What Craig Venter’s Synthetic Cell Says About the Origins Debate

A gentleman named Johan posted this as a comment and it was so good I felt it deserved it’s own blog post:

I couldn’t find any referral to the the Craig Venter Institute’s recent achievement.

Some atheists regard it as another blew to Christianity but in my view it is another scientific achievement that supports Perry’s hypothesis. It proved beyond doubt that DNA is a code . It also proved that DNA is able to code for any type or form of information. It is even able to store the names of the names of the relevant researchers etc.

Here is a quote from the the best open abstract summary I could find about their achievement that is not password protected:

As in the team’s 2008 publication in which they described the successful synthesis of the M. genitalium genome, they designed and inserted into the genome what they called watermarks. These are specifically designed segments of DNA that use the “alphabet” of genes and proteins that enable the researcher to spell out words and phrases. The watermarks are an essential means to prove that the genome is synthetic and not native, and to identify the laboratory of origin.

Encoded in the watermarks is a new DNA code for writing words, sentences and numbers. In addition to the new code there is a web address to send emails to if you can successfully decode the new code, the names of 46 authors and other key contributors and three quotations:

“TO LIVE, TO ERR, TO FALL, TO TRIUMPH, TO RECREATE LIFE OUT OF LIFE.”  -JAMES JOYCE

“SEE THINGS NOT AS THEY ARE, BUT AS THEY MIGHT BE.”  -A quote from the book, “American Prometheus”

“WHAT I CANNOT BUILD, I CANNOT UNDERSTAND.” – RICHARD FEYNMAN

The link: http://www.jcvi.org/cms/press/press-releases/full-text/article/first-self-replicating-synthetic-bacterial-cell-constructed-by-j-craig-venter-institute-researcher/

Absolute proof of the coding abilities of DNA.

I am a Gynecologist and an amateur Java programmer. The similarities between object orientated computing and DNA is amazing.

Continue the good work,

Johan

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19 Comments

Johan says:

When is something (anything) the result of a previous planned activity and when is it just a coincidence? This is the essence of arguments relating to the existence or nonexistence of God. Planning , designing , comprehension etc. are associated with intelligence.

How do we recognize or identify intelligence?

Imagine a radio telescope receiving the following signal . Will it be regarded as a sign of another intelligence? : _ . _. _. I doubt it.

But what about the following ? : _. _._._._. _._._._. _._. _._._._. _._._._.
_._._._. _._._._. _._._._. _._._. _._._._. _._._._. _. _._._._. _._._.
_._._._. _._._. _._._._. _._._. _._. _._._._. _._._. _._._. _._._._.
_._. _._. _._._._. _. _._. _._._._. _._._._. _._. _._._._.
_._._._. _. _. _._._. _._._._. _._._. _._._. _._. _. _.
_. _. _._._._. _._. _. _._._._. _._._. _. _. _._._. _. _._._._.
_. _. _. _._. _._._. _._._._. _._._._. _. _.

10 sec pause _._._._. _. _.
_._._._. _. _._._.
_._._._. _._._. _.

I think any comparable signal will cause quite a stir in scientific circles. The probability of an intelligent source will be very high on the list possible explanations.

A similar code was discovered on our planet but is regarded as the product of an accidental natural occurring event without intelligent guidance.

This is also the basic argument of Perry’s critics. Perry asks for a natural occurring code and the critics response is that the existence of the genetic code is prove enough . But is it?

This argument is comparable to the next.

There was a rock formation known as the “Finger of God” in Namibia . (It collapsed recently -Google “Finger of God”) There are also other examples of similar impressive rock formations. Thus “Stonehenge” was not created by humans but is just a unique natural arrangement of rocks .

The same people attacking Perry’s views will be the first to shoot this reasoning down, but does following arguments really differ? Nature can form amazing rock formations, thus “Stonehenge” is also such a phenomena. A self replicating molecule devolop spontaneously and was able due to this ability, to develop into RNA and DNA. Therefore this self replicating molecules was able to develop a sophisticated code that control life and even their
own replication.

