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.
CharlieM, colewd, other friends:
I appreciate the words of thanks. You all are more than welcome.
This discussion has also given me a chance to solidify my own understanding of these topics and is a way to make my class work interesting as I’m studying histones and chromatin at the NIH school.
4 professors (NIH scientists) take turns teaching my chromotin/histone class. Some have been published researchers in these fields for decades. Some of the diagrams I’ve shown are the same as what I saw in lecture over the last month.
I have no chemistry background, but I can still appreciate the amazing connections of the chemicals in these machines despite my lack of knowledge in chemistry.
stcordova,
No it isn’t. You haven’t quantified the genetic complement required to orchestrate or specify any of this. Each cartoon describes a tiny fragment of sequence.
10% of the genome could be functional and still be ‘specified and orchestrated’, to precisely the extent shown. You could pull up cartoons til doomsday and not cover more than a few megabases of functional sequence.
Just think of what you could do with some actual evidence for that.
Glen Davidson
Science and biology are not being observed to exist either, and they don’t even have the benefit of being an explanation for phenomena.
I think he intends to keep posting images until the server runs out of space.
As if Paley’s argument from incredulity was freshly minted and convincing.
What good is 10% of a rube goldberg machine?
Mung,
Science and biology exist in the same sense that music, politics, language etc exist. You think that means they cannot be observed … well, true, they are not concrete ‘things’. But to deny their existence would be eccentric. It is not necessary to ‘believe in them’.
God, meanwhile, is an explanation for phenomena in the sense that volcano spirits or wind gods are.
petrushka,
Creationism in the internet age.
stcordova,
Sharing your current education is very useful for me. The workings of the cell are fascinating especially the epigenetic workings of DNA you are describing. Can you articulate any more how you think proteins store information? This has to be part of DNA repair, I think:-)
The point I was making is that all the parts of the HOTAIR pencil (writer and eraser) are a carefully orchestrated Rube Goldbergesque design that enable skin cells at the soles of the feet be different from the skin cells at the eyelids. Such exquisite orchestration is aesthetically inconsistent with the idea the rest of the biological system is junk. HOTAIR was thought to be junk (that’s why the discoverers called it HOTAIR, as sort of a joke).
The only way I think the genome has large amounts of junk is through genetic deterioration. This deterioration has been empirically and theoretically supported on many levels.
That is to say, if it’s junk today, it doesn’t mean it was junk in the past. People were healthier, stronger, and much smarter in the past. I don’t think it is a coincidence so much of ancient knowledge was handed down by word of mouth. It seemed normal for people to memorize entire works of literature like Homer’s Illiad and Odyssey or the Bible in ancient times.
I’ve said I don’t know how much is junk, but I have hunch it isn’t just by considering the possibility we could extrapolate what I showed above to the rest of the genome. It seems aesthetically reasonable as an idea, just like the Peacock’s tail.
It’s easy to believe what was discovered for the once-upon-a-time-junk-DNA called HOTAIR could be discovered for many other RNAs whose function we’ve not elucidated. HOTAIR discoverers, Rinn and Chang, have lists of tens of thousands of transcripts with similar hints of function but have not yet been explored.
The ability of HOTAIR to help differentiate skin of the soles of the foot vs. the skin in an eyelid is a powerful example of why information can’t be just restricted in the coding regions. That sort of information just isn’t in the coding regions, the information has to reside elsewhere in places like –… junk DNA!
Mung,
Ask Behe.
Behe is not as smart or knowledgeable as Sal.
stcordova,
I prefer practical inconsistencies to aesthetic ones. Would you be happier if the genome had 0% junk and were 0.32 Gb in length?
BY WHOM? Reference please? If you are repeating that same dumb mistake that noncoding DNA = junk, I will get Larry Moran to come round and lob a brick through your window.
stcordova,
That ‘genetic deterioration’ has resulted in the same transpositional sequences being repeated throughout the genome, accounting for fully 50% of it. Do you really think that came about by point mutation?
Allan Miller,
Once again I will note that HOTAIR, or at least significant parts of it, shows sequence conservation. Nobody looking at comparative genomes would think it was junk.
I suppose you don’t think the Germans bombed Pearl Harbor.
By that same logic, God exists.
Science and biology are not concrete ‘things.’ Neither is God. How do you go about observing that which has no concrete existence? What makes belief in science and belief in biology different from belief in God?
Biologists don’t stone people?
Well, most don’t, anyway.
Glen Davidson
Only if they grow it themselves.
I actually know next to nothing about DNA repair. Too much to learn, hehe!
But in response to your question, you actually saw one of the ways proteins store information. Histones are proteins! The diagrams above with the histone tails (the one with the “27” marked in the diagram) shows how a single amino acid on a protein can receive a chemical marking.
The average protein size is about 400 amino acids long (some are far bigger than that, btw). Each amino acid is numbered.
