The Dawn Treader

Jeff-- Very helpful, and very nicely done. I'm printing out your post to use as a reference.

Hi Jeff,
I assume that you didn't want this thread to be about epistomology and not about your DNA arguments, because you don't post your PPT presentation or a summary of the arguments. I must mention, though, that the theory of evolution does not predict random DNA either. Proving that there is information in DNA (there is information, lots of it) does not prove design any more than proving that there is information in snowflakes proves that snowflakes are handmade. Very simple rules can produce startling "designs". The question is where is the information coming from.

Me:
I assume that you didn't want this thread to be about epistomology and not about your DNA arguments
I managed to obscure my meaning with my keyboard dislexia. Should have said:
I assume that you want this thread to be about epistomology and not about your DNA arguments
but looks like you understood what I meant.

Shall I reply, or would you like this to be an epistomology thread? I'm sheepish about hijacking another thread.

It is based on a faith that science will eventually provide a naturalistic answer to solve today's mysteries.Well, sort of. It's a "faith" based in large part on an excellent track record. We know from experience that just because we can't today explain something in naturalistic terms doesn't mean that there is no such explanation. Does it automatically follow, then, that everything can be explained in naturalistic terms? Not necessarily. But given the comparative track record of naturalistic versus supernatural explanations, it's not a bad bet at all to go with naturalism in a particular case.

I can name dozens (probably hundreds) of cases where naturalistic explanations have supplanted supernatural ones as the generally accepted explanation. Can you name even three examples of the converse? I seriously doubt it.

In my opinion, Drew didn't win. He lost, because he allowed you to dictate the terms, and played the game the way you play it. Instead of arguing that "just because science hasn't presented an explanation yet doesn't mean it won't," he should have been challenging YOU to present POSITIVE evidence to support YOUR assertions, rather than allowing you to allow poking holes in opposing assertions to pass as making your own case.The irony is that skeptics, like Drew, are quick to disparage anything requiring faith … and quick to rely on faith, albeit unknowingly.No, what we discourage is things that require blind, unearned faith. And frankly, to argue that what scientists accept "on faith" is anything at all like what you do is to seriously diminish the meaning of "faith" as Christians would normally apply it.

What's funny to me is that your takedown of Drew is almost precisely correct. But if you were to apply this exact same reasoning to the arguments presented by ID proponents, you'd find the ID arguments lacking for precisely the same reasons. Faith-based; non-falsifiable (which IIRC you have elsewhere argued isn't necessarily a bad thing); more concerned with what we don't know than what we do; presents non-existent facts as "evidence"; appeals to future evidence: ID "theory" is guilty of every single one of these offenses.

ID theory starts from the presupposition (faith) that there must be a creator, and sets about trying to find ways in which we can prove this to be true. It's not falsifiable in any meaningful sense, because there's no realistic conceivable evidence that would disprove it. It spends an inordinate amount of time talking about what evolution doesn't tell us. It talks about differentiating between the appearance of design and actual design as being hypothetically possible, but gives us no such tools to actually do the differentiation, nor does it give us clear-cut examples of one or the other. And it is most certainly philosophy disguised as science, appealing to future knowledge ("the testable model is coming Real Soon Now") to advance a purely philosophical point of view.

The only thing that surprises me is that you can't (or won't) see it.

The biggest problem with ID proponents is that for all their high-minded talk of teaching the controversy and comparing models, they want to put the cart before the horse. They want to start advancing their philosophical point of view before they even have the models and evidence to back it up. And despite having come up with no compelling evidence for ID to date, they "continue to hunt around in the dark and appeal to future evidence to vindicate their models [such as they are today]." Which brings me to this:Therefore, if the truth is that God created life, the researchers will continue to hunt around in the dark and appeal to future evidence to vindicate their models.Don't you see? I could just as easily claim that "Therefore, if the truth is that there is no God and life is a cosmic accident, ID researchers will continue to hunt around in the dark and appeal to future evidence to vindicate their models."

