It's been very hectic around here recently. In addition to the usual end of semester craziness, there's been one thing after another to fill my time. The book I've been editing forever had a major deadline last Monday, which pretty well killed that weekend. This past weekend was occupied by the MAA section meeting in Roanoke, VA, which I decided fairly last minute to attend.
Of course, it hasn't been all stress and hard work. My birthday was yesterday (I'm 42!), and since yesterday was also the day of the semester-ending math department picnic, everyone sang me happy birthday. But still, it's been hard to find time for blogging lately. There's been plenty of fodder certainly, but I'm a painfully slow writer and it takes me forever to write anything.
I almost rushed to my computer to protest the outrage that occurred tonight on Dancing With the Stars. Can you believe that Willow and Mark were eliminated? They were one of the best pairs! Of the seven couples remaining there were three who basically trip over themselves every time they go out on the floor, but apparently they get lots of people to phone in on their behalf. Just ridiculous.
I only barely raised an eyebrow at this post, at Uncommon Descent, where Vincent Torley expressed vexation at my recent, blunt assertion that ID is dead. He fires some specious mathematical arguments in my general direction, and at some point I'll probably reply, but that little project might have to wait at the end of a lengthy queue. (Short reply: If mountains of physical evidence from every branch of the life sciences says that something happened, but a back-of-the-envelope calculation based on an abstract model says it didn't happen, then it's the model that's wrong.) If anyone would like to save me the trouble of replying further in the comments, feel free to do so.
Sometimes, though, an outrage occurs that is so epic, that some comment is called for. One such happened tonight. I had decided to cook a Cornish hen for dinner. Four hundred degrees for an hour works pretty well, I find, so I turned on my oven while I prepared the bird. The oven made the clicking noises it usually makes when I turn it on, and the display informed me that it was now preheating. I spent several minutes liberating the hen from its packaging, and giving it a rub of salt, pepper, Hungarian paprika and garlic powder. Yum! I put it in its roasting pan and opened the oven door.
The oven was ice cold.
Now, this particular oven has always been slow to heat up. The heating element is concealed in the oven's casing, which makes for easier cleaning but slower pre-heating. But not this slow! I checked the stove top, but no dice. No heat at all. I tried turning off the oven and starting over, but still no dice.
I thought perhaps a circuit breaker had been tripped, but no. Everything else on the oven was working fine: the oven light, the timer, the clock, the warning light that tells you one of the burners is active. But no heat. At all. This is not good. It seems to me the problem must be with the heating element itself, which means in turn that it is certainly not something I could fix myself. In fact, it probably means I need to get a new oven. Which is annoying, since this one is only a few years old.
As for the hen, well, it turns out that my toaster oven is just big enough to accommodate the roasting pan. Back in business!
The more I think about it, though, the more annoyed I get about Willow and Mark. There hasn't been an outrage like this since Shawn and Derek got robbed back in season fifteen. I mean, seriously, how do you top this:
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Good luck with the oven. I assume you checked whether the top burners work? If so, you can probably get by with those for a while.
Good luck with your oven, and happy birthday. Any chance it's still under a warranty since it's fairly new? BTW, nothing much to say about Torley's arguments; same old, same old.
I agree with Sean about Torley.
1. Calculating odds of a protein springing up ab initio rather than through RM+NS? Check.
2. Claiming these long odds can't happen when they obviously can? Check (for confirmation, I just produced Torley's "impossible" 1E164 chance event in Excel. 165 lines of "Randbetween(1,10)" later, he's wrong).
3. Assuming any short string not functionally useful in organisms today could never have a function in the past? Check. Same 'ol same 'ol.
However I do wonder whether its politically dead or not. I haven't heard much lately about teachers or principles or school boards trying to use the ID schtick to get creationism back in schools, but maybe that's just due to my lack of awareness. Is it still a used strategy?
My condolences on your loss.
I'm assuming the oven is electric and that the elements for the burners are working. In older ovens, like mine, the element is exposed and when it fails it obvious because the metal core is exposed where the ceramic covering has failed. One thing about Google Search I have found most helpful, is that somewhere, someone, has posted on a blog or video the steps necessary to make simple repairs of appliances. Just put in the make and model number and see what comes up. In my situation, I had the part from Amazon in two days, in the original factory wrapper and installed it in five minutes.
As far as I'm concerned, Dancing With the Stars, with all its apparatus and retinue, should be placed in an industrial oven--a steel-mill blast furnace would serve--and baked to a highly carbonized state.
"If mountains of physical evidence from every branch of the life sciences"
More like modest accumulations of data, and mountainous piles of preferred interpretation and speculation. The facts are forcibly in. Stasis and extinction are the reliable norms.
The life sciences have nothing to offer in the way of protein assembly, much less the feedback that would make protein assemblies useful accidents. Show one paper that makes a nickel's worth of sense about the random formation of ribosome.
Good heavens, Eric, you're not accusing me of committing Hoyle's fallacy, are you? Don't be so silly. Nothing in the papers I cited contained any reference to proteins spring into existence in one fell swoop. What's more, two of the three authors I cited were highly respected evolutionists, and the third author had previously written articles in PNAS and other peer-reviewed publications.
Jason, re your short reply: mountains of physical evidence from every branch of the life sciences do indeed say that something happened, but that "something" is descent from a common ancestor. This evidence says nothing about whether the process was a wholly unguided one, or whether known natural processes are capable of explaining the diversification of life into numerous forms. And as I stated at the end of my post, common descent is not the same thing as evolution.
Larry T--
Thanks for the advice. The oven is electric, but the stove top is also not working. No heat from the oven, no heat from the stove top. But everything else works, as I mentioned. Alas, the oven is outside the warranty.
