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question for evolutionary biologist.

Discussion of everything related to the Theory of Evolution.

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Re: question for evolutionary biologist.

Postby Rap » Mon Aug 27, 2012 3:21 am

Look, lets be clear about what Ventner et. al. have done. They have taken the DNA from one species (A), tacked on some non-functional additions to the DNA to make it different, but functionally the same. They then inserted that DNA into the cell of a closely related species (B), and that B cell was transformed into a type A cell, functionally. If the DNA is like the "computer program" for the cell, all they did was add some comment lines to the code and insert it into a similar cell, and that B cell transformed to an A cell, functionally. They did not create nor engineer a new DNA in the functional sense. This is not to dismiss what they have done, because their next step is to start fiddling with the functional part of the DNA in order to learn how the cell works. How to understand the code rather than just read the code. Sure, they know every base pair in the DNA and what proteins are encoded by that DNA, but they don't fully understand the chemistry and mechanics of the cell that follows from this DNA and the proteins it creates.

Second of all, just because no evidence of life arising from non-life has been found does not constitute a proof that none exists. Typical "creationist" logic.

I mean, I believe in God, and I have faith that he created the universe, I just don't know how, and I don't ever expect to. The evidence for evolution and the logic of evolution is overwhelming, so I think (not believe!) that it is true, it's a small step on the path to understanding God's universe. Anyone frantically trying to disprove evolution because it denies God is arrogant and has little faith. Anyone who believes evolution denies God is also arrogant and has little faith. When it comes to life, we may be like cave men trying to understand what makes the sun go round. Oh, its Apollo, the sun god. No it isn't. Yes it is. It's such a tired, tired argument.
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Postby Forests » Mon Aug 27, 2012 5:47 pm

The only alternative to abiogenesis is creation, which is not exactly free of fairies. As I said, no one knows. The documentary crews weren't around, so all we can do is surmise. Some of us choose to believe in gods, some don't.


That is not fully true becuase there is also panspermia, see for example the book Intelligent Universe by Fred Hoyle. However panspermia does not need to completely replace abiogenesis, a bit of both may explain it.
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Re: question for evolutionary biologist.

Postby wbla3335 » Tue Aug 28, 2012 4:59 am

Panspermia is a mechanism for the dissemination of life, not its origin. Francis Crick was a proponent of panspermia for life on Earth.
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Re: question for evolutionary biologist.

Postby scottie » Tue Aug 28, 2012 11:23 am

Jackbean

It is Venter's claim that his team “created a new species without any biological precursor.”
It was he that referred to this as a “proof of concept”

If you have an argument with that, it is not with me but with real biologists and engineers.

Now your comment
And even if they have created something new, that doesn't mean it had to happen that way in nature.

They did create something new, and the “proof of concept” was the fact that this occurred by direct intervention from an outside source (his team). My argument is that this is the way species arrive and Venter has demonstrated that.

Now your argument is
“that doesn't mean it had to happen that way in nature.”


Well ok if that is the case, put out your own scenario as to how it happened. At the moment you are simply relying on a belief that nature can do this randomly and without direction.
Many brilliant minds have tried and they can't even agree amongst themselves.
So please, show how that can happen and we are in a serious scientific discussion.
If you can't then your view is based, not on science but on a philosophy.

What I say however is; don't conflate belief with science, because if you do then you are obliged to prove your belief scientifically.
Everyone is entitled to believe whatever they wish and there is nothing wrong with that. After all Wbla3335
believes in abiogenesis. Of course its not science, but nothing wrong with that. :)

He is also having great trouble in understanding the difference between creating life and creating a species.
Science by it very nature can't explain how life was created because science is constrained by natural laws.
Life is not a physio/chemical entity that can be explained by natural laws.
He also is having trouble understanding that, as I of course have in believing in fairies at the bottom of the garden. :)

Science however can and has explained and indeed demonstrated, how a new species without any biological precursor can be created. It is not a natural way because it had to be engineered by minds.

My argument is and has been that species did not arrive by the due process of natural laws.
Species have only arrived by some outside intervention.

Venter and his team have demonstrated this by his proof of concept bit of engineering.

Has anyone been able to provide a proof of concept of the natural processes?
The answer is a resounding No.

