Friday, May 19, 2006

My Response to ‘Anonymous Dawn’

` A friend of mine from the Midwest has provided a fairly typical example of the protests of believers and many others against skepticism. I admit, as I had read through Skeptics and True Believers the first time, I had filled the margins with protests, such as; “Just because it's anecdotal doesn't mean it's not true.”
` Of course it doesn’t! No one is saying that. It may just take a while to grasp the significance of it.
` After a time, you realize that a skeptic does not assume that something isn’t true just because there is no empirical evidence for it. That is simply nonsensical! A skeptic simply suspends belief.
` The point of skepticism is to be reasonably certain of what's going on, and this has always been my greatest interest. Hence, I was willing to grasp skepticism. Lots of people I know are not, generally this seems to be because actually being sure of something does not interest them as much as feeling sure of it.
` Not only that, but my friend here is adamant about using Intelligent Design as proof of God. Which is, incidentally, what ID proponents try to use it as.
` Of course, I have already accumulated much in the way of undeniable proof of ID proponents explicitly saying that ID is religiously based creationism and that it is a way to ‘introduce’ people to Jesus.... who has nothing to do with science at all.
` The only thing that science is concerned with is observing the world, and, if possible, confirming those observations, and, if confirmed, using them for things and constructing explanations for why they work. This has nothing to do with the goals of religions.
` Religions are concerned with believing in and worshipping deities and suchlike in order to gain rewards, and not conducting experiments. Though religious mythologies have useful rules and tips about living one’s life, they are not practical for such things as manipulating the world and understanding why you can do so.

` Which is what science is for!

` Another goal of certain religions, however, is to spread the word. This is what Intelligent Design is all about. However, its main scientific content is merely that of mainstream science after it has been tossed into an ideological blender.
` This is partly because IDists want their religion(s) to be taken as seriously as something that is as successful as science has been at understanding the world – which explains why they insist that both the scientific method and the knowledge which yields from using the scientific method (i.e. why lightning occurs, how to save a cardiac patient’s life, how to get to the moon, and other practical matters) is all a bunch of religious dogma.
` Do IDists have a theory that explains more things about the diversity of life than evolution? No, and they admit as much. In case it is not obvious, their prime tactic is to sit around, attacking both science and scientists, especially those in the biological fields.
` Though a small handful of IDists have degrees in some kind of science, they nevertheless are not using the scientific method and tend to ignore or distort almost all evidence of evolution, or facts pertaining to it.

` Ah, but I am getting ahead of myself and forgetting about my original response! Indeed, let us review what Anonymous Dawn has said about rejecting skepticism and supporting her ideals:
Speaking of skeptics -- I'm skeptical of YOU, Spoony. I think it takes a vastly bigger leap of faith NOT to believe in a creator and to declare the whole universe a giant cosmic accident than it does to believe in intelligent design.
` Since you say you’re so skeptical of what I have to say, then why not try to refute it using skepticism? Seriously, can you please tell me how it takes a leap of faith to not have faith? According to your own apparent definition, there can’t be a way to not have faith in anything!
` If I actually did believe that God didn't exist, that would be a leap of faith. Believing that something does not exist is called a ‘negative belief.’
` However, skepticism is all about being open-minded. Any of us, in principle, will accept any crazy thing in the universe as long as it can be demonstrated. Purple sea monsters? Show me one! I’ll accept any fact, because facts can be demonstrated!
` You see, when a skeptic does not know whether or not something exists, they don't go out and form beliefs about it. (Opinions, maybe, though those are not concrete.)
` I don't believe anything about the concept of God. Therefore, how could I believe that God doesn't exist?