Vince Torley,
You seem to be an ID proponent. I will assume that your argument for ID can be summarized in the following points (please forgive me if I am wrong on these and feel free to correct):
1. Certain systems in biological organisms would have a low probability of arising from natural, unguided processes.
2. Because of point 1, it is likely that there is a designer that intentionally created such biological systems.
3. ID is a scientific endeavor. This proposed designer need not be a supernatural being.
Based on those points, let us assume that the designer is not a supernatural being. Given a natural designer, then, it must be the case that such a designer arose from natural processes. What is the probability of such a designer arising via natural processes, though? Surely the probability of that happening would be lower than the probability of a protein forming naturally, would it not? Therefore, we are forced to conclude one of the following:
1. There is no designer.
2. The designer is a supernatural being.
3. There is a designer that designed our purported designer.
4. There is a designer, but that designer arose via undirected natural processes.
Obviously, conclusion 3 is just leading down the road of infinite regress. If we invoke another designer, then how did that designer get there? We must rule out this conclusion.
Conclusion 2 would be possible, but pointless. Why would we continue to refer to the whole endeavor as ID, rather than creationism, which is what the idea that biological systems were created by a supernatural being is typically called. If you invoke a supernatural being to explain the existence of biological systems, it becomes immediately impossible to falsity your hypotheses; the supernatural being could interfere with any potential testing.
Conclusion 1 obviously renders the whole ID endeavor false, so let's deal with conclusion 4. As discussed above, the probability of a designer arising naturally would necessarily be lower than the probability of the systems it purportedly designed doing so. If we assert then that, despite the low probability, the designer arose naturally, we cannot really rule it out. However, what have we gained? We started from the premise that the natural evolution of biological systems is too improbable and been led to the premise that an event of even lower probability actually occurred. Why not just accept that the natural evolution of biological systems occurred? That would have the added advantage that we actually have observed the existence of these biological systems, while we have not done so for a purported designer of those systems.
It seems to me that conclusions 3 and 4 are wholly unsatisfactory. That leaves only conclusions 1 and 2. Therefore either ID is false or ID is just creationism with a new name.
Vince Torley:
I was referring to your UD piece, in which you take Axe's data and then you do some additional analysis on it. Here's the relevant part:
This calculation assumes that a mutation in a protein-producing mechanism has a probability of producing a useful protein equivalent to [the set of useful proteins]/[the set of all possible 150-string proteins]. This ignores the actual process of descent with modification from earlier mechanisms. Its tornado in a junkyard math. You now continue:
It looks to me like you've got the same problem here: the chance of getting an "all left handed" protein from a newly mutated protein-forming mechanism is highly dependent on the parent state of that protein-forming mechanism, and you seem to be ignoring that dependency altogether. More modeling evolution (very inaptly as) tornadoes forming airplanes..
One thing creationists ignores - history. It's all "poof" and that's that. Cataclysm, then stasis - but this is contrary to everything we know. As Justice Ginsberg pointed out to the marriage inequality gang yesterday, marriage has evolved. Shock! it's not the same as it was when Adam hooked up with Eve. It's not even the same as it was 30 years ago and 30 years ago it's not the same as it was 50 and 100....
Cheap apologetics is not science or history or philosophy.
Happy Birthday.
Check Scratch & Dent ovens at the big box stores. May luck into a good deal. Know your oven measurements.
Let the seller install, there is an anti-tipover catch that is tricky w/o experience to install and you definitely want it.
Negotiate a complete price: Purchase, install and carry off the old, now maligned oven.
Good luck
"One thing creationists ignores – history. It’s all “poof” and that’s that."
Yeah, but what they don't ignore is the appeal to countless billions of random, spectacular miracles.
Jason;
I am far more moved by the passing of your oven than DWTS; and I like ballroom dance.
I have a 40+ y.o. oven with an uncertain future; I feel your pain.
As for Torley, fuggetaboutim. I've been butting heads with creationists since the 70's and this is all old stuff. They think ignorance proves more than just that there's things we don't know.
sean s.
So... Jason... young man.. well not so young anymore now are we... so.. when are you going to get married and give me grandchildren? What? No girl is ever good enough for you?
You are worried about appearances? Honey please! Start making me a grandson ... even if you have to adopt... get a snowflake baby and implant it in some lady if you have to.. I am not getting any younger....
Jason's mom..
(Jason I sure hope your mom is alive.. and happy birthday)..
Why the anxiety to declare ID dead? Torley poses reasonable objections. Are they all, every last one, meritless? Perhaps the worst thing that can happen to a person is for ideology to consume rational thought. If the pursuit of truth is the objective, why do atheists never formulate their own inquiries?
Torley's objections are, each and everyone, meritless. ID as an explanation for the origin of the earth and life is dead. The ID MOVEMENT lives on; for them ID is an IDeology.
Phil, you are correct: "Perhaps the worst thing that can happen to a person is for ideology to consume rational thought"; and that is exactly what ID IDeology does.
Re.: "why do atheists never formulate their own inquiries?" That is a silly question.
sean s.
I'm not sure its dead; see @3.
They are not reasonable for reasons I explained in @11.
See, you just gave away the game there; showed that you see ID as a religious claim because you view this as a fight of theists vs. atheists.
But many many theists support and perform mainstream science, and the journals publish thousands (if not tens of thousands) of "our own [mainstream; both from theists and atheists, and probably polytheists and pantheists as well] inquiries" every year. For us, it is not about religion, its about finding the best explanation for the data.
sean samis,
“Torley’s objections are, each and everyone, meritless.”
No, they are just dismissible, swept of the table because they are offensive and too unpleasant to deal with. He is showing you science, and you are reacting with your religion.
-
“That is a silly question.”
No, it surely is not. There is nothing but sappy ideas in between any origins theory you care to name and science-grounded reality. The same applies to ideas about mutations and evolution.
I hate having to repeat myself, but you are appealing to absurd collections of fantastic miracles which do not occur in real life.
===
eric,
“you view this as a fight of theists vs. atheists”
Agreed, but the facts are not favoring atheism. Accepting raw materialism requires belief in things that are absurd. I could list them for the x-teenth time, but there is no reason to do so. You have a commitment that overrides science and repels facts.
I didn't dismiss them, I explained why they are wrong, and neither you nor Torley have responded to those explanations in substance. Would you care to do so?
No problem, the universe does appear to have some absurd rules. Evolution and abiogenesis is nothing compared to QM in that department.
You know what I think is even more absurd than QM? You thinking that the universe must be created in such a way as to make intuitive sense to you, a human being. Seems highly narcissistic to me to think that it owes us non-absurdity or that non-absurdity is required of it. Where is it written that the rules that govern the universe must feel psychologically comfortable to and make sense to Phil? If we look at the data and the best available explanation feels absurd to our notion of common sense, then the correct response is to accept that our notions of common sense are wrong.
