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Author Topic:   Converting raw energy into biological energy
Rob 
Suspended Member (Idle past 5869 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 replied

Rob 
Suspended Member (Idle past 5869 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...
Taylor & Francis - Harnessing the Power of Knowledge
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 replied

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

Rob 
Suspended Member (Idle past 5869 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 replied

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

Rob 
Suspended Member (Idle past 5869 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 replied

Rob 
Suspended Member (Idle past 5869 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 replied

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

Rob 
Suspended Member (Idle past 5869 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 replied

Rob 
Suspended Member (Idle past 5869 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

Rob 
Suspended Member (Idle past 5869 days)
Posts: 2297
Joined: 06-01-2006


Message 213 of 314 (419882)
09-05-2007 9:29 AM
Reply to: Message 208 by molbiogirl
09-05-2007 3:02 AM


Re: Behe's Balderdash II
molbiogirl:
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.
I think I see the problem and it's no big deal really...
Look carefully at part of what I quoted here: http://EvC Forum: Converting raw energy into biological energy -->EvC Forum: Converting raw energy into biological energy
All roads lead to Rome, it is said, and similarly there are many ways to synthesize AMP. A book for chemists on my shelf lists eight different ways to make adenine (which is the top part of AMP without the foundation); the remainder of the molecule can be put together in a variety of ways also. Chemists who want to synthesize adenine, however, use completely different routes from that used by cells. Because they involve reactions in oily liquids at extremes of acidity, these conditions would cause the quick demise of any known organism.
(Behe 'DBB' pg 149)
Behe's point is that adenine is added unnaturally by chemists, and that in that case, yes AMP is easy to synthesize.
But they have failed to show that adenine was present in (as orgel confesses here: Taylor & Francis - Harnessing the Power of Knowledge pg 102-104) under relevant or plausible prebiotic conditions.
C'mon Molbiogirl, your the PhD here right?

This message is a reply to:
 Message 208 by molbiogirl, posted 09-05-2007 3:02 AM molbiogirl has replied

Replies to this message:
 Message 217 by molbiogirl, posted 09-05-2007 11:17 AM Rob has replied
 Message 218 by molbiogirl, posted 09-05-2007 2:55 PM Rob has replied

Rob 
Suspended Member (Idle past 5869 days)
Posts: 2297
Joined: 06-01-2006


Message 214 of 314 (419883)
09-05-2007 9:34 AM
Reply to: Message 209 by molbiogirl
09-05-2007 3:08 AM


molbiogirl:
A chloroplast is irrelevant to abiogenesis.
Protocells don't generate energy using chloroplasts.
Are you invoking belief again based upon unproven assumptions?
What protocells?

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

Rob 
Suspended Member (Idle past 5869 days)
Posts: 2297
Joined: 06-01-2006


Message 215 of 314 (419887)
09-05-2007 10:13 AM
Reply to: Message 211 by Percy
09-05-2007 7:35 AM