NOT having a religion does in fact create its own system of religious thinking. When you say “there are no absolutes”, logically, that single belief in and of itself becomes your absolute!
` A seeming paradox I suppose, largely due to the way language is constructed. Just as paradoxical, I suppose, as the fact that everything in the world constantly changes, except for the fact that everything constantly changes.
` What about the fact that you are a unique individual, just like everyone else? What is so paradoxical about these statements when they are technically consistent?
` Language is full of logical holes, including the fact that you can say; ‘The following statement is true: The preceding statement is false.’ But as they say, words are not a good substitute for actions:
` The reason I like trying to get to the bottom of everything in life is because this method of thought is extremely practical in the real world. True, the main ‘dogma’ of science is to not create dogmas in the first place! How else could one be consistent in their methods?

` Having an open mind is the only tried-and-true method of learning anything about the universe. Not having dogmas about the universe and instead listening to the universe is the object of skepticism.
` Just the fact that the Renaissance took us from the Middle Ages to the Enlightenment and now the Space Age is pretty solid evidence that skepticism generally succeeds at taking evidence and creating new ideas that are useful in the real world.
` And so, because it succeeds in carrying out its job so effectively, this ‘absolute’ does not come under suspicion for people who understand how to use it – and actually do.

` How does it work?

` Not having absolutes allows science to avoid dogma as well as redundant and pointless ideas, which would most certainly inhibit its progress. Even on a casual scale, not being sure of things until you’ve checked them out drastically reduces the amount of potential wrong opinions that you have about whatever it is you're wondering about.
` And, as is known extensively, the human mind can easily be duped. Even our senses sometimes deceive us! That is the point of objective observation. (‘Do you see it too?’)
` As far as skepticism being equal to religious thinking, I cannot see why people often make this assumption. I don't worship anything: I don't have faith in anything that cannot be seen: I don’t follow commandments from any supposed deity: I do not form empirically baseless opinions and insist that they are true.
` I'm merely careful about what ideas I accept as facts. That is all.
` Can you please explain to me why you think skepticism is some kind of religion? (Surely you must know that some skeptics are religious, and that they regard the two as separate types of thought?)

If you admit that there ARE in fact absolutes of some kind– natural laws if you will, your belief in those rules becomes eerily similar to embracing a religion, because your belief does in fact govern your behavior and the way that you live your life!
` What do you mean? Are you talking about the laws of nature? In all practicality, natural laws (such as the Laws of Motion) are valid, and as far as anyone can tell, they have not changed much over time.
` However, scientists do not really ‘believe’ in natural laws: They are simply there to be seen, by anyone, anytime, and there is no reason to think they don't exist.
` Furthermore, I fail to see how laws of nature can affect the way someone lives. Can you explain what you mean and tell me who gave you this idea?

Darwinian theory admittedly accounts for a number of modern changes. Mutant bacteria thrive when they become increasingly resistant to antibiotics. Scientists have clearly demonstrated that the median beak size of Galapagos finches has changed in response to changing weather patterns. Similarly, the ratio of light to dark-colored moths in England shifted when pollution made lighter-colored moths more clearly visible to predators. These are certainly clear examples of natural selection in the works.
However, these specific examples demonstrate only one or a few mutations, and the resulting mutant organism is not all that different from its ancestor. In contrast, to account for the very existence all of life, an endless series of mutations would have to have produced vastly different types of creatures from a common source. I’ve seen no clear proof of that, or even reasonably compelling evidence.
` Earth to Dawn: There is no proof of atomic theory, either! Does that mean you reject the concept of atoms? Besides, there is much more evidence for modern evolutionary theory than atomic theory!
` And, as all biological knowledge I can think of makes sense in light of common descent – if not explicitly demonstrating it – and because a lot of this also points to Darwin's theory, could you please be more specific as far as ‘reasonably compelling evidence’ goes?
` Also, what do you mean by ‘vastly different’ in terms of life forms? All organisms have a lot in common with all other organisms, some moreso than others. As a top-of-the-head example, genes that control eye development in mammals are pretty much interchangeable with ones found in both other vertebrates as well as invertebrates. In terms of DNA, plants such as bananas are only 50% different from humans.
` We also have most cellular structures in common with other eukaryotes, and we have bilateral symmetry in common with most other animals. We even have nearly the same bones and organs as any other vertebrate animal.
` Many genes, such as those for limbs and eyes and body segments are similar throughout species. Some genes are even utilized for one purpose in some organisms while having an entirely different function in other organisms.
` In other words, such genes have been ‘recycled’.
` Of course, I am mainly talking about genes, here. However, the phenome (body, instincts, etc.) of an organism is largely dependent on the genome, as you know.