It’s rather agonizing work to find out each component of the protein and then to find out what possible chemical marks are there and where. Some experiments take years to identify a single chemical mark. Histones got a lot of attention, but many (more than half) can likely be marked as well.. and we haven’t found all the marking yet, not even close.
I use the word epi-proteomic, but the common term is post-translation modification (PTM).
It is not a trivial issue either for the chemical marks to be written/erased/read. The machine complexes to read one little mark on a molecule are huge (many molecules) and complicated. You saw one of the eraser complexes like the LSD1/coREST/REST complex. An example of a writer complex was the PCR2 above. All that just to write or erase a single chemical mark!
So when I showed this diagram at the bottom of this comment:
anywhere you see “K” in the diagram, that is a lysine amino acid. The lysine can be modified by adding methyl groups to the lysine and this serves to mark it, dare I say write to it, with information.
There are huge numbers of chemical modifications. And the one I’ve left out, perhaps the most important is when proteins are connected to glycans. When a protein is connected to a glycan, it’s like adding an external hard drive to a computer, the thing can hold even more information.
But any way, here is the diagram of the lysine at the molecular level, you can then hopefully relate it to the diagram in this comment
with all the “K”s in it, where K is a lysine molecule.
Note below there are actually 4 different states the lysine molecule can exist, it’s memory location can store an alphabet of 4 letters: no-methylation, mono methylation, di methylation, tri methylation. The “alphabetic” symbols (I think) would be K, Kme1, Kme2, Kme3.
If we know the exact position of the lysine, like say position 27, we can say, K27, K27me1, K27me2, K27me3. So to identify the a particular mark on the protein/histone 3 we say something like H3K27me3. Btw, that took decades of chemistry to figure some of these markings out because one can’t really see it even with electron microscopes.
The researchers agonized for decades to realize how the following diagram was applicable to the cell’s histones, and histones are only 1 of 20,000-500,000 proteins or protein isoforms:
Mung,
If the criterion for existing is ‘not being a concrete thing’, then your logic is impeccable. I see a gaping hole in the argument, however …
What a strange argument. Science and biology are human endeavours, like language and music. Does French exist? What makes belief in French different from belief in God? Il faut l’expliquer? Vraiment?
God (in this instance) is a mere explanation (among his many other catch-all attributes – the source of morality, guarantor of eternal life, grantor of boons, and so on). French, meanwhile, is not an explanation. You don’t observe something and conjur up unobservable ‘French’ to explain it.
stcordova,
Oh, you’ll love it, it’s rilly complex!
Like a watch found in the beach sand.
Forget it. He’s rolling.
Ah, well. Unintentional self-parody is still self-parody. But belay the “bravo”.
Science never disguised itself as a human and then appeared as a man on the earth to ‘sacrifice’ itself in order to save us from itself, which is weird anyway as it knew what we were going to do before we did it even before we existed.
You and I have a different understanding of the word ‘explanation’ I think. Unless you can tell me what this ‘explanation’ is that you think you have for phenomena?
… of functional regions. The junk regions are under much less constraint exactly because it’s nonfunctional and therefore unlikely to yield transcripts that interacts strongly with other cellular processes.
Unlikely =/= never
So don’t bother telling me about junk-regions implicated in disease. The genome is big, by chance alone the accumulation of mutations in all that junk is bound to produce a trancript that does mess something up.
Despite all the specificity, interations at the molecular level are governed by brownian motion and you’ll get spurious activations sooner or later. The temperature drops a bit in some tissue and suddenly TF’s bind better even to many nonspecific areas. Allan Miller mentioned PCR and what a good example that is, here’s a primertest I ran this morning on a set of primers designed to target only a single gene in the entire human genome (the annealing temperature is run at progressively higher temperatures from left to right):
http://i.imgur.com/4YnXEVe.jpg
Notice how at the lower temperatures how many nonspecific products result.
stcordova,
Thanks Sal. My opinion is that the cell counts on the presents of adequate quantities of proteins and small molecules to operate and stay under control. By control I mean having the ability to perform its functions such as divide, repair DNA and if not repaired, initiate apoptosis. The current thinking is that low levels of vitamin d in the blood creates a chain reaction of under expression, which leads to over expression of critical oncogenes. My thought is that maybe the requirement of many proteins to do a single task is timing related. The more proteins required the less frequent the event. Thoughts?
So is worship of God. But all of nature worships God. Humans are the only creatures that choose not to. Like i said, by your criteria for what exists, God exists.
No really. You’re just confused. Allan’s argument against God depends upon us not being able to observe God the way we observe science and biology.
Yup, Sal, life is really really complicated. Scientists have been studying transcriptional silencing for 30 years. IDists, not so much.
