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A Rational Look at Christianity; Basing Reason in Truth


The latest issue of World Science has an interesting article related to the search for the origins of life. It's entitled "Tiny genome may be melting away, study suggests" and discusses the discovery of the very small -- miniscule by expected comparisons, really -- bacterium known as car­sonella rud­dii. Now, car­sonella rud­dii is a bacterium that lives inside an Ar­i­zo­na in­sect, Pa­chyp­syl­la ve­nus­ta, a.k.a. the Hackberry Petiole Gall Psyllid (pictured at right), which lives on tree sap.

Okay, what surprises the scientist is that little car­sonella rud­dii is much, much smaller than the expected 400,000 letters of genetic code necessary for life. In fact, it is less than half of that size. According to the article, it has "182 func­tion­al genes. These cor­re­spond to 160,000 'let­ters' of ge­net­ic code; pre­vi­ous es­ti­mates had placed the min­i­mal ge­nome at about 400,000." Wow! Even the scientists are amazed:

"It’s un­be­liev­a­ble, real­ly," said Nan­cy A. Moran of the Uni­ver­si­ty of Ar­i­zo­na in Tuc­son, Ariz., one of the sci­en­tists who con­ducted the new re­search. "It’s be­lieved that more genes are re­quired for a cell to work." The find­ing pro­vides new in­sights in­to bac­te­ri­al ev­o­lu­tion, Moran and col­leagues wrote, also in the Oct. 13 Sci­ence.

Does this mean the end of Intelligent Design's claims for evidence of a designer of unknown origin based on the problem of irreducable complexity? Not really. It's important to really look at what's happening with little car­sonella rud­dii. First and foremost we're still talking about 160,000 letters in 182 functional genes. Since the research is seeking the absolute simplest cell, it is not as if the 182 functional genes representing 160,000 letters evolved. That's not possible since evolution occurs only amongst living things. Thus, we are still in a state where this 182 functional genes had to come together by chance -- a highly unlikely scenario as anyone who has ever played the lottery can tell you.

Moreover, it's important to remember that the collection of genes doesn't function as an organism unless they're in a particular order -- much like the words in a book wouldn't make much sense if they were randomly written. Thus, in addition to 182 functional genes coming together, they had to come together in the correct order to be able to work as a functioning, living organism. To get an idea of how improbable this is, think about how many ways 10 things can be ordered. Just getting ten things together by chance is tough enough, but any ten items can be put together 10! (10 + 9 + 8 + 7 + . . .1 = 55) ways. In other words, if there are 10 things that need to come together in only one way, assuming that the 10 things can be brought together naturalistically by chance, there is only a 1 in 55 chance that they will come together in the right way.

Now, consider if there are 182 things (like functioning genes) that need to be put together in a particular order. That is 182! or 182 + 181 + 180 + . . . + 1 possible combinations with (as far as we know) only one being workable assumuing that all 182 genes will come together in one place sheerly by chance. The odds that they would arrange themselves in the correct order by chance are 16,653 to 1 against which is, to put it mildly, quite extraordinary.

Second, little car­sonella rud­dii isn't making it on its own. Like a man strapped to life support, car­sonella rud­dii wouldn't be able to survive independent of the life-sustaining help of its host. You see, car­sonella rud­dii is a parasite that not only has to be with its host to survive, it appears to be actually morphing to become a mere biological organelle of the host. Consider the following from the World Science article:

Like a cash-strapped com­pa­ny that has to merge with a rich­er firm to keep go­ing, they say, the mi­crobe and its genes seem to be lit­er­al­ly fus­ing in­to a larg­er crea­ture, be­com­ing cogs in its cel­lu­lar ma­chi­n­er­y.

Also,

To live, such in­sects of­ten re­ly on res­i­dent bac­te­ri­a that make and share key nu­tri­ents with them. The host and mi­crobes de­pend on each oth­er to live, a re­la­tion­ship called en­do­sym­bio­sis. The bond is so close and an­cient that the mi­crobes live with­in spe­cial in­sect cells that have ev­olved to house them, called bac­te­ri­o­cytes.