` Developmental biology is another area of science that deals with evolution, as the sequence of stages an organism goes through to get to its adult form closely resembles many organisms which the fossil record indicates were its ancestors.
` Comparing the development of two different species also indicates how closely they are related to one another by the point in which development diverges. This is also consistent with genetic data from the same two species, as well as the tracing of fossil evidence.
` And of course, pseudogenes, and other junk DNA (which constitutes over 90% of the genome) also demonstrate the same levels of relatedness as genes. Sometimes, one species will have a non-working pseudogene while the other species has apparently the same pseudogene, yet it is still functional.
` Correlating evidence for evolution goes on and on, through different fields. They each show a striking level of mutual consistency. Perhaps the reason you don’t agree with this is because the IDists are willing to suppress these facts for their ideals. For example, when you say:

Also, Darwin's theory hits a brick wall when it comes to explaining the development of cellular systems.
` This merely reflects such a suppression, some of which you will see demonstrated shortly.
There are a good number of cells that are irreducibly complicated in their design – in other words, they need several components in place before they can function AT ALL, even minimally.
` That would make sense only if we were machines. Which we aren’t. And I know you're not assuming that we are.
For the more simple minded – an everyday life example of irreducible complexity is a common mousetrap, built with several components – base, hammer, spring, etc. It is impossible to kill a mouse with just the base of the trap -- all the components have to be in place before it is capable of catching any mice.
` This is not a valid analogy, as a mousetrap does not develop, nor does it reproduce, nor does it have eccentrically over-complicated and redundant mechanisms that could potentially be changed with the mutation of offspring.
` Mousetraps are simple and static, and they certainly are not capable of imperfectly creating others of their kind. Organisms are anything but that!
` Strangely enough, despite these clear flaws in philosophy, mousetraps can indeed be reduced, which I find rather amusing.
` As Behe has written:

...Which part could be missing and still allow you to catch a mouse? If the wooden base were gone, there would be no platform for attaching the other components.
` What about the floor? The components would still work if they were attached to the floor! Though, what did he have to say to that?
That’s an interesting reply, but you've just substituted another wooden base for the one you were given. The trap still can't function without a base.
` Of course, he’s missing the point – a mousetrap can function whether or not it is reliant on its ‘natural environment’ for a base. Not noticing this alternative is somewhat like saying a pig would overheat and die in the summer because it has no sweat glands. In fact, pigs are reliant on their natural environment for sunblock and cooling-off by seeking out mud and water. (Hippos, however, do have such protective secretions, and are therefore probably superior in this manner.)
` The point is that, while the mousetrap with the self-contained base is superior, the other one can still function fairly well – it just can’t be moved anywhere.
` In fact, John McDonald has
come up with a hypothesis of sorts in which a mousetrap can be reduced to a mere wire and still function as a mousetrap. In fact, he even had fun with making a mousetrap ‘evolve’, though mousetraps are not like organisms, and so this has nothing to do with real evolutionary theory.
` First, you have a piece of springy wire, which a mouse could conceivably trip and become caught between. Though it is crude and not likely to catch mice unless propped against a mouse hole properly, it is still capable of catching mice. Adding a coil reduces stress on the wire, and so the wire would take longer to fatigue.
` Of course, this type of trap can be knocked over by mice, and so an option that would make it easier to steady it would be to staple it to the floor.
` Stapled to the floor or propped against a wall, however, the trap is still capable of catching mice. Stapling the wire to a piece of wood, however, would allow you to move the trap anywhere. The base would also make the staples necessary, though they were not before. And then he goes into developing the hammer and so on, with animations to boot.