Phil, Torley's claims are meritless; basically he argues that general ignorance proves his claims, which is illogical. Ignorance can only "prove" ignorance. No explanation can be verified by ignorance.
His claims are neither offensive nor unpleasant to me, error is too ordinary.
You say the related scientific explanations are absurd, but only because they challenge your IDeology. They are in fact quite reasonable. Some of these scientific explanations have not been verified yet, some will probably be disproved and replaced. This is not faith, this is just our experience with the scientific method.
sean s.
phil whines "evolution requires miracles, miracles, I say!" Says a man who believes in miracles and that the origin of life, the universe and everything requires miracle after miracle after miracle.
A miracle is an event not explicable by natural causes alone - it is something that exceeds the productive power of nature. Nothing you or Torley write about evolution matches this; you both admit that it is only very unlikely not impossible. Most of Jesus' supposed miracles aren't even necessarily miracles - people recover from diseases without the need for non-natural causes. Multiplying loaves and fishes or water into wine, on the other hand.... of course there are natural possibilities for both - just not in the manner described.
I am just wondering how your "naturalism is not enough" works with your career in engineering - do you have to pray continuously to keep a plane in the air? a building from collapsing?, electricity flowing through a wire? Are bull or ram sacrifices required? Doesn't all this extra time spent praying and sacrificing make your firm less competitive than one relying solely on naturalism?
eric,
“No problem, the universe does appear to have some absurd rules.”
Okay. So would you care to get your hands dirty and note some of those rules as they pertain to the things mentioned in this article?
http://www.the-scientist.com/?articles.view/articleNo/42874/title/Beetl…
===
sean samis,
“You say the related scientific explanations are absurd”
No, I’m saying the explanations are not scientific at all. What you have is a storyline. The article I linked to is actual science, actual investigation, actual discovery (excepting the idiotic final quote). Your beliefs about what mutations can accomplish are only beliefs.
Michael Fugate,
“Says a man who believes in miracles and that the origin of life, the universe and everything requires miracle after miracle after miracle.”
Exactly. But the miracles you accept ignore everything normal, and everything known. You believe that random, purposeless events resulted in spectacular organization and function. You’ve lost track of what is possible and what is impossible. If your religion required that Krugerrands grow on peach trees, you would not resist. What a sorry waste of intellect.
===
“A miracle is an event not explicable by natural causes alone – it is something that exceeds the productive power of nature.”
The productive power of random DNA replication failures is on full display. You are able to ignore miles of literature that show the actual results that researchers uncover. You are out of science and into evolutionary religion. Do a ‘mutations’ search with any engine and come back with the articles celebrating the thrilling results.
I realize this is not going to sink in. Facts and data are not the issue. This is not about evidence. It is about what you prefer and your personal volition. You make your own choices, and you, and you alone, will wear the consequences. You are the captain on a ship with one crew member, and if you willingly, knowingly and deliberately steer into an obvious reef, the wreck will be your fault. You will answer, and you will have no advocates. And there will be no appeals.
I wish you well while you are still in control of your destiny.
Phil:
That was easy". You didn't even bother googling "bombardier beetle evolution," before leaping to the conclusion that it must be designed, did you?
Although given the age of this particular trope, my guess is that you didn't come up with it on your own: you heard it from some creationist or got it from some creationist website and just accepted what they said about it uncritically.
...My apologies for improperly closing my html tag...
Yes, they really are. IDers keep calculating the improbability of some string of dna base pairs or protein amino acids as if the final product from billions of years of evolution was randomly assembled from scratch. Since that is not how evolution works, their model is laughably inaccurate. Ironically, what they are calculating is the improbability of special creation; whole complete systems or organisms springing forth from the earth with no precursors or previous generations.
Phil,
Let me try to tackle the problem with your improbability argument from another direction with an analogy. The earth orbits the sun with some velocity, v. It is easy to show from some basic Newtonian physics that the force acting on the earth due to the sun's gravity must be equal to the centripetal force acting on the earth to keep it in orbit. In terms of quantities, the centripetal force is given by mv^2/r, where v is defined as the speed of the earth, m is the earth's mass and r is the radius of the earth's orbit. The gravitational force acting on the earth due to the sun is GMm/r^2, where r and m are defined above, G is the gravitational constant and M is the mass of the sun. Combining these equations, we get
GMm/r^2 = mv^2/r, which after a bit of algebra can be rearranged to yield v = sqrt(GM/r). This implies that for the earth to stay in orbit around the sun, its velocity must have a very precise value. Any faster and the earth files off into space. Any slower and the earth is pulled into the sun and burns up. How improbable is it that given all the possible velocities that the earth could have that it has the exact right velocity to keep it in stable orbit?
Of course, the argument above is ridiculous, and for precisely the same reason that the argument from improbability regarding evolution is. The physics of the formation of the solar system tightly constrains the velocity of any planets formed. We didn't need God to set the velocity; the laws of conservation of energy and angular momentum did the job perfectly well. In similar fashion, laws of chemistry, physics and biology constrain what happens with biological systems. Your improbability argument assumes that DNA sequences form randomly. They do not. They don't form with the help of intelligent guidance, but their formation is certainly not random. This non-randomness renders the improbability calculations invalid.
Phil,
If facts and data are not the issue, then what the heck are you doing posting to a science blog in the first place? Facts and data ARE science, or at least are the fundamental basis of science. If facts and data don't matter to you, go to a religious site and hash it out with like minded people. Here, facts and data are all that matter.
Phil wrote to me that "the [scientific] explanations are not scientific at all. What you have is a storyline. The article I linked to is actual science, actual investigation, actual discovery (excepting the idiotic final quote). Your beliefs about what mutations can accomplish are only beliefs."
No. Standard explanations for evolution are scientific: They are rational, testable, verifiable or falsifiable, and useful.
Phil wrote to Michael f.: "the miracles you accept ignore everything normal, and everything known. "
The point of science is to discover the UNknown; Phil's desire to hobble science to the known is anti-science.