The bac­te­ri­a thus live in a shel­tered world with a sim­ple, pre­dict­a­ble di­et and lifestyle. So they get by with sim­ple ge­net­ic in­struc­tions. If they or their an­ces­tors had any ex­tra, un­need­ed genes, these would ge­ner­al­ly have been lost over the course of ev­o­lu­tion.

The re­search­ers col­lect­ed Pa­chyp­syl­la ve­nus­ta bugs from hack­ber­ry trees on their uni­ver­si­ty cam­pus and around town. They ex­tracted the Car­sonella DNA and se­quenced it, and got a jolt. "It lost genes that are con­sid­ered ab­so­lute­ly nec­es­sar­y. Try­ing to ex­plain it will prob­a­bly help re­veal how cells can work," said Moran.

The sci­en­tists spec­u­late that in the bac­te­ri­um’s ev­o­lu­tionary past, some of its genes moved in­to the in­sect’s own ge­nome, be­gin­ning a pro­cess of gene takeo­ver.

An­i­mal and plant cells have spe­cialized in­ter­nal struc­tures called or­ganelles, ti­ny sacs of ma­chin­ery used for var­i­ous pur­poses. Strong ev­i­dence sug­gests many of these or­ganelles are de­scen­dants of sym­bi­ot­ic bac­te­ri­a that once lived free, but grad­u­al­ly be­came in­cor­po­rat­ed in­to the cell. A trans­fer of genes from the bac­te­ri­um to the host is of­ten part of the pro­cess.

Car­sonella may likewise be turn­ing in­to an or­gan­elle, the re­search­ers wrote.

In other words, little car­sonella rud­dii not only cannot survive on its own without the host, it's actually giving up the ship and fast becoming an organelle in its Psyllid host. So, in other words, while it is a living organism with only 166,000 letters of genetic code, that is not enough to allow it to continue in existence on its own. It can only survive by freeloading on the more complex Psyllid organism, and such dependence is so complete that it is actually merging with the Psyllid as a means of continuing survival.

So, while this is truly interesting, it seems to me that it supports the idea of irreducible complexity because the study seems to suggest that while an organism may need fewer that 400,000 letters of genetic code to be able to "live", such life can only exist if it has a more complex organism already in existence which it can use to serve the functions that it cannot itself serve with its fewer functioning genes. In fact, in this case the researchers believe that little car­sonella rud­dii had to, at one time in the past, been more complex but lost them over time due to its symbiotic relationship with the Psyllid host.

Thus, while there may be some form of life that is possible to live for a short time, it seems to me that this research does little to support the idea that an organism could function, long term, on significantly less than 400,000 letters of genetic code. Certainly, it doesn't appear that the earliest life couldn't have been significantly less than 400,000 letters and survived without some other entity already in existence that had at least that number.

9 comments:

Just remember,

The first organism on the planet didn't have anything trying to eat him. And he didn't leap from nonlife into life in a single step. That's your guys' creation model, not ours.

http://scienceblogs.com/pharyngula/upload/2006/03/abio_theory.gif

Smaller steps.... smaller steps. Dembski and Behe like to foist the specious argument onto scientists that life began in one step because they know it's untenable.

It is a misrepresentation of the pertinent science to assert that scientists posit a single jump from "nonlife" to "life". Those are both loaded terms that mean little when we are talking about the vast spectrum of things that are somewhere in between. Are viruses alive? Are viroids alive? What about prions?



So evolution only occurs with living things?

That's not a scientific statement. How are you defining "living thing"? Viruses evolve, yet they don't fit most definitions of "life".


I can create a computer program that can evolve a solution to a problem, yet it's not in any way alive.

Replicating polymers evolve.

Ideas and memes can be said to evolve, but they are not alive.

Languages evolve, in very much the same way as life does, but languages cannot be said to be alive.


If you really, seriously want to discuss biology, we can do this. But you have to take a serious step and stop just making stuff up.

Do you have a public university near you with a library? One with a biology department?

