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Sunday, November 23, 2014

Synthetic Life Shows the Impossibility of Abiogenesis

Posted by jlwile on May 30, 2010

Dr Craig Venter made the news last week in a big way. As The Guardian put it:

Craig Venter and his team have built the genome of a bacterium from scratch and incorporated it into a cell to make what they call the world’s first synthetic life form.

It’s an amazing feat of biotechnology, and the process he and his team produced might result in some incredible applications down the road. What I find interesting about the process, however, is how well it illustrates that life simply cannot come about as the result of random chemical reactions guided by some sort of selection process. In other words, this stunning achievement really demonstrates the impossibility of abiogenesis.

The scientific report of Venter and his team’s accomplishment can be found on the website of the journal Science1. I finally got around to reading it, and it is truly fascinating. When you look at the details of how they created their “synthetic” life form, you find that Venter and his team relied on already-living systems not once, not twice, but a total of three times. Without relying on these already-living systems, they would not have been able to produce their “synthetic” cell.

So what exactly did they do, and how did they rely on living systems three different times in order to do it? Well, they wanted to build a genome that they knew would work, so they decided to build one that had already been sequenced. They chose a bacterium called Mycoplasma mycoides, which has a small genome, even for a bacterium. Indeed, bacteria from this genus are often studied to determine what the “minimal” genome for life could possibly be. By starting with the sequence of an already-living bacterium, Venter and his team are technically relying on an already-living system, but I won’t count that. After all, they needed to produce a genome that was actually functional, so it makes sense to copy one from a living organism.

How did Venter and his team “make” this genome? That’s where we find the first instance in which they relied on an already-living system to get the job done. They ordered small chunks of DNA (they call them “cassettes”) from Blue Heron Biotechnology, and then they used yeast cells in a three-step process to stitch those chunks together into a full genome. This is actually discussed in a paper previously published in the journal Science.2

Like bacteria, yeast can have DNA in small, circular units called plasmids. These plasmids are separate from the yeast’s chromosomes, and yeast cells have the chemical machinery to allow them to replicate independently of the DNA in the chromosomes. Venter and his team ordered the DNA chunks to have sequences that would force the yeast cells’ chemical machinery to “stitch” the chunks into bigger chunks to form a plasmid.

Now why order DNA in small chunks and then force the yeast cells to stitch them together? Because human science is limited in the amount of DNA it can produce. Currently, human science and technology can produce small segments of DNA artificially, but when the strand of DNA becomes moderately long, it becomes unstable, and the strand breaks. Thus, scientists don’t have the capability of making an artificial genome. They only have the capability to make small chunks of an artificial genome. So Venter and his team employed yeast cells to do what human science cannot do: stitch small chunks of DNA into a complete genome.

Now remember, this technique was published in a previous paper, and that paper was published two years ago. Why didn’t Venter and his team make big headlines back then? Because when they produced their genome this way, it wouldn’t work. In the end, they concluded that the “synthetic” genome they made had too many mistakes in it. In this paper, they figured out a way to avoid making those mistakes. How? That’s where they relied on an already-living system for the second time.

The chunks of DNA were stitched together inside the yeast cells in three separate steps, each time producing a larger strand of DNA. To make sure there were no serious mistakes, they took some of the DNA produced after the second step (strands that were 100-kb long) and mixed it with the DNA from living Mycoplasma mycoides bacteria. As they say in their current paper:

By mixing natural pieces with synthetic ones, the successful construction of each synthetic 100-kb assembly could be verified without having to sequence these intermediates.

In the end, then, they used DNA they knew was functional (because it came from a living bacterium) to test their “synthetic” DNA. This revealed several problems, which they could then go back and fix. This was apparently a painstaking process. At one point, they say they were delayed by many weeks because of the deletion of a single base pair.

So…once they used a living system to stitch together the DNA (because human science cannot do that) and then used a living system to test the stitching after step two, what did they do? They transplanted the “synthetic” DNA into a living bacterium from a slightly different species, Mycoplasma capricolum, whose DNA had been removed.

Why did they do this? Because life is more than just DNA. In other words, a genome is not something that is alive. Think of it as a complex computer program. A computer program can make a computer do some amazing things, but by itself, a computer program can’t do anything. In order to do something, it must be installed in a working computer. In the same way, DNA by itself is not alive. However, it can make a living cell do a lot of great things. Thus, in order to get their “synthetic” DNA to do something related to life, Venter and his team had to put it into an already-living cell.

Of course, they had to do a lot of engineering to accomplish this transplant, because cells recognize foreign DNA. Thus, even though the recipient M. capricolum cell had no DNA, it had the chemical machinery to detect foreign DNA and destroy it. Venter and his team tried to disguise their “synthetic” DNA to look like M. capricolum DNA. To further ensure success, they then destroyed all traces of the enzyme that M. capricolum would have used to destroy foreign DNA.

Now please don’t get me wrong. I am not minimizing what Venter and his team have accomplished. It is a truly remarkable achievement. In fact, part of what makes it so remarkable is how much they relied on living systems to get the job done. In essence, they used living yeast cells to do what no human scientist can do, then they used living bacterial cells to error-check the yeasts’ work, and then they used a living bacterial cell as a recipient for their DNA, because otherwise, it would not have been able to function.

This truly stunning achievement, then, shows just how dependent life is on the existence of life. To make life, you need life. Even the best human science has to offer relied on already-living systems three times in order to “make” a living bacterium.

This just confirms how the concept of abiogenesis is not science. It’s fantasy.

