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Author Topic:   Time factor in self assembly calculations?
peter borger
Member (Idle past 6002 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 16 of 66 (14189)
07-26-2002 4:50 AM
Reply to: Message 14 by singularity
07-26-2002 4:05 AM


You say (among other things) that:

"Surely this is a very simple example of destroying and recreating life sensu stricto?"

According to your definitions it would be the recreation of life.

But according to your definitions the following is also recreation of life: Imagine a population of dividing cells. Add a cell cycle inhibitor. Now, the cells are non-living/dead.
Next, wash away the cell cycle inhibitor. The cells start dividing again. According to your definitions the cells are alive again.

Q: Did you recreate life by adding and washing the cell cycle inhibitor?

Best wishes
Peter


This message is a reply to:
 Message 14 by singularity, posted 07-26-2002 4:05 AM singularity has responded

Replies to this message:
 Message 19 by singularity, posted 07-27-2002 10:58 PM peter borger has responded

  
peter borger
Member (Idle past 6002 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 17 of 66 (14190)
07-26-2002 5:03 AM
Reply to: Message 15 by singularity
07-26-2002 4:37 AM


Dear Shane,

You state:
"It certainly makes more scientific sense than any historical creation story you care to cite".

I care to cite? Where?

Peter


This message is a reply to:
 Message 15 by singularity, posted 07-26-2002 4:37 AM singularity has responded

Replies to this message:
 Message 20 by singularity, posted 07-27-2002 11:13 PM peter borger has responded

  
John
Inactive Member


Message 18 of 66 (14252)
07-26-2002 10:43 PM
Reply to: Message 12 by peter borger
07-25-2002 9:55 PM


quote:
Originally posted by peter borger:
There are dozens of answers to a question.
It is just a matter of choise.
You are free to choose.
Best Wishes
Peter

I don't get it.

Of course I'm free to choose, but that isn't why I debate here. I debate because it forces me to think and the learn.

------------------
www.hells-handmaiden.com


This message is a reply to:
 Message 12 by peter borger, posted 07-25-2002 9:55 PM peter borger has responded

Replies to this message:
 Message 21 by peter borger, posted 07-29-2002 8:51 PM John has not yet responded

  
singularity
Inactive Member


Message 19 of 66 (14269)
07-27-2002 10:58 PM
Reply to: Message 16 by peter borger
07-26-2002 4:50 AM


Peter

Your example is a great point of the heart of my argument. In the nuclear transfer example the nucleus needs the appropriate environment of the cell in which to be a viable living organism, and beyond that the entire cell needs a usitable environment in which to grow. Your example of a cell culture which is prevented from growing through changes in its chemical (and strictly nonliving) environment highlights the main issue of contention- where does the living organism end and the non living environment begin?

To me this points out that organisms and their environments cannot be disentangled and the definition of matter as living or nonliving is a human imposition. The question of whether or not there is or ever has been anything supernatural about our environment is a bigger, less tangible question. Perhaps in the strictest definition the supernatural must be unobservable and unreproducible, otherwise it falls within the bounds of science. Can God can only exist by not existing?????

From my perspective living organisms cannot be considered outside their living and nonliving environment. I am an advocate of the gaia hypothesis and only find room for a fuzzy feeling inducing, godlike presence in the entire interconnectedness of life. The universe is so dazzling as we find it- where is the need to conjure up an invisible cranky, bearded, robe wearing old man who created, tempted and then judged us?

Shane


This message is a reply to:
 Message 16 by peter borger, posted 07-26-2002 4:50 AM peter borger has responded

Replies to this message:
 Message 22 by peter borger, posted 07-29-2002 9:05 PM singularity has not yet responded

  
singularity
Inactive Member


Message 20 of 66 (14270)
07-27-2002 11:13 PM
Reply to: Message 17 by peter borger
07-26-2002 5:03 AM


Hi Peter

I am not implying that you have personally suggested that any creation models are more tenable than evolution. In fact your prime objective seems to be the criticism of evolution without suggesting more viable alternatives, so I was encouraging you to reveal your position. Do you perhaps think that the origin of life and the universe as a whole is irrelevant to modern existance? (I am struggling to think of a human society without a creation story.....was there a primitive isolated tribe in Malaysia discovered in the late 20th century which had no such mythology??)

Shane


This message is a reply to:
 Message 17 by peter borger, posted 07-26-2002 5:03 AM peter borger has responded

Replies to this message:
 Message 24 by peter borger, posted 07-29-2002 9:17 PM singularity has responded

  
peter borger
Member (Idle past 6002 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 21 of 66 (14418)
07-29-2002 8:51 PM
Reply to: Message 18 by John
07-26-2002 10:43 PM


Excellent!

