Well, it seems the big discussion is still going strong, even after six weeks. Incredibly, the comments still seem to be substantive and interesting. So here's another post to continue the discussion. Plus with my own ongoing blog lethargy, it's nice that there's any activity going on around here at all! So feel free to have at it.
- Log in to post comments
More like this
Well, it's been about three weeks since I signed up for a personal account on twitter (you can follow me here if you're interested - my handle is @dnghub), and threw out my first "tweet."
Since then, I've found myself fully immersed in the web tool, and feel like I can say a few intelligent…
Update: welcome Consumerist readers! While I use my own experience to illustrate concerns about third-party online merchants, this post is mainly about the bigger long-term informational problems I see with reputation, reliability, and online communities. Please feel free to weigh in!
A few weeks…
Blog is short for weblog, originally a chronological set of postings about, well, about whatever. Blogs are/were journals that were published publicly but also allowed readers to comment, read, react and in some ways affect the content. How much dialog and two way communication there was depended…
...five different ways!
In a bit of a twist on some of the "Five songs I love" posts I've done, I thought I'd take one of my favourite songs and see if I could find a bunch of different versions of it.
Some songs seem to naturally lend themselves to re-interpretation by different artists, and…
Thanks, Jason. Onward!
Phil,
If you have any evidence to the contrary, I'd love to see it. Public opinion polls or something?
Not really; there's experimental evidence for the Red Queen model in Daphnia and flour beetles, among other critters. Granted, it's not universally applicable--some other species don't seem to fit the model, and I have no idea whether humans do. But you asked how a low mutation rate could possibly be a bad thing, and there's your answer.
Absolutely. Our symbiotic bacteria have evolved along with us; see here for details. Our community of gut bacteria is actually far less diverse and complex than that of most apes, probably because of a combination of genetic bottlenecking and rapid adaptation to a meat-based diet.
For Hathor's sake, I already provided a link to the actual factual scientific experiment that contradicts you.
It doesn't matter how many times you say that DNA repair & replication enzymes are numerous and complex and coordinated and functional. Biologists already know that. Biologists are the people who discovered that they're numerous and complex and coordinated and functional. And we have seen these very same complex coordinated functional enzymes be improved by random mutations and selections. So whatever intuition makes you think that this would require a "miracle," it's wrong. The probabilities are not what you think they are.
Sure, but according to the scenario, more are being made to replace them.
Sometimes. And sometimes slightly "damaging" them makes them function better, or has no effect. Again (see the Joyce and Robertson citation in my last post), we have seen two self-replicating enzymes mutate into a symbiotic relationship. And a large number of amino acids in ATPases can be replaced without affecting their substrate specificity. We have hard evidence that many of these enzymes are just not as fragile as you believe.
Also, remember that when we're discussing abiogenesis, we're talking about primitive enzymes, not the modern versions that have already been polished by four billion years of evolution. The primitive versions would have been even easier to improve by random mutations and selection, since they were so far from optimal to begin with. (And before you ask, yes, there is experimental evidence for this too. When you put bacteria in an alien environment where their fitness goes way down, the proportion of mutations that improve their fitness goes up. It's easier to evolve improvements when there's more room to improve!)
It wouldn't have been a whole suite of specific enzymes back then. Again, we're talking about the first and most primitive version of the system, before gene duplication added a bunch of copies of each enzyme that could be specialized into different functions.
All those researchers studying liposomes and self-replicating RNA enzymes must have managed to capture fairy tales in a beaker, then. Impressive.
Er, you do know "multiply" and "replicate" are different words for the same thing, right? They both mean "reproduce."
But it's an irrelevant point, unless you're talking about the probability of something evolving twice. Evolution isn't
Well, sure. Most species in Earth's history have eventually gone extinct; I'm sure it was a bummer not having the right genetic tools to keep up with the competition. For those species smart enough to care, anyway. Nature's not very kind.
I think it's fine, considering it's a quick illustration by an amateur. (Remember, Wikipedia's limited to non-copyrighted images, remember. They couldn't find a free picture of Aurornis, so some Wikipedia contributor was kind enough to draw one.)
No, it doesn't look like a lizard tail, but why would it? It's got feathers on! You'd have to get up really close to see that the tail still has a long core of flesh and bone.
You're not gonna find all those feathers in the fossil; they're far more fragile than bone, and are more rarely preserved. Most fossils don't have skin and muscles all over them either, but we're pretty sure the living dinosaurs had them!
So...no offense, but are you done trying to make Aurornis into a problem for evolution? Cuz this is getting kind of rambly.
No, not always. One part can be preserved by drift or neutral selection, even if it does not yet serve a purpose. It just can't be significantly harmful, or it would be selected away.
As always, it's something of a trick question. The systems evolved together, over millions of years; there would never have been a time when human ancestors had the stomachs with the entire modern suite of acid-producing features but none of the mucus-producing ones, or vice versa. So your question should really be, "Which system's earliest, simplest version appeared first?"
And the answer--if we're talking purely about the stomach--is almost certainly the mucus production. Every deuterostome (the branch of the evolutionary tree including starfish, sea squirts and vertebrates) has a gut, and all our guts make mucus. The stomach (a chamber of the gut filled with acid) is much more recent. It's a vertebrate innovation.
Mucus lubricates the gut so food can slide through it easily, and helps protect against food-borne disease. The gastric acid production system probably evolved later, as I said above.
However, both systems evolved from parts that were already functional, even before we had guts. To expand on what Eric said, stomach acid is generated by an enzyme in the P-type ATPase superfamily, which is a huge family of evolutionarily-related enzymes. Humans alone have at least 20 different P-type ATPases, all produced by gene duplication and then diversified for various functions. Basically, any time we need to actively push ions or simple molecules across a membrane for any reason, we use an ATPase.
Likewise, mucus is largely composed of chemicals called mucins, and organisms make them for all sorts of functions; even bacterial biofilms are made up of mucins. Mucus is super-useful because it a) lubricates stuff and b) doesn't dry out or break down easily.
So, to put it all together--the general families of mucins and ATPases came first, and then the mucus-lined gut, and then the specific ATPase that pumps acid into the stomach cavity. Then it was just a matter of gradual evolution toward tougher mucus and stronger acid.
Phil,
I guess I'll start it off on the new thread. Regarding your question about acids, that's one of the easier "problems" you have posted. Acids are NOT universally corrosive; some are even necessary for life to continue to exist in the way it does. Citric acid, for instance is a vital component of aerobic respiration. While I don't have a time machine, so I cannot give you all the gory details, in all likelihood an animal without any mucous layer protecting its digestive tract acquired a mutation that gave it the ability to produce some more mild acid. This aided digestion giving that animal a relative benefit over its competitors. Perhaps that animal was able to make use of some new food source even. Further mutations could well have led to more corrosive acids. This would have been a mixed blessing; digestion would be improved at the expense of damage to the digestive system. Nevertheless, assuming that the damage to the digestive tract does not occur prior to the reproductive years, it would be favored by natural selection. Remember, a mutation that improves reproductive fitness, but cuts lifespan is beneficial from the point of view of selection. From there, then, it's pretty easy to see that a mutation allowing mucous production to protect the digestive tract would be a beneficial one.
I'm not surprised at your blanket statement that the bit I cited isn't correct, given your arrogant and insulting comments about people of Jewish faith in another post. But you would be wrong about my take and, since there is no single arbiter on who's position on a theological subject (as foolish in reality) as who qualifies as "the elect" and how they were given membership, I am not misquoting them. They believe that we are unable to avoid sin, and are unable to do anything but serve our own principles and morally unable to choose god, so he, as a show of his "compassion", has chosen some people for salvation - the rest are screwed, nothing can change that point. The strictly traditional view, no doubt, but that is their view.
The fact that you think otherwise simply undermines the total bit of quackery all of it is: the words can be twisted so that anyone arrogant enough to come forward with his/her version of "what is true" can broadcast it and claim they alone have the truth. Emo Philips captured the idiocracy of these things perfectly:
I was walking across a bridge one day, and I saw a man standing on the edge, about to jump off. So I ran over and said
"Stop! Don't do it!"
"Why shouldn't I?" he said.
"Well, there's so much to live for!"
"Like what?"
"Well... are you religious?"
He said yes.
I said, "Me too! Are you Christian or Buddhist?"
"Christian." "Me too! Are you Catholic or Protestant ? "Protestant."
"Me too! Are you Episcopalian or Baptist?"
"Baptist"
"Wow! Me too! Are you Baptist Church of God or Baptist Church of the Lord?"
"Baptist Church of God!"
"Me too! Are you original Baptist Church of God, or are you reformed Baptist Church of God?"
"Reformed Baptist Church of God!"
"Me too! Are you Reformed Baptist Church of God, reformation of 1879, or Reformed Baptist Church of God, reformation of 1915?"
He said, "Reformed Baptist Church of God, reformation of 1915!"
I said, "Die, heretic scum", and pushed him off.
eric,
“Yes, it’s only chemistry.”