REFERENCES

1. Daniel G. Gibson, et al., “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome,” Science Published Online May 20, 2010. Available online with subscription.
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2. Daniel G. Gibson, et al., “Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome,” Science 319:1215-1220, 2008. Available online with subscription.
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Comments

40 Responses to “Synthetic Life Shows the Impossibility of Abiogenesis”
  1. Dr. Venter’s amazing accomplishment is not relevant about whether abiogenesis is possible. Nothing that they did resembles anything like creating a replicating cell out of organic chemicals. Here’s a quick real science take on the work by Olivia Judson. Have you heard of her?

    Also, I wanted to alert you to a PZ post on junk DNA at Panda’s Thumb, as you might have missed it.

  2. jlwile says:

    It’s quite funny that you NOW say that Venter’s work is not relevant to abiogenesis, since YOU sent me an E-MAIL claiming that his research was “closing the gap” between life and non-life and making lab-produced abiogenesis closer to a reality. Once again, just another example of the mental gymnastics that you must do in order to preserve your world view. Man – I am glad that I just follow the data!

    I am not surprised you consider Judson’s piece to be “real science,” since it is really just an opinion piece. She doesn’t discuss the process or the methodology at all, and she includes no data. That, of course, is what you call science. It’s just not what scientists call science. And no, I have never heard of her.

    Once again, you nee to learn to read, as the front page of this blog discusses how I read PZ regularly. That article was first published on his own blog. He gives the standard evolutionary line that there is a lot of junk DNA (something you at one time claimed evolutionary biologists don’t do – more mental gymnastics on your part). Of course, this ignores all the great research which has demonstrated specific functions for many sections of DNA that evolutionary biologists were sure was nothing but junk. This is not surprising, as being an evolutionist requires you to ignore all sorts of data.

    He puts a lot of stock in one paper, which is also not surprising, since that paper happens to agree with his preconceived notions. And, of course, he is ignoring the other scientists who are using the same method discussed in the article but are not getting the same results as the authors of the paper. As Nature News says:

    But Philipp Kapranov of Helicos BioSciences, a biotechnology firm in Cambridge, Massachusetts, says that his lab, which also uses RNA-Seq, is seeing quite different results. He says that he and his colleagues continue to find a high percentage of a cell’s RNA originating from regions between genes. “I don’t know why the results presented in this paper are different from ours,” he says, suggesting that there may be differences in their sequencing protocols.

    Go ahead and keep touting junk DNA! It’s great to keep such a silly notion alive, as it just shows the absurd lengths one must go to in order to believe in evolution.

  3. Now I freely admit most this stuff is over my head… but I will be impressed when someone creates something “ex nihilo.” PS I have a book written by you… but it remains unread! Til this summer!

  4. jlwile says:

    Thanks for your comment, Billy! I hope you enjoy the book when you get around to reading it!

  5. Rich Townsend says:

    Dear Dr Wile

    I agree with you that it is impossible for something as a complex as a cell to arise directly from its raw materials.

    It’s common for creationists to claim that this makes abiogenesis impossible. But of course it does nothing of the sort.

    No scientist makes this assumption – all abiogenesis research is done on the basis that there are some intermediate steps on the road to a cell. Scientists are trying to understand what these steps might look like.

    BTW, you misrepresent the scientific concensus re junk. There have always been those who argue that junk is junk and others that junk has functions – this goes right back to the late 60s and early 70s. You might wish it otherwise but I’m sorry, that’s the case.

  6. CD says:

    I’m sorry, but I completely fail to see how anything here has shown the impossibility, or otherwise, of abiogenesis. This is a bogus claim and simply undermines Dr Wile’s credibility.

  7. jlwile says:

    Rich, nowhere in this post do I say that “it is impossible for something as a complex as a cell to arise directly from its raw materials.” What I do say is that Venter’s team has further shown how the production of life is dependent on life. We can’t even make a fabricated genome without living organisms, and once that genome is made, it can’t do anything until it is put in a living cell. That’s what demonstrates the impossibility of abiogenesis.

    I agree that “all abiogenesis research is done on the basis that there are some intermediate steps on the road to a cell.” This is, of course, a matter of faith, because we don’t have the foggiest clue what those intermediate steps might be. Indeed, as mentioned in two other posts, the attempts to produce these intermediate steps have been a stunning failure by every measurable standard. Thus, you can believe that such intermediate steps exist if you want, but I simply don’t have the faith to do that. I prefer to look at the evidence.

    I certainly do not “misrepresent the scientific concensus [sic] re junk.” Ever since Ohno likened pseudogenes to the fossils that litter the geological column, it has been the standard evolutionary line that there is a lot of junk DNA in most genomes, and it is the result of the evolutionary process. I agree that some SCIENTISTS over the years have contented that there is not much junk in the genome, but they did so DESPITE evolutionary ideas, not because of them. As the PZ Myers article that brought up junk DNA in this thread says, “The bottom line, though, is the genome is mostly dead, transcriptionally. The junk is still junk.” This is the standard evolutionary line, and it will continue to be until it is demonstrated false. At that point, evolutionists will move the goalposts, as they always do.

  8. jlwile says:

    CD, following the evidence “undermines” my credibility only to those who are committed to dogma. The evidence produced by Venter’s team is that life cannot be made without the aid of life. Abiogenesis requires that life be made without the aid of life. Thus, Venter’s team has helped to demonstrate the impossibility of abiogenesis.

  9. CD says:

    No, the evidence provided is that Venter’s team cannot make life without the aid of life. If you want to think of Venter’s team as a proxy for *all possible naturalistic mechanisms*, then I think your credibility suffers yet further.

  10. jlwile says:

    CD, the evidence is that in order to make life, you need life. This is diametrically opposed to abiogenesis. Venter’s team is not a proxy for all naturalistic processes. In fact, his team has all sorts of advantages over naturalistic processes, and they STILL needed life to make life. This, of course, shows the impossibility of abiogenesis.