This message is a reply to:
 Message 18 by John, posted 07-26-2002 10:43 PM John has not yet responded

  
peter borger
Member (Idle past 6002 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 22 of 66 (14420)
07-29-2002 9:05 PM
Reply to: Message 19 by singularity
07-27-2002 10:58 PM


Dear Shane,

You write:
"unobservable and unreproducible, otherwise it falls within the bounds of science. Can God can only exist by not existing?????"

I think that you cannot interchange the words "observe" and "exist". Some things may not be observed but may be existing. For instance, consider organisms that aren't able to observe light. Does it say anything about the existence of light? No. It is just a matter of having the right receptors, or to tune in the right receptors.

And:
"gaia hypothesis"
It is pretty much a hypothesis and very timely.

have a nice day
Peter


This message is a reply to:
 Message 19 by singularity, posted 07-27-2002 10:58 PM singularity has not yet responded

Replies to this message:
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John
Inactive Member


Message 23 of 66 (14422)
07-29-2002 9:17 PM
Reply to: Message 22 by peter borger
07-29-2002 9:05 PM


quote:
Originally posted by peter borger:
I think that you cannot interchange the words "observe" and "exist". Some things may not be observed but may be existing. For instance, consider organisms that aren't able to observe light. Does it say anything about the existence of light? No. It is just a matter of having the right receptors, or to tune in the right receptors.


I agree about interchanging the words 'observe' and 'exist'

The problem I see is that without observation there is no evidence, no common ground. Anything can be postulated as existing and no one can prove the postulate true or false, so long as it cannot be observed. It is a fundamental philosophical problem.

Belief in a very real sense boils down to evidence-- ie observable data-- or no evidence. Science deals with what we can know, not what we can't.

------------------
www.hells-handmaiden.com


This message is a reply to:
 Message 22 by peter borger, posted 07-29-2002 9:05 PM peter borger has not yet responded

  
peter borger
Member (Idle past 6002 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 24 of 66 (14423)
07-29-2002 9:17 PM
Reply to: Message 20 by singularity
07-27-2002 11:13 PM


dear Shane,

You write:
"Do you perhaps think that the origin of life and the universe as a whole is irrelevant to modern existance"

Yes. Science tries hard to explain things that have never been observed. In my opinion that is gratuitous. It should not be the realm of science.

And:
"primitive isolated tribe in Malaysia discovered in the late 20th century which had no such mythology"

If I recall properly, the alleged isolated Malaysian stone age tribe without origin-mythology was a hoax.

Best wishes
Peter


This message is a reply to:
 Message 20 by singularity, posted 07-27-2002 11:13 PM singularity has responded

Replies to this message:
 Message 25 by John, posted 07-29-2002 9:38 PM peter borger has not yet responded
 Message 27 by singularity, posted 07-29-2002 11:07 PM peter borger has responded

  
John
Inactive Member


Message 25 of 66 (14428)
07-29-2002 9:38 PM
Reply to: Message 24 by peter borger
07-29-2002 9:17 PM


quote:
Originally posted by peter borger:
Yes. Science tries hard to explain things that have never been observed. In my opinion that is gratuitous. It should not be the realm of science.

Science cannot infer?

quote:
If I recall properly, the alleged isolated Malaysian stone age tribe without origin-mythology was a hoax.

It is hard to believe that a culture would have no origin myth. Anyone know the name of this tribe?

------------------
www.hells-handmaiden.com


This message is a reply to:
 Message 24 by peter borger, posted 07-29-2002 9:17 PM peter borger has not yet responded

  
peter borger
Member (Idle past 6002 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 26 of 66 (14440)
07-29-2002 10:37 PM
Reply to: Message 15 by singularity
07-26-2002 4:37 AM


dear Shane,

You write:
"....but I think more work in to the recently discovered nanobes from deep sediments might be more crucial."

So I checked the claims about nanobes. If you have a look in biological scientific literature "nanobes" do not get a single hit (try NCBI homepage search program). This clearly demonstrates that they are not considered to be organisms. Furthermore I've read the article by Phillipa Uwins et al (American Minarologist, volume 83, p1541-1550.)
The authors claim a lot.
1) nanobes grow = unwarranted conclusion. Probably it is nothing but crystalisation/polymerisation,
2) nanobes have a heterotrophic metabolism = unwarranted conclusion. polymerisation requires monomers from their environment,
3) nanobes resemble actinomycetes and fungi = so what, there are piles of rock on Mars that resemble a face,
4) nanobes are composed of C, O, and N and that is consistent with living matter = unwarrented conclusion. The atmosphere is also composed of C, O and N.
5) nanobes appear to be membrane bound structures, a cytoplasma and nuclear area = unwarranted conclusion. All they show is that nanobes are morhological distinct microvessels.
6) nanobes have amorphic wall structres = sowhat. Stones have amorphic wall structures.
7) nanobes contain DNA as indicated by DAPI, Acridine orange and Feulgen staining = unwarranted conclusion. The nanobes may stain aspecificly. They did not include negative controls. They did not isolate DNA (very simple procedure).