The more the science in cell biology is uncovered the more it demonstrates that natural processes could not have originated it. It had to have been engineered.

I will in my next post on the other thread point to the latest information on what constitutes a gene,
which take this point even further.
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Re:

Postby JackBean » Tue Aug 28, 2012 11:46 am

Forests wrote:
The only alternative to abiogenesis is creation, which is not exactly free of fairies. As I said, no one knows. The documentary crews weren't around, so all we can do is surmise. Some of us choose to believe in gods, some don't.


That is not fully true becuase there is also panspermia, see for example the book Intelligent Universe by Fred Hoyle. However panspermia does not need to completely replace abiogenesis, a bit of both may explain it.



And where does the panspermic life come from?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Postby JackBean » Tue Aug 28, 2012 11:47 am

I'm sure you will show me, where Venter said that this is proof of creation by God. Or is another example of your favourite quote mining?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Re: question for evolutionary biologist.

Postby wbla3335 » Tue Aug 28, 2012 5:56 pm

scottie wrote:I will in my next post on the other thread point to the latest information on what constitutes a gene, which take this point even further.

You needn't bother. No one here is particularly interested in your inability to understand science or your ability to misinterpret it. Believe in your god if you want. Believe that science supports your belief if you want. We have continually tried to show you how your "evidence" is misguided, but you're not listening. A deaf man cannot hear. A blind man cannot see. A closed mind can be opened, but only if it wants to be opened. Yours does not.
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Re: Re:

Postby Forests » Wed Aug 29, 2012 12:16 pm

JackBean wrote:
Forests wrote:
The only alternative to abiogenesis is creation, which is not exactly free of fairies. As I said, no one knows. The documentary crews weren't around, so all we can do is surmise. Some of us choose to believe in gods, some don't.


That is not fully true becuase there is also panspermia, see for example the book Intelligent Universe by Fred Hoyle. However panspermia does not need to completely replace abiogenesis, a bit of both may explain it.



And where does the panspermic life come from?


there is no origin for life, life has always existed but to answer your question it came from other planets. most scientists agree the big bang was not the start of everything only the early development of this Universe. perhaps there are an infinite amount of multiverses.

if we just equate existence with life then you will see the whole debate about God/s is futile. if life has always existed then where is the room for any external deity? how could an external God create anything if something has always existed? something has always existed so how could there be any external deity? even if god/s did exist then what came before the Gods?? you start thinking about it and it does not add up!! something has always existed and there is no reason to believe was a religious God.

having read the above someone will probably call me an atheist etc but i am not, in my opinion i believe the evidence supports pantheism. if we equate god with the universe itself ie in all matter then there is no external deity, god becomes the universe and that best fits the evidence in my view but it is still a philosophical view of the evidence and I cant go about proving it to anyone.
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Re: question for evolutionary biologist.

Postby Rap » Wed Aug 29, 2012 8:09 pm

Did Ventner et. al. invent a new species? They took the DNA from one species, added some non-functional "comment lines", removed the DNA from a closely related species, inserted the DNA-with-comment-lines into it, and the new cell was viable, functionally the same as the cell it came from.

If the original cell has the capacity to sexually reproduce, can it sexually reproduce with the new cell? If so, its not a new species. If it cannot, then it is a new species. If it does not sexually reproduce, what makes it a new species?
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Re: question for evolutionary biologist.

Postby scottie » Thu Sep 13, 2012 1:22 pm

Jackbean
I'm sure you will show me, where Venter said that this is proof of creation by God. Or is another example of your favourite quote mining?


Where have I stated
Venter said that this is proof of creation by God

Is raising this sort of fabrication, the only way you can debate?

Maybe your hope is that no one will actually read my posts and simply rely on your “creative quote mining” :)

Come come now, I was really hoping you could do better that this.

Rap
Did Ventner et. al. invent a new species? They took the DNA from one species, added some non-functional "comment lines", removed the DNA from a closely related species, inserted the DNA-with-comment-lines into it, and the new cell was viable, functionally the same as the cell it came from.