More: "You believe that random, purposeless events resulted in spectacular organization and function. You’ve lost track of what is possible and what is impossible."
You've not shown that this is impossible, and we KNOW it is possible.
More: "I realize this is not going to sink in. Facts and data are not the issue. This is not about evidence. It is about what you prefer and your personal volition."
Ah. Facts don't matter? Is that a fact? Or only your personal preference? If facts don't matter, why have you (and other creationists) been making so many claims about what the facts are? Were you trying to deceive us? Or are you just very, VERY confused?
Sean T's reply is spot on.
sean s.
So phil in your world, the mutations that allow the continued production of lactase into adulthood were miracles? God purposely altered the DNA of herder populations in Europe and Africa to allow them to benefit from drinking milk? Did God do this to everyone in these populations at once or was it two lucky souls who spread his or her genes around to everyone else in their respective populations?
It is nice to know that ID requires miracles in spite of the DI's claim that it is not religious, but scientific. You have confirmed that it is not science and never can be. Do you really want your God to be responsible for every base in every genome? Have you thought what this means for your God's responsibility? I don't think you have, but people who have - good Christians with a bit more brain than you - conclude that it makes your God a monster. Is that really what you want?
I think I now understand phil's obsession with DNA repair proteins - he actually thinks they are his God. I can imagine if this God had business cards they would proudly proclaim "preventing genomic chaos since 4004 BC". I was pretty sure that one major problem shared by creationists was an impoverished imagination and this just shows how limited it is.
Now Mike, I don't like it when others write about what they claim I think; I doubt you like it either. So in all fairness, we should lay off doing that to Phil. In truth, we don't know what he thinks; we aren't mind readers and what he writes is so inconsistent that no one can accurately infer his thoughts.
sean s.
Actually I find it humorous the things that phil attributes to me. How could I take him seriously? How could he take me seriously? Being consigned either implicitly or explicitly to hell is the least of my worries.
On the other hand, me attributing thinking to phil is a bit of a stretch - so I should have phrased that statement differently. On the other other hand, you don't think my conclusion fits the data? Can't you imagine an "invisible hand" a la Adam Smith moving up and down a DNA strand?
When someone tells me I'm going to hell, I usually ask them if they are going there too. They usually reply something like "not if I can help it!" To which I reply that hell's sounds pretty nice then.
I count two "other hands" from you Mike; you should really get a doctor to check that out.
Your conclusions (about Phil) might fit the data, but so do other conclusions, including some in which Phil merely blundered; something we all do. So your conclusions appear to be cherry picked, which is always a bad thing.
sean s.
What I can't cherry pick data now - how else can I show evolution is true? phil will no doubt win hands down if I don't throw out all the data that doesn't fit the hypothesis, just ask phil; I know he will back me up on that.
Sean:
Theists don't or shouldn't have a problem with the practice. After all, that's what theology is.
"When someone tells me I’m going to hell, I usually ask them if they are going there too. They usually reply something like “not if I can help it!” To which I reply that hell’s sounds pretty nice then."
sean samis.
"Go to Heaven for the climate, Hell for the company."
Mark Twain
eric;
Some theists have no problem with some very reprehensible things. That does not justify doing those things too. Can't make the world a better place by copying bad behavior.
dean;
I was thinking of that exact quote.
sean s.
Wow! so now I accused of bad behavior - even reprehensible. Nice! Try not to take yourself so f--king serious. Glad to know you are making the world a better place by being a dick.
How could some be so proud about the severest form of ignorance? Phil, keep up the good work as your persistent presence here is a service.
Well, Michael, now your claims are just as irrational as anything of Phil's. If pointing out how your behavior resembles Phil's makes me a dick, what does it say about you that even a dick like me knows you're in the wrong? At least I'm giving you a heads-up.
sean s.
eric,
“That was easy”. You didn’t even bother googling “bombardier beetle evolution,” before leaping to the conclusion that it must be designed, did you?”
I’ve posted that TO article here before.
-
“Although given the age of this particular trope, my guess is that you didn’t come up with it on your own: you heard it from some creationist or got it from some creationist website and just accepted what they said about it uncritically.”
If you’re referring to the article I linked to above, I get emails from several science sites, and got this one yesterday. You can view it online for yourself here:
http://www.the-scientist.com/TheScientist/emails/daily/2015/05/04a.html
Now I’m sure that Isaak’s bombardier beetle outline makes perfect sense to you. But to me, it is completely stupid and disconnected from science, reality and the supposed mechanisms of evolution. Did you notice that mutations are not mentioned in the article? Can you elaborate on a few of these “steps” and explain them in the context of random DNA replication failures and natural selection?
==
1. Quinones are produced by epidermal cells for tanning the cuticle. This exists commonly in arthropods. [Dettner, 1987]
2. Some of the quinones don't get used up, but sit on the epidermis, making the arthropod distasteful. (Quinones are used as defensive secretions in a variety of modern arthropods, from beetles to millipedes. [Eisner, 1970])
3. Small invaginations develop in the epidermis between sclerites (plates of cuticle). By wiggling, the insect can squeeze more quinones onto its surface when they're needed.
4. The invaginations deepen. Muscles are moved around slightly, allowing them to help expel the quinones from some of them. (Many ants have glands similar to this near the end of their abdomen. [Holldobler & Wilson, 1990, pp. 233-237])
5. A couple invaginations (now reservoirs) become so deep that the others are inconsequential by comparison. Those gradually revert to the original epidermis.
6. In various insects, different defensive chemicals besides quinones appear. (See Eisner, 1970, for a review.) This helps those insects defend against predators which have evolved resistance to quinones. One of the new defensive chemicals is hydroquinone.
7. Cells that secrete the hydroquinones develop in multiple layers over part of the reservoir, allowing more hydroquinones to be produced. Channels between cells allow hydroquinones from all layers to reach the reservior.
8. The channels become a duct, specialized for transporting the chemicals. The secretory cells withdraw from the reservoir surface, ultimately becoming a separate organ.