Is the genetic code and the way it controls even the self replicating molecules’s replications a footprint ( finger print) of intelligence or not?

Carbon-based Machine says:

Johan, the “finger of god” rock formation is just a pattern. People can look at clouds and look for things like that. Stonehenge was not a naturally occurring rock formation. It was built by the ancient Brits (pre-Druidic times). Looking for this alleged self-replicating molecule that somehow converted over to living cells is futile, since such a molecule doesn’t exist and never did. With all our understanding of chemistry nowadays, we would have found it if it existed.

I have a question for Perry. How would your theory be affected if we discover life on another planet or moon?

GMEstes1 says:

Nasa scientists have discovered a methane haze surrounding Mars. Bacteria produce methane, the simplest organic molecule. Unfortunately the hostile environment seems to be destorying the molecules at a fast rate. I believe the finding are promising, enough that a manned mission to Mars is planning.
Viking Mission may have discovered simuliar bacteria but the probe caused a heat related chemical reaction that destroyed the bacteria?
I can’t see life on other planets affecting molecular life on earth, do you.

Look at http://www.telegraph.co.uk/science-news/4244904/Life-on-Mars-A-factfile.html

Johan says:

Carbon-based Machine.

It was never my intention to turn Stonehenge into a natural rock formation , but only to speculate why is it regarded as a structure built by humans, When Stonehenge’s structures are observed , it is immediately assumed that they were erected by humans. It is not necessary to do any research to prove that it is not a natural rock formation, we just know it is not. Why? They
are also just patterns, but patterns arrange in a why that let us instantly associate them with human behavior.

The self replicating molecule. The dificulties experienced in the quest for the origin of life, let some researches speculate about the idea of a self replicating molecule that preceded RNA and DNA.

DNA is a self replicating molecule. If contains the code for the polymerase enzymes necessary to allow it to make exact copies of itself. All die DNA in the cell nucleus is duplicated ( self replicated) prior to the onset of mitosis. The same happen prior to meiosis before chromosome pairing and exchange of genetic material.

In conditions that prevail in a laboratory, it is possible to replicate segments of RNA molecules without the necessity of an enzymatic catalyst . RNA molecules can act as catalysts to replicate themselves.( Although not as effectively as the enzymes). Catalysts are necessary to allow the different nucleotides to combine. These catalysts are necessary due to the very high energy levels
necessary for the nucleotides to combine. Catalysts allow these combination reactions to occur at much lower temperatures.

Carbon-based Machine says:

I hope that Perry will answer my question about finding life on another planet.

Johan, his main point is that there is a difference between a pattern and a design. DNA and RNA can replicate under the right circumstances, but for them to be successful codes, they must be arranged in a meaningful way. They’re not the alleged self-replicating molecule(s) that abiogenesis theories are looking for. DNA and RNA are also non-living in and of themselves, and they require other cellular machinery and organelles in order to reproduce meaningful information, and even to survive without being degraded. Understanding them at a chemical level is one thing, but they need to be understood at the informational level. Also, the coding would need to contain blueprints for the replication of not only the genetic material, but also for all the organelles, cellular processes, and their replication too. For intelligent design to be incorrect (at the biological level), these nanomachines with a complex programming language and self-replication abilities must have arisen by chance. I’ve taken college-level biology classes, and none of the theoretical abiogenesis hypotheses resolve this informational dilemma. Furthermore, the Miller-Urey experiment, for all practical purposes, demonstrated how unlikely random abiogenesis really is (despite their intentions).

I’m not sure what your point was regarding Stonehenge. There’s archaeological evidence that it was built by people. The ancient Egyptian pyramids have a better chance of being random rock formations than abiogenesis does of being random chemical processes. A cell phone probably has a better chance of randomly coming together than a living cell – even a nanobacterium.