  11. CD says:

    I’m sorry, but I don’t care (at this point) whether abiogenesis is impossible or not. What I care about is a science. By all means point out how much “help” they required from existing life. By all means criticise anyone who tries to imply that this success provides ample (or indeed any) evidence for naturalistic abiogenesis. But to declare that this “shows the impossibility of abiogenesis” is infantile and wrong on so many levels. I would have thought you would understand this basic point.

  12. CD says:

    Hmmm, some poor editing on my part there. Post should read:

    I’m sorry, but I don’t care (at this point) whether abiogenesis is impossible or not. What I care about is a science educator demonstrating exceptionally poor logic. By all means point out how much “help” they required from existing life. By all means criticise anyone who tries to imply that this success provides ample (or indeed any) evidence for naturalistic abiogenesis. But to declare that this “shows the impossibility of abiogenesis” is infantile and wrong on so many levels. I would have thought you would understand this basic point.

  13. jlwile says:

    CD, I really think it is you who doesn’t understand. The logic is quite clear, and it is odd that you can’t seem to grasp it. Naturalistic processes with no goal in mind are at a severe disadvantage compared to a bunch of well-educated, highly-trained scientists working in a lab with the goal of making life. Nevertheless, even with all their advantages, Venter’s team could not produce life without relying on life a total of three specific times. Thus, if they needed to rely on life to make life (with all their advantages), it is clear that naturalistic processes (with significantly fewer advantages) can’t produce life without relying on life.

  14. Captainstegs says:

    Quoting from previous posts.

    “the evidence is that in order to make life, you need life”

    If I might edit this somewhat.

    “the evidence is that, in this instance, in order to make life, they used life”

    Now the statement is accurate.

    With the age of the earth being calculated using radiometric dating (a method that has been backed up using helioseismic dating of the sun) as 4.5 billion years old (practically an infinite amount of time) and an infinite amount of galaxies, solar systems and planets, to say that just because some scientists on one of these planets can’t recreate life without lifes help in only a handful of years shows that you don’t seem to be able to comprehend the vastness of space and time during which these life creating processes could have occurred.

    Even if we use your 10,000 years as a starting basis we still have a practically infinite number of planets where a life creating process could occur. Following the “Infinite monkey theorem” isn’t it logical that the possibility of life occuring on one of these planets by chance is not just possible but probable.

  15. jlwile says:

    Thanks for your post, Captainstegs. The statement was right as it was originally written in the post. There is no need to correct what is already correct. Indeed, every piece of data ever collected by scientists shows that in order to make life, you need life. This is just one more piece of data to throw on the pile. What makes this piece particularly devastating to abiogenesis, however, is how it shows so clearly the dependence that life has on life. A lifeless genome can’t even be produced without life, and then once that genome is produced by life, it can’t do anything unless inserted into an already living cell.

    Actually, the age of 4.5 billion years for the earth is calculated using scientifically irresponsible dating methods and is not consistent with the majority of the data. However, even granting that scientifically irresponsible age, it is certainly not a logical possibility that “life occuring [sic] on one of these planets by chance is not just possible but probable.” You rely on at least two false premises. First, you assume that 4.5 billion years is “practically an infinite amount of time.” That is certainly not true. As you can see from probability, it doesn’t come CLOSE to being enough time to produce any reasonable level of information from random processes. Even the scientifically irresponsible age of the universe doesn’t put a dent in the time needed for random processes to produce a reasonable amount of information.

    Second, you assume an infinite number of planets. There is no way to verify such an assumption, and it is almost certainly not true. Indeed, such a belief relies on three major assumptions:

    1. General relativity is a good description of the universe on a large scale.

    2. The universe is relatively homogeneous (The Cosmological Principle).

    3. The expansion of the universe is properly described in all its essential features by the Big Bang Theory.

    While #1 is probably correct, #2 and #3 are almost certainly wrong.

    You can certainly take on faith that all the data ever collected by science is wrong when it comes to life requiring life and that at some point in some distant past life arose without the aid of life by some completely unknown process. However, I don’t have that kind of faith. I prefer to follow the evidence.

  16. CD says:

    Your bias is very telling here. Your flawed argument could be used at varying points in scientific history to demonstrate the impossibility of human flight without divine intervention, likewise with the generation of lightning, the ability to breath underwater, and any of a range of scienitific achievements that were previuosly regarded as purely the realm of the divine.

    Venter’s team were trying to do exactly what they acheived. Their achievement has little bearing on the question of whether life can be artificially constructed from non-biological components. It merely suggests that we are not yet at that level. Your reaching and refusal to give ground to the obvious suggests no small level of desperation, which I must say is rather unbecoming…

  17. CD says:

    You claim that the scientifically universally accepted dating methods (outside Judeo-Christian-Islam creationists) are scientifically irresponsible based on assumptions of constant decay rates. I am an astrophysicist/cosmologist and would be intrigued how you claim that this is an assumption given the striking evidence from Oklo and astrophysical observations, amongst several others.

  18. jlwile says:

    CD, I am certainly not desperate, and I am no more biased than any other scientist. The fact that you must resort to tactics like saying I am desperate rather that discussing the evidence indicates that you cannot really defend your position.