You are not accurate in your post. May I offer some corrections.
The source DNA was chemically synthesised.
You will find this paper from Venter's team helpful.
http://www.ncbi.nlm.nih.gov/nuccore/296455217

Their comment reads
The genome, which was designed based on Genbank Accession Number
CP001668 (Mycoplasma mycoides subs. capri str. GM12), was assembled
from chemically synthesized oligonucleotides. The sequenced genome
was isolated from a yeast clone. The sequenced clone is
sMmYCp235-1.

This synthetic genome contains all but 14 of the genes of wild type
Mycoplasma mycoides subspecies capri strain GM12. Among the genes
deleted from the genome are components of the ABC glycerol
transporter operon gtsABCD. These genes are involved in the
production of hydrogen peroxide, which is believed to be the
principal virulence factor of the mycoides group of mycoplasmas .
The genome also contains added watermark sequences for
identification of the genome as synthetic and also antibiotic
resistance markers to allow for selection. Overlapping cassettes of
1080 were assembled from chemically synthesized oligonucleotides.
The complete synthetic genome was assembled by transformation
associated recombination (TAR) cloning in the yeast Saccharomyces
cerevisiae, then isolated and sequenced. A clone with the correct
sequence was identified and transplanted in Mycoplama capricolum
subspecies capricolum recipient cells in which the restriction
modification system had been inactivated. This synthetic M. mycoide
genome can be isolated for future work.

The company that provided the initial synthesis was Blue Heron.
http://www.blueheronbio.com/Services/Ge ... hesis.aspx

I think you will find that the “old DNA” was not removed. It couldn't because the cell would have died.
The new DNA was inserted, and to prevent rejection the “restriction modification system” was inactivated.
If you listen to the video on Venter's site you will get a good idea as to what they actually did.
As to your comment about

If the original cell has the capacity to sexually reproduce, can it sexually reproduce with the new cell? If so, its not a new species. If it cannot, then it is a new species. If it does not sexually reproduce, what makes it a new species?

Firstly, your question is simply hypothetical.
The new cell does not reproduce sexually.

Venter describes it as a new species without a biological ancestor.
I would suggest you email him and ask him why he considers it a new species.
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Postby Rap » Thu Sep 13, 2012 6:30 pm

To scottie - being a computer programmer, I don't draw a distinction between a file containing code and another file with the identical code, as far as programming goes. That's what I meant by "taken from". Thanks for the quote - correct me if I am wrong, but, as I understand it, the constructed DNA is identical to the DNA of the first organism, except for a few non-vital deletions, and then an addition of a non-functional length of DNA.

Regarding whether it is a new species, I guess I don't know what constitutes a new species for an asexual organism. Any ideas? Maybe I _should_ email him.
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Re: question for evolutionary biologist.

Postby scottie » Mon Sep 17, 2012 7:55 pm

Rap
Sorry for the delay, I have only limited time to devote to this forum.
Thanks for clearing up my misunderstanding. Good to know your are a computer programmer. I have done some myself, mainly on 4GL relational database stuff
As far as the species point is concerned, the Venter Institute has a FAQ which I think helps.
http://www.jcvi.org/cms/research/projec ... -cell/faq/
They produced a clone of an existing genome and removed some 14 genes.
The syntheticM. mycoides organism has 14 genes deleted or inactivated, including genes that are predicted to be critical to virulence.

Question 9 of the FAQ provides some more information for you.
As far as species categorisation, this site may help.
http://www.mansfield.ohio-state.edu/~sa ... ol3010.htm

On a general point as to whether this is a completely new genome.
The answer is no, as this is just a first stage in that process.
This proof of principle or concept was to determine whether it was possible to create a genome and insert it into a cell. The best way was to construct a genome that was a copy of an existing one which they knew would work. That process took them 15 years.
The next stage then is to commence going down the road of constructing a new genome.

Incidentally the synthetic genome is somewhat different from that of the original even apart from the deletions. What you have referred to as the “non functional” lengths of DNA do actually actually function, however because the proteins produced are just fragments they are effectively neutral to the cellular production. They were able to create a new code for these "non function" lengths because there is a lot of redundant space in the triplet codon for 20 amino acids. There are 64 codons available and they took advantage of the additional 44 that could be used.

You will find the video of the press conference answers a lot of your questions. In particular the question and answer session from around 32 minutes in.
http://www.jcvi.org/cms/research/projec ... ell/video/

Hope this helps
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