Except that science has a long history of throwing out old models when newer one come along that do a better job explaining reality. The process is often painful and involves a lot of conflict, but it happens, and has happened. By and large, religious viewpoints have no such history.At some point, the data will reach the tipping point. Just ask Anthony Flew.Yep. Sooner or later, even the brightest among us will find it easier to throw up their arms and say "God did it." :)The information content in DNA is more analogous to the content of the Hobbit than it is a book full of Merry Christmas printed 500,000 times.Actually, it's somewhere in between. Whereas the Hobbit is made up of 26 letters (not counting punctuation) that can be combined in many, many ways, DNA is made up of only four "letters" which can only be combined in very specific ways. When you further govern this with the fact that "gibberish" combinations will neither self-replicate nor pass themselves on while "working" ("meaningful," if you prefer) combinations will, it's not difficult to find that DNA falls much closer to the snowflake end of the spectrum than to the Hobbit end of the spectrum. This is even further tempered by the fact that you're comparing the complexity of any life to that of a specific book. A less-unfair (but still unfair) comparison would be to compare the information contained in DNA with that in any book ever written/published.I was trying to gauge where fellow PCA'ers were ... and suddenly, the thread starting getting into the philosophy of public education, funding etc.Yeah, if only some jerk hand't brought up that whole tangent. Oh, wait... ;)

Kevin:

Actually, what ID does is apply to bogus use of probability and statistics. Probabilities are only useful for predicting future outcomes, not for determining whether or not past outcomes actually did occur. It was exceptionally unlikely that Giacomo (50-1) and Closing Argument (71-1) would finish first and second in the Kentucky Derby this year, but that doesn't prove that they didn't (and, in fact, we know that they did). There was only a one in 1,221,759 chance that last night's Tennessee Lotto 5 drawing would pick 27-12-35-14-38, but it did. And, in fact, the odds were only one in 146,611,080 that they would be picked in that order, which they were.

And even if you wanted to look at probabilities of past events, they're only useful by way of comparison. You can't just look at the probability of an event having happened a certain way, saying "that's unlikely, therefore it probably didn't happen." You have to be able to assign probabilities to alternative explanations and compare all those probabilities. And even when you've done that, you haven't proven anything; you've just given yourself an educated guess as to where to start looking.

It's pretty clear that a post-hoc look at probabilities is meaningless as an explanatory tool.Scientific conclusions are inductive, not deductive. They can never be proven 100%; only disproven.True, they can never be proven 100%, but a percentage can be assigned, and through this we can decide upon relative likelihoods. And even if a scientific theory isn't proven beyond reasonable doubt, it can still be a useful explanatory tool to the extent that it actually works. We know that Newtonian physics isn't correct, but for a large subset of what we need it works just fine, so we continue to teach and use it for practical applications within its useful scope.

Jay:

DNA and protein sequences are generally not unique; sequences are usually repeated across different genomes, commonly repeated within genomes, and sometimes even repeated within the sequences themselves

Perhaps true ... but the point is, sequence matters. If you resequenced a genome for the heck of it, guess what would happen?

Likewise, if you resequence the letters in my blog post, it quickly becomes unintelligible.

Perhaps you know the length of the simplest protein sequence (in terms of amino acids) ... then tell me how many nucleotides must be correctly sequenced to generate this protein.

The problem with inferring design from this information is that Nature can make information as easily as God, all it needs is energy input.

Yes. Nature can produce objects with very low information content ... like snowflakes and crystals. So far, no one has reproduced a natural, contingent process which generates complex, specified information. Once they do, they will get the Nobel prize ... as I told Drew that day. The folks at the Sante Fe Institute are looking quite diligently.

If you just grant me that the program can make baby programs with some typos and that the environment will like some words more than others, you'll get information.

That is the argument Dawkins makes. It is a form of Berras Blunder. The argument requires an environment which is choosey about the information it selects ... it wants to form a Tolkien novel. This, of course, hardly describes a blind, mechanistic, unguided process. It describes a process that must be pre-programmed to select to a specific design ... in the case of our analogy, it must have a Tolkienish design to it. It would require a second programmer to write the program to select the Tolkienish letters from the random baby programs.

Let’s assume there *is* no obvious natural explanation for a phenomenon. How do you proceed? You guys are right that the argument that “science might come up with an explanation later” is unfalsifiable and lame. I think a better argument is that invoking God is ad hoc and not very parsimonious. You are quick to invoke Him here because you want to believe.