GMEstes1 says:

Thank you for your comments.

I believe Mr. Marshall has presented the results after the DNA and RNA have developed themselves omitting the complete cycle. We reverse engineer the developed helix. The process doesn’t follow a prescribed set of instructions. It seems to be a gigsaw puzzle or trial and error pattern until the correct cell matches a place on the rung completing a rung on the helix.
There are a good many cells that are rejected never making the cut in development.
There doesn’t appear to be an -efficient- master builder assembling prefabricated cells.
If we can apply mathematical computations, a law can be developed.

GMEstes1 says:

Attachment to my previous post;
Mr. Marshall makes excellent presentations on the evolutionary process known as genetic engineering today. The word engineer infers a blue print and a blue print or drawing implies a planner and designer.
Mr. Marshall, for personal reasons, is convinced genetic engineering of the DNA helix is an ordered plan from an outside source. The outside source is intelligent as Mr. Gitt and Mr. Schroeder have proposed. They call the force God
because they see intelligence as the only force capable of producing an intelligent DNA and RNA Helix.
Mr. Marshall is applying the laws of physics to the laws of biological and chemical processes. The question arises, is this applicable and valid ?
Electricity and biology have origins in the subatomic or quantum relm.
Applying a signal generator and injecting noise in a circuit applies to computer and communication systems. Algorythoms produce a desired result through silicon control devices with a coded message of o’s and 1′s at the speed of light through a medium, air or copper.
Intar-Species communications doesn’t dwell on the speed of information rather, the end result with corrum sensing. It relies on the cell and encoded information being a completed and autonomus entity, as I understand it.
In cell integrity, I can’t escape the question of origin. I always end up with the question, where did my cells come from. We are all connected on a personal level to the Big Bang or the development of elements. Then I will evidentually work back to God and then to the question, where does God come from. From there I go one more step, either God always existed or a particle always existed. There is no answer. Only the evidence trail of matter, the physical world we live in. If I can see it and touch it it exist. I recognize me, therefore I am.
I’ll stay with developmental biology as my focus.

patrikbeno says:

http://www.ted.com/talks/craig_venter_unveils_synthetic_life.html

Perry, I guess Venter’s synthetic life proves at least following:

1) DNA can be made error-free by a conscious being, hence error correction mechanism in native DNA are a bit… redundant (and complicated and buggy but don’t mind that) .
2) synthetic life is mechanical. No need for consciousness to be present in these synthetic cells. It is possible without ever-present consciousness.

How do you reconcile this with your ideas?

Patrik, you always ask great questions.

1) Let’s suppose we strip out all the error correction mechanisms. What do you think the prospect for long-term survival will be for that species?

2) They transplanted DNA into a live cell and got it to reproduce based on the new instructions rather than the old one. To call this synthetic life is a half truth at best.

So my question is, do these cells communicate with other cells the way regular bacteria do? Do they do quorum sensing etc? Do they have words for “you” and “me” and “us”?

What parts of the genome code for this capability?

Interesting comment he makes, that one base pair error derailed the project for 3 months. “Accuracy is essential. There are parts of the genome where it will not tolerate a single error.”

patrikbeno says:

Perry,

I am not denying necessity of error correction mechanisms. Of course they are mandatory, for obvious reasons. All I am saying is that Venter managed to create error-free DNA replication, hence he was more successful than God Himself, because *our* DNA replication is error-prone (we need error correction routines just to fix copy errors). Why would anyone intentionally design error-prone copy function? Yet our DNA is error-prone. (This is not about fixing externally inflicted mutations. This is about internal inconsistencies.)

Whether the synthetic cells communicate is irrelevant. They replicate. They live. That is the definition of life, as far as I know.

They developed, simulated and tested it all in computer. In the end, it works same way in computer as in physical reality. No divine consciousness involved nor needed.

