Michael Behe is best known for coining the phrase Irreducible Complexity, but I think his likening of biological systems to Rube Goldberg machines is a better way to frame the problem of evolving the black boxes and the other extravagances of the biological world.
But even before going to the question of ID in biology, I’d like to explore philosophical and complexity questions of man-made Rube Goldberg machines. I will, however, occasionally attempt to show the relevance of the questions I raised regarding man-made Rube Golberg machines to God-made Rube Goldberg machines in biology.
Analysis of man-made Rube Goldberg machines raises philosophical questions as to what may or may not constitute good or bad design and also how we make statements about the complexity of man-made systems. Consider this Rube Goldberg machine, one of my favourites:
Is the above Rube Goldberg machine a good or bad man-made design? How do we judge what is good? Does our philosophical valuation of the goodness or badness of a Rube Goldberg machine have much to say about the exceptional physical properties of the system relative to a random pile of parts?
Does it make sense to value the goodness or badness of the Rube Goldberg machine’s structure based on the “needs” and survivability of the Rube Goldberg machine? Does the question even make sense?
If living systems are God-made Rube Goldberg machines, then it would seem to be an inappropriate argument against the design of the system to say “its poor design for survivability, its fragility and almost self-destructive properties imply there is no designer of the system.”
The believability of biological design is subjective to some extent in as much as some would insist that in order to believe design, they must see the designer in action. I respect that, but for some of us, a system that is far from physical expectation, design is quite believable.
But since we cannot agree on the question of ID in biology, can we find any agreement about the level of specificity and complexity in man-made Rube Goldberg machines? I would hope so.
What can be said in certain circumstances, in terms of physics and mathematics, as far as man-made systems, is that certain systems are far from what would be expected of ordinary non-specific processes like random placement of parts. That is, the placement of parts to effect a given activity or structure is highly specific in such circumstances — it evidences high specificity.
My two favourite illustrations of high specificity situations are:
1. a domino standing on its edge on a table.
2. cards connected together to form a house of cards. The orientation and positioning of the cards is highly specific.
We have high specificity in certain engineering realms where the required tolerances of the parts is extremely narrow. In biology, there are high specificity parts (i.e. you can’t use a hemaglobin protein when an insulin protein is required to effect a chemical transaction). I think specificity of individual interacting parts can be occasionally estimated, but one has to be blessed enough to be dealing with a system that is tractable.
In addition to specificity of parts we have the issue of the complexity of the system made of such high specificity parts. I don’t think there is any general procedure, and in many cases it may not be possible to make a credible estimate of complexity.
A very superficial first-pass estimate of complexity would be simply tallying the number of parts that have the possibility of being or not being in the system. This is akin to the way the complexity of some software systems is estimated by counting the number of conditional decisions (if statements, while statements, for statements, case statemets, etc.)
In light of these considerations we might possibly then make statements about our estimate for how exceptional a system is in purely mathematical and physical and/or chemical terms — that is providing the system is tractable.
I must add, if one is able to make credible estimates of specificity and complexity, why would one need to do CSI calculations at all? CSI is doesn’t deal with the most important issues anyway! CSI just makes an incomprehensible mess of trying to analyze the system. CSI is superfluous, unnecessary, and confusing. This confusion has led some to relate the CSI of a cake to the CSI of a recipe like Joe G over at “Intelligent Reasoning”.
Finally, I’m not asserting there are necessarily right or wrong answers to the questions I raised. The questions I raise are intended to highlight something of the subjectivity of how we value good or bad in design as well as how we estimate specificity and complexity.
If people come to the table with differing measures of what constitutes good, bad, specified, complex and improbable, they will not agree about man-made designs, much less about God-made designs.
I’ve agreed with many of the TSZ regulars about dumping the idea of CSI. My position has ruffled many of my ID associates since I so enthusiastically agreed with Lizzie, Patrick (Mathgrrl), and probably others here. My negative view of CSI (among my other heresies) probably contributed to my expulsion from Arrington’s echo chamber.
