Minimal bacteria and dastardly implications
Over at Concerned Scientist Dan takes issue with my post from yesturday, "Minimal bacteria". He has a graphic showing the proposed steps from simple chemicals to bacteria, juxtapositioned with what he considers to be the creationist paradigm.
The purpose of his post is to ‘correct pseudoscientific arguments’, but since we didn’t make any arguments of that nature he seems to have decided to make some rather bold assumptions about what we meant to say, and work from there:
The obvious implication is that, if the simplest known bacterium requires well over 200 genes to survive in modern laboratory conditions, with ample nutrients, etc., it’s inconceivable that it could have evolved from nothingness (a.k.a. that abiogenesis could have occurred without a Creator)?
The argument against this, of course, is that life–even such as the simplest bacteria– isn’t expected to arise in one magical step from a stewpot of simple chemicals, but slowly, via the steps outlined on his graphic above.
But then– was it possible I was not implying anything about "arising from nothingness"? The post in question was hardly more than a summary of the article, which was definitely not written by creationists. Looking at minimum life forms is certainly relevant to abiogenesis, but from that does it necessarily follow that we posit the ‘minimal bacteria’ as the first step in life from simple chemicals?
We appreciate your clarifying this, Dan, and especially the collection of papers in your footnote– good spring break reading– but it isn’t quite fair to make up arguments for us just because Talk Origins has arguments against them.
Were you not suggesting that there’s a problem with a methodologically natural explanation of abiogenesis, absent of a creator??
Comment by Dan — March 17, 2006 @ 6:43 pm
Where do you think I suggested such a thing? In my post I avoided making any claims simply because I didn’t think the PNAS article supported that; I considered it no more than background material– interesting background material, but still just that. I never made any assumptions that the “minimal bacteria” meant minimal anything else, and I definitely never thought of abiogenesis as a direct step from simple chemicals to a modern day bacterium.
You know we’re quite willing to debate views we actually hold… but it doesn’t make sense to extrapolate an argument anytime someone makes an observation. This blog isn’t one of those places where you get nicely canned arguments at regular intervals, and nothing else. We’re regular students with an interest in these issues (origins of life, evolution, ID) and we don’t intend to spend all our time arguing pro and con; often we’ll be just focused on learning more, reading and discussing papers that are relevant to these topics but don’t carry specific arguments.
ID people might see all of microbiology as evidence for design, but that doesn’t mean whenever we think about microbiology we’re making a design argument.
Comment by Freawaru — March 17, 2006 @ 10:15 pm
Of course, the fact that “ID people might see all of microbiology as evidence for design, but that doesn’t mean whenever we think about microbiology we’re making a design argument.” might be true. But, given some postings such as this: http://goodmath.blogspot.com/2006/03/king-of-bad-math-dembskis-bad.html
it is hard to see how honest the ID movement is. Granted, my math and biology isn’t that great, but even I read Behe’s Black Box and thought that he was ignoring something. His personal viewpoint was that things must be designed, and as such, he ignored possibilities much more likely to pass a credulity test. For the fun of it, I had my wife (finishing her Master’s in Statistics) review some of Dembski’s arguments, and even she, without the Phd (yet), could easily poke holes in the assumptions that Dembski uses, and hers were the same as Chu-Carrolls. Of course, one observation does not equate to the “truth”, but given that in my simple experiment I did not reveal Chu-Carrolls posting first, that does make me feel more comfortable in discounting Dembski. Of course, looking at folks such as PZ Myers, and the group and PT and TalkOrigens, my comfort level in my base assumption that ID is squirrely is reassured. Most of the posters on those sites are on the forefront of evolutionary research, and of course, ID has yet to truly face the gauntlet of peer review.
On the flip side, ID seems to predisposed by it’s current advocates towards the Christian god. Unfortunately, that is it’s major downfall in the public’s view. Since the majority of supporters of ID in the US appear to be Christian fundamentalists, that detracts from it’s attractiveness as a whole. The DI isn’t ashamed at all to espouse it’s views on narrowly focused “christian” radio stations, but once again, it has not published a major body of work that would allow it to fit in with currently established evolutionary theory, or even come close to upsetting current evolutionary theory.
To compound matters, from a purely spiritual point of view (and one cannot discount this viewpoint, since it is the channel that IID seems to focus on drawing it’s support from), forcing God to fit into a narrow view of every time that something new appears in the fossil record that it must be his DIRECT handiwork simply appears to be the frail human psyche needing to rest on a miraculous event to provide a crutch to make those individuals feel special. That is rather belittling to God, since it makes his actions be centered on us. Given the sheer vastness of creation, that appears rather selfish on humanity’s part.