` Let me make it clear, though, that the point of this exercise is not to say that a mousetrap can evolve. The point is to demonstrate that half a mousetrap is better than no mousetrap at all, and that parts that are added later may necessitate the previous parts.
` Or, as McDonald says: ‘Each newly added part is optional at first, and could be removed without destroying the function. However, modifications to the new parts or to other parts make the new parts necessary to the mousetrap function.’
` Though it does not demonstrate evolution, I bring this up because it illustrates a very significant concept.
` And, though Alex Fidelibus, Don Stoner, and Ken Miller have come up with yet other ways a mousetrap could be assembled in a stepwise fashion, functioning at each step, somehow I think you’ll be much more interested in my response to this:

Just one example of what I understand to be an irreducibly complex cellular system is the flagellum of some bacteria -- the flagellum requires a number of cellular components before it works -- a stator, rotor, and motor. Furthermore, I’ve also read reports that have shown that around 40 various kinds of proteins are found in a working flagellum. I’ve never seen a sufficient explanation for the evolution of a flagellum based upon Darwinian theory.
` Of course you haven’t; you’ve been getting your information from people like Michael Behe, who – for one thing – admitted in court that he hasn’t read much about the subject.
` Indeed, Kenneth Miller, who is both a professor of biology and a Christian, has indeed done his homework in this area. What does he have to say to Behe? First, he makes clear what argument Behe is using:

‘For nearly than a century and a half, one of the classic ways to argue against evolution has been to point to an exceptionally complex and intricate structure and then to challenge an evolutionist to "evolve this!"
` As [Behe] realizes, however, the mere existence of structures and pathways that have not yet been given step-by-step Darwinian explanation does not make much of a case against evolution. Critics of evolution have laid down such challenges before, only to seem them backfire when new scientific work provided exactly the evidence they had demanded.
` Behe himself once made a similar claim when he challenged evolutionists to produce transitional fossils linking the first fossil whales with their supposed land-based ancestors (Behe 1994: 61). Ironically, not one, not two, but three transitional species between whales and land-dwelling Eocene mammals had been discovered by the end of 1994 when his challenge was published (Gould 1994: 8-15).
` Given that the business of science is to provide and test explanations, the fact that there are a few things that have, as yet, no published evolutionary explanations is not much of an argument against Darwin.
` Rather, it means that the field is still active, vital, and filled with scientific challenges. Behe realizes this, and therefore his principal claim for design is quite different. He observes, quite correctly, that science has not explained the evolution of the bacterial flagellum, but then he goes one step further. No such explanation is even possible, according to Behe. Why? Because the flagellum has a characteristic that Behe calls "irreducible complexity."’
` Which you are quite familiar with, evidently: Like a complex machine, Behe contends that any hypothetical intermediate stages of a complex system would not be functional, and so could not be selected for. Therefore, it is impossible to come up with a realistic explanation!
` On top of this, Behe fails to mention that most of the proteins in a cell are closely related to other proteins that have another function. These provide clues to evolution that he does not even address.
` In evolutionary terms, all that needs to happen for another protein to ‘speciate’ is a gene to duplicate a protein, and in one of these genes, chance upon any of a number of small mutations which cause one protein with an established function (or functions) to do something or other that is different.
` (This also applies to entire chain-reactions that facilitate signaling in cells. In the case of photosensitive cells, there is barely any difference between the complex ‘chain’ that allows sensory perception of light and other signals found in other types of cells. But, I am rambling....)
If you believed Michael Behe's assertion that biochemical machines were irreducibly complex, you might never bother to check.... Musser and Chan did check, and found that two of the six proteins in the proton pump were quite similar to a bacteria enzyme known as the cytochrome bo3 complex. Could this mean that part of the proton pump evolved from a working cytochrome bo3 complex? Certainly.
` ...[There are] modern organisms that have full, working versions of the cytochrome bo3 complex. Can we make the same argument for the rest of the pump? Well, it turns out that each of the pump's major parts is closely related to working protein complexes found in microorganisms. Evolution assembles complex biochemical machines, as Musser and Chan proposed, from smaller working assemblies that are adapted to fit novel functions. The multiple parts of complex biochemical machines are themselves assembled from smaller, working machines developed by natural selection, as shown in Figure 2
` So, there are actual, known small, working mechanical assemblies that can be combined into larger assemblies, which can be, in turn, combined into yet larger ones? Behe, on the other hand, completely ignores the possibility of such existing structures and insists that the whole thing would have to be assembled from individual units all at once.
` Miller gets back to flagella shortly. In the meantime, he mentions that Behe has also asserted that structures such as cilia are ‘irreducibly complex’ only if you ignore facts.