My conclusion: this article is a hoax. If it really had been something it would have been published in Nature, Science or other leading scientific journal. Don't believe the hype!

best wishes,
Peter


This message is a reply to:
 Message 15 by singularity, posted 07-26-2002 4:37 AM singularity has responded

Replies to this message:
 Message 29 by singularity, posted 07-30-2002 12:58 AM peter borger has responded

  
singularity
Inactive Member


Message 27 of 66 (14450)
07-29-2002 11:07 PM
Reply to: Message 24 by peter borger
07-29-2002 9:17 PM


Hi Peter

I will admit to not knowing the full background of the stone age malaysian tribe story- it was more to illustrate the point that all societies seem to need some story of their ultimate origin (being a hoax fits this suggestion). We are all compelled to take sides in this debate to varying degrees.

More importantly I think a self consistent concept of where we came from is very important if we are going to take control of our future. Taken to the extreme religious fundamentalism can be used as justification for plundering our environment and endangering our survival as a species based on the premise that we are going to a better place anyway (or worse as in the heavens gate sect). If this world is just a soul sorting machine with a rapidly approaching use by date as suggested in christian theology then we don't owe it to future generations to keep it habitable. Evolution gives us a more progressive philosophy, with room for cooperation and altruism along side competition and progress. It places more importance on our children's survival than on some intangible reward (ala "eat all your dogma and you can have heaven for dessert").

I also think few would try to argue against the proposition that science has offered many more tangible benefits to its "followers" than any religion (despite circumcision and compulsive handwashing by early christians). How many people could say with any authority that they would rather live in a prescientific society such as the middle ages?

Lastly you said:

>Science tries hard to explain things that have never been observed. In >my opinion that is gratuitous. It should not be the realm of science.

I think it would be gratuitous if science was presented as irrefutable, but the basis of science is that it thrives on change. In contrast religious advocates also "try hard to explain things that have never been observed" and then attempt to present them in a factual context that is both inflexible and untestable.

I will admit that there is in scientific fields a necessary inertia against changing basic ideas and that most scientists conduct their work by using previous results as a premise. But any scientist would leap at the opportunity to rewrite a basic principle if they could produce the evidence for it. Einstein's refinement of gravitational theory is a good example. Once the first substantial evidence was found the field took off and as the theory was further substantiated it became generally accepted.

I think it is reasonable to highlight the limitations in our current understanding of the details of evolution (not surprising given the fact we have only had reasonable genetic tools for the last 10 years) but to dismiss it without offering a more plausable (and testable) alternative that fits all the evidence gathered so far does nothing to further our understanding of the origin of biological diversity.

Shane


This message is a reply to:
 Message 24 by peter borger, posted 07-29-2002 9:17 PM peter borger has responded

Replies to this message:
 Message 28 by peter borger, posted 07-30-2002 12:13 AM singularity has responded

  
peter borger
Member (Idle past 6002 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 28 of 66 (14458)
07-30-2002 12:13 AM
Reply to: Message 27 by singularity
07-29-2002 11:07 PM


Dear Shane,

You write:
"I think it is reasonable to highlight the limitations in our current understanding of the details of evolution (not surprising given the fact we have only had reasonable genetic tools for the last 10 years) but to dismiss it without offering a more plausable (and testable) alternative that fits all the evidence gathered so far does nothing to further our understanding of the origin of biological diversity."

With our reasonable genetic and molecular biological tools it has become clear that evolution theory cannot account for:
1) the origin of life,
2) the origin of genes,
3) (the origin of) biodiversity.
So, in conclusion: Darwin was wrong, and so are all evolution biologists. It will take ages before they will admit this, since there is no naturalistic alternative. Evolution theory is the best naturalistic explanation they have. Frankly, I am not interested in the best naturalistic explanation as it is not in accord with our observations. I am interested in truth. I don't mind whether the truth should include a Creator.