    I am simply following the data. The research involved in the field of abiogenesis is radically different from the research involved in human flight, the ability to breathe underwater, etc. etc. The reason for that is simple. In each of those other pursuits, progress was made, and the research continued to show improvement toward the goal. Instead, abiogenesis research has been a spectacular failure, with no progress being made. Indeed, as Simon Conway Morris (an evolutionist who WANTS to believe in abiogenesis) says:

    Francis Crick can write ‘An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle’…More than two decades on from Crick’s ruminations, however, it still remains the case that the notion of an infinitesimally unlikely series of chemical reactions – that from our perspective can be described only as a ‘near miracle’…remains the unbidden and silent observer at much of the discussion of how life originated. Yet, as Iris Fry (note 85) reminds us, such terminology is effectively that of creationism. Put this way, nearly everyone will ask that the now unwelcome guest should vanish through the adjacent wall

    Once again, Venter’s team’s work demonstrates that life depends on life. The construction of a genome cannot even be accomplished by a group of talented researchers without the help of living organisms. If talented researchers spending millions of dollars over many years with that specific goal in mind cannot do so without the aid of living organisms, undirected natural processes clearly will not be able to do so.

    You say that you are interested in why I claim that the assumption of constant half-lives is irresponsible. Please read my posts on the subject:

    One Reason I Am Skeptical of an Ancient Earth

    Kicking and Screaming

    Please note that “universal” acceptance means nothing to me. Science is not done by majority vote. It is done by following the data. If you are interested in majority votes, please go into politics, an area more suited to such ideas.

  19. Captainstegs says:

    At the end of the day the problem that most of us have is that we don’t know all “the data”. But luckily for us there are scientists and clever people who have analysed a hell of a lot of it and interpreted it into simple soundbites that people can at least try and understand. And without having enough time to analyse all “the data” and with the majority of informed people telling me that the earth is approximately 4.54 billion years old, based on “the data”, I am of course going to believe their interpretation of “the data”.

    I like this article; http://www.asa3.org/ASA/resources/Wiens.html#page%2019

    it provides a good overview from a christian of the 40 or so different methods of radiometric dating that you have dismissed in full as being inaccurate. It also gives a good breakdown of how ice cores are used for dating. They count the layers, not just by depth as you claim in your articles but by actually counting layers. They do this by looking at the bubbles in the layers, bigger bubbles in the summer, visible for up to 60,000 years, and also by electrical conductivity, spring ice has higher nitric levels and is therefore more conductive, observable for 60,000 years, and finally by summer dust levels observable up to 160,000 years. Three different ways that all concur and all of which you have again no doubt dismissed.

    With regards Dendrochronology in 2004 a new calibration curve INTCAL04 was internationally ratified for calibrated dates back to 26,000 Before Present (BP) based on an agreed worldwide data set of trees and marine sediments (varves). Do you dismiss this as well or are multiple tree rings occuring now at a rate of around 2 extra rings every year all around the globe just to fit in with your 10,000 year date of the earth?

    If I held a viewpoint based on data I believed to be accurate and I could see 100 colleagues with more experience and more data than me who held diametrically opposite views I know I’d think I’d gone wrong somewhere, rather than to be vain enough to think that everybody else was wrong. I tend to agree with this view of your goodself http://answers.yahoo.com/question/index?qid=20061025130926AAWg3Ig
    in the way that you claim you’re following ‘the data’ and yet dismissing a good 50 different methods of ageing the earth out of hand because it doesn’t fit in with your world view. You will never amend your views as you have too much riding on the beliefs that you put forth in the books that you sell.

    The statement that ‘life depends on life’ to be created of course wraps around again and again on itself until you say that God must have created life in the first place as something can’t come from nothing, apart from God of course, cause he’s…well…”Magic” and has always been here in a way that defies both time and space.

    All Atheists or Christians must accept that something can come from nothing or must have always have been. For Christians this is God, for Atheists why can’t this be life. I don’t see how the argument that ‘life must always have been in order to create life’ carries any less weight than ‘God must always have been in order to create life’. Not that I believe that life has always existed I am just putting forward an argument that the fact that you need life to produce life doesn’t prove God’s existence.

  20. Captainstegs says:

    Just a small thing. I was having a read of your “kicking and screaming” post. Which claimed to show one of the 40 or so chemicals used in radiometric dating being out by a factor of 100,000. Assuming this experiment is right and you take the 100,000 error and apply it to the 4.5 billion year old date of the earth (which has in fact been calculated using more than just the one method admittedly) then you still have an earth that is 45,000 years old. 4 times older than the age that you give the earth.

    Doesn’t this show “the data”, that you put forward as proof that radiometric dating is flawed, giving you a date for the earth that is massively different than the one that you propose.:-) Or are you going to say that your 100,000 error rate was what was out by a factor of 4.

    On a slightly different tangent, if the earth is only 10,000 years old, why has the rest of the universe been around for 13 billion years or so, as calculated by looking at the light that has reached us from the ends of the universe. Or is this wrong as well? Did it take 13 billion years just to come up with the design for the earth?

  21. CD says:

    The desperation is merely an observation based upon your refusal to admit that your initial claim is ridiculous – that a successful attempt at bio-engineering somehow implies that naturalistic abiogenesis is not just less likely (which would still be a rather odd claim to make), but is actually impossible. Your credibility is all but vanishing here, Jay, with such obstinancy.

    Who cares what Simon Conway Morris has to say – a Christian with his own strong biases based upon his faith and strict adherence to his own left-field ideas. And surely we are not arguing from authority here are we? I think Nobel Laureate Jack Szostak would have something to say about this. To claim that there has been no progress in abiogenesis is either dishonest or exceptionally naive, especially in light of Szostak’s work, developments in the RNA World hypothesis, and the many other areas of study.