Who is quick? We have had fifty + years of data gathering going on. Let's start to form some models, and make some predictions. And then keep looking. One model is going to begin to emerge as the best possibility. I am not for abandoning the search as tgirsch always seems to think I am. I think that is a straw man to say all creationists are for abandoning science and sitting around and holding Bible studies. I have never advocated that.

Re: your "wife is gone" illustration.

I am not acting quite as quickly as you seem to think. And, I am not for calling off the search either. The point is, if we are really interested in truth, then we are going to have to start considering all the models on the table. Put everyone's idea to the test.

Incidentally, your "wife is gone" illustration is a good one to support another point I have been trying to convince tgirsch and kevin (tgirsch's blogging partner) of for some time. When we are looking for explanations of past events, we have to consider plausible scenarios. The way you decide what is plausible versus what is not plausible is to assess likelihood to different scenarios. Likelihoods is another term for probabilities. I am continually told, however, that probabilities for past events don't count. Your illustration shows that they do. Many thanks for that.

I agree to your point ... we need to be rigorous about eliminating natural explanations. It is a valid point. I am not arguing for a quick out ... or for lazy scientists.

Thanks for the good discussion!

Jeff:The odds of Lucy winning powerball four years in a row are simply staggering.The odds of her winning it once are staggering, but that doesn't mean she didn't. But nothing about your example counters mine. The unlikelihood of her legitimately hitting it four years in a row makes you guess that she was cheating. But until you can come up with evidence that she was cheating, it's nothing more than a well-informed guess.I am comparing the odds of two things ... the likelihood that chance as an explanation works, and the likelihood that it does not.Apples and oranges. Unless, of course, you can actually assign a specific probability figure to either of those odds. But that's not what you do. You're not comparing anything, really. All you're doing is assigning a probability value to the possibility that chance could produce where we are today, and saying that it's so unlikely as to be impossible. What you don't do is assign probability values to the other possible outcomes that chance could have produced, or a probability value that Designer X produced our current outcome, or a probability value that Designer X could have produced something different. Until you assign a probablility value to the proposition that something other than chance (and I mean a specific something here, not just "anything else") got us to where we are today, you're not "comparing" anything.

And your own wording reveals this. You're comparing the probability that something happened against the probability that it didn't, and that's not meaningful. It's analogous to you comparing the odds that Giacomo would win the Derby against the odds that the horse wouldn't, and saying that this suggests Giacomo didn't actually win it.

Getting back to your Lucy example, that's flawed, too. Because in this example, you know she won the lottery four times. What you're actually comparing in this case is the probability that she won it legitimately against the probability that she cheated. But whether or not she actually had the right numbers is not in question.

Further, the lottery example doesn't fly too well anyway, because the "winning numbers" would have to have been specified by Lucy a priori. The better comparative example for design versus evolution is rather than pointing out that Lucy won in those four years, just say that the numbers in 1995 were 32-14-23-08-15-02, and in 1996 the numbers were 21-18-07-11-23-14, and in 1997 the numbers were 01-17-34-29-27-06, and in 1998 the numbers were 30-14-18-07-19-26. The odds that those four sets of numbers should be picked are astronomical. But what you ignore here is that four sets numbers had to be picked. The probability argument against evolution is akin to hitting a golf ball and saying "Wow, of all the zillions of blades of grass it could have landed on, how unlikely that it should land on this one," while ignoring the fact that it had to land somewhere.

And this bears repeating about the Lucy example: that the likelihood of her cheating is much greater than the likelihood of her legitimately winning four times does not prove anything. It's merely suggestive, and gives us a place to start looking for evidence. But until we find such evidence, we really don't know anything at all about it.In fact, if she won 50 years in a row, your argument is basically to say we should ignore probabilities because it already happened.That's not at all what we're saying, and I think you do a disservice to our argument to suggest this.