In addition, there are scientific alternatives. They do not include the origin of life and the origin of genes (because of the principle of genetic uncertainty), but they can be tested by the predictions they do.
Best Wishes
Peter

[This message has been edited by peter borger, 07-29-2002]


This message is a reply to:
 Message 27 by singularity, posted 07-29-2002 11:07 PM singularity has responded

Replies to this message:
 Message 31 by singularity, posted 07-30-2002 3:24 AM peter borger has responded

  
singularity
Inactive Member


Message 29 of 66 (14460)
07-30-2002 12:58 AM
Reply to: Message 26 by peter borger
07-29-2002 10:37 PM


Hi Peter

In response to your points:

>1) nanobes grow = unwarranted conclusion. Probably it is nothing but crystalisation/polymerisation.

Nanobes are non-crystalline for one thing. Secondly they appear to grow on a variety of common surfaces (glass, copper or polystyrene). If it was a simple polymerisation process then why have nanobe colonies never been observed on these surfaces unless they have been exposed to sandstone samples from the sea bed? What is the magic ingredient if not life of some kind? If it is an inorganic process then why does the process occur the same way on different substrates?

2) nanobes have a heterotrophic metabolism = unwarranted conclusion. polymerisation requires monomers from their environment,

The authors never conclude that they have established the metabolism of nanobes in their original paper (American Mineralogist, Vol 83, 1541-1550 (1998)). They only state that the preferential growth of nanobe colonies on areas later found to have organic contamination from human fingerprints in the petri dishes suggests that nanobes have some need for organic substrates (ie are heterotrophic). And don't jump up and down about the contamination issue- it doesn't change the fact that nanobes were originally observed in the sandstone samples or more importantly that nanobes have been observed.

>3) nanobes resemble actinomycetes and fungi = so what, there are piles of rock on Mars that resemble a face.

And tortias that resemble jesus.....

I think it is not an unwarranted observation that something which they are proposing may be a living organism looks very similar to known living organism (except for being an order of magnitude smaller). It is a necessary part of the argument- looks like life-> behaves like life-> is chemically consistent with life---> might be life
This observation is only part of the argument. If it looked nothing like life that would be a form of contrary evidence. They are establishing the lack of contrary morphological evidence.

4) nanobes are composed of C, O, and N and that is consistent with living matter = unwarrented conclusion. The atmosphere is also composed of C, O and N.

You are ignoring the details here. The composition of the atmosphere is C:N of about 1:70:29 from memory. The nanobes C:N is about 60:10:30 (from figure 9 in the original article). This is about the same as it observed for living organisms. More importantly there is insufficient metal or counterion present to suggest the formations are mineral in nature. Again showing a lack of contrary evidence.

>5) nanobes appear to be membrane bound structures, a cytoplasma and nuclear area =unwarranted conclusion. All they show is that nanobes are morhological distinct microvessels.

In one image there is a suggestion of a darker area toward the centre of the cavity which they suggest as a possible nuclear area, but could just as easily be a sectioning artifact given the difficulties they report in preparing the TEM samples. The conclusion that they observed membrane bound structures is fairly hard to dispute though. Again this is a small but essential piece of the whole argument.

6) nanobes have amorphic wall structres = sowhat. Stones have amorphic wall structures.

This is a big misunderstanding. Stones have distinct crystalline structure on a microscopic scale. Other examples of microscopic bodies which were mistaken for organisms based on morphology alone have crystalline microstructure. They are rightly eliminating the possibility these structures are mineral in nature.

7) nanobes contain DNA as indicated by DAPI, Acridine orange and Feulgen staining =unwarranted conclusion. The nanobes may stain aspecificly. They did not include negative controls. They did not isolate DNA (very simple procedure).

DAPI displays a specific flouresence when it binds to AT rich DNA sequences and is the best indication DNA presented in the paper but is admittedly qualitative. They did not isolate DNA for two reasons. Firstly they are a microscopy group rather than a microbiology/genetics group. Secondly isolation of DNA is not always a "very simple procedure", especially when working with tissues which have never been successfully extracted before. The nanobes display unusual cell wall properties, grow slowly and represent a very small sample as individual colonies- all of which would impede DNA isolation.
Even if the DNA tests are false positives the organisms may not contain DNA but could still be considered living. Their size is not inconsistent with a different mode of reproduction. Too much is unknown at this stage.

My conclusion is the same as theirs: it could be a new form of life but more research is needed. Your implication that the absence of any papers in the biological literature suggests nanobes a hoax is a bit of a stretch. Would a search of the astronomical literature of 1700 AD have proved that pluto didn't exist? Try to stick to the reported evidence even though it is limited at this stage. At the very worst this could be a misinterpretation of some very compelling initial evidence. Bacteria slightly larger than nanobes (200nm) have been isolated and genotyped so the interpretation isn't unreasonable.