    By all means claim that abiogenesis is doomed to failure. By all means claim that the difficulties we have faced in creating life suggest that there is more to life than naturalistic processes. But to claim that Venter proves the impossibility of abiogensis, and to claim that there has been no progress in abiogenesis just makes you yet another “internet pseudo-scientific wack-job” – a technical term we use in cosmological circles…

  22. jlwile says:

    Captainstegs, I agree with you that no one has the time to review all the data, but nevertheless, when you are interested in a topic, you should look at all the data you can. To do anything less is essentially a cop-out. I also agree that you should seek the views of other scientists who are experts in the field of interest. Indeed, I have, and a lot of them agree with me. More of them don’t agree with me, but science is not done by majority vote. It is done by analyzing the data. You fall into a very bad trap by assuming that because the majority of scientists believe something it must be true. First, we know that isn’t a reliable method of determining things, as the majority of scientists have been demonstrated wrong several times in the past. Second, it stifles scientific progress. Most of the great scientific revolutions occurred because a handful of scientists disagreed with the majority. In the end, if you look at the majority of scientists as your high priests and simply accept their dogma, you are not being scientific. You are being dogmatic. It is not vain to follow the data – it is the only reasonable scientific thing to do.

    I read the ASA article long ago, and it has all sorts of errors in it. I certainly would not take any advice from someone who makes so many mistakes in his discussion. For example, in the section you specifically linked, he says “All of the different dating methods agree–they agree a great majority of the time over millions of years of time.” That is, of course, quite false. Indeed, not only do the radiometric dating methods often conflict with each other, they also often conflict with accepted dates. He says “Vast amounts of data overwhelmingly favor an old Earth.” Once again, he is dead wrong. In fact, very little data favor an old earth. The majority of data favor a young earth. He says “Radioactive decay rates have been measured for over sixty years now for many of the decay clocks without any observed changes.” Once again, that is completely false. Radioactive half-lives have been demonstrated to be variable under several conditions.

    The worst parts of Wiens’s paper, however, are his details on the process of radiometric dating. He doesn’t seem to have much knowledge of the literature. For example, he claims that the isochron plot he shows in figure 4 is supposed to be a “a check to ensure that the system has not been disturbed.” Of course, that is not true, as Ozima and his co-authors have shown (Ozima, M., et al., Origin of the anomalous 40Ar—39Ar age of Zaire cubic diamonds: excess 40Ar in pristine mantle fluids, Nature 337:226 – 229, 1989).

    Ice cores are also a terribly unreliable dating method. In order to learn about how poor the are, you can read this.

    Your comments about dendrochronology also show that you have not investigated that method of dating, either. There is no need to postulate many rings per year in order to see how dendrochronology supports a young earth. You simply have to understand how these overlapping tree-ring chronologies are made. When they try to overlap the master tree ring patterns, they measure the degree of overlap with a “t-value.” The higher the t-value, the more reliable the overlap. INCAL04 uses really low t-values at many points: t-values that other studies have shown allow for the overlap of completely unrelated trees.

    If it makes you feel better to give insulting links about me so that you can avoid facing the data, that’s fine. However, it is just another example of how rushing to judgment without looking at the data can lead you to massively wrong conclusions. The answerer (and presumably you) claim that you can’t trust anything in my books except physical chemistry or sub-atomic physics. That is demonstrably false, given the amaing success that students who use my curriculum have when they end up pursuing science at university.

    The statement that “life depends on life” is simply a summary of the data. If you choose not to believe the data, that’s fine. You can have faith in anything. Just don’t claim to be scientific when you are forced to ignore the data to maintain your worldview.

  23. jlwile says:

    Captainstegs, if you would actually read that post, you would see that I never reference a change of a factor of 100,000 for a radioactive half-life. I use a factor of 100,000 as the difference in energy between electrons and nucleons, and there is a factor of 100,000 between the predictions of the old-earth and young-earth scenarios for the zircon data. If you want to learn, you actually have to read. Of course, rather than trying to apply some sort of simplistic model to this issue, I use the variations in half-life simply to show that what has been confidently expressed by those who want to believe in an old earth is actually demonstrably false. Radioactive half-lives are certainly not constant in many situations.

    Your question about light travel also shows that you have not looked into this issue much at all. There is no conflict between a 10,000-year-old earth and light that comes from sources that are several billion light-years away. Indeed, all you have to do is learn a bit of general relativity to understand this. Please educate yourself here and here.

  24. jlwile says:

    CD, it is fine if you want to continue to attack my credibility instead of address the issue. It just demonstrates who the desperate one is in this “conversation.”

    I actually care what Simon Conway Morris says. He spends a huge amount of time in his book chronicling the abject failure of abiogenesis research, and he makes a very strong case, even though he still insists that abiogenesis must be possible SOMEHOW. I think this demonstrates the difference between you and me. I read Morris’s book and was impressed by how much evidence he presented. You are simply impressed by the fact that Dr. Jack Szostak is a Nobel Laureate. Thus, you will take his word over the evidence. That’s an argument from authority, and it means very little to anyone interested in science. In fact, it smacks of dogma.

    Please feel free to consider me an “internet pseudo-scientific wack-job” if it makes you feel better. After all, if you can’t answer with data, I understand that your only other option is to hurl insults. Once again, I think it is clear who the desperate one is in this “conversation!” Thanks for demonstrating this to all my readers!

  25. CD says:

    Ha ha, you bring up Morris and then claim that it is me that is arguing from authority. Oh, I see what you did there. You have not addressed a single of my criticisms which is most certainly obvious to your readers. And what data am I supposed to be presenting?

    Again, please explain how your claims that there is no progress in abiogenesis can stand in the face of Szostak’s work.

    Again, please explain how a successful feat of bioengineering demonstrates that abiogenesis is not merely unlikely, not merely difficult, but actually impossible.