Jeff:If we throw out inferences, then the scientific study of the past would be crippled.Where have I (or anyone else, for that matter) suggested that we should "throw out inferences?" We must understand their limitations, and that's an entirely different thing.I am not interested in the odds of whether something happened. You have straw manned me to death. ... I am interested in explaining how something happened ... not if it happened.No, I really haven't strawmanned you to death, and in fact, I call BS on this how/if evasion. You repeatedly point to mostly-manufactured probabilities as compelling evidence that something (naturalistic evolution) couldn't have happened (and, in fact, you do something similar later in this same comment). As far as I can see, that's been the sole purpose of introducing probabilities into the discussion. All those statistics prove is that our current situation is exponentially unlikely, but that doesn't make it impossible, and until you point out a more likely alternative (and can demonstrate that it's more likely, and can provide compelling evidence that in addition to being more likely, it actually did happen that way), you've got nothing. The entire probability line is a farce. And as long as you continue to appeal to it, I will continue to call you on it.It is completely rational and we exercise this kind of logic all the time. We eliminate each unlikely possibility and pursue explanations until we find one that seems likely ... then we search for confirmation of the leading explanation.No, you've got the order a bit wrong here. We don't rule out unlikely explanations unless we've got a more likely one. We don't question the vast improbability that this particular raindrop should land in this particular spot just because that happening is so statistically unlikely. It's only when a more likely explanation presents itself, or when the phenomenon completely contradicts everything we think we know about how stuff works, that we start looking for alternate causes/explanations. And even then, our intuition is often wrong, and the seemingly improbable turns out to be true. (After all, it seems highly improbable that I should be moving at nearly 70,000 miles per hour while I'm sitting here in my desk, and yet it's true.)We can abandon the pure random chance theory because it is patently absurd.Can we? How do we know that it's patently absurd? It's not because we "know" she cheated (although we strongly suspect this), it's because we know cheating is possible, and because we've seen it done, and because the comparative probability of a cheat is far greater than the comparative probability of not cheating. And still we can't say with certainty that she cheated. As unlikely as it may seem, it still remains possible that Lucy did legitimately win the lottery four times in four years.

That's the gaping hole in your logic here. You're equating "extremely improbable" (or even "exponentially improbable") with "impossible," and the two are simply not equivalent.

There's also the possibility that there's more information that we simply don't have. For example, if Lucy used $2,000 per day of her winnings from the first jackpot to buy more lottery tickets in year two, the likelihood of that second win is much greater.What I am arguing here is simply that we can start to abandon the improbable explanationsThis is only allowable when you can present more probable alternatives, along with evidence that those alternatives actually transpired. Until you can do that (and you've done neither), all you can do is suspect.

Once again, it seems that your argument (and that of virtually all ID proponents) is that "what I say must be true because what they say seems highly unlikely to be true." Never advancing your own theory or model, only attacking the prevailing model (with which you have personal philosophical conflicts).

As to the ET stuff, I won't speak to the merits or detriments of it, because I haven't studied it at all, and we've been sidetracked far enough already.

Jay:

Biological sequences have information. Your arguments about rearranging the letters in a blog post or in a protein sequence demonstrate this and I am not disputing it. Again, the question is, how did it get there?

Not just information. A very special type of information. It is precisely specified information that is non-contigent upon any known non-natural processes and is extremely complex. It is important to keep identifying the nature of the information we are talking about. The only kind of thing that can produce highly complex, highly specified, completely non-contingent information is intelligent agents who purpose to put the information there.

Until you or someone else can identify a natural process that produces this unusual kind of information, then it is improbable that it suddenly just got there by the magic of time. You are just saying, "trust me, nature can do that sort of thing" but offering no explanation or examples. That is an appeal to faith.

Our program example does describe a blind, mechanistic process. Our example world selects Tolkien-ish things because that is its nature. Our real world selects world-ish things because that is its nature.

Your analogy does not work, in my opinion, because of your equivocation on the word "select". The "selection" process exemplified by natural processes does not look anything like software development.

It is like someone showing off the evolution of Ford Mustangs over the past thirty years, and saying nature is doing exactly the same thing. The comparison simply does not work, because Mustangs, like software programs, are designed.

Maybe since I work on software for a living, your analogy does not work for me. When I write a program to do something, I am quite intentional about what I am doing. Your claim that nature could essentially write meaningful methods and procedures with no intentionality is again a faith based claim, from my perspective.

Let's try this. Explain how a monkey jumping on a typewriter could bang out the Hobbit given enough time. That kind of analogy would make sense.

The evidence that Nature does make specified information is strong. For example, look at the fossil series. The oldest fossil layer contain only microscopic, single-celled organisms with less information that newer fossil layers with huge, multicellular organisms like dinosaurs. It did not have to been this way. We have discovered millions of fossils, and complex organisms are always in the more recent strata. The trend is always toward increasing information.

