DNA Was Designed By A Mind

parados wrote:

real life wrote:

parados wrote:

real life wrote:

I guess I understood his reference to the 'lethal defect' in the rna world hypothesis coupled with his nonbelief in miracles ( he quotes approvingly of the need to 'reject improbabilities') to be fairly conclusive.

But have it your way. There COULDA been a miracle, you're right.

Really? You understood it? LOL.. yeah.. I guess you agree with what you "understood". You just don't agree with Shapiro.

So what do you think he means when he cites others that urge us to 'reject improbabilities' ?

Robert Shapiro, Professor Emeritus and Senior Research Scientist in the Department of Chemistry at New York University wrote:

Nobel Laureate Christian de Duve has called for "a rejection of improbabilities so incommensurably high that they can only be called miracles, phenomena that fall outside the scope of scientific inquiry." DNA, RNA, proteins and other elaborate large molecules must then be set aside as participants in the origin of life.

Seems like you've taken the opposite approach.

Not at all. RNA is created in a container. Whether the container it is in is considered life or not is irrelevant in the discussion of how RNA came about. Shapiro only says it is improbable for the container to have been dead prior to RNA forming.

What he says is that he rejects the improbable 'rna world' scenario.

Robert Shapiro, Professor Emeritus and Senior Research Scientist in the Department of Chemistry at New York University wrote:

"In the very beginning, you couldn't have genetic material that could copy itself unless you had chemists back then doing it for you," Shapiro told LiveScience.

from http://www.livescience.com/animals/060609_life_origin.html

I'm pretty sure he's not saying it COULDA happened.

A possible candidate for Shapiro's driver reaction might have been recently discovered in an undersea microbe, Methanosarcina acetivorans, which eats carbon monoxide and expels methane and acetate (related to vinegar).

Biologist James Ferry and geochemist Christopher House from Penn State University found that this primitive organism can get energy from a reaction between acetate and the mineral iron sulfide. Compared to other energy-harnessing processes that require dozens of proteins, this acetate-based reaction runs with the help of just two very simple proteins.

The researchers propose in this month's issue of Molecular Biology and Evolution that this stripped-down geochemical cycle was what the first organisms used to power their growth. "This cycle is where all evolution emanated from," Ferry says. "It is the father of all life."

real life wrote:

parados wrote:

real life wrote:

And if they did successfully replicate when 'physical forces split them' what was the imperative to develop rna or a replicator of any kind?

Who says there is an "imperative"? Other than you? Evolution isn't driven by "imperatives".

Evolving a huge molecule such as a replicator would be very 'expensive' in terms of resources for a small organism.

Based on what? What are your assumptions on the resources? What are you assumptions on the energy source? If evolving a huge molecule would be "expensive" for a small organism then how can a small organism have DNA? Isn't it too expensive in resources? Your argument lacks sense based on what is presently found in microorganisms. Organisms often have more resources available to them than they can ever use.

Quote:

If the critter is already successfully replicating, what would the 'survival advantage' be vs. the extreme amount of resources needed within a limited space to develop such a massive molecule?

What extreme amount of resources? The energy required for a microorganism is not large compared to the energy sources used by present microorganisms. Microorganisms don't begin to stress the sun's energy. They don't use all the energy of vulcanism when they are found there. They don't use all the energy of any energy source that I can think of. Resources? What resources are limited? If life forms on clay, there is no way that life could use all the resources available to it since the clay compared to the microorganism is almost infinite. Carbon is certainly not severely limited in supply on the earth. Nor is hydrogen or oxygen. The only thing an organism requires is that available resources are replenished in some way. Something that is quite common on the earth. Water flows and moves chemical from one spot to another. Life as we know it wouldn't exist without the movement of chemicals on the earth. Water percolates through the earth while leaching out chemicals. All that is required is that the chemicals be delivered to the organism in a manner that makes it available without destroying the organism. (Osmosis might be something you want to investigate.)

Your argument that a microorganism has limited resources is completely false.

real life wrote:

parados wrote:

real life wrote:

parados wrote:

real life wrote:

I guess I understood his reference to the 'lethal defect' in the rna world hypothesis coupled with his nonbelief in miracles ( he quotes approvingly of the need to 'reject improbabilities') to be fairly conclusive.