On the other hand, with purely man-made designs, particularly Rube Goldberg machines, I think there is a legitimate place for questions about the specificity of system parts and the overall complexity of engineered systems. Whether such metrics are applicable to God-made designs in biology is a separate question.
What you see as a kludge is to anyone who thinks about it, clever design. For stability in flight birds require a low centre of gravity. Placing these muscles (and bones strong enough to anchor them) above the wings will raise the bird’s centre of gravity and thus affect their stability.
As far as I know birds are unique in having this muscular arrangement. Humans have deltoid muscles which raise the arms in the manner you recomment for birds.
This is a fairly major anatomical change to have taken place.
I suspect that if evolution hadn’t had to kludge the birds’ musculature, you would be pontificating that a LOWER center of gravity would make flight impossible or difficult — given (of course) the very different shape birds would have. Hopefully, you understand that all the parts have to work together, and moving the muscles around would entail moving bones and other organs.
Your argument sounds much like “there’s no way to put a powerful engine in a car, because the transmission would strip out the first time you accelerated.”
Are you being serious? Try telling that to any brain surgeon, or Jimi Hendrix, or Da Vinci, or an olympic archer, or my wife knitting a cardigan, or a person who fixes mobile (cell) phones, or a hairdresser, or a chef, or a toymaker, or a card magician, or a pickpocket, and so on and so on.
Okay, you may need the services of a medium for the second and third examples 🙂
Handwaving seems to confer some advantage.
CharlieM,
All your examples are of course examples of grasping objects. Hands are very good for that, not so good for flying, running, digging, climbing up tree trunks, or any of the other various tasks that other species’ forelimbs are good for. Of course you will respond that we can make tools for all those purposes, but that just evades the point. Is your self-esteem so weak that you have to buttress it by standing atop a pyramid of all other tetrapods?
Look Flint, you have no idea what evolution can do (beyond changing allele frequency) and you sure as hell cannot test your claim that evolution had to kludge the birds’ musculature. So perhaps you should stop with your proclamations and post some science
As former tree climber I can say that hands are very good for allowing humans to ascend tree trunks. As for digging they are good for that too.
But alas we were not designed to fly.
Don’t be silly.
http://theskepticalzone.com/wp/author/flint/
Yet we fly.
Sal said:
Well, in the profession of engineering we judge the goodness of the design of a system by how well the resulting system meets its requirements. But I have noticed over the years that when you IDists talk about “design” you rarely talk about requirements. Different people will allocate different requirements to a system, and the requirements may change over time, but where’s the philosophical problem?
Sal said:
Again, this comes down to requirements. Ultimately the machine does not have needs; it satisfies (or doesn’t satisfy) the needs of it’s owners/users. Survivability may or may not be of high concern.
It is your belief that genetics determines the organism, it is not mine. My belief is that genes make the proteins required to build up the organism. The regulation involves the activity of genes but this is instigated at the level of the organism and the cell.
No they don’t. Birds use genes that make the substances required for bird wings. Some genes will be the same as dinosaur genes, some will differ. I appreciate that because they are closely related their genetic makeup will be very similar, but this just tells me that birds and therapods are made from virtually the same materials.
Rotors are not manufactured from separate pieces for ease of manufacture, it would be easier if they were fashioned from one single piece. No, they are made this way to take account of strength to weight ratio, erosion forces, aerodynamic forces, operating temperature and weathering.
The wing of a bird needs to deal with the same forces. The fairly rigid structure of the “hand” is achieved because the bones are fused, the primary flight feathers are fused to the bone and the barbs are locked together by means of the barbules. The rigidity of the leading edge is achieved by the extension of the patagial ligaments. Feathers suffer from erosion and there is put in place a means of replacing them without severely affecting the viability of the individual. This is not, by any means, an exhaustive list of needs.
All this and the wing also need to be folded away so that it doesn’t hamper activities such as foraging, perching, walking, mating or nest building. There are a multitude of features that have to interact and combine in order for a flying bird to function and survive.
Quit with the simplistic misrepresentation.
Who cares? I wrote “genetic material,” which isn’t limited to :”genes.”