But this again misses the point. We know that organism with biological information appeared instantaneously in earth history ... and did so repeatedly because of life exterminating events in earth history.

I completely agree with your point about gradually increasing complexity ... but the original life forms were photosynthetic and fully functioning. They had functioning systems -- they could convert light to food ... from day one.

We need to offer a plausible pathway for fully functioning systems on day one.

Who is giving up quickly? You are. When I say hasty and quick, I am referring not to time but to the weight of evidence for and against any natural explanation for a phenomenon.

Actually, I am not calling for giving up ... seriously, go back and read my post and comments.

What I am calling for is a model to make predictions so that we can see how good the model is.

An example would be ... what kind of early life forms should we expect to see ... how about truly simple life forms with a minimum complexity of a dozen proteins or so. Something like that.

I am not saying this proves DNA evolved by chance, I am saying that not only is it not absurd to consider that chance did it, it is absurd not to consider it.

Actually, it is absurd to consider chance can do anything. It would be a philosophical faux pas to do so ... since chance is not a thing. It is a concept. It has no ontological status ... in other words, I cannot reach out and touch chance, see it, smell it, weigh it, talk to it, burn it, detect it ... etc, etc.

Chance literally cannot cause anything.

What I believe you are saying, is, we need to consider that an improbable explanation is possible. It is improbable, though possible, that I am a butterfly dreaming that I am a blogger ... improbable, but possible. I will consider it. I will also, most likely, reject it and go with the more likely explanation that I am a blogger engaging in a pleasant conversation with an interesting and polite person who has a Phd and is therefore much smarter than I am ;-)

It is like someone showing off the evolution of Ford Mustangs over the past thirty years, and saying nature is doing exactly the same thing.Well, kind of. With the mustangs, we can look at the blueprints, talk to the designers, query them as to why they did what they did, etc. We can witness the entire process from concept to design to manufacture.

But note the trap you've just stepped into here. Even with intelligent designers involved, the Mustang of today is vastly different from the Mustang of just 30 years ago, and the product has evolved. The mistakes have been weeded out, but they existed.

So what your Ford Mustang analogy proves is what I and others have argued all along: that there is no necessary contradiction between evolution and intelligent design. We reject intelligent design not because it contradicts evolution (at least at a very high level, it doesn't), but because there's been no significant evidence put forth to support it.When I write a program to do something, I am quite intentional about what I am doing.This type of argumentation misses the point. What you are essentially arguing is that it's impossible for a computer programmer (or anyone else, for that matter) to model a random universe, because "intent" has gone into their design of that model. That's silly. If I build a model that's designed to closely model natural processes, my intent concerns the model itself, not the thing that the model represents.

I could make a copy of a random rock, too, but that doesn't make the original rock "designed."First, billions of years are not available. In geologic time, life appeared instantaneously on this planet ... it did not have billions of years to evolve from protocells.Well, we think that's how it happened, but that's far from conclusive. But now you're conflating abiogenesis with evolution. For the sake of argument here, how about we concede that God snapped His fingers and made the original life form appear. We're concerned with what happens after that. All the evidence we have concerning what happened after that first moment (or moments) of life points to evolution.

Whoa! You wrote a treatise. I'll check out your links ... and accept my apologies for the pigmy comment boxes. They are annoying me too.

But the whole ID movement is based solely on the intuition that life is too complicated to be accounted for naturally, evidence be damned.

Based on your understanding of the ID movement ... which is derived from Talk Origins. Go read Dembski's book called Intelligent Design and then let's talk. Until then, I feel like you are presenting talking points pulled from a tip sheet on how to win arguments against creationists.

Well heck, everything is a faith-based proposition when you put it that way. But as we've argued many times before, that doesn't make all propositions equal in merit. And in fact, it doesn't make all faith equal in merit, either.

I am glad to hear you say this. You are the first skeptical friend who has admitted this.

What differentiates faith is the "logos" (Greek for justification) behind the faith. Faith with no logos is blind faith. Faith with logos is earned faith (i.e. trust). Logos, incidentally, is the carefully chosen Greek word used as the name of Christ in John 1. I do not think that was a coincidence. ;-)

As stated above, this conflates abiogenesis and evolution. Even if we concede God's involvement in abiogenesis (I don't), this has zero net effect on the theory of evolution.