No, sorry. The questions I asked were:
“Why is there a reaction if I pour vinegar on soda? Just chemistry?”
The answer is no. There is a reaction because I pour the vinegar on the soda. See how that works?
===
Michael Fugate
“A decent analogy of chemical reactions is to think of a bolt and a nut…a fender onto a frame of a car…driving over a pothole…If I put a nut on the end…If you wanted to get the pieces apart…You would use a tool like your fingers…a wrench or pliers”
But unfortunately, you can’t express this decent analogy without referencing living things, or things designed by living things.
-
“A glucose molecule 6 carbon, 6 oxygen, and 12 hydrogen atoms – a stable configuration – when in the presence of oxygen gas will eventually convert into carbon dioxide and water….There is no living thing needed to make these things work – just basic chemistry and random molecular movement.”
So that is how glucose molecules break down, with no living thing needed. How is it made?
===
Anton Mates,
“But it’s an irrelevant point, unless you’re talking about the probability of something evolving twice. Evolution isn’t”
Tall odds against something happening are always relevant. But isn’t convergent evolution supposed to be about things evolving twice?
-
“You’re not gonna find all those feathers in the fossil; they’re far more fragile than bone, and are more rarely preserved.”
They didn’t get lost here:
http://news.nationalgeographic.com/news/2014/07/140702-archaeopteryx-fo…
-
“Likewise, mucus is largely composed of chemicals called mucins”
Yeah, they’ve identified at least 19 mucin genes in humans. But once you have one, the rest are inevitable, because the first one will be duplicated in a random event, and then mutations can prepare the new one to fill another evolutionary niche, and so on.
-
“So, to put it all together–the general families of mucins and ATPases came first, and then the mucus-lined gut, and then the specific ATPase that pumps acid into the stomach cavity. Then it was just a matter of gradual evolution toward tougher mucus and stronger acid.”
See how easy that was?
===
Sean T,
“Remember, a mutation that improves reproductive fitness, but cuts lifespan is beneficial from the point of view of selection. From there, then, it’s pretty easy to see that a mutation allowing mucous production to protect the digestive tract would be a beneficial one.”
Yeah, I can see that. That was an easy problem to solve.
===
dean,
“given your arrogant and insulting comments about people of Jewish faith in another post.”
You’ll have to refresh my memory on that. I’m a Zionist, and generally don’t make disparaging remarks about what I consider the chosen people.
You know, I read that while Jews make up less than .2% of the world population, they’ve pulled down more than 20% of all the Nobel prizes awarded? How weird is that? Mutations maybe?
-
“since there is no single arbiter on who’s position on a theological subject…as who qualifies as “the elect” and how they were given membership”
If you discovered that there is ‘the elect’, you’ll probably find arbitration about the membership at the same source.
-
“They believe that we are unable to avoid sin, and are unable to do anything but serve our own principles and morally unable to choose god, so he, as a show of his “compassion”, has chosen some people for salvation – the rest are screwed, nothing can change that point.”
That’s a pretty sad perspective. Maybe they’ll do their own analysis and get straightened out.
Take a bird whose chicks are under horrendous selection pressure, add a few gene duplications and other assorted DNA replication errors and anything can happen...absolutely anything!
http://www.newscientist.com/article/dn26689?cmpid=NLC%7CNSNS%7C2014-121…
As is yours - for folks capable of rational thought, you and they are equals.
Take a bird whose chicks are TOUCHED BY THE HAND OF GOD and anything can happen…absolutely anything!
Fixed for you Phil. ID in a nutshell - meaningless as science but perhaps meaningful as theology.
This is of course not true for evolution. God can poof, but evolution takes time - although living things today can be quite complex - they weren't always. But we have explained this to you so many times and you have shown time and again you don't know enough basic chemistry and biology to make sense of the articles to which you link. Anton has pointed this out patiently and in incredible detail and yet we just get the same old tired creationist tropes thrown back at us. I don't know how many times we need to demonstrate that you have no argument before you will realize it - maybe never.
Michael Fugate,
Well that's all very fine stuff, the early simplicity that you believe, but can't know anything at all about since there nothing now that isn't hideously complex. But how is glucose made?
Michael Fugate,
Also, I think you’re glossing over the bird deal. I realize that you have limitless faith in accidents, but things like this really call for some serious thinking. There is just so much involved. How many trial and error DNA replication errors would you suppose occurred the gametes produced by the parents to wind up with an evolutionary strategy like that? What would you call that anyway? Temporal juvenile mimicry? And the behavior? That’s a hell of an accidental trick right there…moving like a caterpillar till you hear the dinner bell? What genes would you suppose could even be damaged to account for something like that?
https://www.youtube.com/watch?v=FwSGk1_Y4rY
Phil,
...so what happens if somebody else pours the vinegar on the soda instead of you?
What happens if nobody pours it intentionally, the vinegar just happens to spill onto the soda because of an earthquake or something?
If nothing happens differently in these cases, then why do you say that the reaction depends on you and not just on its own chemistry?
He could probably have expressed it in terms of landslides, or frost-thaw weathering of rocks, or something like that. Most people would find that analogy slightly less accessible, though!
Anyways, if you think that mere design by living things is sufficient to grant chemistry its special magic, I'm not sure what your problem is with deistic or theistic evolution. Why not just say that all those mutations and whatnot are the result of divine intent, therefore it all works out?
Glucose can be made by spark discharges in a suitable atmosphere--rich in carbon dioxide and water vapor, I think. And it's been found in those carbonaceous meteorites, so there must be some abiotic process that makes it in space.
Scientists have also built artificial chemical systems that synthesize glucose, mostly by mimicking the enzyme pathways used in photosynthesis; the actual components of these systems are not living, though.
Not really. Consider the next radioactive atom to decay, somewhere on Earth. The odds against that particular atom decaying, at that particular time, are astronomical. But it'll still happen.
Granted, the odds of something happening can be relevant to deciding whether it did happen, if you're doing a Bayesian analysis--but then you need prior probabilities as well, and those are rarely available in the real world. That's why statistical hypothesis tests do not estimate the probability that the hypothesis is correct, by and large.
Nope, it's supposed to be about two different things evolving to have similar functions. Dig down into their fine-scale anatomy or genetics or whatever, and you find that they really aren't the same thing. Bat wings don't look like bird wings up close.
Admittedly, there's an exception if you're talking about convergent evolution of very simple structures, like two populations experiencing the same nucleotide change at the same locus of the same gene. In that case, there's really only one way for it to happen, so the convergent structures will actually be identical. However, the very simplicity of a structure means that the odds of its appearing twice are not that low.
Sure, but that article makes a big deal about how unusually well-preserved that fossil is. All the other Archaeopteryx fossils we dug up over the last 150 years "showed such feathers on only its wings and tail."
Likewise, Aurornis was probably covered with lots more feathers than you can see in that one fossil.
Yup, exactly. To quote from the abstract of "Evolution of the Large Secreted Gel-Forming Mucins" in "Molecular Biology and Evolution",
"The emerging picture is one of expansion of mucin genes by gene duplications, followed by internal repeat expansion that strictly preserves frameshift. Computational and phylogenetic analyses have permitted the proposal of an evolutionary history of the four human mucin genes located on chromosome 11 from an ancestor gene common to the human von Willebrand factor gene and the suggestion of a model for the evolution of the repeat coding portion of the MUC5B gene from a hypothetical ancestral minigene."
Easy for whom? Took a couple billion years to evolve, took human scientists a couple thousand years to study, took me half an hour to Google up their findings. I guess my part was easy...
OK, I'll bite. How many? Show your work!
"Batesian mimicry" is the technical term. Same deal as the caterpillars we talked about earlier that mimic dangerous snakes.
Well, a lot of nestlings and other baby animals have special alarm behavior patterns--although usually they consist of huddling and being very still--and a lot of them can also recognize a parental call and modify their behavior accordingly. So the building blocks are there. It is a cool trick though!
Dunno, I'm no neurogeneticist. Japanese quail have been successfully bred for short or long tonic immobility (freezing and silencing behavior) in their chicks, so there definitely are some genes governing such behavior, but I couldn't tell you what they are. I'd probably look at a) genes expressed in the amygdala, which mediates fear reactions, b) genes associated with unusual movement patterns, like the ones in rodent models of movement disorders, and c) genes associated with call recognition, which is fairly well studied in songbirds.
Incidentally, the caterpillar-like plumage of these nestlings is shared by another related bird, the Brazilian Laniisoma, and phylogenetics suggest that this is a synapomorphy within their clade. So that gives us an idea of when the plumage evolved. I'd hazard that the movements evolved later, since they wouldn't help much if you didn't look like a caterpillar in the first place!
I think I have said all I can say and will only add that it is impossible for someone to understand science if they have not progressed from the concrete operational stage to the formal operational stage. For most people, this happens before or early in their undergraduate careers, but for some, it never happens due to both nature and nurture. I have seen high school and college students in the concrete stage try to memorize their way through science courses and it usually doesn't work and even if it does they have no future in science except as technicians repeating a rote procedure.