This stage -- secretory glands connected by ducts to reservoirs -- exists in many beetles. The particular configuration of glands and reservoirs that bombardier beetles have is common to the other beetles in their suborder. [Forsyth, 1970]
9. Muscles adapt which close off the reservior, thus preventing the chemicals from leaking out when they're not needed.
10. Hydrogen peroxide, which is a common by-product of cellular metabolism, becomes mixed with the hydroquinones. The two react slowly, so a mixture of quinones and hydroquinones get used for defense.
11. Cells secreting a small amount of catalases and peroxidases appear along the output passage of the reservoir, outside the valve which closes it off from the outside. These ensure that more quinones appear in the defensive secretions. Catalases exist in almost all cells, and peroxidases are also common in plants, animals, and bacteria, so those chemicals needn't be developed from scratch but merely concentrated in one location.
12. More catalases and peroxidases are produced, so the discharge is warmer and is expelled faster by the oxygen generated by the reaction. The beetle Metrius contractus provides an example of a bombardier beetle which produces a foamy discharge, not jets, from its reaction chambers. The bubbling of the foam produces a fine mist. [Eisner et al., 2000]
13. The walls of that part of the output passage become firmer, allowing them to better withstand the heat and pressure generated by the reaction.
14. Still more catalases and peroxidases are produced, and the walls toughen and shape into a reaction chamber. Gradually they become the mechanism of today's bombardier beetles.
15. The tip of the beetle's abdomen becomes somewhat elongated and more flexible, allowing the beetle to aim its discharge in various directions.
Sean T,
"If facts and data are not the issue, then what the heck are you doing posting to a science blog in the first place?"
My wording was poor. I should have said that facts and data are not actually what you guys are interested in. You can substitute rationales and analogies on cue, which is what I expect Eric to do rather than get grimy trying to coordinate mutations and any of Mark Isaak's idiotic increments. You don't find evolutionists huddled up and grooving about DNA replication screw-ups. They have to be dragged to that party, and they won't stay there very long.
A reprimand from a fellow ingrate is nothing compared to the one you'll receive from the Intelligence who's responsible for your being, Michael. Consider it training for the inevitable, but take comfort; your accuser has some judgement coming his way too as there is a Standard for behavior that supersedes even his own.
Phil,
People who understand science see "Isaak’s bombardier beetle outline" as just part of the normal scientific process. Given some phenomena (such as a bombardier beetle) and questions about it (how did it come to be?) scientists
(1.) gather as much information as they can about the phenomenon and related things (other beetles and insects)
(2.) develop a proposed explanation based on known facts.
(3.) step-by-step verify or falsify the proposed explanation.
(4.) flesh-out the details of the process as more information is discovered.
(5.) Repeat.
"Isaak’s bombardier beetle outline" appears to satisfy step (2.)
Mutations would not be mentioned in the article you read because those would be found in steps (3.) or (4.) If all this appears stupid to you then that demonstrates that you really don't understand science.
Science is like cooking, it's a process that usually cannot be judged until it's pretty far along. If you don't know how to cook, your place is not in the kitchen.
sean s.
Of course I can't, I'm not a geneticist studying insects. But each step has articles cited and you can follow those links if you are truly interested in learning what scientists know about beetle evolution. I also can't calculate the electron structure of a high-Z atoms ab initio from quantum mechanics (AFAIK, nobody can), but that doesn't mean angels are needed to push the electrons around and keep them in their place. Human lack of complete detail of a process is not evidence of design; this is just the same old false dichotomy you're using. My link showed there is a plausible set of evolutionary steps for its development, with most if not all of the major steps observed independently. That is certainly not everything. But its far more evidence in favor of an evolutionary origin than the evidence you have for design of the beetle, because you have bubkis. Nothing. Nada. Evolution is the best supported theory because you have no empirical support at all for your hypothesis. And evolution will contnue to be the best theory for the bombardier beetle's traits until such time as you come up with positive evidence of a designer intereving in nature. Go out, dig up a billion year old genetics lab, and you'll have something. Find a lunar monument and you'll have something. Observe the spontaneous creation of a creature and you'll have something. Probability calculations on their own? Not something.
The main difference here is that scientists try and 'get grimy' as much as they can, and are mostly resource limited in how grimy they can get (i.e. how many and how detailed experiments they can do to learn more). In contrast, design proponents avoid griminess like the plague. What experiments has your community done on your designer hypothesis, Phil? Any? Any in the offing? Any test for designer you've come up with yet?
If bombardier beetle genetics is not yet grimy enough, its because we haven't gotten there yet. If Designer characteristics, mechanisms of design, and timing is not yet grimy enough, its because you all seem to not want to even look at it.
Aware, In spite of sean's humorless, puritanical tone-inspired carping, I am positive I understand much more about the thoughts going on in phil's brain than you do about any god. Heaven forbid someone might be offended though and I hope you take none.
As for the beetle genes - this is relatively simple. As of 2013, only two beetle genomes had been sequenced. When more have been completed, it will be possible to search those elements of the genome which differ between bombardier beetles and their near relatives. Localization of those genes involved will soon follow. Do you have some money to pony up, phil, I am sure if you offer someone will take up the challenge. What do you want to bet that they will find the beetle has altered existing ancestral metabolic pathways through random mutation and natural selection?
One of the great success stories has been the use of the dog genome in finding human genes involved in genetic disorders. I brought this up before, but if you refuse to believe in common ancestry - then you won't know what to do with it. You would rather avoid cognitive dissonance at all costs - how else could you be immune to so much evidence?
sean samis,
“(2.) develop a proposed explanation based on known facts….“Isaak’s bombardier beetle outline” appears to satisfy step (2.)”
How does it do that? What known facts are you referring to?
Can you at least speculate about how random mutations and natural selection produced the valve mentioned in the Science Daily article…just that one thing?
I don’t expect anyone to dig in with this, and all the things that are either irrelevant, presumptuous or just flat stupid about Isaak’s article. I’d like to get this shameless clown in front of a high school science class and rip him a new invagination with his own theory. I really can’t fault you guys for balking.
===
eric,
“Of course I can’t, I’m not a geneticist studying insects.”
I don’t think a specialist is going to be able to help out in reconciling how random DNA replication failures result in precise, coordinated systems. But you do claim to understand how evolution works. I don’t really see how you can if you can’t reasonably apply the baseline mechanisms for it.