Re: There's been work done since 2004
Percy:
Science is tentative, so there can be no guarantee (no proof) that we've nailed down the environmental conditions of the early earth. No proof ever. Increasing evidence might increase our confidence, but it can never reach certainty.
Science is believed by most to be empericism. It is theorized, tested, and confirmed (ie. it is proved). We then have what we call evidence.
That is what good science is...
What you're talking about is theory, and that is tentative. Because based upon the evidence, we can make all kinds of theories.
As I said in message 1:
I think that some of you have simply moved past the evidence and take for granted that it is possible based upon your 'methodological naturalist' bias. Molbiogirl spoke of a theoretical explanation for the problem of energy conversion. And I must confess that it is probably internally coherent, but there is no external evidence to support or test it. I want to discuss the subject.
Percy:
To understand how strong a rebuttal this is you have to understand your original claim, which was that ATP can't be produced unless you already have some ATP.
And I have since repositioned the question to reflect the real problem and I am told it is irrelevant becase of the a priori fact that it happened in some form as yet unknown. A position which you appearently support.
The real problem is that the processes which assemble the known energy conversion systems, are themselves built with processes that depend upon the production of ATP. That is what the evidence shows.
You are assuming the existence of protocells and abiotic chemical soups that are not relevant to current biological function. And you have no proof or evidence for these systems. They are merely assumed to be true, because otherwise, life's appearance is illogical and not thermodynamically favored by a material cause.
Lewontin is well known for his belief in evolution. And he is honest about what it is, and why he proceeds.
Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door.
(Wiki-evolution /Richard Lewontin, 1997. Billions and billions of demons, The New York Review, p. 31, 9 January 1997)
Darwin's theory of evolution by natural selection in particular is hopelessly metaphysical, according to the rules of etiquette laid down in the Logic of Scientific Inquiry and widely believed in by practicing scientists who bother to think about the problem. The first rule for any scientific hypothesis ought to be that it is at least possible to conceive of an observation that would contradict the theory. For what good is a theory that is guaranteed by its internal logical structure to agree with all conceivable observations, irrespective of the real structure of the world? If scientists are going to use logically unbeatable theories about the world, they might as well give up natural science and take up religion. Yet is that not exactly the situation with regard to Darwinism? The theory of evolution by natural selection states that changes in the inherited characters of species occur, giving rise to differentiation in space and time, because different genetical types leave different numbers of offspring in different environments... Such a theory can never be falsified, for it asserts that some environmental difference created the conditions for natural selection of a new character. It is existentially quantified so that the failure to find the environmental factor proves nothing, except that one has not looked hard enough. Can one really imagine observations about nature that would disprove natural selection as a cause of the difference in bill size? The theory of natural selection is then revealed as metaphysical rather than scientific. Natural selection explains nothing because it explains everything.
(Richard Lewontin / “Testing the Theory of Natural Selection” Nature March 24, 1972 p.181)

This message is a reply to:
 Message 211 by Percy, posted 09-05-2007 7:35 AM Percy has replied

Replies to this message:
 Message 216 by Percy, posted 09-05-2007 11:07 AM Rob has replied

Rob 
Suspended Member (Idle past 5869 days)
Posts: 2297
Joined: 06-01-2006


Message 220 of 314 (419989)
09-05-2007 9:00 PM
Reply to: Message 218 by molbiogirl
09-05-2007 2:55 PM


Re: Behe's Balderdash II
molbiogirl:
AMP = Adenosine Mono Phosphate
That means (pay close attention now) Adenine + Ribose + Phosphate
Behe is talking about the synthesis of AMP, not just the synthesis of adenine. My earlier cite (re: aqueous solution) stands.
No it doesn't... and I'll be answering that other reply shorlty...
Adenine + Ribose + Phosphate = AMP
Where'd you get the adenine? That comes in my next response...

This message is a reply to:
 Message 218 by molbiogirl, posted 09-05-2007 2:55 PM molbiogirl has not replied

Rob 
Suspended Member (Idle past 5869 days)
Posts: 2297
Joined: 06-01-2006


Message 221 of 314 (419992)
09-05-2007 9:05 PM
Reply to: Message 217 by molbiogirl
09-05-2007 11:17 AM


Re: Behe's Balderdash II
Molbiogirl:
Prebiotic Adenine Revisited: Eutectics and Photochemistry, Leslie Orgel, Origins of Life and Evolution of Biospheres, Volume 34, Number 4, August, 2004
Orgel writes: [b]"Recent studies support an earlier suggestion[b/] that, if adenine was formed prebiotically on the primitive earth, eutectic freezing of hydrogen cyanide solutions is likely to have been important. Here we revisit the suggestion that the synthesis of adenine may have involved the photochemical conversion of the tetramer of hydrogen cyanide in eutectic solution to 4-amino-5-cyano-imidazole. This would make possible a reaction sequence that does not require the presence of free ammonia. It is further suggested that the reaction of cyanoacetylene with cyanate in eutectic solution to give cytosine might have proceeded in parallel with adenine synthesis."
Rob:
Behe's point is that adenine is added unnaturally by chemists, and that in that case, yes AMP is easy to synthesize.
Molbiogirl:
Orgel disagrees!
Did you even read what Orgel said?
Where did he say that it was found or tested or proven?
He said, if it was formed prebiotically... Do you know wahat the word if means. Or is it like the word is that some folks in high positions seem to have trouble with?
Seriously!
I am far from dissapointed...
Edited by Rob, : No reason given.