Bruce,

I'm not making stuff up. I do know what I'm talking about (or I read enough to back up what I'm saying). I do have a public university near me and I do know and have talked to biology teachers both at the high school and universtiy level who accept ID.

Why do you find it necessary to be insulting? Because I'm busy today, I'll respond to the rest when you respond to that.

I wasn't trying to be insulting.

They were serious questions.


Do you want to pursue this or not?

A simple math question for you

You wrote

"Now, consider if there are 182 things (like functioning genes) that need to be put together in a particular order. That is 182! or 182 + 181 + 180 + . . . + 1 possible combinations with (as far as we know) only one being workable assumuing that all 182 genes will come together in one place sheerly by chance. The odds that they would arrange themselves in the correct order by chance are 16,653 to 1 against which is, to put it mildly, quite extraordinary."



How many bacteria do you think are in one cubic inch of soil?

How many amino acids are in a pond of prebiotic soup?



Odds as long as 16,000 :1 are decimal dust when we're talking about organisms and chemical processes that number in the quintillions.

1. “Do you have a public university near you with a library? One with a biology department?” certainly reads like an insult to me since it follows on “But you have to take a serious step and stop just making stuff up.” Given your tendency in the past to come on with statements that are insulting, I tend to doubt your claim that this is perfectly innocent.

2. I am not a creationist. Creationism is a very particular thing, and so to the extent your link describes the difference between creationism and evolution, it doesn’t apply to me. However, since you are clearly suggesting that ID suffers the same problem, I am responding.

3. "Odds as long as 16,000 :1 are decimal dust when we're talking about organisms and chemical processes that number in the quintillions." Actually, we’re talking about one -- the first one. There weren’t quintillions at the time that the first one came into being. Thus, this is a very large red herring.

4. You act as if I’m unaware of polymers, repeating polymers and hypercycle. But that process really doesn’t change anything. Here’s why: I am not disagreeing with the existence of polymers and repeating polymers. Certainly, DNA and RNA are polymers. So we’re already starting with the first step. Moreover, I have no problem that DNA is a repeating polymer (RNA may also be, I just don’t know and haven’t looked it up yet). Here’s the problem, however: hypercycle. You throw it out there as if hypercycle is somehow proven. But it’s not -- it’s a theory that so far isn’t meeting up with the facts.

Here is what Principia Cybernetica Web (not a "creationism" site) has to say about hyptecycle:

The idea of a hypercycle was developed by Eigen and Schuster (1979). They noticed that biological organization results from a cooperation of several autocatalytic systems that augment each other.

* * *

Each autocatalytic component benefits from forming a hypercycle because cooperation increases its reproduction rate. The evolution of hypercycles was never observed experimentally. Thus, the only evidence comes from mathematical simulations. Eigen and Schuster (1979) found that homogeneous systems with uniform components may be evolutionary unstable. They differentiate and a new form (e.g., dissipative structures) emerges at the level of the entire hypercycle. Thus, hypercycles may develop by duplicating of the original gene and subsequent differentiation of genes. This process corresponds well to the Turchin's scheme of metasystem transition.


Note that he says that evolution of hypercycles comes only from mathematical simulations -- no observed data. Add to that the following from Theoretical and Computational Approaches to the Study of the Origin of Life By D. SEGRÈ, Lipper Center for Computational Genetics and Department of Genetics, Harvard Medical School, AND D. LANCET, 2Department of Molecular Genetics and The Crown Genome Center, The Weizmann Institute of Science (again, not a "creationism" piece of work):

One of the fundamental characteristics of a living system is the capacity to make more of itself. The simplest chemical system bearing such attribute is an autocatalytic molecule, i.e. a molecule capable of accelerating the rate of its own production from precursors. (Lifson, 1996; Orgel, 1992; Szathmary and Maynard Smith, 1997). Autocatalytic molecules were experimentally designed in the laboratory, and it was shown that molecular self-replication in vitro is indeed possible. Examples involve modified nucleotides (Li and Nicolaou, 1994; Rebek, 1994; Tjivikua et al., 1990), as well as short peptides (Lee et al., 1996). One of the most attractive forms of autocatalyisis is the one involving bio-polymers, as explored by Orgel’s through the template-directed synthesis of oligonucleotide analogues (Orgel, 1992; Schwartz and Orgel, 1985; Sievers and von-Kiedrowski, 1994). Despite the increasing success in the design of autocatalytic molecules, it should be mentioned that no relevant example has been reported within any life form. Neither DNA nor RNA is truly autocatalytic, as they require the aid of specialized enzymes. How likely is it that nature could randomly hit upon a contrived self-replicating molecule similar to molecules whose synthesis presently requires the careful engineering of experienced organic chemists? This is a question that would require considerable future pursuit.