It`s your claims that “information-carrying” molecules and ‘histone codes’ have to be highly specific and exquisitely orchestrated that lacks support. Every single methyl group is an independent bit of information? Really? Storing a unique address for every neuron? Sez who?
It`s also quite unrelated to the what-%-of-DNA-is-junk question (well, except that there’s a benefit in being able to exclude transcription factors from whole domains of a genome that is 85 – 90% junk; in a more efficient genome, silencing generally has some specific (!) biological relevance…)
Whooo boy!
Just wait til he finds out about glycosoaminoglycans. It`s like adding a RAID to a computer. The possibilities are endless.
.
.
.
Oh crap!
<desperately tries to put cat back in bag>
Not sure of your meaning here. As normally configured, a RAID (Redundant Array of Inexpensive Drives) doesn’t add additional storage, it’s a means of protecting against head crashes or other data corruption that can happen on one drive, but is unlikely to happen across an array of drives all of which hold identical information. In other words, it’s a real-time backup system.
I agree its not. It is a physical structure and as such can never be as all-encompassing as an archetype.
I am intrigued that something can be specialized in many ways. What ways would these be? And can you give an example of the limb of any animal that is less specialized than the human arm?
I hope no one counts on RAID as a backup. It keeps critical systems running, but it isn’t a backup. Sorry, but I’ve run into too many people who don’t do backups.
Flint,
Well, I was lamely trying to riff on the idea that, in Sal-world, storage capacity = information content.
The theoretical storage-capacity of a single (partially sulphated) glycosoaminoglycan chain is impressive. Of course it`s information that`s heavily duplicated / highly redundant; I suspect the same is true of the histone codes. Just because the potential information storage is massive, that doesn’t mean that`s how it`s implemented…
It just so happens I heard a speaker at the ENCODE 2015 conference talk about the vitamin D receptor! Most of my detractors here don’t like the NIH ENCODE initiative, if you haven’t noticed. 🙂
Ok, how this relates. I highly recommend this 2-minute video first. Notice the role of HAT underexpression in cancer:
HAT is affected by vitamin D. How do I know that?
I heard it straight from an ENCODE researcher (link below) in the first 7 minutes of one ENCODE 2015 talk on Vitamin D. Around the 7 minute mark, he shows a slide that shows the relation of the Vitamin D receptor and the Epigenetic Histone Acetylation Complex (HAT). The other complexes like the nucleosome/chromatin remodelling complex and the mediator complexes are pretty important too!
So what does that imply? Not enough vitamin D results in HAT under operation. So even if there is enough HAT, it can’t be properly recruited without enough Vitamin D. So this particular ENCODE researcher helped show the connection.
The later part of the lecture is pretty deep and it went into more ENCODE specific stuff. But anyway, here is Wesley’s 35 minute talk at ENCODE 2015 if you are remotely interested. I have to confess, I didn’t comprehend but 20% of the talk at the time, but like most people there, including the scientists, we didn’t understand a lot either.
If one was molecular biologist the computer parts of ENCODE weren’t understandable, if one was a computer guy the biology parts weren’t that understandable, and if one was a medical doctor then some parts of all of it was not understandable, that’s why the meeting was convened to help everyone start talking the same language. So here it is:
I’ve run into that — not personally, but on a site that I use.
RAID is great for dealing with disk failures, providing that they don’t all fail at the same time. But when the RAID controller itself fails, and it turns out to be an obsolete model that you cannot find a replacement — then you are in deep trouble.
I don’t mean that it’s specialized for many things. I just mean that it has many features that add to its specialization. Now what exactly do we mean by “less specialized”? Generally in biology we mean “closer to the ancestral condition”, but it could also mean “capable of a greater variety of actions”. A typical rodent forelimb is certainly closer to the ancestral mammalian condition than is a human one, and is capable of grasping, walking, climbing, and digging, so it seems to me less specialized in both senses.
I would say less specialized means less affected by perturbations in the environment.
The majority of humans would die within a few months if the electrical grid failed world wide.
Rats, maybe not so much, although rats in northern climates depend on humans for food.
Actually, a RAID is a backup-oriented system, but it’s not intended to be an offline, secure duplicate of your files. It’s only a way of not losing everything if your one and only drive crashes. The point is that it doesn’t increase your storage capacity, it only makes that capacity a bit more bulletproof.
And yes indeed, a RAID has a single point of failure (the controller), so it’s not quite as redundant as truly mirrored drives, with separate controllers and buses.
Human can also use their forelimbs for grasping, (also with each hand independently), walking, (many infants use them in this way prior to walking) , climbing, and digging. And, over and above this, there are many things that humans use their forelimbs for that rodents do not (unless you know different) ?
Here are a few uses I can think of:
making tools, punching, strangling, smothering, signalling intentions, throwing objects, counting, breaking eggs, clapping, hugging, interlocking digits to get greater purchase when lifting, cupping the ear to assist in hearing, shielding the eyes, judging and measuring distance, pointing. writing, CPR, trout tickling, doing the hand jive and a few other unmentionable things.