Comment by Christian — March 18, 2006 @ 4:03 pm
Christian: Thanks for your comment. Perhaps the major difference in our viewpoints is our opinions of credibility… but unfortunately such opinions will always be somewhat subjective. Dembski’s Ph.D. is from the University of Chicago– one of the best mathematics departments in the country– and his book on the design inference was peer-reviewed by Cambridge University Press as part of the series Cambridge Studies in Probability, Induction, and Decision Theory. To me, this doesn’t mean it’s right, but it does mean it has at least as much credence as a random internet poster like Chu-Carroll, whose critique hasn’t been peer-reviewed.
So, since I’m not willing to accept either Dembski’s or TalkOrigin’s word for it, I have to take the rather tedious route of verifying each of their claims before accepting them. As a college student without even a B.A. in math or biology and a limited amount of time I can take away from classwork, this is a rather slow process…. it’s spring break now, and at the top of my reading list is the website you linked, some papers on the subject by Dembski– I like to try to pull together both sides of the argument when I can :)– and then probably a few more papers on probabilities and the Fisherian and Bayesian approaches, so I can have a half-chance of figuring out who is right. But then… our breaks are never real breaks, and I’ve got several long assignments to finish for class as well, so I’m not sure how far I’ll get even now. Sorting through the mathematics behind specification and making my rather intuitive understanding of it rigorous has been a project I’ve wanted to get on all semester.
So far I haven’t seen any arguments for Darwinian evolution that stand a careful parsing– or, in the vocabulary of the day, ‘critical analysis’. I know I’m not an evolutionary biologist and there is a great deal of literature I haven’t read… but the general quality of the arguments I get for evolution is so poor that I’m not very much inclined to take the pronouncements of the evolutionary biology community as anything like fact. This doesn’t mean I consider everything they say nonsense, but it does mean I feel obliged to verify– in that same slow, tedious way– most of their claims before accepting them.
My conclusion then… to keep on reading, finding out more, joining in discussions and debates at our IDEA Club. Science can never give us brute facts anyway; we’re just interested in the best explanation from the publicly available (empirical) data. I would be the first to say ID has a long way to go, and I definitely haven’t stopped criticizing it, or listening to the arguments for evolution; but based on what I’ve seen so far, ID seems to be that best explanation currently available.
Comment by Freawaru — March 18, 2006 @ 9:18 pm
“Science can never give us brute facts anyway; we’re just interested in the best explanation from the publicly available (empirical) data.”
This defines your problem.
First, observations are considered brute facts. Sometimes they are affected by the theory they are verifying or falsifying, but they are useful for that purpose anyway, which is what counts.
Second, science (and you) should never be interested in the content of an explanation of old observations, but if the explanations are useful for predictions of new.
Ie, I’m not a biologist, but when I see some (of many) evolutionary predictions and then see them verified, and never falsified, I trust that theory regardless if I understand and appreciate every detail of it. (And I don’t, trust me. ;-)
Is general relativity “the best explanation” for gravity? No way, it’s too complicated to use wherever it isn’t needed. Plain old newtonian gravity is much easier to understand the innards of and use.
Here it’s also easy to see ID’s shortcomings. It has never made any predictions.
Comment by Torbjorn Larsson — March 19, 2006 @ 1:04 am
Torbjorn– maybe I should have been clearer, but I was categorizing observations under the ‘data’ used in science, rather than as part of the theory it produces. And yes– in an ideal world, at least, these data and observations are theory independent.
We have a slightly different take on the predictive value of both neodarwinian evolutionary theory and intelligent design. In neodarwinism, what particular predictions have so greatly impressed you?
Have you looked at all at the historical use of the design paradigm as a heuristic– in physics, for example?
Comment by Freawaru — March 20, 2006 @ 8:23 pm
´When you ask for specific examples of evolutionary predictions, and there is 150 years and thousands of peer-reviwed papers, I get suspicious. Are you going to debate each and every one of them?
Anyway, for my personal layman impression, the Pharyngula or The Loom blogs gives impressive accounts. Here is a cool one that discusses the prediction and discovery of collagen II in lampreys: http://scienceblogs.com/pharyngula/2006/02/lamprey_skeletons.php It also makes new predictions to check up in the future.
There is no “design paradigm” in physics! Maybe you are referring to the weak anthropic principle. That’s an application of an obvious variant of the anthropic principle, that phenomena need to be consistent with that we exist, the tautological weak one. It’s a general type of prediction that we obviously can make use of whenever we find it advantageous, to make our observations.
It has been valuable for heuristically predicting some observations, for example a resonance in the triple alpha process, which happens in suns.
The observational value as such is merely an ‘ad hoc’ with no theoretical value. It didn’t explain the value of the resonance in the theory, which is the prediction that we are really interested in when we speak of predictions from theory. Later a theory from first principles did the explanation.