Shane


This message is a reply to:
 Message 26 by peter borger, posted 07-29-2002 10:37 PM peter borger has responded

Replies to this message:
 Message 30 by peter borger, posted 07-30-2002 2:43 AM singularity has responded

  
peter borger
Member (Idle past 6002 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 30 of 66 (14466)
07-30-2002 2:43 AM
Reply to: Message 29 by singularity
07-30-2002 12:58 AM


dear Shane,

You say in reply:
1) "What is the magic ingredient if not life of some kind?"
A carefull scrutiny will reveal that this proces has nothing in common with life. Probably it is a selfpropagating reaction.

2) "organic contamination from human fingerprints in the petri dishes suggests that nanobes have some need for organic substrates..."

..to attach to.

And:
"..nanobes were originally observed in the sandstone samples"

Sandstone containing N and C?

3) "I think it is not an unwarranted observation.."
You are free to think whatever you like.

And:
"It is a necessary part of the argument- looks like life-> behaves like life-> is chemically consistent with life---> might be life"

I do not follow your logic. Firstly, "it looks like life" is an utterly subjective observation. Maybe someone else doesn't think it looks like life. Maybe it resembles some filamentous micro-organisms, but so do carpet fibers. As mentioned before, even if you find molecules that have a similar consistency as biomolecules it doesn't say anything. It is a fallacy similar to: blood and seawater have similar levels of ions, so our ancestor was an aquatic ape (this has actually been proposed by some evolutionist). These fallacies are called non-sequiturs, meaning that the conclusions drawn are not followed from the evidence presented.

4) "The composition of the atmosphere is C:N of about 1:70:29 from memory. The nanobes C:N is about 60:10:30 (from figure 9 in the original article). This is about the same as it observed for living organisms. More importantly there is insufficient metal or counterion present to suggest the formations are mineral in nature."

One doesn't need ions to polymerise.

5) "In one image there is a suggestion of a darker area toward the centre of the cavity which they suggest as a possible nuclear area, but could just as easily be a sectioning artifact given the difficulties they report in preparing the TEM samples. The conclusion that they observed membrane bound structures is fairly hard to dispute though. Again this is a small but essential piece of the whole argument."

You cannot present the nanobes as having a nucleus based on this observation. They do not show any membrane bound structures. It is wishful thinking.

6) "This is a big misunderstanding. Stones have distinct crystalline structure on a microscopic scale. Other examples of microscopic bodies which were mistaken for organisms based on morphology alone have crystalline microstructure. They are rightly eliminating the possibility these structures are mineral in nature."

What is the big deal being not of mineral nature. They've already shown that the nanodes are non-mineral of nature. So it may be not stones, but it certainly has nothing in common with life.

7) "DAPI displays a specific flouresence when it binds to AT rich DNA sequences and is the best indication DNA presented in the paper but is admittedly qualitative. They did not isolate DNA for two reasons. Firstly they are a microscopy group rather than a microbiology/genetics group."

This is no argument. They could have asked anybody in their institute to provide conclusive evidence of the nature of the DNA. If they send the nanobe to me I will extract the DNA (if present).

And:
"Secondly isolation of DNA is not always a "very simple procedure", especially when working with tissues which have never been successfully extracted before."

This is also no argument. If DNA is involved it can be extracted. The authors claim that they are able to see the nanobes-colonies by eye, thus indicating that heaps of DNA can be isolated. (By the way how do you think these nanobes synthesise their DNA?)

"The nanobes display unusual cell wall properties, grow slowly and represent a very small sample as individual colonies- all of which would impede DNA isolation."

You are mislead by the author's jargon: cell growth, cell walls, membranes, DNA etc.

And:
"Even if the DNA tests are false positives the organisms may not contain DNA but could still be considered living. Their size is not inconsistent with a different mode of reproduction. Too much is unknown at this stage."

That would be something and I expect to read it in Nature or Science, not in the American Mineralogist.

7) "DAPI displays a specific flouresence when it binds to AT rich DNA sequences and is the best indication DNA presented in the paper but is admittedly qualitative."

And may also bind aspecifically to C-N-0 compounds. As long as the authors do not include appropriate controls I am not able to interpret their results.

You say:
"My conclusion is the same as theirs: it could be a new form of life but more research is needed."

Your conclusion is unwarranted.

Question: Why hasn't a follow up of this study been published on DNA isolation? There was ample time since 1998.
Answer: Because there is no DNA involved.

best wishes
Peter


This message is a reply to:
 Message 29 by singularity, posted 07-30-2002 12:58 AM singularity has responded

Replies to this message:
 Message 32 by singularity, posted 07-30-2002 4:48 AM peter borger has responded

  
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