I am not trying to conflate evolution. When I talk about "chemical evolution", I am talking about abiogenesis ... the primordial soup and all that. Still, I would think that you would want to keep God out of all of it, not just speciation, true?

You mean like a model that predicts that life should become more diverse and complex over time, and which will actually be confirmed by fossil records? That sort of model?

Yeah. Kind of like the model I subscribe to. But we can do better than that. Let's get specific. I want to see some predictions from your model which really stick your neck out.

BTW, A human fossil dating back to the Cambrian period would be just as devastating to a Biblical model as it would to an evolutionary model, btw. The Bible describes progressive creation ... man is created on day 6, not day 1.

Well, it would be if that were what he was arguing, but it's not. To my knowledge, Jay has never even argued that God isn't somehow responsible. Just that we've been too hasty to attribute things directly to God in the past, and thus should be careful about doing so now.

You are probably right. Jay is a theistic evolutionist, I believe. I will go along with your statement.

The intruder in the basement analogy works for this discussion, I think. I would agree that many have jumped to "there is an intruder in the basement making those sounds" conclusion. The point stands, even if Jay was not disputing it, that the fact that science has offered physical explanations for things does not mean that everything has a physical explanation. It simply is a logical faux pas to assert such a thing.

Hey, now, wait a minute! When I make these same arguments about "truth" you bristle and call me a relativist and scream all kinds of foul play. How come you get to hide behind it now, when it's convenient for you?

This comment completely lost me.

That's true given a LOT of unstated assumptions. You're assuming that Lucy isn't the only one playing the lottery, for example; you're assuming that she hasn't taken a disproportionate amount of her winnings from the first fair-and-square hit and reinvested them; you're assuming that she hit the jackpot each time (whereas you can "win the lottery" and get just your ticket price back, and that's pretty common); etc.

Good point. I did make assumptions. Lucy bought one ticket each time. Lucy won the grand prize powerball each time. Tens of millions of tickets were issued each time. Her odds of winning each time were 50 million to one ... or something even higher.

First, why don’t you post your power point presentation so we can have a look at your data?

You keep saying “why don’t we start to form some models” - this is what biologists have been doing for hundreds of years. Here is a page that explains three scientific models of abiogenesis. ID-ists/creationists have always been free to propose scientific models also. Still, as you know, there is no scientific creationist/ID model, unfalsifiable claims and criticism of evolution.

Next, you make some claims that again make me wonder if you are really looking for scientific truth:

... but the original life forms were photosynthetic and fully functioning. They had functioning systems -- they could convert light to food ... from day one.
We know that organism with biological information appeared instantaneously in earth history ... and did so repeatedly because of life exterminating events in earth history.

This is the sort of thing that makes scientists really mad when arguing with ID proponents: it seems to me that you have knowingly changed the question to reflect the answer that you want. We most certainly do not know any of these things. You seem to be claiming either one or both of the following, neither of which is supported by the facts:

1) All living things were killed off and new life emerged de novo many times in the Earth’s history.
I have never heard a biologist make this claim. If you really believe this, you have a lot of things to explain. I could write a whole post on just this point, but here’s one big problem for your claim: if all biological life was destroyed and arose de novo several times, why can I construct a phylogenetic tree using rRNA sequences that demonstrates that they had a common ancestor before all of these life-exterminating events?
2) The first life appeared “instantaneously” and was viable and photosynthesis-ready “from day one”.
Life did not appear “instantaneously” on “day one”, it appeared almost a billion years after the Earth formed.

The problem in front of us is most definitely not “how do we assembly a working cell ‘instantaneously’ from ‘day one’”.

Let us spell out explicitly what we know:
About 4.5 Billion Years Ago: Earth Forms
About 3.8 Billion Years Ago: Earliest known blue-green algae

I think if you were really interesting in eliminating natural explanations, you would mention that the Earth existed for (4.5 – 3.8 billion years ago, plus or minus big error bars) about 700 million years before blue-green algae appeared. Some of this time the Earth was not hospitable to cellular life (but may have been hospitable to self-replicating molecules), but this certainly does not reduce the problem to:

We need to offer a plausible pathway for fully functioning systems on day one.