Perhaps with some training there might be hope for Phil, but he needs to realize that there is a problem before he can take the steps to solve it. Best of luck.
No, there wouldn't be. In order to be a successful student there must at least be a desire to learn. Phil has demonstrated that he doesn't have that; indeed, he believes he is the only one with the answers. Failed cause there.
By the way, considering the particular system Phil brings up (caterpillar mimicry in cinereous mourner chicks), it's only fair to ask creationists to apply some serious thinking for a change.
When an evolutionary biologist looks at this system, it's pretty straightforward to analyze. The nestlings mimic a caterpillar. From this, based on evolutionary theory, you could predict that:
a) a caterpillar that looks like that lives within the home range of this bird;
b) this caterpillar is toxic or otherwise dangerous to eat; and
c) the nestlings are at risk of being eaten by some predator which also encounters the caterpillar, but avoids attacking it.
And indeed, all these things turn out to be true. Also, the only other species which is known to share this particular mimicry pattern is a closely related one, suggesting that it evolved in their common ancestor.
Now, questions to consider if you're a Serious Thinker working from the creationist perspective:
1) This strategy only improves the chick's odds of survival because it is threatened by predators, the caterpillar is also threatened by predators, and the predators are at risk of eating the caterpillar and becoming sick or dying as a result. In other words, if there weren't several species of animal busily trying to murder each other here, there would be no point in the caterpillar's poison, its distinctive appearance, or the chick's mimicking the caterpillar. So if you believe in a Fall and an originally perfect natural world without pain or death, what were all these animals doing back then? Were they just killing time by pretending to hunt each other down? And if these traits were built into them in anticipation of a future Fall and a subsequent need to avoid predators, then why did only this particular pair of bird species receive them? Are other birds more deserving of having their babies devoured?
2) From a more general intelligent design perspective, what's the point of this system? If it's there to save baby birds from a horrible death, it's not working very well; most young birds die before they can reproduce anyway. Why not just design the birds to be bite-proof, or design the predators to avoid attacking baby birds? Likewise, it doesn't maximize the survival of the caterpillars (who are more likely to be attacked because they can be confused for tasty baby birds) or the predators (who are more likely to starve because they can't find suitable prey.) On the other hand, if the Great Designer just wanted to make some birds that looked like caterpillars because that's artistically awesome, why did he/she/it/they happen to stick those birds in the one spot on Earth where mimicking this caterpillar gives you a slight survival edge?
3) If species are not descended from a common ancestor, why do we only see this particular mimicry in a group of closely related species, and not in other birds that live in the same area and nest in the same sort of habitat?
Anton,
I've been really busy, and traveling tomorrow. I will get back with you Monday.
===
Michael Fugate,
You're perspective is very narrow. There are lots of very heavily educated people who think your views are terribly flawed.
You've expressed some confusion about genetic information. You might check out A. E. Wilder-Smith. Henry F. Schaefer is also pretty interesting. There is a downside to spending too much time in support group settings. If you want a razor edge on your worldview, you need to sharpen it on something hard.
Wilder-Smith didn't work in genetics, AFAIK. He was a chemist who published most of his research before we even knew DNA was a double helix (and a young-earth creationist who believed the Paluxy tracks were real, FWIW). If you have a question about genetic information, might I suggest consulting an actual genetics textbook? Written sometime in the last 20 years, even? "Introduction to Genetic Analysis" by Griffiths, Wessler, Carroll and Doebley is a good one.
That he is.
I would suggest this series by philosopher John Wilkins and papers by Paul Griffiths on genes and information.
http://evolvingthoughts.net/2014/06/genes-the-language-of-god-0-preface/
Anton Mates,
Sorry for the delay.
-
“…so what happens if somebody else pours the vinegar on the soda instead of you?”
Then they would have their own reaction event, but it would not be related to mine.
-
“What happens if nobody pours it intentionally, the vinegar just happens to spill onto the soda because of an earthquake or something?”
That’s possible, if there were enough accidental events leading up to a container of vinegar being positioned to spill on a pile of soda.
-
“If nothing happens differently in these cases, then why do you say that the reaction depends on you and not just on its own chemistry?”
Not just me. There would be quite a lot of conscious deliberation involved before the reaction could take place.
-
“Anyways, if you think that mere design by living things is sufficient to grant chemistry its special magic, I’m not sure what your problem is with deistic or theistic evolution. Why not just say that all those mutations and whatnot are the result of divine intent, therefore it all works out?”
I can see why that would be a logical next step for a materialist frustrated by complexity, but I’m old school…actually ancient school.
-
“Glucose can be made by spark discharges in a suitable atmosphere–rich in carbon dioxide and water vapor, I think. And it’s been found in those carbonaceous meteorites, so there must be some abiotic process that makes it in space.”
I couldn’t find anything specifically about glucose and those sources. But the point is about chemistry and living things. Decomposition and production are two entirely different things.
-
“Tall odds against something happening are always relevant.
Not really. Consider the next radioactive atom to decay, somewhere on Earth. The odds against that particular atom decaying, at that particular time, are astronomical. But it’ll still happen.”
Yeah, but that is inevitable vs. possible, not the same thing. Everything has to be evaluated for plausibility in terms of probability. That’s why we use words like rare and common.
-
“How many trial and error DNA replication errors would you suppose occurred the gametes produced by the parents to wind up with an evolutionary strategy like that?
OK, I’ll bite. How many? Show your work!”
But I would never make the claim that accidents would produce such a thing, so I have no work to show. But, I think you eloquently stated the general principle:
“You’d need a lot more than 102 million years–or 102 billion years, for that matter–for a bacterial population to experience every possible mutation.”
In my view, you can’t put this back in the closet after excusing E coli for not evolving. This has to be applied across the board to every single supposed accidental step.
-
“…nestlings and other baby animals have special alarm behavior patterns–although usually they consist of huddling and being very still–and a lot of them can also recognize a parental call and modify their behavior accordingly. So the building blocks are there.”
Yeah, but it’s the accidental mortar between the building blocks that I’m always interested in.
-
“From this, based on evolutionary theory, you could predict that…And indeed, all these things turn out to be true.”
I don’t understand how predictions really work in an unguided system. But my perception of evolutionary theory is that it is largely a catalogue of responses for all situations. To mimic the leading apologist, it sounds like science, but it is really only the appearance of science.
-
“So if you believe in a Fall and an originally perfect natural world without pain or death, what were all these animals doing back then?”
There are conflicting views about this. I accept that nature was altogether radically different then. But your question is well-taken, and if I shared your views, I would definitely dwell on it and other things, like rapid speciation.
-
“From a more general intelligent design perspective, what’s the point of this system? If it’s there to save baby birds from a horrible death, it’s not working very well…..If species are not descended from a common ancestor, why do we only see this particular mimicry in a group of closely related species, and not in other birds that live in the same area and nest in the same sort of habitat?”
I have no good answers to such questions. I don’t know, and needn’t pretend to know. The same questions could be applied forward to the millennium when, as I understand it, things will be restored.
-
I referred to Wilder-Smith and Schaeffer in response to what I perceived as Michael’s contention that advanced education inevitably leads to a particular mindset. I chose these two because I think they both have serious credentials.
===
Michael Fugate,
“I would suggest this series by philosopher John Wilkins and papers by Paul Griffiths on genes and information.”
I skimmed some of the posts you linked to. I can understand the motivation for wanting to view genetic information to just a metaphor, but I don’t think many people would really agree with that, or see a need for it. They chose the word “codons” for a reason. I think Wilkins is trying to sweep a landfill under a rug.
But if I can pose some different questions, you’ve expressed at various times that your point of view and conclusions put you in an advantageous and enlightened position. What is the actual value of that? What is the downside of not believing the things that you believe? Would you say it is about happiness or mental health, or some other kind of success?
truth
Phil,
How would it differ? Would the reaction rate be different? Would the chemical products be different? Is there any way a scientist could look at the mixture and conclude, "Ah, this must have been the product of Phil's intelligent design, not Anton's intelligent design, or simple mindless material processes?"
Sorry, but that wasn't my question. Why do you say that the reaction depends on you at all? Mix a liter of vinegar and a cup of baking soda. What features of the resulting reaction differ depending on whether it was you who mixed it, or someone else, or a chain of accidental events?
In my view, none of them do. Once you know the chemistry, you're done. Whether conscious, living things were part of the causal chain that led to the reaction is an interesting historical question, but it has nothing to do with the reaction itself. The chemicals just do what they do.
It should be findable on Google; that's how I found it. Or look up "formose reaction" for another example.
Well, yes. The point is that chemistry occurs as normal whether or not living things are involved. Life isn't magic.
No, they're the same thing viewed from different angles. Most chemical reactions decompose one set of chemicals and produce another. In any case, I was giving examples of the abiotic production of glucose.
No, it's not inevitable that any particular atom will decay, unless you have an infinite amount of time to wait around.