If it is correct, then we should be unable to find examples of functional cilia anywhere in nature that lack the cilium's basic parts. Unfortunately for the argument, that is not the case. Nature presents many examples of fully-functional cilia that are missing key parts. One of the most compelling is the eel sperm flagellum (Figure 3), which lacks at least three important parts normally found in the cilium: the central doublet, central spokes, and the dynein outer arm (Wooley 1997).....
` The key element of the claim was that: ".. any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional." But the individual parts of the cilium, including tubulin, the motor protein dynein, and the contractile protein actin are fully-functional elsewhere in the cell. What this means, of course, is that a selectable function exists for each of the major parts of the cilium, and therefore that the argument is wrong.
` In other words, by looking at the real world, Behe’s statement that such elements of cilia are nonfunctional on their own is demonstrably false.
` Now, concerning bacterial flagella:
To begin with, there is more than one type of "bacterial flagellum." Flagella found in the archaebacteria are clearly not irreducibly complex. Recent research has shown that the flagellar proteins of these organisms are closely related to a group of cell surface proteins known as the Class IV pilins (Jarrel et al 1996) Since these proteins have a well-defined function that is not related to motility, the archael flagella fail the test of irreducible complexity.
` Clearly, when he speaks of the bacterial flagellum, Behe refers to flagella found in the eubacteria. Representations of eubacterial flagella appear in Darwin's Black Box (Behe 1996a: 71) and have been used by Dr. Behe in a number of public presentations. Surely these structures must fit the test of irreducible complexity? Ironically, they don't.
` In 1998 the flagella of eubacteria were discovered to be closely related to a non-motile cell membrane complex known as the Type III secretory apparatus (Heuck 1998) These complexes play a deadly role in the cytotoxic (cell-killing) activities of bacteria such as Yersinia pestis, the bacterium that causes bubonic plague. When these bacteria infect an organism, bacteria cells bind to host cells, and then pump toxins directly through the secretory apparatus into the host cytoplasm. Efforts to understand the deadly effects of these bacteria on their hosts led to molecular studies of the proteins in the Type III apparatus, and it quickly became apparent that at least 10 of them are homologous to proteins which form part of the base of the bacterial flagellum (Heuck 1998: 410).
` This means that a portion of the whip-like bacterial flagellum functions as the "syringe" that makes up the Type III secretory apparatus. In other words, a subset of the proteins of the flagellum is fully-functional in a completely different context – not motility, but the deadly delivery of toxins to a host cell. This observation falsifies the central claim of the biochemical argument from design – namely, that a subset of the parts of an irreducibly complex structure must be, "by definition nonfunctional." Here are 10 proteins from the flagellum which are missing not just one part but more than 40, and yet they are fully-functional in the Type III apparatus.
` In addition, it should be obvious now that ID proponents generally do not acknowledge the idea that a biological component could evolve for one purpose and later be used for another. In other words, they assume that, just because something performs some function, it would have had to evolve for that purpose alone.
` This is not consistent with evolutionary theory, because it is not consistent with evidence from the real world.
` For an example that comes to mind off the top of my head, this is like saying that wrist bones would have to have evolved as opposable digits.
` The skeletal and muscular structure of a giant panda's wrist does indeed show a grasping digit. However, the original function of wrist bones are to allow flexion, presumably for locomotion as in the case of Tiktaalik, the ‘limb-finned fish’.
` Similarly, to say that one system cannot transform into another assumes that both skin and forelimbs would have to have evolved to allow bats to fly with their webbed fingers, or that the eye originally evolved to see images, or that the tail evolved for swinging from trees, or that the malleus and incus evolved to allow mammals to hear.