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“But each step has articles cited and you can follow those links if you are truly interested in learning what scientists know about beetle evolution.”
Did you do this? Do they go into all kinds of detail about how new genes, and new genetic controls and regulatory mechanisms for these genes were produced by random mutations?
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“scientists try and ‘get grimy’ as much as they can, and are mostly resource limited in how grimy they can get”
Nonsense. The actual scientists deal with what is there and how it works. Some will include an obligatory reference to evolution. But nobody undertakes the problem of numerous systems and subsystems developing in parallel accidentally. They can’t. It is not conceivable.
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Michael Fugate,
“how else could you be immune to so much evidence?”
Common genes is not evidence. It is data that you interpret as evidence. Dogs and humans do not have identical genomes. If shared genes suggest common ancestry, then unshared genes suggest the opposite.
Just a FYI to #30: The velocity of the earth can have a lot values and still orbit the sun. Your formula was to calculate a circular orbit, but at any given initial position relative to the sun, any velocity from 0 to that positions escape velocity will result in a closed elliptical orbit. Orbits that cross the suns diameter will cause a collision, but otherwise, absent any friction, there are no decaying orbits to cause a crash into the sun. If you consider only life supporting orbits, the range is much more limited, but still quite large, so the example is not really a suitable comparison.
Phil asked me, "What known facts are you referring to?"
Isaaks' list specifically mentions some, and his audience (others studying the topic) will bring their own knowledge too. Those of us who are not in this field would need to do our homework. That includes you and I.
Phil asked me, "Can you at least speculate about how random mutations and natural selection produced the valve mentioned in the Science Daily article…just that one thing?"
I can speculate all day on this but having no expertise the results would have little value. We need to wait for the experts to do their job.
Phil complained, "I don’t expect anyone to dig in with this, .... I really can’t fault you guys for balking."
Given your lack of expertise, we can fault you for not balking.
Phil commented to eric that "...nobody undertakes the problem of numerous systems and subsystems developing in parallel accidentally. They can’t. It is not conceivable."
Nobody? You keep track of what every scientist does? You know what they are all doing? Ain't buyin' that ...
The genetic studies you long for are an immense project. They will not be done in your lifetime or mine; history does not revolve around us.
sean s.
phil, have you ever considered getting off your butt and studying nature instead of just reading about it on creationist websites?
If you did, you might find that thousands and thousands of beetles (which as JBS Haldane noted you hypothetical creator has an inordinate fondness) produce chemical defenses from pygidial glands. There is this cool one near my house in the genus Eleodes that is big, black, and flightless that stands on its head when disturbs and releases a foul odor. If you have ever handled beetles you would know this. Other things are that beetles have hard shells that are relatively inert (great for storage toxins) and that sphincters are a dime a dozen in the animal world (a ring of circular muscles hardly rocket science).
Even the bombardier model has evolved in two separate subfamilies of carabid beetles. If one peruses the TOL website, one finds that we currently understand almost nothing about the relationships among beetles. As sean points out this will take years and years of dedicated research to figure out - something in which neither you nor any other creationist will take part; the only thing you can cling to is the "god of the gaps" theology that keeps your god alive in what we don't know. If there isn't a mystery to solve, then for you there is no god. We know there are more mysteries than we can ever solve, so your theology will always be safe. The rest of us with even the tiniest bit of curiosity will be trying to actually find out how something works and how it evolved.
eric,
“Reread step #s 4-8 in your quote of my link. That meets the requirements of what you just asked.”
No, those don’t really go into the depth below the jargon zone. It’s easy enough to say that “the invaginations deepen”, but things like that don’t just happen. You understand how evolution works, so you know that some kind of alterations have to occur.
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“it is a series of sequential, positive adaptational mutations that can lead to the valve structure you want us to explain.”
Exactly. But I’m not expecting you to actually do that.
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“We observe whether organisms with partial (i.e., ‘intemediate’) structures exist because if they do, that shows that the intermediate adaptations were either positive, neutral, or at least not negative enough to kill off the line of descent.”
Well, what would you point to as partial structures?
===
sean samis,
“Those of us who are not in this field would need to do our homework. That includes you and I.”
Well yeah, but I don’t think the experts can really help out with on how things developed. But I’m entirely open to any papers you want to link to.
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“I can speculate all day on this but having no expertise the results would have little value. We need to wait for the experts to do their job.”
Oh, don’t short yourself here. The mechanisms of evolution are not that hard to understand. There are only two. The difficulty is in applying those. We have a few days before this thread dies, so I’ll try to get us started on the valve deal.
===
Michael Fugate,
“phil, have you ever considered getting off your butt and studying nature instead of just reading about it on creationist websites?”
Yes I have. Only rarely will I ever refer to anything but secular sources.
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“If you did, you might find that thousands and thousands of beetles…”
Indeed. There are lots of remarkable variations, but that just taxes the idea that they are the result of random DNA replication failures. There can’t be any modified descendants unless something went wrong. I’m glad my worldview does not depend on things like that.
Phil wrote that, "The mechanisms of evolution are not that hard to understand."
You are asking us to speculate on sequences of genetic mutations; those can be quite complex.
"We have a few days before this thread dies, so I’ll try to get us started on the valve deal."
Standing by.
sean s.
Sigh. You know the more lengthy explanation. I know you know this. Why do you feign ignorance? A beetle has many beetle kids. Their genomes vary due to both sexual mixing and mutation. Some of them have deeper invaginations than others; some of them have shallower invaginations than others. Differential survival rates means the next beetle generation will have deeper or shallower invaginations depending on which trait gave an advantage; in cases where it's a close call, the distribution may widen in the next generation rather than narrowing/going in a specific direction, or something like genetic drift may come into play.
As for which specific mutations occurred, I don't know. I've told you I don't know already. That's what geneticists seek to learn. And regardless of whether some scientist I'm unaware of already knows the answer to that question, or whether no scientist currently knows the answer to that question, ID has no evidence to support it so is a worse explanation.
The carabid beetle family contains all sorts of variations on the 'defensive squirting gland' structure.
Not bombardier beetles, but interesting...
http://arstechnica.com/science/2015/05/a-missing-link-between-prokayote…
phil, if you really are interested in learning something, then I suggest the following:
Given this being about beetles, let's start there.