  26. jlwile says:

    I quoted Morris in the post that discusses a wealth of data related to abiogenesis. Thus, I presented evidence. You did nothing but mention a Nobel Laureate who happens to agree with you. Thus, YOU were arguing from authority. I was presenting evidence. This once again demonstrates who is the desperate one. Thanks for your help!

    What data are you supposed to be presenting? Perhaps some data that show abiogenesis is possible. You have given none.

    To see how far Szostak is from any kind of abiogenesis, all you have to do is read his and Ricardo’s Scientific American article (“Origin of life on earth”) from last year (301:54-61). Here is their summary of how they think it occurred:

    There COULD BE pools of cold water, PERHAPS partly covered by ice but kept liquid by hot rocks. The temperature differences would cause convection currents, so that EVERY NOW AND THEN protocells in the water would be exposed to a burst of heat as they passed near the hot rocks, but they would almost instantly cool down again as the heated water mixed with the bulk of the cold water. The sudden heating would cause a double helix to separate into single strands. Once back in the cool region, new double strands–copies of the original one–could form as the single strands acted as templates. As soon as THE ENVIRONMENT NUDGED protocells to start reproducing, evolution KICKED IN. In particular, AT SOME POINT some of the RNA sequences mutated, becoming ribozymes that sped up the copying of RNA–thus adding a competitive advantage. Eventually ribozymes began to copy RNA without external help. It is relatively easy to IMAGINE how RNA-based protocells MAY HAVE then evolved. Metabolism COULD HAVE arisen gradually, as new ribozymes enabled cells to synthesize nutrients internally from simpler and more abundant starting materials. Next, the organism MIGHT HAVE added protein making to their bag of chemical tricks. With their astonishing versatility, proteins would have then taken over RNA’s role in assisting genetic copying and metabolism. Later, the organisms would have “learned” to make DNA, gaining the advantage of possessing a more robust carrier of genetic information. At that point, the RNA world became the DNA world…

    It’s a great bedtime story. But what does he have to back it up? The fact that certain well-engineered bits of RNA can link other bits of RNA together and some bubbles that he has the audacity to call protocells? Nice try, but I want some evidence, not bedtime stories!

    Of course, it’s important to point out that the “RNA world” hypothesis is just one of many hypotheses related to abiogenesis. As I see it, there are at least eight current hypotheses regarding the origin of life, all supported by well-known people like Christian de Duve, Stuart Kauffman, Michael Russell, etc. The very fact that there are so many competing hypotheses shows that there has been no real progress. In science, as progress is made, hypotheses are winnowed down to one that actually seems to work. There are so many hypotheses out there about the origin of life right now, you know that there have been no serious experimental results with which to exclude at least the most outlandish of them.

    Again, it is easy to see how Venter’s work shows the impossibility of abiogenesis. When a team of DESIGNERS who have THE SPECIFIC GOAL in mind of creating a living cell cannot do it without the help of already-living cells, it is clear that unknown random chemical reactions acted on by some unknown selection process will not be able to create life without the aid of life. Perhaps an analogy will help. Venter’s team is like a man trying to jump a ravine using a high-powered motorcycle and a ramp. It turns out that even with the motorcycle, he cannot jump the ravine. Now what does that say about the possibility of a man jumping the ravine with just his legs? In light of Venter’s work, you are forced to believe that the man can jump the ravine unaided, even though the man with the motorcycle cannot.

    You might have that kind of faith. I don’t.

  27. CD says:

    We will almost never know how abiogenesis occured – hoping for evidence from that age of the Earth is only going to breed disappointment. What is required are plausible avenues along which life may have developed. That is about all we can hope for. That is precisely what we have developing with the varying hypotheses. You may find these inadequate. You may find this indicative of the insurmountable task of naturalistic abiogenesis, and you may well be right. BUT TO STATE THAT NO PROGRESS HAS BEEN MADE IS *LYING* – you may not think much of that progress, but by claiming no progress, you with one hand dismiss the work of many scientists and their research groups. Disgraceful behaviour for someone who thinks of themselves as a scientist.

    And your ananlogy fails immediately. Venter’s team were trying to do exactly what they acheived. Construct a living cell from a reengineered and artificially constructed loop of DNA by inserting it into the pre-existing machinary of a DNA-absent cell. They were not attempting to build a cell from scratch. Venter knows more than anyone that he does not yet have the technology or knowledge to do this. Claiming that Venter was attempting to do this is *LYING*. And claiming that Venter’s research shows that abiogenesis is impossible is either dishonesty or just stupidity. Given the trail of lying above, I’ll go with dishonesty for my first guess.

  28. CD says:

    Why do I have to provide evidence for abiogenesis? I have not once argued for naturalistic abiogenesis (although it is my own belief that this is how life originated.) I have merely pointed out your dishonest reasoning. In all of my writing, I have not shut the door to non-naturalistic causes. I am concerned with your reasoning and rhetoric – given your position as an educator of children – rather than arguing against your beliefs. I have creationist colleagues, friends and relatives who would be rather disappointed in your argumentation.

  29. jlwile says:

    “We will almost never know how abiogenesis occurred.” If that’s the case, it is irrational to think it ever did occur. And no, it is not lying to state that no progress has been made, because no progress has been made. There is no evidence to suggest that it ever occurred, and no evidence to indicate which of the many different fairy tales is more scientifically likely. Once again, you can believe in one (or more) of the fairy tales if you like. I just don’t have the faith to do so. I must follow the evidence, which shows the impossibility of abiogenesis.

    Indeed, these experimental results clearly show that abiogenesis cannot occur, because even with all their advantages, Venter’s team could not create life without the help of life. All the scientific evidence clearly shows that life needs life. These experiments simply demonstrate that in a very stark way.