But have it your way. There COULDA been a miracle, you're right.

Really? You understood it? LOL.. yeah.. I guess you agree with what you "understood". You just don't agree with Shapiro.

So what do you think he means when he cites others that urge us to 'reject improbabilities' ?

Robert Shapiro, Professor Emeritus and Senior Research Scientist in the Department of Chemistry at New York University wrote:

Nobel Laureate Christian de Duve has called for "a rejection of improbabilities so incommensurably high that they can only be called miracles, phenomena that fall outside the scope of scientific inquiry." DNA, RNA, proteins and other elaborate large molecules must then be set aside as participants in the origin of life.

Seems like you've taken the opposite approach.

Not at all. RNA is created in a container. Whether the container it is in is considered life or not is irrelevant in the discussion of how RNA came about. Shapiro only says it is improbable for the container to have been dead prior to RNA forming.

What he says is that he rejects the improbable 'rna world' scenario.

Robert Shapiro, Professor Emeritus and Senior Research Scientist in the Department of Chemistry at New York University wrote:

"In the very beginning, you couldn't have genetic material that could copy itself unless you had chemists back then doing it for you," Shapiro told LiveScience.

from http://www.livescience.com/animals/060609_life_origin.html

I'm pretty sure he's not saying it COULDA happened.

Yep, if you read the ENTIRE quote. Shapiro says life started from dead chemicals. He also says that RNA was created in a containerized life form.

But you really missed this part.. (on purpose?)

Quote:

A possible candidate for Shapiro's driver reaction might have been recently discovered in an undersea microbe, Methanosarcina acetivorans, which eats carbon monoxide and expels methane and acetate (related to vinegar).

Biologist James Ferry and geochemist Christopher House from Penn State University found that this primitive organism can get energy from a reaction between acetate and the mineral iron sulfide. Compared to other energy-harnessing processes that require dozens of proteins, this acetate-based reaction runs with the help of just two very simple proteins.

The researchers propose in this month's issue of Molecular Biology and Evolution that this stripped-down geochemical cycle was what the first organisms used to power their growth. "This cycle is where all evolution emanated from," Ferry says. "It is the father of all life."

Shapiro is skeptical: Something had to form the two proteins. But he thinks this discovery might point in the right direction. "We have to let nature instruct us," he says.

Did DNA replication evolve twice independently?[/size]

Leipe DD, Aravind L, Koonin EV.
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Bethesda, MD 20894, USA.

DNA replication is central to all extant cellular organisms. There are substantial functional similarities between the bacterial and the archaeal/eukaryotic replication machineries, including but not limited to defined origins, replication bidirectionality, RNA primers and leading and lagging strand synthesis. However, several core components of the bacterial replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic replication apparatus. This is in sharp contrast to the principal proteins involved in transcription and translation, which are highly conserved in all divisions of life. We performed detailed sequence comparisons of the proteins that fulfill indispensable functions in DNA replication and classified them into four main categories with respect to the conservation in bacteria and archaea/eukaryotes: (i) non-homologous, such as replicative polymerases and primases; (ii) containing homologous domains but apparently non-orthologous and conceivably independently recruited to function in replication, such as the principal replicative helicases or proofreading exonucleases; (iii) apparently orthologous but poorly conserved, such as the sliding clamp proteins or DNA ligases; (iv) orthologous and highly conserved, such as clamp-loader ATPases or 5'-->3' exonucleases (FLAP nucleases). The universal conservation of some components of the DNA replication machinery and enzymes for DNA precursor biosynthesis but not the principal DNA polymerases suggests that the last common ancestor (LCA) of all modern cellular life forms possessed DNA but did not replicate it the way extant cells do. We propose that the LCA had a genetic system that contained both RNA and DNA, with the latter being produced by reverse transcription. Consequently, the modern-type system for double-stranded DNA replication likely evolved independently in the bacterial and archaeal/eukaryotic lineages

Unless you want to argue that the early lipid membrane envisioned by Shapiro is actually a sophisticated semipermeable membrane, then the critter only has use of what's inside.