If you are interested in heuristics, there are many such. One is the observation bias. Since we exist, we know there exists life in at least one solar system. The probability was 100 %. Therefore, there exists life in every solar system! At least, this is what heuristics can tell you, in the absence of specific theory.
Comment by Torbjorn Larsson — March 21, 2006 @ 1:54 am
Debate every point? I probably don’t disagree with you on all of them— after all, even supposing evolution was false, this would not– statistically– mean all of its predictions were false. And every discarded theory in the history of science has a certain amount of productivity to its name, or it would never have been considered “good science”. I just wondered what particular sort of predictions so impressed you, since my own survey of the 150 years of history left me distinctly unimpressed.
The article you linked to is interesting. I don’t generally read Pharyngula (it’s a bit too political for my taste: “Let’s kill everyone who doesn’t agree with us!” ) but I do read The Loom.
And no, I wasn’t thinking of the anthropic priciple– Hoyle was the only one who tried putting that to use, right? but was referring to some earlier comment threads about the foundations of science and how early physicists worked with the idea of a designed, ordered universe as a heuristic– and how the predictions they made from that idea were surprisingly successful.
I don’t follow the logic in your last paragraph. Let’s call the set of all solar systems where life exists L, and the set of all solar systems S={s1,s2,….si}
So your first statement: ∃ si such that {si ∈ L}. Okay. Call this entire statement statement q . Given life in our solar system, the probability that life exists in our solar system is 1. No problem there; P(q|q)=1. Where does the next one, ∀ si ∈ S, {si ∈ L} come from?
Comment by Freawaru — March 21, 2006 @ 9:05 pm
“was referring to some earlier comment threads about the foundations of science and how early physicists worked with the idea of a designed, ordered universe as a heuristic”
I have no idea of what you mean.
Before science really took off, many scientists were religious. They considered the universe as a proof for their religion, called some parts of theories “laws”, and did a lot of stuff we don’t do any more in science.
Perhaps that is what you mean. But of course observations and theories are ordered; there is even theories that say that a large enough universe must have parts with order (statistical mechanics, Ramsey theory). To say that that is a design paradigm would be to misuse observer bias, since we live in such an ordered part.
“Where does the next one, ∀ si ∈ S, {si ∈ L} come from?”
That is observation bias. We have only studied one solar system, but it is all the observations we have. So we apply it to all other systems heuristically. It’s an illustration of why heuristics and ad hocs are easily wrong, and not to be trusted.
Comment by Torbjorn Larsson — March 22, 2006 @ 4:02 am
Okay, I think I understand… you’re working with a sort of inductive hypothesis; if every member of the set we’ve observed has the given property, we suppose this is a property of every member of the set?
Surely what we’ve studied of our universe has all been ordered? And it didn’t have to be, we could have been reasoning human beings attempting to study science, and found it entirely incomprehensible? Or less ordered, less designed-looking?
Do you really think our universe is large enough that it might be as random, unintelligible, unordered as anyone could posit, and still a part such as ours would be ordered in the — well, very ordered– way we see all our observable surroundings to be?
Or are you working with the much larger set available through multiverse theory, where all possiblities are played out in various universes, and this just happens to be the one that looks ordered?
Of course people used to do things in science we wouldn’t do anymore. But when we look at their writings, the ‘old lab notebooks’, the interesting question is– which methodology, which unwarranted assumptions worked, and which didn’t? For instance we consider astrology and alchemy more than quack science, they are also, to the extent they are part of the history of science, “failed science”, since they didn’t work.
Kepler, Galileo, Newton worked with the assumption that the universe had been put together by a perfect designer, and they were “reverse-engineering” so to speak. Newton went so far about talking about his physics as “getting into the mind of God”. We don’t do that anymore in science. But why was it such a fruitful heuristic?
Remember my claim here is very limited; I am not making an inductive argment that because what we see is ordered, everything is ordered, and therefore designed. My observation is simply that this design paradigm has been– surprisingly– productive.
Comment by Freawaru — March 22, 2006 @ 3:08 pm
Oh, I see. We mainly agree, except that I don’t think that descriptive ideas of some, not all, early scientists merits to be called ‘paradigm’, or that it was a useful heuristic.
The order that we happen to live in, speculation of its generality aside, gives our theories predictability. So we observe the method of science to work, now and then.
Comment by Torbjorn Larsson — March 23, 2006 @ 3:50 am
Were you not suggesting that there’s a problem with a methodologically natural explanation of abiogenesis, absent of a creator??
What explanation for abiogenesis includes enough testable detail to be scientifically meaningful?
Comment by Wiliam Bradford — July 30, 2006 @ 2:39 am