More semantic babble. That’s what I wrote, just not in your literalistic pedantic fashion that adds nothing but your sanctimony.
Mostly the same genes, but with mutations, many selected. Almost none will be the same as (non-avian) dinosaur genes.
Yes, deal with that fact for once, rather than ignoring the issues.
Yes, so would bone, the difference being that there is no inherent limitation requiring wings to be made of many bones.
Anyway, you’re really appallingly wrong about the pieces being made for ease of manufacture. Of course they are, once it’s been decided that they’ll be made from pieces. You’re equivocating with your “objection,” the pieces are indeed made to facilitate manufacture, whether or not it might be “simpler” (questionable, really, when everything’s factored in–but you don’t care) to make them in one piece.
They’re complex, ignoramus, that’s why they’re made from pieces. Your twaddle is meaningless.
So what does this have to do with starting from basically the same bones (aside from the digit numbering question) as non-avian dinosaur “hands”?
Nothing, you’re merely equating the two very different matters because you’re attempting to ward off the obvious conclusions.
Yes, duh. Why fuse together a lot of ancestral bones when it would be simpler and less prone to mistakes to begin with one bone? Your “analogy” with helicopter rotors is just pathetic, a disanalogy.
Yes, but it is entirely beside the actual point, which you never address in your rambling, unthinking manner.
Did you just find that out?
Glen Davidson
A diagram of one the God-made molecular Rube Goldberg machines from this paper:
http://www.nature.com/nrm/journal/v9/n7/full/nrm2439.html
This machine is one of the many that read the buzzillion Random Access Memory devices called histones. Histones are part of the memory schemes that are part of the computers we call cells. Below is just one of the possible reading processes of the histones (the bead marked H2A, H2B, H3, H4 and a tube H1). The wires connecting the beads are DNA which are Read Only Memory devices.
Reading complexes like this one can read both the RAM from the histones and the ROM from the DNA. To quote Clint Eastwood from the movie Firefox, “What a machine!”. 🙂
This is a schematic of the God-made Rube Goldberg machine we call a metabolism. It is a simplified schematic of course:
Hi Glen. You say I am not:
That bizarre and unpromising start is your version of events, not mine. So from your unpromising start remarkable results have been achieved.
I believe that the bird’s wing, and also the forelimb of all non-human vertebrates are the equivalent of the human arm which was interrupted at a lower stage of development. Any limb that is used for locomotion is not then free to be used for more creative tasks. We humans by raising ourselves to the upright position have freed our forelimbs and thus they have contributed to the means by which human art and technology has advanced. We as individuals have become creators of novelty. By use of our hands we can bring to fruition objects which were conceived in our minds. At the present time we are becoming expert in manipulating inanimate matter but our minds are still at an early stage of evolution.
Thanks for giving the full reference. But that’s a paper about transcription factors, not about histones as “random access memory” or DNA as “wires” or “ROM”.
I take it, Sal, that you have abandoned all pretense to rational discourse and have reverted to What Good Is Half An Eye incredulity.
It’s back to 1803 Paleyism for you!
ROFL and there we have it – the argument from “diagram with lots of arrows and abbreviations”. PRAISE THE LAWD.
From the prestigious scientific journal nature a depiction of the Writers, Erasers, and Readers of the histone Random Access Memory devices.
John Harshman is pretty upset the the journal doesn’t use scare quotes to say “Writers”, “Erasers”, “Readers” apparently because he doesn’t like the idea people are perceiving these nano-machines in this way since they might inspire thoughts that these are kind of sophisticated nano-machines more complex and more specified than Payley’s watch:
Here is the power point from the website the diagram is from:
http://www.nature.com/nrd/journal/v13/n9/fig_tab/nrd4360_F1.html
This diagram is a simplification, the read and write machinery is very complex:
Amazing stuff. Preach it brother.
And to think the same “prestigious” journal publishes dusins of papers every year demonstrating it all evolved.
And you never once provided a real design explanation for fusing a bird wing from many bones. I should point out that even worse is our coccyx, which has a small function in anchoring muscle as IDists/creationists like to point out, but which is an unnecessarily fragile organ made of many tail vertebrae–hardly the way to make a good muscle anchor.