The probability of any particular atom decaying is low, but atoms still decay all the time. The probability of any particular mutation occurring is low, but mutations still occur all the time. It's exactly the same thing.
Really? Do you find it plausible that Paris is the capital of France? What was the probability calculation you ran to arrive at that conclusion?
Oh, well, great. Then my answer to your question is, "I don't know how many, but if you ever figure it out someday, we can discuss whether that number's a problem for evolutionary theory."
Only those accidental steps which would require every possible mutation to precede them. Which is...none of them.
That could be problematic, because most of science consists of making and testing predictions about unguided systems.
And yet, according to you, the responses creationism/ID provides to scientific questions are things like:
If evolutionary theory is just pretending to be science, it seems to be doing a far more convincing job than the competition.
I don't think he ever made such a contention. On the contrary, he stated that advanced education does not lead to a scientific mindset unless it's accompanied by the right kind of cognitive development.
But you're wrong. They're legitimate scientists, but when it comes to evolutionary theory, neither of them has serious credentials.
Schaefer in particular is a very accomplished quantum chemist , but his work has nothing to do with evolution. He does not study genetics, biology or information theory. Citing him as an authority on "genetic information" is like citing Richard Dawkins as an authority on submarine maintenance.
Phil, do you know who chose the word "codons?" Here's a hint: he's a scientist who fully accepts the theory of evolution.
Sorry, I know that doesn't narrow it down very much. More specifically, he's a molecular biologist who helped decipher the genetic code, and established C. elegans as a model organism for developmental research. Here's a quote from him:
"...we need to put everything into an evolutionary framework, simply because complexity arises in biological systems by accretion and modification and not by reinvention."
So, yes, he coined the word "codon;" he also concluded that evolution is foundational to biology. Why should we be deeply impressed by one fact but not the other?
Given that everything that happens within a cell is chemistry, why would any chemist think intelligence were required? He or she certainly wouldn't think that when discussing chemical reactions - read any chemistry book.
Of course, being a scientist is an elitist skill like being an athlete or a painter or a musician. Not everyone can do it. This doesn't make scientists better - just different. Humans like stories and creating and relating stories is another skill. As one recent commentator related, she was a creationist because she thought it made a better story than evolution. If we look at indigenous religions of which early Judaism is an example - they centered on how to live sustainably in one place. To do this you needed to know what is (science) and knowing that what you ought to do (religion). Religion converted the knowledge of the environment into a stories (song, dance, poetry, painting, sculpture, etc.) that people could easily remember and would guide their actions. The important thing is that there is a feedback between is and ought. Our understanding of nature is not fixed and therefore our understanding of what we ought to do can't be either. We need storytellers who can keep with what is to inform people what needs to be done - we don't need a story from 2000 or more years ago, but one from today.
“Once you know the chemistry, you’re done. Whether conscious, living things were part of the causal chain that led to the reaction is an interesting historical question, but it has nothing to do with the reaction itself. The chemicals just do what they do….The point is that chemistry occurs as normal whether or not living things are involved. Life isn’t magic.”
I think a lot of reactions are very unlikely to occur without coercion and controlled circumstances. Miller’s experiment is a good illustration.
-
“No, they’re the same thing viewed from different angles. Most chemical reactions decompose one set of chemicals and produce another. In any case, I was giving examples of the abiotic production of glucose.”
How easily does this happen? -
“The probability of any particular atom decaying is low, but atoms still decay all the time. The probability of any particular mutation occurring is low, but mutations still occur all the time. It’s exactly the same thing.”
Well that is definitely the story line, but in view of so many things showing only tepid evolution, the supposed availability of cooperative mutations looks like a false backdrop. You still have to juxtapose things like the whale tale with E coli going nowhere for xillions of years.
-
“Oh, well, great. Then my answer to your question is, “I don’t know how many, but if you ever figure it out someday, we can discuss whether that number’s a problem for evolutionary theory.” “
Well yeah, but you’re asking me to disprove something with math that is accepted without it. The question was “how many trial and error DNA replication errors would you suppose occurred…?”
-
“Only those accidental steps which would require every possible mutation to precede them. Which is…none of them.”
That still doesn’t work. You were right the first time.
-
“On the contrary, he stated that advanced education does not lead to a scientific mindset unless it’s accompanied by the right kind of cognitive development.”
Right out of Cool Hand Luke. You got to get your mind right.
-
“They’re legitimate scientists, but when it comes to evolutionary theory, neither of them has serious credentials. Schaefer in particular is a very accomplished quantum chemist , but his work has nothing to do with evolution. He does not study genetics, biology or information theory.”
I don’t buy this argument at all. The most serious objections to evolutionary theory do not lie in the far reaches of information theory. They are very basic. They were noted in the PT hit piece, which was probably written by someone way out of his field.
-
“Phil, do you know who chose the word “codons?” Here’s a hint: he’s a scientist who fully accepts the theory of evolution.”
No, I didn’t, but I’m not surprised that he would accept the theory. But the issue was information. A specific thing happening is not a metaphorical event. Codons are about codes…messenger RNA is about a message.
-
“…we need to put everything into an evolutionary framework, simply because complexity arises in biological systems by accretion and modification and not by reinvention.”
This is an interesting statement…a thought directive of sorts. But if you start at the supposed ancestral beginning, this doesn’t hold up. You can’t just gene duplicate and modify your way to over-qualification.
Anton, please pardon my missing salutation. This was the result of composing offline in fits, starts and holiday interruptions.
Here is an analogy - a non-scientist arguing with scientists against evolution is like a non-athlete playing basketball against Michael Jordan in his prime. the non-athlete is never going to be good enough and only the most delusional would think he or she could win. A non-biologist scientist arguing against evolution is like Michael Jordan trying to play baseball. Will he probably be better than most non-athletes, no doubt, but if he can't hit the curveball no amount of ego and drive will make it happen. Only the most delusional of chemists of physicists think they understand biology better than biologists (we know these scientists are out there - just doesn't make them any less delusional). As with any analogy there will be exceptions, but they are going to be rare.
If you want to learn biology take a biology course from a real biologist - don't take a chemistry course or a theology course - don't take the course from a chemist or a theologian.
Phil,
Miller combined four common gases and shot some electricity through them; he had no idea what chemicals would be produced by this. I have difficulty imagining a less "coerced" result!
And of course they were controlled circumstances; that's what an experiment is. If you disregard every experiment designed by a human researcher, what would be the point of scientific research into abiogenesis at all?
Not sure what you mean? The formose reaction, for example, occurs spontaneously if formaldehyde is combined with a base and a metal such as calcium.
That's like saying "Why hasn't this uranium atom decayed for xillions of years, when xillions of other atoms have decayed in that time?" It's still the same thing.
Yes, I am, because it's only creationists who say that this particular bit of math is even relevant. Evolutionary scientists don't claim that the probability calculations you've suggested would prove evolutionary theory. By and large, they think such calculations are ill-defined and uncomputable, and say nothing about the validity of evolutionary theory one way or the other. So if you want to claim that you can disprove evolutionary theory this way...well, it's up to you to produce the math.
Very basic!? But that would mean that all that ID fanciness about irreducible complexity and complex specified information was just pseudoscientific window-dressing! Oh man, the Discovery Institute will be mortified.
Seriously though, it's true that the most popular objections to evolution are far from technical. But that doesn't mean expertise isn't important if we want to evaluate those objections. Anyone can pound the table and say "Evolution is wrong because there are gaps in the fossil record!" But if you want to find out whether they're right, it helps to check with the people who actually know the fossil record backwards and forwards. And you and I aren't among those people. Neither is Henry Schaefer.
The piece was written by Reed Cartwright, then a doctoral student in evolutionary biology, now an assistant professor studying computational evolutionary genetics. I'm not sure it's possible to have your work be more closely related to the topic than that.
No problem! It's not like there's a dozen contributors to keep track of on this thread anyway.
Anton Mates,
“Miller combined four common gases and shot some electricity through them…
And of course they were controlled circumstances; that’s what an experiment is.”
Yes, but he was not simulating a natural environment. You don’t generally find vacuum pumps, valves, pure gases, regulated heat and electrical charge sources, water-cooled condensers and p-traps all put together in a closed loop, in a naturally occurring setting. That’s what I meant by controlled circumstances.
Concentration and proximity are severe problems for an unguided process. If you were a chiral amino acid molecule in a drop of water looking for a date, you might as well be on another planet if she’s on the other side of the drop. That does not make Stanley a pimp though, because for all his efforts, nobody even danced.
-
“If you disregard every experiment designed by a human researcher, what would be the point of scientific research into abiogenesis at all?”
I’m all for the research of just about every kind. But abiogenesis means no bio, which means no intellect to design and manipulate with.
-
“Not sure what you mean? The formose reaction, for example, occurs spontaneously if formaldehyde is combined with a base and a metal such as calcium.”
Yes, but the point was about living things. How often does nature randomly combine formaldehyde, a base and a metal like calcium to produce glucose?