Tiny critter = Very limited resources.

Quote:

Shapiro is skeptical: Something had to form the two proteins. But he thinks this discovery might point in the right direction. "We have to let nature instruct us," he says.

Shapiro is by no means considered on board.

Brandon9000 wrote:

His approach is apparently to attack us for not having proof of every step in our reasoning, and then to pretend not to see when we ask him for evidence to support his own beliefs. I would think that it would be apparent even to him how unfair that is.

What's unfair, Mr. 'We Have the Exact Mechanics Down' ?

You are the guys who claim, 'we've got all the evidence and you've got none'.

So why's it unfair to ask you to produce evidence?

real life wrote:

Quote:

Shapiro is skeptical: Something had to form the two proteins. But he thinks this discovery might point in the right direction. "We have to let nature instruct us," he says.

Shapiro is by no means considered on board.

skeptical of that being the initial life but not skeptical of life forming from dead chemicals.

Interesting stuff here.

Quote:

Did DNA replication evolve twice independently?[/size]

Leipe DD, Aravind L, Koonin EV.
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Bethesda, MD 20894, USA.

DNA replication is central to all extant cellular organisms. There are substantial functional similarities between the bacterial and the archaeal/eukaryotic replication machineries, including but not limited to defined origins, replication bidirectionality, RNA primers and leading and lagging strand synthesis. However, several core components of the bacterial replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic replication apparatus. This is in sharp contrast to the principal proteins involved in transcription and translation, which are highly conserved in all divisions of life. We performed detailed sequence comparisons of the proteins that fulfill indispensable functions in DNA replication and classified them into four main categories with respect to the conservation in bacteria and archaea/eukaryotes: (i) non-homologous, such as replicative polymerases and primases; (ii) containing homologous domains but apparently non-orthologous and conceivably independently recruited to function in replication, such as the principal replicative helicases or proofreading exonucleases; (iii) apparently orthologous but poorly conserved, such as the sliding clamp proteins or DNA ligases; (iv) orthologous and highly conserved, such as clamp-loader ATPases or 5'-->3' exonucleases (FLAP nucleases). The universal conservation of some components of the DNA replication machinery and enzymes for DNA precursor biosynthesis but not the principal DNA polymerases suggests that the last common ancestor (LCA) of all modern cellular life forms possessed DNA but did not replicate it the way extant cells do. We propose that the LCA had a genetic system that contained both RNA and DNA, with the latter being produced by reverse transcription. Consequently, the modern-type system for double-stranded DNA replication likely evolved independently in the bacterial and archaeal/eukaryotic lineages

http://www.ncbi.nlm.nih.gov/pubmed/10446225

real life wrote:

Unless you want to argue that the early lipid membrane envisioned by Shapiro is actually a sophisticated semipermeable membrane, then the critter only has use of what's inside.

Shapiro didn't restrict his container to a lipid membrane. it was one of the choices he lists but is not the only one.

Dishonesty from you again real life.

parados wrote:

real life wrote:

Quote:

Shapiro is skeptical: Something had to form the two proteins. But he thinks this discovery might point in the right direction. "We have to let nature instruct us," he says.

Shapiro is by no means considered on board.

skeptical of that being the initial life but not skeptical of life forming from dead chemicals.

how do I say this tactfully..................

without initial life, there is no other life

(you can't win if you don't play)

real life wrote:

Interesting stuff here.

Quote:

Did DNA replication evolve twice independently?[/size]

Leipe DD, Aravind L, Koonin EV.
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Bethesda, MD 20894, USA.