How about getting some flour beetles - http://insected.arizona.edu/mealinfo.htm
these are easy to grow colonies on oatmeal or bran.
Measure adult or larval characters to find variation - you will find it.
Do a selection experiment by starting new colonies with say bigger or smaller beetles or faster or slower development times - something that is variable.
The other thing is put out some pitfall traps in your yard or some other open space. Measure variation in a beetle species in nature. Find out what it is and try to start a colony.
Actually studying nature will so much more profitable than reading silly creationist books and articles.
sean samis,
“You are asking us to speculate on sequences of genetic mutations; those can be quite complex.”
Yeah, I know. And those sequences would be very narrow and specific, and therefore very unlikely. That’s why dreamy scenarios like Isaak’s will never grind into the details.
That said, about that valve. Were I you, I’d start with a germ cell mutation involving a gene duplication, or perhaps multiple copies. That would put you ahead of the game on the proteins that can manage the chemicals involved, and probably strength characteristics as well. And if I understand how this valve works, it would not require neurological input. It resembles a check valve, automatically sealing on back pressure.
But it can’t be as big as a dinner plate, and it has to wind up correctly positioned relative to the reservoir outlet in the chamber. Things like this will have to be addressed by further mutations.
Any objections so far?
Regarding: “Yeah, I know. And those sequences would be very narrow and specific, and therefore very unlikely. That’s why dreamy scenarios like Isaak’s will never grind into the details.”
Here you claim to know things you cannot know yet, which means your “speculations” begin with the unwarranted assumption that there’s nothing to find. You are setting this up for failure.
Regarding: “Any objections so far?”
It’s premature to make any comment. Your “speculations” have no specific content. They are too general, too ambiguous. You have a long way to go, and many specifics to add before there’s anything for others to comment on.
Except of course you started with an opening claim that poisons your effort.
sean s.
sean samis,
"You are setting this up for failure."
Well, there are lots of ways for it to fail, but you can point out if I’m being overly pessimistic.
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“You have a long way to go, and many specifics to add”
It isn’t me. This about how evolution works.
I’m figuring that having one or more duplicated genes, the next thing that needs to happen is for this altered genome to become fixed in a local population. This isn’t guaranteed, and if it happens it will take some time, but there is definitely an advantage. It means that every new germ cell produced could wind up with replication errors that could further change the duplicate gene so that it could contribute to the formation of our valve.
Anything disagreeable so far?
With a duplicated gene fixed in the population, theoretically any germ cell involved in reproduction it is capable of catching a replication error that can help the duplicate evolve to assume some new role. Whatever the change, if it confers some kind of benefit, then this mutation can possibly also become fixed. And again, should this happen, it allows every new germ cell to be player in the mutations game. It seems to me that fixation has a throttling effect.
If cells 1905 and 77319 both have mutations in their inherited duplicate gene, the twain might never meet, or the alterations could be incompatible. So I would think that for the most advantageous sequence to occur, fixation is critical because it removes particular lineages from the process.
I’m not sure how many changes would be required to actually change the duplicate gene into one capable of defining our valve. But more importantly, at some point, other systems undergoing alterations would have to come into play.
Phil,
Your requirement that mutations would have to be “very narrow and specific” is a set-up for failure; it’s not even something evolution would require.
Regarding “Anything disagreeable so far?”
As before, You have a long way to go, and many specifics to add. And even then, everything you speculate could be wrong because there are many different pathways to the result.
sean s.
No analysis of potential evolutionary pathways provides any evidence or argument for design. Its just the old, very very tiresome now, false dichotomy. So, your efforts to me seem dead in the water right from the start.
If you want to come here and argue for design, then how about giving us the ID hypothesis for the who, what, where, when and how of design? How about a proposed mechanism? How about predicting some physical artifact (in the broad sense) of the design event that we can find? A Precambrian rabbit? Billion year old biology lab? Moon monolith? Anything?
I would go with something much simpler - like how ID can tell that the 2 point mutations (a C > T and a G > A) associated with lactase persistence in humans were "designer-directed" and not random changes?
sean samis,
“Your requirement that mutations would have to be “very narrow and specific” is a set-up for failure; it’s not even something evolution would require.”
I don’t see what you could possibly mean here. For a series of mutations to alter a duplicate gene, they will have to occur in that same gene until it is able to do something else. Read the section on Neofunctionalization here http://en.wikipedia.org/wiki/Gene_duplication
I’ve actually spotted you a couple of light years worth of accidental productions in this. If it doesn’t look like a realistic process, it isn’t my fault.
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“You have a long way to go”
No, it is the process you accept that has a long way to go.
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“even then, everything you speculate could be wrong because there are many different pathways to the result.”
That’s horse shit. It is also a false set-up for success.
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eric,
“No analysis of potential evolutionary pathways provides any evidence or argument for design.”
I haven’t mentioned design, and usually don’t because I’m a creationist. ID is too tepid for my tastes.
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“Its just the old, very very tiresome now, false dichotomy”
No, you’re just reapplying the best-in-field fallacy. In your mind, the top loser is a winner.
You could, of course, do what I’m doing, and try to actually apply your theory. But you will not, I believe, for a couple of reasons. The first is that you’ve convinced yourself with debate tactics rather than science. The second, I suspect, is that you’ve thought about this just enough to recognize some of the problems and don’t want to go near it. None of you guys seem to be interested in realistically appraising what you believe.
The biggest problem in constructing a developmental framework for how something would evolve is trying to avoid thinking in human terms.
If engineers are designing a special application valve, several disciplines would be involved. In my business, the process specialist would provide normal operating pressure and temperature, and the chemicals the valve would be exposed to. Mechanical engineers and material specialists would use this to select the type of valve design needed. (In some situations, what we call wetted parts might require a particular alloy, and this might be clad to something else for either strength or economic reasons.)
The valve the bombardier beetle uses in its defense mechanism is subject to all the same considerations, but they all have to be addressed by a trial and error process. The number of trials would necessarily be immense simply because there are so many ways to fail. But while the design parameters are similar for engineered valves and the beetle’s, the former is deliberately produced in response to a need. The latter is not. If it acquires a functional configuration, it is only happenstance. Mark Isaak betrays this reality in his outline in statements like these:
“Quinones are produced by epidermal cells for tanning the cuticle.”
