheres Vol. 29, No. 5 / October, 1999

Hmmm I can't find it anywhere...

I found this little gem by Orgel (a real scientist). And it is from 2004. Did I miss the adenine formula from 1999 you are so exited about on pages 102 through 104? It's a PDF so you'll have to look at it yourself.

He covered a lot of different modes of conceivalbe synthesis, and it looked pretty bleak to me. Seems a confrirmation of Behe until you prove something...

http://www.crbmb.com/cgi/reprint/39/2/99.pdf

Your assertions have proved fallacious before molbiogirl; self replicating enzymes, viruses, and now AMP? Where do you get your information?

Edited by Rob, : No reason given.


This message is a reply to:
 Message 196 by molbiogirl, posted 09-05-2007 1:00 AM molbiogirl has responded

Replies to this message:
 Message 200 by kuresu, posted 09-05-2007 2:14 AM Rob has responded
 Message 208 by molbiogirl, posted 09-05-2007 3:02 AM Rob has responded

  
kuresu
Member (Idle past 623 days)
Posts: 2544
From: boulder, colorado
Joined: 03-24-2006


Message 200 of 314 (419852)
09-05-2007 2:14 AM
Reply to: Message 199 by Rob
09-05-2007 2:08 AM


Re: Behe's Balderdash II
Try harder. Here's the article:
http://www.springerlink.com/content/q148256677847857/
All I did was try google scholar. Didn't work, but it told me to try the whole web. And lo and behold, I see the title of the article (minus vol., num., and date). I click on it, and it's from the same volume, number, and date listed by molbio.

Was it really that hard?


This message is a reply to:
 Message 199 by Rob, posted 09-05-2007 2:08 AM Rob has responded

Replies to this message:
 Message 201 by Rob, posted 09-05-2007 2:21 AM kuresu has responded

  
Rob 
Suspended Member (Idle past 3958 days)
Posts: 2297
Joined: 06-01-2006


Message 201 of 314 (419854)
09-05-2007 2:21 AM
Reply to: Message 200 by kuresu
09-05-2007 2:14 AM


Re: Behe's Balderdash II
Well I appriciate that Kuresu. I just hope I don't have to eat any words. I hate crow...

Unfortunately, I cannot view it. The font is so large that it would be impossible to navigate.

Perhaps you can educate me on the proper computer wizardry to make it legible, or simply copy and paste the relevant citations here.

Edited by Rob, : No reason given.


This message is a reply to:
 Message 200 by kuresu, posted 09-05-2007 2:14 AM kuresu has responded

Replies to this message:
 Message 202 by kuresu, posted 09-05-2007 2:29 AM Rob has responded

  
kuresu
Member (Idle past 623 days)
Posts: 2544
From: boulder, colorado
Joined: 03-24-2006


Message 202 of 314 (419856)
09-05-2007 2:29 AM
Reply to: Message 201 by Rob
09-05-2007 2:21 AM


Re: Behe's Balderdash II
um, zoom out? it's a pdf, right? You're using adobe, right? Adobe has a zoom in/out feature.

You know, that magnifying glass in the tool bar?

Sheesh. Are you so computer illiterate that you can figure out the boards dbCodes but can't see a graphic element? Or use the "help" function?


This message is a reply to:
 Message 201 by Rob, posted 09-05-2007 2:21 AM Rob has responded

Replies to this message:
 Message 203 by Rob, posted 09-05-2007 2:33 AM kuresu has not yet responded

  
Rob 
Suspended Member (Idle past 3958 days)
Posts: 2297
Joined: 06-01-2006


Message 203 of 314 (419858)
09-05-2007 2:33 AM
Reply to: Message 202 by kuresu
09-05-2007 2:29 AM


Re: Behe's Balderdash II
When I click the link you gave, an HTMl doc comes up. No adobe...

I'm going to try registering with SprignerLink.

Edited by Rob, : No reason given.


This message is a reply to:
 Message 202 by kuresu, posted 09-05-2007 2:29 AM kuresu has not yet responded

  
molbiogirl
Member (Idle past 751 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 204 of 314 (419861)
09-05-2007 2:45 AM
Reply to: Message 197 by Rob
09-05-2007 1:20 AM


I get zilch, zero, and nada, when doing a web search for your bit...

[sigh]

A man who doesn't know how to google.

Pubmed, Rob. Look in pubmed.

Or, if pubmed is too much for you to handle, try scholar.google.

Have you even tried to read the giant chunk from that paper that I posted upthread?

All I was saying is that the factory itself (in this case a chloroplast) is made in the cell by way of a process that uses ATP.