Furthermore, the host cell not only accepted useless synthetic chromosome. It also threw away part of the original chromosome (which we assume has been product of cell’s consciousness, hence it was more important than synthetic one, and meant something more essential than synthetic one). Yet synthetic chromosome wins. From this point of view, host cell’s integrity has been violated and its consciousness not only failed to keep its genome intact, it also blindly accepted useless substitute.

With respect to infamous DNA junk theory, this either says that there WAS a junk in DNA, or now IS, or both.

So, again, how do you reconcile?

“Venter managed to create error-free DNA replication”

I’m not sure what you’re trying to say here. Are you suggesting that the future generations of this cell will always be error proof?

They did not simulate it all on a computer. They simulated pieces of it on a computer and were successful enough to design a new genome for the cell. They did not model the entire operation of this cell on a computer. Not even close.

Notice that they didn’t produce this new genome with a series of random copying errors. Notice that in Venter’s press conference the cell has ZERO tolerance for error in some parts of the genome.

I don’t know whether the original chromosome was part of the cell’s consciousness or not. I do not even know if cells are conscious. I suspect that they could be.

You make it sound as though you think that I think that cells cannot be fooled. Or accept substitutes…. or ???? Please explain what you are trying to say.

You have on your computer files that, to date, have never been accessed by any user or the operating system. You could delete them today and so long as you use your computer, never need them. Only in a very particular instance might some of those files ever be needed. Alternately you could corrupt those files any way you want and nobody would ever notice.

Does that make the original files junk?

patrikbeno says:

We’re on different wave lengths, sadly. But I try to clarify…

“I’m not sure what you’re trying to say here. Are you suggesting that the future generations of this cell will always be error proof?”

Irrelevant. And no, they won’t, not without error correction, of course. I just say Venter proves that it is possible to design error-free copy algorithm so that you don’t need to fix your own copy errors (internal errors), only mutations caused by extraneous influences (external errors). If your copying function is 100% correct, you only have to deal with external errors. I would not expect divinely designed DNA to have internal errors.
Just an idea to think about, not any definitive rebuttal of your position.

“They did not model the entire operation of this cell on a computer. Not even close.”

Irrelevant. And I am not saying that. They simulated function of the new synthetic genome, and parts of the original genome that was expected to “interface” with the new synthetic genome.
But since you claim that cell exerts consciousness and its sense of purpose to create an information in order to function and fulfill the purpose, I find it interesting to see that genome designed in computer works as expected in reality. Would your hypothesis be true, I would expect cell’s holistic counsciousness and sense of purpose, as well as internal error correcting schemes to interfere with the synthetic genome. This did not happen.
Again, just an idea to think about, not any definitive rebuttal of your position.

“Notice that they didn’t produce this new genome with a series of random copying errors. Notice that in Venter’s press conference the cell has ZERO tolerance for error in some parts of the genome.”

Irrelevant. See above.

“I don’t know whether the original chromosome was part of the cell’s consciousness or not. I do not even know if cells are conscious. I suspect that they could be.”

I understand your hypothesis was that consciousness is an “immaterial purposeful agent” standing on top of the cell and driving (programming) its chemistry. You say information is needed for cell to function, and consciousness is needed to provide purpose to information and drive the evolution. Do I interpret your view correctly?

If I do, and if you are right, there’s no part of the cell that cell’s consciousness is in. It is on top of it. If it’s on top if, it cannot be affected by any mutations to chemistry, internal, external, natural or synthetic. Cell’s consciousness cannot be fooled by changes into chemistry. Any changes, synthetic or not, would be considered errors, and fixed by the error correcting schemes, programmed by immaterial consciousness.

Assuming my interpretation of your position is correct, I claim that the Venter’s achievement casts a shadow of serious doubt on your “conscious cell hypothesis”. That’s why I speak about this.
Again, just an idea to think about, not any definitive rebuttal of your position.

“Please explain what you are trying to say.”

I hope I did, in previous paragraphs.