    I know you can’t handle the evidence, so the first thing you tried to do is insult me. Since that didn’t work, you now accuse me of lying. Of course, that doesn’t work, either, as I am not lying. I am accurately reporting the results and accurately reporting their implications. You just don’t like their implications, so you are desperately trying to throw things to the wall until something sticks. Note that you didn’t refute my analogy at all. You simply tried to distract by saying that Venter’s team wasn’t trying to create life from scratch. They weren’t trying, because they COULDN’T.

    Venter’s team was trying to create life according to their design. They couldn’t do it without the help of life – at three different points. Thus, it shows the impossibility of abiogenesis, as life is required for life. I know you don’t like the results, but that doesn’t change them. Rational people will understand the implications of their results, while those who are obsessed with dogma will do everything they can to deny them.

    Do not worry about my position as an educator. As I have shown in my response to Captainstegs, my courses produce university-level science students who are head and shoulders above their peers. Thus, my rhetoric and logic have been demonstrated to work very well when it comes to science education! That’s just one more piece of evidence indicating your comments are not based on serious scientific considerations.

  30. Josiah says:

    If I may throw my opinion at the original issue, I’m afraid I have to agree with CD. You certainly cannot say that the manner in which these scientists created life disproves the posibility of Abiogenesis, any more than the failure or an Alpine expedition to produce a Yeti or the attempt by said explorers to forge evidence of a Yeti disproves the possibility of a Yeti. But it does not, as Shooter apparently argued, “narrow the gap” in the least. It has no effect whatsoever on the question “can life be formed from scratch by chance” if somebody tried to create life according to a method Chance wouldn’t have access to.

    I might add that you neglected a fourth use of life, indeed intelligent life, in the persons of the scientists who set this all up in the first place. Even if Venter’s team could produce a bacterium without the other lifeforms, I’d want very clear evidence that the influence of this fourth lifeform had been minimized before disregarding the biggest stumbling block for evolutionists. Otherwise I believe the process would be termed “intelligent design” and equally unrelated to the question at hand.

  31. CD says:

    >Venter’s team was trying to create life according to their
    >design. They couldn’t do it without the help of life – at
    >three different points. Thus, it shows the impossibility of
    >abiogenesis, as life is required for life.

    I’m sorry, but your continued insistence on this being a logical argument simply makes you an idiot.

  32. CD says:

    Thanks Josiah – nice to see someone can appreciate logic on this blog! I agree with all your points, although your last is the eternal bugbear in trying to demonstrate to creationists/IDists the power of evolution in genetic algorithms :)

  33. Percy says:

    Hi Jay – great blog!

    I think you might be misreading CD’s point. Abiogenesis is life arising from non-life. You say that Venter’s research that proves that abiogenesis is impossible, but in that case how can you believe that God created Adam from the non-living dust of the Earth. CD can correct me if I’ve got this wrong, but I think he’s saying that both creationists and evolutionists accept the possibility of abiogenesis but disagree on how it might have happened.

    Venter’s team is taking one approach to artificial life, other teams are taking other approaches, some that attempt to begin from scratch with custom vesicles (to serve as a primitive cell membrane) and custom genomes. Your claim that life arising from non-life without God is impossible depends upon the failure to solve what is a very tractable biological engineering problem. You can hope that they won’t solve the problem in your lifetime, but you might instead want to stake out a position now that anticipates their eventual success, else you’ll have to backpedal.

    –Percy

  34. jlwile says:

    Josiah, I think that you (like CD) can’t seem to understand the implications of this research. Of course this achievement shows the impossibility of abiogenesis. Venter’s team WANTED to produce life according to their design. The only way they could achieve that goal was to enlist living creatures to do the synthesis for them. When a team of designers with the specific goal of producing a living organism can’t do the job without the help of living organisms, it is clear that undirected processes with no goal will not be able to produce a living system.

    Your analogy isn’t correct, as a Yeti might be found by another group with the same goal and better equipment or a more likely search area or something like that. Thus, with AN ADVANTAGE, another group might succeed where the first group failed. In this case, the situation that HAD ALL THE ADVANTAGES could not get the job done. To assume that a situation that HAS SIGNIFICANTLY FEWER advantages will produce an outcome that the situation with all the advantages couldn’t produce is simply ludicrous.

  35. jlwile says:

    CD, thanks once again for demonstrating that you cannot argue your point – all you can do is insult. That might work on irrational blogs, but it doesn’t work here.

  36. jlwile says:

    Hi Percy. Thanks for the comment! It all comes down to what ABILITIES exist in the situation. It is true that strictly speaking, creationists and evolutionists both believe in abiogenesis in the sense that they believe in organic life coming from a non-organic source. The difference, of course, is the source. Creationists believe in an intelligent Creator as the source, evolutionists (generally) believe in natural processes.

    So…let’s look at the abilities. Venter’s team is full of smart people with lots of money and equipment. They couldn’t do it without the help of living organisms. Natural processes have FEWER advantages than Venter’s team, so if Venter’s team couldn’t do it, natural processes can’t. The Creator, however, is probably smarter and more resourceful than Venter’s team. Thus, the Creator can get the job done.

    Nowhere in this post do I say another team might not be able to produce artificial life without relying on living organisms. Indeed, a team with more expertise and more resources might be able to do what Venter’s team could not. I doubt it, but I certainly wouldn’t rule it out. However, that would not be surprising. More resources and more expertise COULD produce what Venter’s team could not. Of course, that would still be depending on life, because as Joshua says, the team is full of living organisms. For those who believe in material abiogenesis, however, they have to think that natural processes (which have far fewer advantages than Venter’s team or any future team) can do what Venter’s team could not. That’s an irrational position.