You need to at least state your bold assumption that no living thing or self-replicating molecule existed for even a single second of the 700 million years before blue-green algae appeared 3.8 BYA. Let’s be precise so I know you are not just trying to recruit lay people who want to believe what you are arguing.

This brings up the issue of “billions of years”. The reason I keep saying billions of years is that the Earth is about 4.5 billion years old and you are using present-day biological sequences to do your analysis. 4.5 billion (age of the Earth) – 0 (now) = 4.5 billion. Don’t like those numbers? Here are some more conservative numbers: 3.8 billion (oldest known blue-green algae) – 0 (now) = 3.8 billion.

Now I see you are trying to analyze very old DNA sequences, whose information you are somehow estimating from latter-day sequences. (Again, let us have a look at your methods and your data.) It is reasonable to estimate this information, but this is again an estimate with big error bars, and you need to state your assumptions.
Not just information. A very special type of information. It is precisely specified information that is non-contigent upon any known non-natural processes and is extremely complex. It is important to keep identifying the nature of the information we are talking about. The only kind of thing that can produce highly complex, highly specified, completely non-contingent information is intelligent agents who purpose to put the information there.
What exactly do you mean by “complex, specified, non-contingent information”? I am a biologist who analyzes the information in biological sequences for a living, and I have never heard this jargon until now.

If you are going to define this information as something that only God can make:
“the only thing that can produce highly complex, highly specified, completely non-contingent information is intelligent agents”
then you are right, only God can make it, but you must agree that this begs the question. Again, let’s not frame the question to yield the answer that you want.
Until you or someone else can identify a natural process that produces this unusual kind of information, then it is improbable that it suddenly just got there by the magic of time. You are just saying, "trust me, nature can do that sort of thing" but offering no explanation or examples.
No. I offered an explanation and several examples: 1) the clear development of information in the fossil layer, 2) biological “micro-evolution” (a.k.a “evolution”) which is so evident it makes even creationists use the E-word, and 3) the spontaneous formation of information in things like snowflakes.

Here’s another: they are many examples of proteins that are only present in mammals and therefore evolved in the last hundred million years, billions of years after life began. Sure, maybe God came and touched things up a few billion years later, but again, the most parsimonious explanation is that this information was created by an organism adapting to this world.

Further, your argument (God must have made DNA because we cannot yet explain it naturally to my satisfaction) is classic “God of the gaps” - it works for any gap in human knowledge. Do you see how a few hundred years ago the same argument applied just as well to explain the plague using God: “until you or someone else can identify a natural process that produces this disease, then it is improbable that it is not a punishment from God”? Do you see how if humans had been satisfied with this sort of argument, we would have never cured the plague? Can you see why scientists are so hostile toward this sort of argument?
That is an appeal to faith.
No, it is not an appeal to faith, it is an appeal to parsimony and existing biological evidence.

On to the Hobbit analogy:
Your analogy does not work, in my opinion, because of your equivocation on the word "select". The "selection" process exemplified by natural processes does not look anything like software development.
I am not comparing software development with natural selection, I am comparing software with DNA.

I am not equivocating about my definition of the word “select”: the tendency of the world to encourage the survival of self-replicating things that are better suited to this world.
It is like someone showing off the evolution of Ford Mustangs over the past thirty years, and saying nature is doing exactly the same thing. The comparison simply does not work, because Mustangs, like software programs, are designed.
Okay, pardon the tangent, but I have to set the record straight. This is your second reference to the so-called “Berras Blunder”, which was a metaphor not a blunder. Here is exactly what Berras said:

Everything evolves in the sense of "descent with modification," whether it be government policy, religion, sports cars, or organisms. The revolutionary fiberglass Corvette evolved from more mundane automotive ancestors in 1953. Other high points in the Corvette's evolutionary refinement include the 1962 model, in which the original 102-inch wheelbase was shortened to 98 inches and the new closed-coupe stingray model was introduced; the 1968 model, the forerunner of today's Corvette morphology, which emerged with removable roof panels; and the 1978 silver anniversary model with fastback styling. Today's version continues the stepwise refinements that have been accumulating since 1953. The point is that the Corvette evolved through a selection process acting on variations that resulted in a series of transitional forms and an endpoint rather distinct from the starting point. A similar process shapes the evolution of organisms."