“Does that make the original files junk?”

Yes, considering your scenario, I think they are junk. But I sense we just stumbled upon conflict in our individual interpretations of the term “junk”.
So I ask, what else would qualify as junk, to you?

GMEstes1 says:

Assigning consciousness to cellular life is thought provoking. If cells have consciousness then it implies the womans’ body does monthly perform a natural flush of an egg. Want to chase that rabbit?

Designing error free cells is a great process, it would stop many birth defects caused by foreign substances not natural to the body and abolish many unwanted genetic dieases if that were possible. This may have an effective promising future. We need to work for the best possible outcome.

Genetic engineering has always led to an out cry from the religious extreme right and I don’t expect any difference to emerge.

MikeFromOhio says:

Hi, Perry and others,

First off, I apologize if I am a bit off subject here. I am an software architect (EE from OSU) that found your Atheist Riddle and various talks on YouTube to be quite interesting. I think you are asking the right questions. How did DNA get here? Why aren’t there any other codes arising from physical processes?

It would be interesting to try and evolve a rudimentary DNA using a computer algorithm that simulates evolution. I have written a paper about Genetic Programming and learned a lot about what this technique can and cannot do, but no one, to my knowledge has tried to evolve a bare bones “code”.

Seems like such a prototype would be a nice way to take your questions to the next level of understanding. Curious if anyone might be interested.

Mike

MikeFromOhio says:

Sorry I have one other comment.
Perry you made the following comment about evolution:

Remember, the Darwinian formula is
Random mutation + natural selection + time = Design
But genetic programs work on this formula:
Random mutation + deliberate selection + time = Design

Actually Genetic programs and evolution in general work like this:
Variation(Population) + PhenotypeBasedSelection + Time = Design

There are 3 keys differences here to your description. First, Evolution needs a population to work with (typically 10k or more in computer simulations). Next is Variation (mutation is only one of the ways nature varies structures that evolve. And thirdly, selection is done on the phenotype of the individuals in the population (not the genotype, like in your example text-mutator). In other words, your simulated environment should have NO knowledge of the genotype structures in your population — only the “expression” of those genotypes (i.e. what they do in your simulated environment).

Anyway, lets discuss this more, especially with respect to evolving a bar-bones CODE from some type of molecule-based-like evolution algorithm. I am not saying this will even work, but by trying we will understand a great deal more about the questions you so brilliantly ask.

Cheers
-Mike

Johan says:



First an error correction . The intended time gaps didn’t materialized in my original post. Here
is a better attempt.

But what about the following ? : _. P _._._._. P _._._._. PP _._. P _._._._. P
_._._._. PP _._._._. P _._._._. P _._._._. PP _._._. P _._._._.P _._._._. PP _.
P _._._._. P _._._. PP _._._._. P _._._. P _._._._. PP _._._. P _._. P _._._._. PP
_._._. P _._._. P _._._._.PP
_._. P _._. P _._._._. PP _.P _._. P _._._._. PP _._._._. P _._. P _._._._.PP
_._._._. P _. P _. _._._. PP _._._._. P _._._. P _._._. PP _._. P _. P _. PP

_. P _. P _._._._. PP _._. P _. P _._._._. P P _._._. P _. P _. PP
_._._. P _. P _._._._.PP
_. P _. P _. PP _._. P _._._. P _._._._. PP _._._._. P _. P _. PPP

10 sec pause _._._._. P _. P _.PP
_._._._. P _. P _._._. PP
_._._._. P _._._. P _. PPPP

P = 2SEC GAP
PP = 4 SEC GAP
PPP = 10 SEC GAP
PPPP = VERY LONG VARIABLE GAP ( HOURS TO YEARS OR NEVER ) AND THAN
THE SAME SIGNAL RECEIVED AGAIN.