Well, of course you have no explanation, but certainly a lot of opinion that you like to trot out as if it matters.
Yes, no one ever disputed that. You can’t explain the development process according to design principles, but can say a whole lot of things that no doubt prop up your beliefs in some non-rational fashion.
Not necessarily. Ape hands work for locomotion and are fairly capable of “more creative tasks,” and presumably could be better at the latter while still working for locomotion, although dual use always requires some compromise. For that matter, our hands continue to be used for locomotion in a number of situations, although unquestionably that role has diminished with bipedality.
There just is evolution in biology. We’re not at an “early stage of evolution,” we’re just in the process.
Glen Davidson
How it was designed (not all of the details, but at least some) and the evidence we have for how it was designed.
Present these, Sal.
If you don’t, you’ve just got a homily.
Glen Davidson
stcordova,
When you don’t use scare quotes, there’s always a chance that some creationist will fail to understand that you’re being metaphorical. That’s the problem.
It’s beginning to look a lot like spamming.
Hi Glen. You keep going on about my lack of explanation for the fusion of bird’s wing bones. But if you have understood what I have been saying you would see that this is exactly what I would expect for a limb that is based on the general pentadactyl limb. It has been modified and somewhat simplified in its bone structure to serve the narrow purposes that birds put it to. Birds have evolved from terrestrial animals with a more general form of the limb.
Yes, but you have provided no reason for why bird wings should be based on the pentadactyl limb. Unthinking evolution has to (contingently), design does not.
Yes, and the limitations of the evolutionary processes provide an explanation for it.
You don’t.
Glen Davidson
CharlieM,
So we all agree on what happened. You just feel the need for a mechanism to explain what happened that’s mysterious, mystical, downright incomprehensible to anyone other than you, and for which there is no evidence. Is that a reasonable summary?
Here is a God-made set of interchromosomal Rube Goldberg machines that uses a Rube Goldberg machine (the sender) in one chromosome to express and send junk DNA to another chromosome to trigger its Rube Goldberg machine (the receiver).
Below is a depiction of the receiver Rube Goldberg machine’s operation.
It is an example of a trans-acting non-coding RNA that is involved in gene regulation. You will see now how junk DNA is recruited in the regulatory schema whereby the junk RNA from junk DNA is incorporated into a polycomb protein complex that interacts the histone RAM and DNA ROM:
The junk DNA in question:
https://en.wikipedia.org/wiki/HOTAIR
From
http://www.cell.com/trends/biochemical-sciences/abstract/S0968-0004%2810%2900030-7?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0968000410000307%3Fshowall%3Dtrue
Odd.
the linked article calls it a gene, not junk.
Well well, look at this biology textbook, it refers to biological systems as Rube Goldberg machines! Bwahaha!
ttps://books.google.com/books?id=arRGYE0GxRQC&pg=PA7&lpg=PA7&dq=rube+goldberg+biology&source=bl&ots=jpz8lQ_Mnd&sig=v-BmJULCW7xqS-hvyrEheSPTh3o&hl=en&sa=X&ved=0ahUKEwjGtdDi8JDLAhVG2T4KHdtqCn8Q6AEITDAL#v=onepage&q=rube goldberg biology&f=false
stcordova,
First of all, the link doesn’t work. But second, your uncontained glee at being able to find a particular pair of words somewhere in some book is inexplicable to me.
What do you get when you combine Paley’s Watch with a Rube Goldberg machine?
Bwahaha! From the prestigious scientific journal Nature:
Because the foolishness of God is wiser than the wisdom of men.
As I observed earlier, evolutionary biologists tend to look at Rube Goldberg as silliness not evidence of cleverness. The simpler clock is viewed by the author as “intelligent”. He’s got it backward. Rube Goldberg clocks evidence more genius, not less.
The human biological clock is Rube Goldbergesque!
To quote the late John Davison, “I love it so!”
Do you like have a scientific argument, Sal?
Or is intoning “Rube Goldberg” just comforting to you?
Glen Davidson
Yeah.