“The channels become a duct, specialized for transporting the chemicals.”
This is forgivable on a literary basis as there is no practical way to express functionality without doing it in terms of necessity. But nonetheless, specialties produced by a random, unguided process can never really be ‘for’ anything.
Sigh. Okay: no analysis of potential evolutionary pathways provides any evidence or argument for creationism.
Its not a fallacy, its the only way science can work. If we want to perform experiments, we have to decide what factors to test and what not to test. We have to decide what experiments are likely to succeed and which aren't. These things require judgments based on theories and hypotheses, so yes in fact we must pick one or more out of what we have to proceed with doing science. We cannot wait, using no hypothesis or theory at all, until some theory meets Phil's standard of evidence (whatever that is - you haven't specified) - that would be ludicrous.
Do you know what it looks like when people wait around until some theory meets some abstract level of evidence rather than being best in show? It looks like the creationism research program - a decades being on the table, but no experiments. No progress. Not even an attempt at discovery or innovation.
Its been done, thousands of time. A lot of modern paleontology is based on it. Paraphrasing your inner fish: if evolution is right, there will be an intermediate between fish and limbed species. It will have existed approximately 375 million years ago, so we should look for it in rock dated about that old. (Note that creationism would predict none of these things; not the fossil, not the age, not the type of rock, nothing. It would be useless for planning and evaluating this proposal's likelihood of success). Hey look, we found exactly what evolution predicted would be there!
“Do you know what it looks like when people wait around until some theory meets some abstract level of evidence rather than being best in show? It looks like the creationism research program – a decades being on the table, but no experiments. No progress. Not even an attempt at discovery or innovation.”
You are apparently unaware of history when it comes to science and scientists.
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“Its been done, thousands of time.”
No, it has not. If it had, it would be easy for you to do it yourself. But, as always, you are welcome to produce even one paper or study which actually acknowledges and deals with the complications that would be involved in producing new genes and new features with DNA replication errors. They are not there. And you know they are not there.
We are about a millimeter into an obviously very complex developmental scenario, and the only thing that you can offer is that ID breaks the petty rules of materialism. You haven’t proposed anything that will tilt the odds in favor of your own theory. As I noted earlier, this is not about science, or knowledge, or data, or evidence. And it sure as hell isn’t about statistical realities, plausibility or common sense.
Tiktaalik was a fish, not a track star. You need to prove out your mechanism before you accept things like that.
You asked for an application of the theory. I gave you one: the theory of evolution was applied by Neil Shubin to help him figure out what sort of undiscovered fossil he might be able to find. It was used by him to help him figure out what age/strata of rock he should look in. That's an application. Its an application creationism would've been utterly useless for. The discovery of DNA occurred approximately 100 years after Darwin; people were applying the theory long before Crick and Watson. Now for sure there are lots of uses for evolution in genetics, but the theory was and continues to be very applicable outside of that field too.
I almost hesitate to ask, but with your 'do it yourself' line, are you really insisting that I personally hypothesize a new organism and go out and dig it up before you will accept that the theory has applications? Because that's an absurd requirement. If OTOH you're asking me to cite another scientist's application, I did that in the last message; you completely ignored it.
eric,
“You asked for an application of the theory. I gave you one: the theory of evolution was applied by Neil Shubin to help him figure out what sort of undiscovered fossil he might be able to find. It was used by him to help him figure out what age/strata of rock he should look in.”
No, what I’m asking for is a fair evaluation of the mechanism that is supposed to accomplish all the changes that supposedly occur between the fossils. If the mutations/selection idea, and it is just an idea, doesn’t shake out, the fossils are meaningless.
By the way, Shubin will have to do some adjustments on his iconic discovery. It is believed that Polish tetrapods were already on their feet at least 15 million years before his fish was racing towards terrestrial limbs.
http://news.nationalgeographic.com/news/2010/01/100106-tetrapod-tracks-…
Phil wrote that he’s asking for “a fair evaluation of the mechanism that is supposed to accomplish all the changes that supposedly occur between the fossils. If the mutations/selection idea, and it is just an idea, doesn’t shake out, the fossils are meaningless..”
At first glance, that seems a fair request, but it’s not all Phil’s asking for. He wants this fair evaluation, and he wants it NOW. He seems to object to waiting for it; he seems to want a conclusion NOW.
That is neither fair nor reasonable.
sean s.
Mutation/selection isn't an idea, it's been observed in many cases. Lenski's experiments are a good example. I suspect you are asking that we not extrapolate from observed cases to unobserved ones, but rather observe mutation and selection in the case of each and every proposed speciation event before we claim it occurred via evolution. This is unreasonable. If we observe it occurring in some cases, then (a) it can occur in other cases, and (b) it becomes the best explanation for what occurred in other cases until such time as you present an alternative mechanism that better describes, predicts, and explains the data. Put up your alternative mechanism; otherwise this one is the best.
Hey Jason, do we get an epilogue? How did you resolve your oven problems?
"Lenski’s experiments are a good example"
But not good enough. Ants build anthills, but they did not build the Himalayas.
So you ARE saying we can't extrapolate from one case to others but must show you evidence of every single evolutionary speciation event?
No, I’m saying that that is not a valid extrapolation. The Lenski icon adapted to use an alternate food source that it already had the genes for in 31,000 generations. Try and apply that, to this:
“Over the next 15 million years ancient cetaceans evolved into diverse forms, exploiting the rich resources in the sea.”
http://www.teara.govt.nz/en/dolphins/page-6
You can’t appeal to zillions of years, because there is an accepted time frame. And you can’t ignore things like longer times to sexual maturity, longer gestation times, smaller populations and fewer offspring.
You also cannot reasonably extrapolate one very modest adaptation into countless features and support systems all developing simultaneously, having started from scratch. Lenski’s heroes needed one lousy enzyme. The whales would need countless new genes, specialized proteins, and phenomenal genetic control systems. It doesn’t work. It isn’t realistic.
Prove it! I bet you can't.