In other words, hypercycle is a nice theory, but the facts ain’t there yet. It may turn out to be the case and it may be the key that proves ID wrong, but at the moment, it is still a nascent theory with no evidence that it is the way it actually happened. In other words, because hypercycle has not been connected to biological evolution by the evidence, you still have a collection of DNA that somehow has to self-organize into a strand in the correct order. Because the "tiny step" that you apparently trumpet is a phantom, the odds of that happening by sheer chance are very long.

5. Speaking of odds, the odds of 16K:1 are the odds only of them organizing in the right order. You have to add to that the odds of them all being in the same place at the same time, the odds of them being in a “soup” where they have the elements that they need to generate the rest necessary for life, and the odds that the "molecular motors" that are found in cells could somehow exist or be manufactured by the free floating DNA which will, for reasons unknown, perform the tasks needed to create the living cell.

'1. “Do you have a public university near you with a library? One with a biology department?” certainly reads like an insult to me since it follows on “But you have to take a serious step and stop just making stuff up.” Given your tendency in the past to come on with statements that are insulting, I tend to doubt your claim that this is perfectly innocent. '

Given your past tendency to assume that disagreeing comments conceal veiled insults, I can see how you did it with this one as well.

The "serious step" has directly to do with my question about a public university nearby to you. But we'll go slow and see how it goes. How this is an insult is beyond me. Are you saying I'm suggesting that the nearness of a university would somehow by its magical proximity have bearing on the validity of your post? What you're seeing is exasperation and an attempt to gauge the possibility of you following up on this discussion before I dive in. I have noticed a previous tendency of yours to dip a toe in and retreat. Are you going to stick with this one? We'll see.

Let's take the next two points as one. They're quite the same point.


'2. I am not a creationist. Creationism is a very particular thing, and so to the extent your link describes the difference between creationism and evolution, it doesn’t apply to me. However, since you are clearly suggesting that ID suffers the same problem, I am responding.

'3. "Odds as long as 16,000 :1 are decimal dust when we're talking about organisms and chemical processes that number in the quintillions." Actually, we’re talking about one -- the first one. There weren’t quintillions at the time that the first one came into being. Thus, this is a very large red herring. '

So let's slow down a bit. I posted the graphic that shows multiple steps between non-life and life. I post it by way of illustrating that the consensus scientific model is that chemicals took multiple steps of replication and increasing complexity before developing into something we'd call life. Forget for a moment that the left hand of the graphic is labeled "creationism". Just look at the right half as an illustration of multiple steps. I'll concede as any scientist would that we don't know all of the steps yet, though we have a very good idea of some of them. But there is a very simple question I want to ask you:

What is YOUR model? And while we're at it what is the model that you think you are arguing against? If you think the odds are too long for a non-intelligent design solution, please illustrate what model you think this particular intelligent design solution that you propose above is in conflict with. Is it one step, non-life to life? Or is it multiple steps? If your model is not the creationist model, please illuminate for me if you share the one-step model or not.

Because of your "odds" assertion, I'm assuming you're arguing that the scientific model is one step. Of course it is multiple steps, which makes your odds mathematically inaccurate.

Let's be very clear about what you are asserting. Are you asserting that a string of replicating molecules needs to assemble a string of genetic code that's 182 genes long in order to be what we call "life"? Or that it takes a string of 182 genes to be merely self-replicating? If you are indeed talking about "life", what definition are you using? Instead of using the word "life", can you please define it in terms of what aspects this thing would have.