I just thought I provided evidence that Paley’s watch was discovered in humans and that it was also a Rube Goldberg machine. I mean, it’s right there in the pages of the peer-reviewed prestigious scientific journal Nature.
It even uses the phrase:
Science is wonderful ain’t it? It helps us see all the Rube Goldergesque designs God has made in biology.
Makes me want to study science even more.
Ah, it’s about word use and a bad analogy.
Impressive.
Glen Davidson
OK, you believe in God. Got it.
Oh my Flying Spaghetti Monster (OM-FSM)!
I noted this phrase by Aziz Sancar:
Turns out Aziz won the Nobel Prize. He’s a real scientist to boot! Wow!
http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2015/sancar-facts.html
contrast with
So if a structure is really, really complicated and really, really stupid, then goddidit.
Sorry about that. Here ya go, I made the tiny url link just for you.
Page 7, figure 1.7:
http://tinyurl.com/j4rka6v
I’m happy to find out other people think biology is like a Rube Goldberg machine like I do, even a Nobel Prize winner. Great minds think alike. 🙂
You realize, of course, that this has been used for decades as an argument for evolution.
When evilutionists use it, creationists jump in and accuse them of second guessing the mind of god.
I have, for years, argued that top down design is impossible, for all the reasons you cite.
You’re right, Petrushka, us TSZers need to set them creationists right — biology is a Rube Godberesque design. Dang right.
Please provide a reference wherein someone claims that the stretch of DNA in question is asserted to be junk-DNA. From any period in time.
I really don’t get the obsession with labels. It’s irrelevant to me what anyone wants to call these things, machines, architectures, systems, codes, information storage, transfer, translators bla bla bla. It is completely irrelevant what label you decide to stick on to it to figuring out how they came to exist.
If they’re machines, then macines evolved. If they’re codes, then codes evolved. If they’re systems, then systems evolved.
First, putting a smiley after an absurd statement doesn’t insulate you from having made an absurd statement. Might as well stop. Second, that textbook’s use of “Rube Goldberg Machine” is nothing like what you intend, suggesting that you do indeed just look for particular words without even noticing how they’re being used; god goggles in operation. In that text, the term is used only as an illustration of a causal chain in order to compare it to a regulatory cascade.
I had once imagined that you could be engaged in discussion, but I find that I was mistaken. You are uninterested in science, just apologetics, and you simply search the literature for words you can use and ignore the rest. As you do with the comments here. As you will do with this comment. And so, the most one can do is occasionally point out your errors and distortions in hopes that someone else will be informed. This is an unsatisfying goal, and I’m not sure how long I will bother to continue.
http://www.nature.com/nature/journal/v458/n7235/full/458240a.html
Additionally from Carl Zimmer
By the way Rumraket, from Rinn himself in the Nature paper:
Rinn looked for histone marks even though these were not protein coding genes, but rather ncRNA “genes”.
So much for your nay-saying about histone epigenetic memory in non-coding regions.
Sal, are we still talking about Percentages of functional vs nonfunctional?
How’s you count going?
Can you make predictions using this power? Or do you just look at things and say, yes, that is as expected?
stcordova,
Let me point out that hotair shows a fair amount of sequence conservation. You know, the sort of thing that can be used to distinguish functional sequences from junk.
Not in this thread, we’re talking Rube Goldberg machines.
But, I’m not the one asserting a number for non-functionality like Rumraket and other are. They claim to KNOW in the absence of direct experiment.
I’m content to say, “I don’t know, I have a hunch. Let’s see what future experiments uncover.” I guess 50%.
That HOTAIR was a pretty amazing non-coding “gene”.
And how could such an amazing feat be realized and coordinated?
Histones, baby, histones and other epigenetic factors and the readers, writers, and erasers of epigenetic RAM.
Here is another examples where the histone reader complex moves to histones bearing certain epigenetic marks and then the complex interacts with non-coding RNAs:
https://www.dovepress.com/long-noncoding-rnas-from-identification-to-functions-and-mechanisms-peer-reviewed-fulltext-article-AGG#F4