-
“it’s only creationists who say that this particular bit of math is even relevant.”
Well, yeah. I think it is pretty apparent that evolutionary biologists are not going to start asking questions about probabilities at this point in time.
-
“Evolutionary scientists don’t claim that the probability calculations you’ve suggested would prove evolutionary theory.”
Well I should think not, especially when every single random step is unlikely, and most of them not less than miraculous. But it would be more accurate to call them advocates. The duty of scientists is to use all means possible to dismantle and falsify theories, not protect them from scrutiny.
-
“By and large, they think such calculations are ill-defined and uncomputable”
I would say extremely tedious to define, and immensely complex and discouraging to try and calculate. It’s better to just say that something just evolved. Hell, it’s not like anyone is going to be taken to task for it.
-
“and say nothing about the validity of evolutionary theory one way or the other.”
It has to. Evolution depends on random, fortuitous events occurring. Systems with multiple complex components necessarily demand that each of those must evolve (and maintain some kind of selectability) simultaneously by this method. The more numerous the components are, the lower the odds are that utile accidents will occur. It is a grotesquely complicated and implausible mess, which is exactly why evolutionary scientists excuse each other for not bringing it up.
-
“The piece was written by Reed Cartwright, then a doctoral student in evolutionary biology, now an assistant professor studying computational evolutionary genetics.”
Well then he is probably bright enough to produce some computational probability studies on the parallel occurrence of random beneficial DNA replication errors. Then he won’t have to whine about Schaeffer and incredulity.
Hey Phil, Ken Miller is a God-fearing Christian. What do you think: http://www.millerandlevine.com/evolution/behe-2014/Behe-2014.pdf ?
Michael Fugate,
“Hey Phil, Ken Miller is a God-fearing Christian. What do you think: http://www.millerandlevine.com/evolution/behe-2014/Behe-2014.pdf ?”
I would quarrel with that appraisal, as Miller is Catholic. But that aside, I would also quarrel with Behe for missing the point of his own probabilities arguments. There is no place to hide from adaptation, whether it is drug resistance, blind cave species or intriguing things like this:
http://phys.org/news127667797.html
The issue, in my mind, is not whether or not adaptive mutations occur. It is whether they occur exclusively on the random basis that current theory by and large demands. In other words, I think that it is probable, if not obvious, that some alterations occur in response to environmental stresses.
Phil,
Hmm. So when you said, "they chose the word 'codons' for a reason," what did you mean, exactly? Because the reason he chose it (it was Sydney Brenner) obviously didn't make him conclude that the genome must be intelligently designed. Why should it make us conclude that?
Codons and messenger RNA are little molecules smacking into each other chaotically until they happen to interact in the right way to make other little molecules do something which, ultimately, keeps the whole metabolism ticking along. "Codes" and "messages" are ways for human scientists to make sense of this system. That's why it's a human scientist who invented the word "codon."
C'mon, he's a scientists talking to other scientists there. "We need to" is just Brenner suggesting an important research focus; he's not charging anybody with thoughtcrime.
Yes, but at the ancestral beginning, you didn't have the sort of complex systems that need to be explained through gene duplication.
(Also, of course, your complaint here is about abiogenesis, not evolution. I don't think it's terribly valid either way, but it's definitely not under evolutionary theory's jurisdiction.)
The natural environment was being simulated inside the apparatus. All the pieces of technology you list above are necessary to produce that simulated environment, but that doesn't mean they're actually part of it!
That's how simulations work, you know? If you want to simulate a desert environment, you bring in a heater. No, real deserts do not contain artificial heaters. But you're not building a desert, you're simulating one.
If that weren't true, the only way to simulate a natural environment would be to build a life-sized replica of Earth or something!
That's funny, I can think of tons of unguided natural processes that effectively sort and concentrate various chemicals. Or don't salt pans, gold veins, coal seams, petroleum reservoirs, mineral crystals, and puddles of water exist in nature?
Thankfully, this is not at all true. Otherwise we'd be in trouble, considering that much of our body chemistry consists of chiral amino acids floating around in water looking for dates!
So I ask again: Wouldn't that mean it's impossible for humans to conduct useful abiogenesis research, because scientific research is always consciously designed and conducted? Indeed, by your argument, how can scientists study any natural process without "contaminating" their results with their own intelligence?
Your point was. But that point goes out the window if you're unable to show why the "livingness" of living things matters to their internal chemistry. Can you identify a chemical process that works differently inside and outside a living body?
No idea, but the ingredients are abundant; you just need borate minerals. And formaldehyde's all over the place; indeed, it was the first organic molecule to be identified in interstellar space!
That said, you don't find high concentrations of formaldehyde (or glucose) on the surface of the modern Earth. That's because living organisms really like to eat them, so those substances don't last.
Oh, they investigate lots of probabilities. But if creationists think this particular probability is evolution's Achilles' heel, then it's rather baffling that they don't do out the math and hold up the results in triumph!
No, it doesn't.
The statistical fallacy you're committing here is sometimes called confusion of the inverse, or the inverse fallacy. You're thinking that if the probability of various traits or systems appearing is low, under evolutionary theory, then the probability that evolutionary theory is correct must also be low given that those traits/systems do in fact exist in nature. And that's a very intuitively attractive idea, but it's wrong. Bayes' Theorem doesn't work that way. Those two probabilities can be completely, wildly different.
More succinctly, P(A|B) != P(B|A), where A is "evolutionary theory is correct" and B is "whales developed echolocation" or "dinosaurs turned into birds" or whatever biology factoid you're pointing out today.
And note, it's not biologists who say your reasoning is flawed here. It's statisticians and mathematicians, most of whom have no particular interest in defending evolutionary theory. (I teach stats, and we spend a lot of time discussing this particular fallacy, precisely because it is so intuitive for the majority of students.)
Well, that at least is true.
Wrong in two ways. First, it is not necessary for all components to maintain selectability, if some of them are preserved by genetic drift or neutral selection until they are integrated into the larger system. Second, these components do not need to evolve simultaneously, provided the earlier, simpler versions of the system are still adaptive for some reason. Before the vertebrate gut had mucus + acid, it just had mucus, and the mucus was already useful--but not for the same reason it would be useful later on.
Correction: the lower the odds are that a particular, pre-specified useful accident will occur. But the odds that at least one useful accident will occur go up. With more numerous components, there are more ways to go wrong but also more ways to go right.
Then you can top them all, just by bringing it up yourself. Show us the math! Rub it in our faces!
Yes, he is. Feel free to read them and comment!
I see Phil didn't read the piece I suggested or he would stop saying ignorant things about simultaneous mutations - not to mention all mutations are deleterious.
Did you know that the weather requires random, fortuitous events occurring?
Even more ignorant is his wankerish comment on Catholics. What a dick.
I was just thinking how the mutation story and the Christian story parallel each other. Christians claim that one mutation is never enough to get a positive result that you need a least two, but most likely more. Not only that, they need to be simultaneous. Yet God sent only one savior to one single population to save the entire world. Why not two, or three or one to every nook and cranny of the earth all simultaneously rather than this slow 2000 year crawl. Who wouldn't believe that was an intelligent design? Yet with the Christian way, so many people have been born and died in the past 2000 years with knowing about Jesus. Maybe Christianity wasn't designed after all - just a bunch of random fortuitous events.
Michael Fugate,
“I see Phil didn’t read the piece I suggested or he would stop saying ignorant things about simultaneous mutations – not to mention all mutations are deleterious.”
Actually I perused it once, and read it slowly a second time. And better still, I linked to a much more impressive adaptation event.
-
“Even more ignorant is his wankerish comment on Catholics.”
I thought, based on prior experience, that you might bristle if I expressed doubts Miller’s misplaced faith. There is a weird cog-diss deal with some atheists who loathe the idea of a living God, while harboring unwanted reverence for Catholicism. Thankfully, I was not exposed to the dictates of a magisterium in my youth, but having now spent many hours in the CCC, I can understand the effects. With all due respect, there are significant differences between that system and sola scriptura Christianity.
I don't see reverence for catholics here Phil-you're just being called out for being an gsrden variety bigot who's using religion as a cover because you don't have the spine to own up to your statements.
Phil:
Well, you're almost there. The alteration in how many individuals carry an allele or gene does occur in response to environmental stresses. That's is very much part of evolutionary theory; what I've just described is what 'selection' is.
And the probability of a mutation itself might alter if you're including things like background radiation dose and the presence of chemical teratogens in food sources in the category 'environment.' Heck, such things might even differentially alter the proability of mutations, making some mutations more likely than others based on factors such as bond strength between base pairs. However what we have no evidence for - and what would be trivially easy for creationists to show if it was true - is some Lamarkian-style response in which mutations increasing neck length in giraffes get more probable when trees branch and produce leaves higher up.
.
That's just silly. Abiogenesis means the genesis occurs without biological compounds. It doesn't mean the experiment has to be carried out by nonbiological scientists. A typical scientist can study an atypical process, yes? Being typical doesn't preclude them from being able to study an atypical process, does it?