Your odds are roughly 16,000 to one of what exactly happening?


"5. Speaking of odds, the odds of 16K:1 are the odds only of them organizing in the right order. You have to add to that the odds of them all being in the same place at the same time, the odds of them being in a “soup” where they have the elements that they need to generate the rest necessary for life, and the odds that the "molecular motors" that are found in cells could somehow exist or be manufactured by the free floating DNA which will, for reasons unknown, perform the tasks needed to create the living cell."

Before you start stacking odds on top of odds, let's get the first part straight. As I said, let's slow down here. Let's make sure we both understand what you asserted in your first post before you start dashing onward.

Your odds are roughly 16,000 to one of what exactly happening? Please describe for me what existed before we roll the "sixteen thousand sided-die". Assuming the lucky chance occurs, what should we see after the die roll, and what was there before the die roll, or what should we have expected to see if the die roll hadn't been successful? What aspects of "life" would this thing exhibit before and after this die roll? And is this thing in the "before" state the only thing like it in its environment? Why or why not?

1. I leave it to the reader to decide if they agree with my assessment or yours. Moreover, I never feel required to continue a conversation since, as I just stated in another blog, this isn't a debate blog. I think that sometimes the supposed rebuttals speak for themselves.

2. I like to go slow. Let me know whenever you don't understand what I'm saying.

3. You posted a series of steps comparing "Creationist ideas of Abiogenesis" and "Real Theory of Abiogenesis." Obviously, given that you are accusing me of skipping steps, you are putting me in the creationist camp. I am telling you that if it is the consensus model (which I doubt), then the model is flawed because the evidence doesn't support it. I posted the long quote from Theoretical and Computational Approaches to the Study of the Origin of Life so that you can see what scientists are actually acknowleging, i.e., that there's no evidence that hypercycle participated int he development of living organisms. Does that matter to you? Apparently not since you skip over it in your response.

4. My model? I don't have a model, personally. I don't make stuff up (contrary to your assertion). What ID is saying is simly this: there is evidence in the record showing that naturalistic explanations do not and cannot explain what we are seeing. Thus, we have to take into account the possibility that what we see is not the result of pure naturalistic processes.

5. My odds are what they are based on the need to get from repeating polymers to a DNA strand of sufficient length and order to be able to have sufficient information to be able to support life. They acknowledge the first two steps of the chart you posted, polymers and repeating polymers, exist. In fact, that is my starting point. It is from that point that there has to be some naturalistic self organizational process. That process (you suggest to be hypercycle) doesn't work for the reason stated in my earlier post. Thus, the leap that you are so offended at is present and scientists know it! It is only on the Internet that we see people trying to make the assertion that this is somehow settled thought.

So, as you said, let's go slow: the odds I am posting is simply the odds that DNA will organize into a sting in the appropriate order assuming that all of the DNA is acutally in existence in one place at one time. It goes no farther than that one small step in the totality of steps needed for a functioning cell to exist.

"scientists are actually acknowleging, i.e., that there's no evidence that hypercycle participated int he development of living organisms. Does that matter to you? Apparently not since you skip over it in your response."

I did not skip over it in my response. I explicitly stipulated it for now, and conceded that scientists don't know the whole picture yet. I explained that I linked the image for illustrative purposes. Before a hypercycle discussion, I'd still like a good deal of clarification on the subject of your original post.

"My model? I don't have a model, personally."

I also asked you to describe the model you are arguing against. If you do not have a model of your own, please explain for me what specifically is going on in the scientific model that for example your 16,000:1 odds represents.

So your starting point is repeating polymers. Okay.

But then you say:

"My odds are what they are based on the need to get from repeating polymers to a DNA strand of sufficient length and order to be able to have sufficient information to be able to support life."


"the odds I am posting is simply the odds that DNA will organize into a sting in the appropriate order assuming that all of the DNA is acutally in existence in one place at one time."

So I have some questions regarding this. You say you start with repeating polymers. Are these polymers DNA or something else like RNA? Are you including the transition from some other repeating polymer to a DNA-driven organism in your 16,000:1 event? Are these self-assembling polymers?