I ran this past our pet hamster and he wasn’t impressed. Maybe you should add hand gestures to their list of capabilities.
That’s actually false.
The issue is not with the ENCODE initiative, it’s with the grandiose conclusions not suppored by evidence being made in the popular press. It’s effectively misinformation.
It’s important work they do, but rather than being responsible scientists and doing the kind of measured, honest presentations of their results we hope scientists should do, they go and make super-hyped declarations about paradigm shifts in the media. A media that is of course all too keen to hop along with attention-grabbing headlines.
I take it bothers you that ENCODE proponents are inspiring the idea that the human genome is more than 10% functional. If people go around believing it is 50%, 60%… 99.5% functional, that would really bother you.
Let’s assume for the sake of argument the functionality numbers aren’t that high in reality, say 15% functionality instead of 2% or 10%, would a false belief of 100% functionality be such an unacceptable cultural change?
How badly would such a belief, that the human genome is packed with 99.5% Rube Goldbergesques designs — how badly would such an idea affect the progress of science? I don’t see why it should, a creationist like me got so excited about the idea and that I wanted to learn more about science, not less. I wanted to teach more about the details of how these machines connect (as I have done in this discussion), not less.
Is the real problem the fact that such a change in a cultural mindset might make people more inclined to worship an invisible God because of the great genius and humor and unnecessary wasteful extravagance they perceive in biological systems? It’s not really because it will hinder the progress of medical discovery is it?
I take time to find and discuss the details of biological systems and rather than you guys marveling at the intricacy of these contraptions, I get criticized for spamming. I’d think you guys would have enjoyed actually discussing science and facts just like the HOTAIR non-coding DNA and it’s ability to connect to a writer and eraser, almost like a pencil.
What’s there to fear if ENCODE changes the culture?
Rehashing Paley’s argument with copy and paste is spamming.
Drawing unwarranted conclusions may impress your zombified “students,” but it isn’t adult discourse.
Not responding to criticism and repeating your bullshit claims ad nauseam is just rude.
You really ought to listen more and talk less.
Would you be happier if I said, “Wow, evolutionary biologists should be amazed at what mindless processes like mutation and natural selection can do, amazing.”
“Look at the Rube Goldbergesque designs in biology like the non-coding HOTAIR ‘gene’. Evolutionary biologists should be celebrating these amazing products of mindless processes of mutation and natural selection.”
Or, “I have a hunch the genome is much more functional than previously thought because NIH initiatives like ENCODE, Roadmap, E4 and the glycobiology interest group. If we find more function, evolutionary biologists should be amazed at what mindless processes and natural selection can construct. Simply amazing.”
There I said it, no mention of God, but rather an appeal to mindless undirected forces. Are you happy now. 🙂
Have you even read any of the responses to your posts?
The standard conclusion reached by most evolutionary biologists is that about two percent of the human genome codes for protein, and eight percent does something else, such as regulation. Putting gene in scare quotes is not warranted. Genes are genes because they have function and because their sequence matters.
You have thoroughly rubbished your thread by conflating non-coding with junk, and then not-so-subtly implying that lots of DNA formerly thought of as junk is actually functional.
You have argued dishonestly by avoiding talking about the actual percentages of DNA that has newly found function. In short, after all your blather, you haven’t raised the percentage above ten.
I provided good evidence we could suspect introns (which are 25%) of the genome, are functional. I provided evidence transposable elements (17-21%) are functional for 2 reasons (somatic transposition to make unique neoron trascriptomes and genomes, yes genomes), and histones on transposable elements. I talked in another thread about pseudogenes and as decoys for miRNA in a regulator schema. I discussed lncRNAs in the long coding RNA thread, etc. etc. These are good indicators of a functional hunch.
In contrast, you have not provided one experimental proof of 90% non-functionality. Not one lousy unequivocal experiment.
Granted the lines of evidence I offered must be extrapolated to give high levels of function, but at least I cited experiments and lab measurments which is more than what the critics here have done.
Genetic load. Onion test. That’s two.
Knockout experiments would make at least two and a half.
Granted, they are Larry Moran’s arguments, not mine. Perhaps he didn’t originate them either, but that’s my source.
On no one’s authority but my own intuition, I would accept the possibility that junk might affect evolvability by supplying an occasional mutation to function. that might be how regulatory networks originated.
I suspect, however, the Michael Behe and Doug Axe will not be in the forefront of unraveling such things. In fact, I can’t think of a single contribution to knowledge by anyone in the ID movement. All the research assumes stochastic mutation, drift, and selection.
petrushka,
As I understand it, in many cases knockout experiments are a poor indicator of functionality because of the redundancy built in to genetic networks.