Everyone including Berra and the guy who is trying to sell the phrase "Berra's Blunder" knows Corvettes are designed. You can say he was making a bad metaphor, but to accuse him of “blundering” implies that he forgot Corvettes are manmade, which is lame.

The fact that Berra cannot compare two things without being accused of “equating” the two things (and yes, he was accused of equating them) says more about the people he is arguing with than about Berra.

Yes, Berra was knowingly begging the question of design, but come now: there are two kinds of things in the world: things that are natural and things that are manmade. In this case, natural things are under consideration. That leaves only manmade things to use for analogies. If he had used something natural, you could accuse him of begging the question of design just the same, since whether natural things are designed is exactly the question under consideration. You are using rules that prevent him, but not you, from making any analogy at all without “blundering”.

About Lucy, the thing I and tgirsch and others find unsatisfying about your analogy is that evolution involves concurrent, not sequential trials. In the primordial soup, there were countless macromolecular precursor Lucy’s floating around simultaneously for millions of years before life began. Right now, there are countless Lucy’s alive and simultaneously playing the biological lottery. (And this is ignoring my original objection, which is that you are a direct descendant of a winning Lucy, so she had to win for you to be sitting here musing about all this in the first place.) In evolution, many Lucy’s play at the same time, and if you want to calculate probabilities, you must have some way of considering those Lucy’s that played and did not win.

I am after the Truth, too, the question is how do we get at it.

What we scientists are doing is investigating scientific truth as a way of learning the Truth.

You seem to want to do science. You want to publish in our scientific journals, you want to teach your findings in our science classes, so, sorry, you have to use science to do that. If you want to do science, you have to make falsifiable claims and you have to propose a testable model.

Go ahead and do meta-science, or whatever you want to call it, but do not expect scientists to accept it as science.

Jeff:Go read Dembski's book called Intelligent Design and then let's talk. Until then, I feel like you are presenting talking points pulled from a tip sheet on how to win arguments against creationists.Actually, while I've not read Dembski's entire book (or Behe's), I've read articles by both, seen interviews with Dembski, etc. And no, I'm not following any talk origins script (in fact, I rarely go there).Again, I think you are missing the point. Improbable things can happen. But is that where you start looking? Is that the best spot to place your hope and trust? You seem to be asking me to accept coincidence after coincidence after coincidence after coincidence ... and just say, wow, what incredible luck.Actually, I'm not asking you to do that at all. I'm asking you, instead, to look at all the scenarios to which we can assign probabilities, and start from the least improbable. Kind of like the old Sherlock Holmes saying: when you eliminate the impossible, whatever remains, however improbable, must be the truth.

But this is the fatal flaw in your logic that you just don't seem to be getting. You're looking at probability in a vacuum. You're saying that because scenario A is remarkably improbable, scenario A should be eliminated or should not be seriously considered. But that only works if there exists some Scenario B for which the probability is much greater. In that case, you eschew scenario A in favor of scenario B, unless there's some fatal flaw in scenario B that eliminates it.

Unfortunately, voodoo math aside, you can't assign any sort of probability to the God hypothesis, so it's a question that math and science simply cannot answer (something Descartes learned the hard way). In any case, science isn't particularly interested in whether God did anything; it's more interested in how things happened. Whether God did it or not, science would still strive to understand the progression of events and the processes involved, and it ought to be able to accurately detect those, unless God intentionally obfuscated His work -- something that seems to me to be highly unlikely.[Probabilities] are not proof. They are merely data points of evidence, that is all.This is exactly correct. Which means that probabilities essentially tell us nothing meaningful about how life began. So why introduce them into that discussion? :) As I said, it's meaningless to say that "Scenario A is exceptionally improbable" unless you can quantify a more probable alternative. With your lottery winner example, there are easy to quantify alternatives: Lucy cheated. With the origins of life, your preferred alternative is impossible to quantify probabilitically, so we have no means of using probabilities to assess the likelihood of truth or falsity. All you have, instead, is intuition (it just "seems" or "feels" right), but that's not at all scientific.I am not after scientific truth. I am after Truth. Truth with a capital T.Fair enough, and we all ought to be. The problem is, no tool has a better track record of getting us closer to capital-T Truth than science. Not even remotely.