You say "to be able to support life"... again, I'd like a clarification. Define "life". When you say "to be able to support life", does that mean immediately after the 1 in 16k event, or after additional steps? When you use the term "life" was this thing not alive just before the 1 in 16k event (by your definition of life) and was it alive just after it? What is this thing capable of? Does it have a cell membrane or not? Is it self-replicating? Was it self-replicating before the 16k:1 event?

You said before that only living things evolve. Don't replicating polymers evolve? Why or why not? What definition of "evolve" are you using if it excludes replicating polymers?

Also germaine to the 1:16,000 question is is this thing in the "before" state the only thing like it in its environment? Why or why not?


"Moreover, I never feel required to continue a conversation since, as I just stated in another blog, this isn't a debate blog. I think that sometimes the supposed rebuttals speak for themselves."

This and another response in a different thread causes me to rethink the wisdom of responding to your blog at all.

I'm sorry to hear that you think this is a debate. That explains what I see as your response to me: adversarial.

Bruce,

Sorry about the delay, but I have a life outside of this blog.

While I said that I am willing to go over things slowly, I am not willing to go over things that aren't pertinent. Here's my view of the events thus far:

1. I post the original post pointing out that there is a significant jump from DNA to the living organism described in the article.

2. You post a response that accuses me of ignoring the small steps of science. You linked a page that had what I understand to be a position you support that including hypercycle in the steps from polymer to living organism.

3. I post a quote from an article that points out that hypercycle has not lived up to the position of being part of that chain of events since there is no evidence that hypercycle is involved with any living organisms. Hence, hypercycle appears to be a dead end and there is no small step available.

4. You concede that hypercycle is not yet supported, but in an act of faith equal to anything a Christian undertakes, you suggest that "we have a very good idea of some of [the steps]." (Of course, I disagree with this bald, unsupported statement.) You then begin to ask me a series of questions which is where we are.

Now, I don’t see any reason in particular to answer your questions about self-assembling polymers and cell membranes. In all sincerity, it seems to me that the questions you ask are irrelevant if there is no scientific step connecting "repeating polymers" to "living organisms" (as you seem to acknowledge). It is like you are staring at a chasm wider than the Grand Canyon and are trying to find a rock that moves you nominally closer to the far side. Even if you are successful in finding a slightly closer rock, you aren’t going to come anywhere near closing the gap.

So, with that in mind, I will answer your questions in this way: I don’t care whether we are talking RNA or DNA. Take you pick -- whichever one is best for the idea that there is a step-by-step method linking "repeating polymers" to a living organism is fine with me. After all, I am not here to stand in the way of proof that ID is wrong. I support ID because I think it is true. If you can show me legitimately how this chasm is bridged, I don’t care how you do it. But beware -- no one has bridged it yet. Moreover, they really have no idea how to bridge it -- and that’s the problem for evolutionism.

Oh, and I am not going to answer any questions about repeating polymers or cell membranes unless you first tell me what difference it makes. I am not going to spend time chasing down answers to questions if they don't advance the conversation.

BTW, I do agree it is legitimate to ask what constitutes life. I am aware that the line between life and non-life can get a bit fuzzy sometimes. So, let me tell you what qualities something generally has before it is considered alive. To constitute a living organism, something has to have at minimum the following characteristics (when functioning properly):

1. It is capable of self-replication.

2. It is capable of independently acting on the outside world.

3. It has the ability to ingest nourishment and excrete waste.

4. It has the ability to respirate.

5. It can only come from other life.

Now, I am aware that 5 begs the question in the question of the origin of life, so I don’t expect you to abide by that in any answer you may give. To the best of my knowledge, every single organism that we would call living has each of these characteristics. So, with the exception of number 5 which is irrelevant when we’re talking about the first cell, I would consider something to be alive only when it has the other four qualities.

Oh, and whenever two people take opposite positions on an issue, it is technically a debate. It doesn’t need to be contentious, but I would suspect that if we were to examine posts in the past to determine which of us ordinarily sounded contentious first, you would have a significant edge.

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