    So the only way I would be forced to backpedal is if someone can demonstrate the production of life through totally natural processes. Since the data clearly say this can’t happen, I am not in danger of having to backpedal. Of course, if I am wrong (and that is always possible), I will have to backpedal, but I am not going to ignore what the data say just because I might be forced to backpedal someday. That would also be an irrational position to take.

  37. CD says:

    It is you, Jay, that cannot understand logical implications. How can you claim that Venter’s team has ALL the advantages available to it to create life? Have you been given prescience to KNOW of all future developments in bioengineering, that you KNOW that no future advances will be sufficient to overcome the limitations that Venter’s team has faced?

    You are claiming that because this team with all the advanatges availble TODAY has failed, all future teams must necessarily fail. That Venter’s team’s lack of success is sufficient to make the most absolute claims about the entire future of bioengineering.

    What is so laughable is that you actually believe this argument has merit, and are willing to defend it so vociferously in spite of the sad spectacle you are making of yourself.

    You may well be right – naturalistic abiogenesis may be impossible, and a divine being (perhaps your Yahweh) brought life into existence. But your desperation to believe this has crippled your ability to reason rationally.

    The impossibility of naturalistic abiogenesis may be the reason why Venter “failed”, but in no way does Venter’s “failure” demonstrate that naturalistic abiogenesis is impossible.

  38. Percy says:

    Hi Jay!

    I think you may still misunderstand what Venter’s team was trying to accomplish. You don’t think they were trying to create life from scratch, do you? As I mentioned in my previous post, there are other teams trying to do this, but not Venter’s.

    >So the only way I would be forced to backpedal is
    >if someone can demonstrate the production of life
    >through totally natural processes.

    As long as you’re claiming that it is the creation of life through natural processes that is impossible and not abiogenesis, sure. I somehow got the impression you were saying that abiogenesis is impossible, which would rule out both natural and supernatural processes.

    >Since the data clearly say this can’t happen…

    What data would that be? If you’re referring to the fact that Venter’s team failed to accomplish something they weren’t trying to do then I don’t think you have any data.

    If the only way you would have to backpedal would be if we observed the creation of life through natural processes then you needn’t concern yourself about any of the teams working on artificial life. Even if these teams accomplish all their fondest goals, they still would not have created life through unassisted natural processes.

    –Percy

  39. jlwile says:

    CD, you really need to think about this, as you clearly don’t understand the results. Indeed, you don’t even understand what I wrote about the results. NOWHERE did I say that other teams will fail at their attempts to produce life without the aid of living organisms. The fact that you seem to think I said that demonstrates that you haven’t bothered to seriously read my post or think about what Venter’s results mean. If you spent less time trying to hurl insults and false accusations, you might have time to actually think about what the result of Venter’s team actually means. Of course, insults and false accusations are usually the resort of those who don’t want to think.

    What I clearly said was the Venter’s team has significant advantages over NATURALISTIC PROCESSES. They had a goal of making life. Naturalistic processes do not. They had lots of intelligent designers working to get the job done. Naturalistic processes do not. They had all sorts of equipment to help them. Naturalistic processes do not. Thus, if they needed the help of living organisms to get the job done, naturalistic processes don’t have a chance of getting the job done without the aid of life as well.

    It is amazing that you try to chastise me about my conclusion, when you can’t even understand what I clearly wrote. Venter’s team did, indeed, demonstrate the impossibility of abiogenesis, since even with significant advantages over naturalistic processes, they still had to use life in order to make life.

  40. jlwile says:

    Hi Percy. Thanks for your thoughtful comment. The goal of Venter’s team was to produce a synthetic organism. Certainly, if they could have done it without the aid of living organisms, they would have. After all, you just need to read both papers (the two-year-old one and the current one) to see how much delay was caused by those pesky living organisms. However, as I said in the post, they couldn’t even create moderately-long strands of DNA without the help of living organisms. Thus, if they COULD have created their synthetic organism without the help of yeast and bacteria, they would have. However, they couldn’t.

    >As long as you’re claiming that it is the creation of life
    >through natural processes that is impossible
    >and not abiogenesis, sure.

    When I say “abiogenesis” in the post, I am referring to the generally-accepted view of abiogenesis – that life came from non-living matter through natural processes. When we are talking about sources of intelligence producing life, that is generally called “intelligent design.” So of course, I am simply saying that given Venter’s team’s advantages over naturalistic processes, it is clear that if they had to enlist the help of living organisms, then naturalistic processes aren’t going to be able to make life without living organisms.

    >What data would that be?

    The data that show the impossibility of abiogenesis are manifold. “Signature in the Cell” is a good place to start if you want to learn the data. In addition, both The Design of Life and Life’s Solution (written by someone who WANTS to believe abiogenesis is possible) discuss the appalling lack of progress in abiogenesis research. However, Venter’s team’s result does, indeed, add to the data.

    >If the only way you would have to backpedal
    >would be if we observed the creation of life
    >through natural processes then you needn’t
    >concern yourself about any of the teams
    >working on artificial life.

    Yes, I do. I think this is where you are not quite understanding the implications. Teams working on synthetic life provide an excellent indicator of what it takes to make life. Indeed, they are probably a better indicator than most origin-of-life experiments. After all, when an origin-of-life experiment fails, the experimenters can always fall back on the idea that they didn’t model the early conditions correctly, didn’t have the serendipity to experience the one-in-bazillion situation that was necessary to make life arise, etc., etc. However, when a team that isn’t interested in modeling the early earth tries to make something that is alive, it gives us a window on what it would take for naturalistic processes to make something that is alive. Venter’s team tells us what it takes to make life – it takes living organisms.

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