This message is a reply to:
 Message 217 by molbiogirl, posted 09-05-2007 11:17 AM molbiogirl has replied

Replies to this message:
 Message 222 by crashfrog, posted 09-05-2007 9:10 PM Rob has not replied
 Message 224 by kuresu, posted 09-05-2007 9:19 PM Rob has not replied
 Message 227 by molbiogirl, posted 09-05-2007 9:29 PM Rob has replied

Rob 
Suspended Member (Idle past 5869 days)
Posts: 2297
Joined: 06-01-2006


Message 223 of 314 (419994)
09-05-2007 9:13 PM
Reply to: Message 216 by Percy
09-05-2007 11:07 AM


Re: There's been work done since 2004
Rather than digressing into a discussion of the nature of science and the relationship between evidence and theory, let me just reiterate that we will never reach certainty about the conditions on the early earth.
And that is why it is hopelessly metaphysical as Lewontin said.

This message is a reply to:
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Replies to this message:
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Rob 
Suspended Member (Idle past 5869 days)
Posts: 2297
Joined: 06-01-2006


Message 228 of 314 (420003)
09-05-2007 9:38 PM
Reply to: Message 227 by molbiogirl
09-05-2007 9:29 PM


Re: Behe's Balderdash II
Do any of you have one shred of evidence of a prebiotic organism that is not totally theoretical ie. non-existent?
And theorized evidence is not evidence...
I mean evidence in the real world, (emperical) ie. the fossil record or discovered elsewhere, for any form of prebiotic organism?
I ask, because there is an earthload of evidnce for biotic organisms. And they're not made the way all of these masses of data and theoretical research assume and predict that prebiotic organisms were made.
What good is a 'scientific' prediction (theory) that cannot be tested?
And you know the best part...?
I don't have to say, 'if these bilogical organism were able to synthsise ATP or adenine or any other structure or enzyme et al... then perhaps it was a result of this or that bla bla bla...'
No, I don't have to say that... Because they actually exist! And they do synthesize this and that, and we have evidence of that, and that, and that, and that, bla bla bla bla etc.
And you know what else... it's proven science. It's not tentative.
Science is a search for proof. We start with theory and evidence. We then seek to find a match.
All you have is theory. No evidence and no match.
Edited by Rob, : No reason given.
Edited by Rob, : No reason given.
Edited by Rob, : No reason given.
Edited by Rob, : No reason given.
Edited by Rob, : No reason given.

This message is a reply to:
 Message 227 by molbiogirl, posted 09-05-2007 9:29 PM molbiogirl has replied

Replies to this message:
 Message 230 by kuresu, posted 09-05-2007 10:02 PM Rob has replied
 Message 232 by jar, posted 09-05-2007 10:12 PM Rob has replied
 Message 239 by molbiogirl, posted 09-05-2007 10:25 PM Rob has replied

Rob 
Suspended Member (Idle past 5869 days)
Posts: 2297
Joined: 06-01-2006


Message 233 of 314 (420012)
09-05-2007 10:13 PM
Reply to: Message 230 by kuresu
09-05-2007 10:02 PM


Re: Behe's Balderdash II
The question is...'Why do you assume prebiotic organisms to begin with?

This message is a reply to:
 Message 230 by kuresu, posted 09-05-2007 10:02 PM kuresu has replied

Replies to this message:
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