DNA replication is central to all extant cellular organisms. There are substantial functional similarities between the bacterial and the archaeal/eukaryotic replication machineries, including but not limited to defined origins, replication bidirectionality, RNA primers and leading and lagging strand synthesis. However, several core components of the bacterial replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic replication apparatus. This is in sharp contrast to the principal proteins involved in transcription and translation, which are highly conserved in all divisions of life. We performed detailed sequence comparisons of the proteins that fulfill indispensable functions in DNA replication and classified them into four main categories with respect to the conservation in bacteria and archaea/eukaryotes: (i) non-homologous, such as replicative polymerases and primases; (ii) containing homologous domains but apparently non-orthologous and conceivably independently recruited to function in replication, such as the principal replicative helicases or proofreading exonucleases; (iii) apparently orthologous but poorly conserved, such as the sliding clamp proteins or DNA ligases; (iv) orthologous and highly conserved, such as clamp-loader ATPases or 5'-->3' exonucleases (FLAP nucleases). The universal conservation of some components of the DNA replication machinery and enzymes for DNA precursor biosynthesis but not the principal DNA polymerases suggests that the last common ancestor (LCA) of all modern cellular life forms possessed DNA but did not replicate it the way extant cells do. We propose that the LCA had a genetic system that contained both RNA and DNA, with the latter being produced by reverse transcription. Consequently, the modern-type system for double-stranded DNA replication likely evolved independently in the bacterial and archaeal/eukaryotic lineages

http://www.ncbi.nlm.nih.gov/pubmed/10446225

Interesting isn't it that life could exist without double stranded DNA? DNA might have evolved after organisms already existed.

Didn't you claim it couldn't real life? Hmm.. really interesting. Real life is more than happy to post stuff without seeing the real implications of it.

real life wrote:

parados wrote:

real life wrote:

Quote:

Shapiro is skeptical: Something had to form the two proteins. But he thinks this discovery might point in the right direction. "We have to let nature instruct us," he says.

Shapiro is by no means considered on board.

skeptical of that being the initial life but not skeptical of life forming from dead chemicals.

how do I say this tactfully..................

without initial life, there is no other life

(you can't win if you don't play)

Don't worry about tact real life.

You might want to worry about intelligence in posting articles that dispute your claim.

So.. does the last article you posted contain "evidence?" I am just curious as to why you posted it.

real life wrote:

Tiny critter = Very limited resources.

Really? Based on what?

So if you give a microorganism unlimited resources it won't be tiny any longer? What happens to it real life?

parados wrote:

real life wrote:

Unless you want to argue that the early lipid membrane envisioned by Shapiro is actually a sophisticated semipermeable membrane, then the critter only has use of what's inside.

Shapiro didn't restrict his container to a lipid membrane. it was one of the choices he lists but is not the only one.

Dishonesty from you again real life.

I gave you the option of proposing a much more advanced membrane. Go for it.

(hint: think about why Shapiro, an award winning chemist, DIDN'T propose a more advance membrane)

They are not proposing that living organisms existed without DNA.

parados wrote:

real life wrote:

Tiny critter = Very limited resources.

Really? Based on what?

So if you give a microorganism unlimited resources it won't be tiny any longer? What happens to it real life?

It's not how many resources are in the neighborhood , it's how and if they are able to control those resources.

Organisms are able to absorb some substances and reject others.

Also they are able to excrete some substances and retain others.

The proposed 'lipid membrane' would be a significant hindrance to absorption, excretion , etc.

How does the critter keep toxic waste product from building up inside?

How does the critter 'feed' itself with a fresh supply of chemicals that it needs to keep the metabolic activity going?

Today, sophisticated double-layered cell membranes, made of chemicals classified as lipids, separate living cells from their environment. When life began, some natural feature probably served the same purpose. David W. Deamer of the University of California, Santa Cruz, has observed membrane-like structures in meteorites. Other proposals have suggested natural boundaries not used by life today, such as iron sulfide membranes, mineral surfaces (in which electrostatic interactions segregate selected molecules from their environment), small ponds and aerosols.

real life wrote:

Brandon9000 wrote:

His approach is apparently to attack us for not having proof of every step in our reasoning, and then to pretend not to see when we ask him for evidence to support his own beliefs. I would think that it would be apparent even to him how unfair that is.

What's unfair, Mr. 'We Have the Exact Mechanics Down' ?

You are the guys who claim, 'we've got all the evidence and you've got none'.

So why's it unfair to ask you to produce evidence?

Because you simply ignore every request asking you to provide evidence for your theory of the formation of life on Earth. How many times do I have to say it?