Shouldn’t we differentiate between random patterns and designed pattens. I think there is a
definite difference. Perry, in my opnion, refer to designed patterns as opposed to randomly appearing patterns. The latter is purely a coincidence and the former the fruit of an active mind,.

My point regarding Stonehenge : To argue that Stonehenge is a natural occurring phenomenon is similar to the arguments used promote the belief that the development of the genetic code is purely random event.

My question is how do we differentiate between designed and random events?

The foundation of science is observation and science’s development is guided by improvements in the equipment used to make these observations.

Perry’s observation that only minds create designed patterns is still valid. The Venter Institute’s research strengthens his arguments.

Johan

Johan says:

IS THE CRRAIG VENTER INSTITUTES’S SYNTHETIC CELL REALLY A
SYNTHETIC CELL?
…or was it a synthetic chromosome?

The scientists at the institute changed Mycoplasma capricolum into Mycoplasma mycoides
JCVI-syn1. A synthetic copy of the M mycoides genome was created and introduce in a
modified M capricolum cell . A new synthetic variant of M mycoides was created that
contains a “watermark” with the names of scientists , a web address and three wll known
quotations , all written in genetic code. This new variant is called Mycoplasma mycoides
JCVI-syn1. A remarkable scientific achievement.

Why do I question the term synthetic cell? DNA is hardware NOT SOFTWARE. The
sequence of the organic bases in the DNA molecule represent a code and form the software.
Software needs hardware to execute its INTENDED program. The hardware necessary on a
cellular level is three types of RNA (m, t en r RNA)

The software residing on the DNA molecule is able to create some of the necessary hardware
on its own. The Venter Institute’s transplanted genome had to produce mRNA . mRNA is
hardware produce in way that it contains copies of the genetic software.

The original M capricolum contained the other hardware necessary for the genetic software to
function. I refer to rRNA and tRNA.

The mRNA, tRNA and rRNA form an essential hardware unit that is necessary for the proper
execution of the genetic programs. These programs control chemical reactions. Life is a
multitude of finely controlled continuously occurring chemical reactions. The genetic code
control each and every one of these reactions via enzymes. ONE ENZYME SPECIFIC FOR
ONLY ONE OF THESE REACTIONS and a specific genetic code exists for each of these
enzymes.

My conclusion is that the creation of Mycoplasma mycoides JCVI-syn1 was a great
achievement, but its individual cells are not totally synthetic. Only the chromosome is
synthetic.
More like swapping hard dicks but swapping hard disks in a system that is more advanced than
anything that is presently existing in the computer industry.

Here is a link to an excellent article about protein synthesis and the “ mRNA–tRNA–rRNA
unit” and protein synthesis http://mmbr.asm.org/cgi/content/full/69/1/101 .

Johan

PRECISELY. My apologies to Patrik for not responding yet, been very busy but I will. But you’ve said exactly what I intended to say. Right down to your analogy about swapping hard discs. They didn’t build no computer, pal. They just switched the memory storage and the program.

This was no synthetic cell. It’s a re-programmed genome, all made from borrowed parts. And it’s very carefully designed by very smart people. Nothing random or accidental about it.

Great achievement, no doubt. And a deeply misleading PR stunt.

Johan says:

Hi Perry and Patrik.

Patrik said :”Furthermore, the host cell not only accepted useless synthetic chromosome. It also threw away part of the original chromosome ”

Venter Institute said:”The complete synthetic M. mycoides genome was isolated from the yeast cell and transplanted into Mycoplasma capricolum recipient cells that have had the genes for its restriction enzyme removed.”
They deliberately crashed the “hard disk” of the “original cell” by removing the restriction enzyme that prevents “foreign code” from producing mRNA.

The new “hard disk ” they inserted contained the code to suppress any activity on old hard disk.

Institute said: “The M. capricolum genome was either destroyed by M. mycoides restriction enzymes or….”

The most logical explanation is the restriction code of the new genome suppressing the old code. This is what restriction enzymes are intended to do.

Johan

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