Phil, my grandmother was a Southern Baptist who loathed Catholicism. Her brother married a Catholic and converted. She refused to visit his grave because it was in a Catholic cemetery. Not only that, she believed that Baptists were not a sect derived from the reformation, but had existed outside Catholicism from the beginning of Christianity. She was truly an ignorant woman - much like you. Your claim that Protestants are more Christian than Catholics is just another sign of your delusion.
So now you admit that beneficial mutations can and do occur? Keep backpedalling and soon you will accept evolution in all its glory. Go tell your friends and family the good news.
Anton,
“So when you said, “they chose the word ‘codons’ for a reason,” what did you mean, exactly? Because the reason he chose it (it was Sydney Brenner) obviously didn’t make him conclude that the genome must be intelligently designed.”
Of course it didn’t. But all this came up in response to Michael suggesting that the use of the word ‘information’ is just a metaphorical representation. My point is that I think there are a lot of evolutionary biologists who would not agree with that notion.
-
“ “Codes” and “messages” are ways for human scientists to make sense of this system.”
No, it is information, like the contents of an encyclopedia.
-
“The natural environment was being simulated inside the apparatus. All the pieces of technology you list above are necessary to produce that simulated environment…”
No, there is no simulation of any kind. It was a controlled environment which in no way emulates outer space or an early earth. Technology is not a natural circumstance.
-
“I can think of tons of unguided natural processes that effectively sort and concentrate various chemicals. Or don’t salt pans, gold veins, coal seams, petroleum reservoirs, mineral crystals, and puddles of water exist in nature?”
Sure, but you don’t generally see anyone using any of those in origin of life experiments.
-
“Wouldn’t that mean it’s impossible for humans to conduct useful abiogenesis research, because scientific research is always consciously designed and conducted?”
Of course it does if the object of the game is to show how abiogenesis occurred with no intellectual input.
-
“Can you identify a chemical process that works differently inside and outside a living body?”
Yeah, glucose production.
-
“if creationists think this particular probability is evolution’s Achilles’ heel, then it’s rather baffling that they don’t do out the math…”
But you’ve done out the math yourself when you were excusing E coli for not being able to cough up one lousy transport enzyme in 102 million years, or 102 billion years. That’s the nature of a random protein production system….so many possible errors, so few functional results. But a loss of function like that makes you wonder why the divergence from salmonella ever occurred at all, doesn’t it?
-
“You’re thinking that if the probability of various traits or systems appearing is low, under evolutionary theory, then the probability that evolutionary theory is correct must also be low…”
Of course. You have to go through all kinds of convolutes to conclude anything else, and something as subjective as Bayes' theorem doesn’t change the probabilities.
-
“the lower the odds are that a particular, pre-specified useful accident will occur. But the odds that at least one useful accident will occur go up. With more numerous components, there are more ways to go wrong but also more ways to go right.”
But this conflicts with your rationale for the E coli. This is what I was talking about when I said that there is a catalogue of responses that have to be mastered in order to maneuver through the problems. There are no problems with evolutionary theory because there is a response for everything. Problems are just prompts.
Michael Fugate,
“Your claim that Protestants are more Christian than Catholics…”
No, that is not really my claim. Aside from the fact that many, if not most Protestant denominations are in decline and often involved in rank apostasy, they used to enjoy a reasonable common scriptural focal point. Catholicism does not work like this at all. Their doctrines are subject to change at the whim of the cathedra.
The point is that Miller being Catholic does not make him a God fearing Christian. Technically, he is supposed to be Vicars of Christ fearing.
-
“So now you admit that beneficial mutations can and do occur?”
In my view, the changes I referred to above would be better called something else. They do not appear to be the result of random replication errors.
Phil,
Point of order--where did he do that? I've only seen Michael use the word "metaphor" once in this conversation, and it wasn't in that context.
And so far you haven't advanced any evidence for that opinion; you've just noted one evolutionary biologist who liked the word "codon."
The contents of an encyclopedia are ink and paper. They mean something more to us humans, who read and write the thing. If there's a god or gods who wrote our genetic code, it might have all sorts of extra layers of meaning to them, but there's no way for human science to know about that.
This doesn't actually mean that information is "metaphorical"--I think you're misusing that word. It just means that information is observer-dependent.
Hey look, it's NASA simulating outer space. Why, they're using technology to do it, the cheaters! And here's the army simulating battles in Iraq, but there's fake blood everywhere and that guy's wearing a mangled plastic arm! They don't have fake blood and costume prosthetics in real battles!
It doesn't seem like the rest of the world agrees with your "simulations aren't allowed to use technology" rule, Phil. In fact, it seems like simulations require technology, unless it's something you can simulate by waving your arms and talking in a funny voice.
You do, actually, but so what? They were just examples that disprove your claim that "concentration and proximity are severe problems for an unguided process." If oil and salt and water and gold can be concentrated, so can amino acids or sugars or nucleotides.
Okay, so then, wouldn't all natural science be equally impossible? I mean, earthquakes, plant growth, planets orbiting stars, bacteria dividing...all those phenomena occur with no intellectual input, at least so far as science is concerned. Do you reject scientific research on all of them?
How does it work differently in those two settings?
No, I didn't. I did the math (very roughly) on how long would it take E. coli to experience every possible mutation it could experience. Since no scientist anywhere is claiming that E. coli has experienced every possible mutation ever, that doesn't help the creationist case.
What probability would you like to compute, how do you plan to compute it, and how will you use it to demonstrate the implausibility of evolutionary theory.
I don't really know where to begin with this. Are you claiming that ancestral E. coli had the citrate-eating ability and then lost it? How do you know that? And if so, why would that make you wonder why E. coli diverged from salmonella? Populations diverge and then lose traits all the time. A ton of olfactory genes have become nonfunctional in humans since we diverged from other primates.
Uh, that's like insisting, "right triangles have three equal sides, and no lousy Pythagorean theorem changes that fact!" Bayes' theorem is practically the foundation of working with conditional probabilities. If you're going to write it off as "subjective" (what does that even mean?)...well, good luck inventing your own theories of probability and statistics from scratch, I guess?
No, it doesn't. Evolving the ability to metabolize citrate is only one way to improve your fitness (if you're in a citrate-rich environment, anyway). There are many other ways to do so. So it's not surprising if one E. coli lineage comes up with that adaptation while many others don't.
Of course, all of this is moot. As I pointed out earlier, wild-type E. coli doesn't live in a citrate-rich environment like Lenski's research population, so we don't even know if it would have been adaptive for the wild-type bacterium to develop citrate-munching abilities. Maybe that's not a trait natural selection ever favored before...who knows?
Anton,
“Point of order–where did he do that? I’ve only seen Michael use the word “metaphor” once”
Well, I could be taking him wrong, but I believe that is the point the writer is trying to make in the link Michael provided in #17 above. I’ll let you decide:
http://evolvingthoughts.net/2014/06/genes-the-language-of-god-0-preface/
Also, in #21, he said the following:
“Given that everything that happens within a cell is chemistry, why would any chemist think intelligence were required? He or she certainly wouldn’t think that when discussing chemical reactions – read any chemistry book.”
I take that to mean that what happens in cells is nothing more than chemical reactions, so the use of the word information is only metaphorical.
If that is the case, in my opinion, taking offense at the concept of actual information is because of the ideological implications.
-
“The contents of an encyclopedia are ink and paper.”
Well, that’s the raw chemistry, but it is the organization of characters into words that represent concepts, ideas and facts that makes it information.
-
“If there’s a god or gods who wrote our genetic code, it might have all sorts of extra layers of meaning to them, but there’s no way for human science to know about that.”
I’ve seen articles about those other layers, but the point is that either the code was designed, or it arose by accident. I don’t see that latter as being a particularly reasonable belief.
-
“It doesn’t seem like the rest of the world agrees with your “simulations aren’t allowed to use technology” rule”
You missed the point. If you’re truly trying to reproduce the actual circumstances of an early earth, then you are limited to what was there, or a very close approximation of what was there. The devices in Miller’s experiment were not there. You can come close to duplicating the vacuum of space with a vacuum chamber, and test things in this device. It is an entirely different thing to try and prove that there is no designer by using a designed apparatus.
-
“They were just examples that disprove your claim that “concentration and proximity are severe problems for an unguided process.”
No, those are real problems. Miller’s experiment was not conducted in a stadium. He used a loop to concentrate chemicals.
-
“..all those phenomena occur with no intellectual input, at least so far as science is concerned. Do you reject scientific research on all of them?”
Of course not. Within reasonable limits, I don’t reject any kind of research.
-
“ “Can you identify a chemical process that works differently inside and outside a living body?”
…glucose production.
How does it work differently in those two settings?”
The processes for arriving at glucose are different. Plants don’t use the formose reaction to produce it.