OK. Now I know you don't bother reading my posts.

One more time.

To produce ATP, a chloroplast does not use ATP. It uses NADPH and FADH.

The "factory" you are referring to runs on NADPH and FADH to set up a proton gradient and to move electrons.

(An E. coli uses NADH.)

That's on wiki. You can find wiki, can't you Rob?


This message is a reply to:
 Message 197 by Rob, posted 09-05-2007 1:20 AM Rob has responded

Replies to this message:
 Message 205 by Rob, posted 09-05-2007 2:52 AM molbiogirl has responded
 Message 206 by Rob, posted 09-05-2007 2:53 AM molbiogirl has not yet responded

Rob 
Suspended Member (Idle past 3958 days)
Posts: 2297
Joined: 06-01-2006


Message 205 of 314 (419862)
09-05-2007 2:52 AM
Reply to: Message 204 by molbiogirl
09-05-2007 2:45 AM


Molbiogirl:
The "factory" you are referring to runs on NADPH and FADH to set up a proton gradient and to move electrons.

How is the factory built? that was the point... Not what it runs on...

And was that article Kuresu found on adenosine or adenine? Because Behe was talking about adenine.

Edited by Rob, : No reason given.


This message is a reply to:
 Message 204 by molbiogirl, posted 09-05-2007 2:45 AM molbiogirl has responded

Replies to this message:
 Message 209 by molbiogirl, posted 09-05-2007 3:08 AM Rob has responded

  
Rob 
Suspended Member (Idle past 3958 days)
Posts: 2297
Joined: 06-01-2006


Message 206 of 314 (419863)
09-05-2007 2:53 AM
Reply to: Message 204 by molbiogirl
09-05-2007 2:45 AM


Molbiogirl:
A man who doesn't know how to google.

Fifteen years as of oct 11 of this year. I only have eyes for her.


This message is a reply to:
 Message 204 by molbiogirl, posted 09-05-2007 2:45 AM molbiogirl has not yet responded

  
Rob 
Suspended Member (Idle past 3958 days)
Posts: 2297
Joined: 06-01-2006


Message 207 of 314 (419864)
09-05-2007 2:55 AM


Guess I'll have to wait until morning... yawn
  
molbiogirl
Member (Idle past 751 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 208 of 314 (419865)
09-05-2007 3:02 AM
Reply to: Message 199 by Rob
09-05-2007 2:08 AM


Re: Behe's Balderdash II
I found this little gem by Orgel (a real scientist). And it is from 2004.

From the paper you claim to have read:

Nucleoside 2 or 3 phosphates sometimes give nucleoside 2 or 3 cyclic phosphates in good yield in this way. More recently it has
been shown that AMP can be converted to ADP and ATP by cyanate in the presence of insoluble calcium phosphates (Yamagata, 1999).

Yamagata, 1999. That's the paper I cited, Rob.


This message is a reply to:
 Message 199 by Rob, posted 09-05-2007 2:08 AM Rob has responded

Replies to this message:
 Message 213 by Rob, posted 09-05-2007 9:29 AM molbiogirl has responded

molbiogirl
Member (Idle past 751 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 209 of 314 (419866)
09-05-2007 3:08 AM
Reply to: Message 205 by Rob
09-05-2007 2:52 AM


And was that article Kuresu found on adenosine or adenine? Because Behe was talking about adenine.

Adenosine IS adenine.

How is the factory built? that was the point... Not what it runs on...

A chloroplast is irrelevant to abiogenesis.

Protocells don't generate energy using chloroplasts.

Edited by molbiogirl, : expletive deleted


This message is a reply to:
 Message 205 by Rob, posted 09-05-2007 2:52 AM Rob has responded

Replies to this message:
 Message 210 by Doddy, posted 09-05-2007 6:18 AM molbiogirl has not yet responded
 Message 214 by Rob, posted 09-05-2007 9:34 AM molbiogirl has not yet responded

Doddy
Member (Idle past 4019 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 210 of 314 (419871)
09-05-2007 6:18 AM
Reply to: Message 209 by molbiogirl
09-05-2007 3:08 AM


molbiogirl writes:

Adenosine IS adenine...


...with a ribose attached to it.


Help to inform the public - contribute to the EvoWiki today!

What do you mean "You can't prove a negative"? Have you searched the whole universe for proofs of a negative statement? No? How do you know that they don't exist then?!


This message is a reply to:
 Message 209 by molbiogirl, posted 09-05-2007 3:08 AM molbiogirl has not yet responded

  
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