-
“no scientist anywhere is claiming that E. coli has experienced every possible mutation ever…”
Oh, I think they come close to doing that quite often. It’s how evolution works:
“Only about one nucleotide pair in a thousand is randomly changed every 200,000 years. Even so, in a population of 10,000 individuals, every possible nucleotide substitution will have been "tried out" on about 50 occasions in the course of a million years, which is a short span of time in relation to the evolution of species”
http://science.howstuffworks.com/life/evolution/evolution5.htm
-
“Are you claiming that ancestral E. coli had the citrate-eating ability and then lost it?”
I don’t have to claim that. They can do that now in an anaerobic environment. They are just inferior to Salmonella their supposed evolutionary cousins. (Actually, they use a citrate test to determine which one they have: http://www.austincc.edu/microbugz/citrate_test.php)
Since they already have the genetic mechanisms to process citrate, and are just missing a transport enzyme, the most parsimonious thing to assume is that they lost it and haven’t won it back in the mutations lottery yet, except in Lenski’s iconic lab.
-
“Bayes’ theorem is practically the foundation of working with conditional probabilities. If you’re going to write it off as “subjective” (what does that even mean?)”
It means exactly that, because the premises are conditional…subjective. That’s why books have been written proving and disproving the existence of God, both using Bayes’ theorem. This article deals with the subjectivism as it relates to the theory:
http://plato.stanford.edu/entries/bayes-theorem/
Phil,
They are chemical reactions nothing more nothing less - anything having to do with language is human short hand - Dennett calls it the "intentional stance."
Phil,
And you do realize given that there are 1000s of protestant groups all of which disagree in some part doctrinally, that they too are making it up as they go along. If they were all following the Bible or if the Bible were in any way clear there would be only one Christianity, but obviously there isn't.
Phil:
In the bottle. The bottle itself does not invalidate the experiment, just like the fact that NASA builds vacuum chambers does not invalidate their findings.
It is exactly the same.
Bottle 1: contains vacuum. We use it to study how things behave in a natural (non-man-made) vacuum.
Bottle 2: contains aenerobic chemicals. We use it to study how things behave in a natural (non-man-made) aenoromic chemical environment.
Why would #1 be valid despite the bottle being built by humans and #2 be invalid because the bottle was built by humans?
eric,
“Bottle 1: contains vacuum. We use it to study how things behave in a natural (non-man-made) vacuum.
Bottle 2: contains aenerobic chemicals. We use it to study how things behave in a natural (non-man-made) aenoromic chemical environment.
Why would #1 be valid despite the bottle being built by humans and #2 be invalid because the bottle was built by humans?”
Because of the goal and nature of the experiments. If you want to simulate how crude oil is naturally formed from organic material, you can approximate that with garbage, heat and pressure. But you can’t use complex, controlled process equipment to separate naphtha, gasoline and diesel fuel from crude oil and then claim that that you have illustrated natural processes and natural products. The same holds true for the Miller’s or any other experiment that uses technology that exceeds natural circumstances. The results might be interesting, useful and valuable, but it is in no way natural, and it surely doesn’t prove that no intellect is necessary. It proves that it is.
Michael Fugate,
“They are chemical reactions nothing more nothing less – anything having to do with language is human short hand”
No, chemicals are just the ink and paper. In the case of a replication enzyme recognizing an error, there is some kind of input. Removing that error is a reversal, not a continuance towards equilibrium. Replacing the sequence is no different than correcting a misspelling. This is obviously more than just chemical reactions. It is about signals and actual information.
-
“And you do realize given that there are 1000s of protestant groups all of which disagree in some part doctrinally, that they too are making it up as they go along.”
This is a common refrain, but the thousands of groups is more about locality and personality that raging doctrinal disputes. There are devoted house churches in China using one or two handwritten pages, and large churches with endless resources. Christians are not Christians because they have mastered systematic theology. There are plenty of advanced subjects, but the basics are unpretentious, and necessarily juvenile.
In the NASA vacuum chamber, a pump is used to produce the vacuum but the response of chemicals to that vacuum is the same regardless of the source. In the biology anaerobic chamber, electrodes and heating elements are used to produce sparks and heat but the response of chemicals to that environment is the same regardless of the source. As long as we do the experiment correctly, nature can't tell the difference because on the scale of atoms and molecules, there won't be any difference. The chemicals being studied cannot tell the difference between heat produced on the outside of the glass by sunlight and heat produced on the outside of the glass by an electric heater. So it doesn't matter that the heating mantle was designed, because as far as the chemicals in the bottle are concerned, heat is heat.
The only time source makes a difference is if the artificial source is producing a different signal (i.e. different spectrum of heat, or different voltage/current/duration spark) than the natural one. That is a perfectly credible criticism to level at some scientific experiments - that they are not modeling reality accurately, and so the results may not accurately predict what nature does/did - but the one thing that criticism does not do, is support your argument that all OOL experiments must be ruled out as a class because the experiments used human-designed equipment. That is an utterly foolish argument to make for, as I've said, as long as the condition produced is the same, there is no difference between an artificial process to get there and a natural process to get there.
It is not. No matter what you believe. It is just chemistry. The signals/information baggage is placed there by humans as a shortcut to understanding. You are introducing intention into a system that has none.
So Catholics are just as Christian as Protestants? How about Jehovah's Witnesses? Mormons?
Nothing that Protestant groups believe is incorrect? They are all equally good? Infant v. adult baptism doesn't matter? How about Biblical inerrancy? Creationism?
Nope doesn't matter one bit.
IIRC, replication enzymes do not recognize errors. Instead, there are specific repair enzymes that do so, and they can do that because most types of replication errors produce consistent results and the enzyme chemically interacts with that result. So for example, methylation is a fairly common result of some types of duplication errors, and there are enzymes floating around the cell that will attach to methylated sites and demethylate them. The enzyme itself has no idea whether its fixing a problem or creating one; it's just chemically reacting to the methyl group.
AFAIK, enzymes can't tell the difference between a novel change and a 'reversal' because it has no knowledge of what the DNA string looked like in the past. How could it? Do you know of a mechanism that would allow one folded polymer to "know" if a chemical reaction would return a reactant to a previous state?
This is in fact the 'molecular fail' of the broader ID claim that mutation can break functions but not build them. The chemicals involved in duplication and mutation could not possibly tell the difference between a 'breaking' and a 'building.' They cannot see the past to tell what the original DNA strand looked like, and they cannot see the future to tell what phenotypic result will occur. Thus the ID claim is physically impossible. Chemicals do not and cannot know the result of the reactions they participate in, thus they cannot selectively perform only those reactions that 'break' funcionality and never those reactions that 'build' functionality.
Here is a pretty good clue the things that happen within cells are just mindless unintentional chemical reactions. I can stick any DNA sequence with a "start codon" into any cell and it will "read" it and "translate" into proteins - even if the cell has no use for that protein or if the protein itself doesn't have any "functional" shape (it could be too few amino acids ("stop codon"). One could also put a "beneficial mutation" into a strand of DNA causing a mismatch - the "repair" enzymes will see that error and correct it - even though leaving it would benefit future generations.
The same with "signals" - purely chemical reactions - this is why disrupters can influence development. Take a look at the history of thalidomide - it binds and inactivates the protein cereblon which is important in limb formation. Cereblon would be bond and inactivated by other inhibitors in the fetus, but those inhibitors would be produced at specific times. The cells and molecules can't tell the difference between an inhibitor at the "correct time" and one at the "incorrect time." Just mindless unintentional chemical reactions and nothing more.
The intentions are all opposed externally on the system - it is like looking a shapes in clouds and claiming a designer made the cloud into a "horse" to amuse your picnic. Wait, I am not sure you don't already believe that.
Michael Fugate,
“So Catholics are just as Christian as Protestants?”
Not necessarily. I am a minimalist about salvation, so I am soft on that issue. But in form and function, the Catholic catechism is pretty consistently at odds with New Testament doctrine.
-
“How about Jehovah’s Witnesses? Mormons?”
You could add quite a few more. some very interesting like Iglesia ni Christo or the Church of Christ. Generally, these all have one or more characteristics that I have problems with. The first is peculiar, historically late-breaking, enlightened central figures. The second is when they claim to be the one and only authentic Church. The third is what they believe about Christ.
-
“…the things that happen within cells are just mindless unintentional chemical reactions…The same with “signals” – purely chemical reactions”
As I recall, there are some 250 different kinds of cells in humans, and with notable exceptions, they all have identical copies of a the same DNA molecule. If you’re comfortable with the idea that cell differentiation is just chemistry, and no actual information or specific signals are involved, I won’t argue the point.
===
eric,
I don’t know what to say about why replication enzymes do what they do. But they definitely function to preserve the original.
“Some of the mistakes are corrected immediately during replication through a process known as proofreading, and some are corrected after replication in a process called mismatch repair. When an incorrect nucleotide is added to the growing strand, replication is stalled by the fact that the nucleotide's exposed 3′-OH group is in the "wrong" position….During proofreading, DNA polymerase enzymes recognize this and replace the incorrectly inserted nucleotide so that replication can continue. Proofreading fixes about 99% of these types of errors, but that's still not good enough for normal cell functioning.
After replication, mismatch repair reduces the final error rate even further. Incorrectly paired nucleotides cause deformities in the secondary structure of the final DNA molecule. During mismatch repair, enzymes recognize and fix these deformities by removing the incorrectly paired nucleotide and replacing it with the correct nucleotide.”
http://www.nature.com/scitable/topicpage/dna-replication-and-causes-of-…
Perhaps they are just using the word 'recognize' metaphorically to express the fact that they appear to know exactly what they are doing.
That is exactly what they are doing. Along with words like proofreading, recognize, fix, etc.
Most scientists do not write with the assumption that a creationist will come along and interpret every metaphor and anthropomorphization literally. And in fact in many articles scientists will use such language intentionally in order to help nonscientists understand...because the only other option is to use terms of art and jargon. It is infinitely easier to say a molecule recognizes an error than it is to describe chemical potentials and which reactions are thermodynamically and kinetically favored in a given environment. That doesn't mean the molecule has eyes. It means the chemical structure of the molecule reacts with the chemical structure of the given environment in a specific and predictable way.
So when a creationist such as yourself comes along and is determined to take a completely mainstream science article that the authors would never dream anyone could think supported creationism, they usually can.
I guess what you've shown here is that we are in a no-win public communications situation. Either talk in accurate yet opaque jargon, or talk in common vernacular and have creationists twist such descriptions of the same processes 180 degrees away from their intended meaning.
Err...second paragraph I'm missing the verb phrase. "supported creationism and twist it, they usually can."
As an aside, this was so regularly done to SJ Gould that he felt forced to make several public "no, they're wrong and misinterpreting my work" statements ahead of the release of his Structure of Evolutionary Theory. Because folk like you are so eager to find any justification for your ideas, that you will take mainstream positions and pore over word choice rather than listening to the substantive message that the scientist is trying to convey.
"Most scientists do not write with the assumption that a creationist will come along and interpret every metaphor and anthropomorphization literally"
I think both the scientists are simply describing what happens. But if you're correct, it should be easy enough to rewrite the quote above using accurate literal technical language instead of metaphors. How should it actually read?
Phil,
I don't think that's the case. If you look at the comment thread, for instance, Wilkins agrees that DNA can be taken as encoding information. He thinks information is subjective or observer-dependent, but that's not the same as a metaphor.
(And BTW, under most mathematical definitions of information, it can be generated just fine by chemical reactions--or any random process, in fact.)
But a simulation is not trying to reproduce the actual circumstances of the system it's simulating. That wouldn't be a simulation, it would be a copy. A simulation is trying to reproduce a subset of the behavior of the system it's simulating. Seriously, you might want to check the dictionary on this.
Miller was simulating the atmosphere of the ancient earth and testing its ability to generate organics. What he used to synthesize, heat and contain that atmosphere in the first place is simply of no consequence to the simulation. Just as it doesn't matter how NASA's vacuum chambers are constructed and powered, provided they do their job of making a vacuum.
OK, so why not? If you accept that research on some mindless natural processes is valid even though it's conducted by intelligent, conscious scientists, then what makes abiogenesis research off-limits?
That's simply because the chemical prerequisites for the formose reaction aren't present in a plant. If you inject a plant with a mixture of formaldehyde, base and calcium...well, it probably won't be a very happy plant, but the formose reaction will proceed as normal inside. The "livingness" of the plant won't change that.
Plants do use the Calvin cycle to produce glucose, and that also works the same in a nonliving setting. The chemicals don't know or care if they're involved in life.
"Every possible nucleotide substitution" ≠ "every possible mutation." The number of distinct individual substitutions is huge, certainly. But it's still only a tiny fraction of the total set of possible mutations, which would also include insertions, deletions and substitutions of multiple nucleotides at once.
Ah, I see what you're thinking. Trouble is, if you assume that E. coli lost the enzyme, you still have to account for its original appearance; you've just moved that back before E. coli and Salmonella diverged. Taking that into account, I don't think it's more parsimonious to say that "the enzyme appeared in the common ancestor of E. coli and Salmonella and then disappeared again in E. coli", than to say that "the enzyme appeared once in Salmonella."
Of course, this is a toy phylogenetics problem. There are actually a lot of other bacterial species on this branch of the evolutionary tree--Shigella, etc. Many of them can aerobically metabolize citrate, many of them can't, and it's way beyond my expertise to figure out what the most parsimonious pattern of transitions here would be.
Anyways, back to my previous question--why does any of this pose a problem or inconsistency for evolution?
I thought that's where you might be going. Here's the thing, though: the theorem is no more "subjective" than "2+2 = 4". It's just a mathematical statement about how various probabilities have to be related. But it has powerful implications for subjectivist world views.
The link to subjectivism works like this. A "subjectivist" interpretation of probability says that a statement is more credible, more believable, if it's more probable. In that sense, you are a subjectivist, or at least you've been taking a subjectivist stance throughout this entire conversation. Every time you say something along the lines of "evolutionary theory is wildly improbable, therefore unbelievable," you're making a subjectivist claim.
So, if you're a subjectivist and you want quantitative justification for your belief, you need those probability calculations, and therefore you need Bayes' theorem. As your article says, "the Theorem's central insight — that a hypothesis is confirmed by any body of data that its truth renders probable — is the cornerstone of all subjectivist methodology."
Oh, yes. But the problem there does not lie with Bayes' theorem, but with the probabilities being plugged into it. The theorem says that you could calculate the probability of God's existence given some piece of evidence, if you knew a) the unconditional probability of God's existence, b) the probability of the evidence being observed if God exists, and c) the probability of the evidence occurring if God does not exist. Trouble is, of course, it's awfully hard to find agreement on more than one of those values. They're...subjective, it seems.
If you try to estimate the probability of evolutionary theory being correct vs. intelligent design, you run into the same sort of dilemma. And that's exactly why I said the probability calculations you suggested are uncomputable and irrelevant. They depend on other probability estimates that are subjective at best and unknowable at worst.
How are you going to get your heat and pressure, except through a complex, controlled process?
How are you going to create and provide the "garbage," and ensure that it matches the composition of the natural organic materials that lead to oil, except through a complex, controlled process?
The two experiments you describe are equally complex, controlled, man-made, intellect-driven, or any other word you care to use. Seems to me that you just don't like the second experiment because of its result; fractionating crude oil by applying heat and pressure produces a level of order and complexity that makes you uncomfortable, so you claim that this particular experiment wouldn't count because there was human intelligence in the mix.
Which is kind of funny, because there are mindless natural processes that do fractionate crude oil, producing natural deposits of asphalt, natural gas, naphtha and so on.
I think we can agree that particle accelerators use a crapload of high technology. Does it follow that they're useless for telling us about the natural behavior of subatomic particles?
No, its not easy, that's the point. To descibe it accurately and literally takes much more specialized expertise and the resulting text would only be comprehensible to people with a strong science education. Which would completely fail to accomplish the goal of a paper that was published in the journal Nature Education, which is to educate nonscientists.
Anton:
This bears repeating. AFAIK IDers don't even have a mathematically workable definition of information that would yield the results they claim. They have qualitative statements about information, but no mathematical description of it that allows you to analyze reactions and which yields the analysis result 'intelligent processes can produce it, unintelligent ones cannot.' IOW, their claims are irreproducible because they have no independently reproducible methodology for determining what information is.
OTOH, if you look at standard mathematical treatments of information theory (the use of Shannon Entropy is what I'm thinking about), they allow for information to be produced by random processes quite easily.
It is like taking Genesis literally when it is so obviously metaphorical. Why people still do this is beyond me.
One really does need to do some reading in psychology, philosophy, cognitive development, etc. to understand why we use the language we use. As I mentioned before Dennett called this the "intentional stance" you can check it out on Wikipedia or better yet read is book on Intuition Pumps. Hell, you might learn how to think better (one could only hope).
The things called "signals" in cells that "turn on" or "turn off" "transcription" are chemicals and they act through chemical reactions. Forming chemical bonds, changing conformations, and so on.
Here's an exercise for you Phil. Pull up a weather site, notice blue lines with triangles, red lines with semicircles, purple lines with both or red and blue with both, Hs and Ls - these are imposed by humans onto patterns of air pressure. If you go out and look, you won't see them painted on the sky. You might see and feel clouds, wind speed & direction, temperature, and humidity, etc. Humans are using patterns, extracting information from those patterns, but is there agency behind the air molecules shaping them into cold fronts?
Because we can id rocks or soils, does that mean there is agency behind the patterns we detect?
It wouldn't be easy, but it'd certainly be possible. Strike "recognize [x]," replace with "contain an active site to which [x] binds via Van der Waals, hydrophobic and other chemical forces, which triggers a change in the enzyme's conformation." Strike "mistake"/"error", replace with "change in base sequence." And so forth.
It wouldn't be as clear reading for most people, though!