` (In reptiles, the malleus and incus are part of the lower jaw. Across the numerous transitional forms, one jaw joint recedes and another develops so that many species have both joints at once. Eventually, the ‘reptile’ joint shrinks into nothingness and the malleus and incus are integrated in the hearing mechanisms.)
` To say that something would have to have evolved for one specific purpose ignores the fact that modern evolutionary theory does not predict that anything is evolving in any particular direction over long distances of time. Nevertheless, this is an assumption I hear a lot from IDists.
` With that hopefully understood, Miller goes on to say:
Proteins that make up the flagellum itself are closely related to a variety of cell surface proteins, including the pilins found in a variety of bacteria. A portion of the flagellum functions as an ion channel, and ion channels are found in all bacterial cell membranes. Part of the flagellar base is functional in protein secretion, and once again, all bacteria possess membrane-bound protein secretory systems.
` Finally, the heart of the flagellum is an ion-driven rotary motor, a remarkable piece of protein machinery that converts ion movement into rotary movement that makes flagellar movement possible. Surely this part of the flagellum must be unique? Not at all. All bacteria possess a membrane protein complex known as the ATP synthase which uses ion movements to produce ATP. How does the synthase work? It uses the energy of ion movements to produce rotary motion. In short, at least four key elements of the eubacterial flagellum have other selectable functions in the cell that are unrelated to motility.
` In other words, various components of the flagellum are known to have a selective purpose, just as skin has an important purpose even when it is not utilizing the limbs of certain squirrels or marsupials as a gliding surface.
` So, yes, Behe has said that, in principle, the flagellum cannot be reduced to selective parts for natural selection to work with.
In reality, the flagellum has already been reduced to advantageous parts which can conceivably be assembled into an entire flagellum.
` As Miller puts it:
What this means, in scientific terms, is that the hypothesis of irreducible complexity is falsified. The Darwinian explanation of complex systems, however, is supported by the same facts.
` Indeed, ‘the scientific community [does] not greedily embrace its startling claims’, as Behe has suggested they should, because this argument (as well as others of his) are demonstrably false. There is undeniable proof of the existence of things he claims don’t exist, the absence of which are what his entire ‘irreducibility’ is based on.
` Yet, Behe says that instead; ‘The dilemma is that while one side of the elephant is labeled intelligent design, the other side might be labeled God.’ In fact, the reason his arguments are not accepted by biologists and the like because they are already familiar with this type of thing and are in a position to spot flaws like these.
` On the other hand, followers of Behe’s arguments (like most people) are unaware of such obvious falsities.

` What else does Kenneth Miller have to say in the paper I have used here? Feel free to read away! In fact, there is more where that came from, if you like.
` You may also be interested to know that, according to this humorous interview with Stephen Colbert, Miller says that he chooses to believe that God does not deceive the human race. All the evidence for evolution (which he sees daily) is not a lie. He believes that God has set the process of evolution into motion, creating himself and Colbert, and perhaps even Bill O'Reilly.
` And as for supposedly having no hypothetical path of evolution that could lead to such a flagellum, Matzke clearly contradicts this notion. It's a bit technical, however. Even more technical is an informative article entitled Type III secretion systems and bacterial flagella: Insights into their function from structural similarities.
` As you should know by now, Behe was apparently not aware of most scientific papers on this subject, probably including those last two. So, just because
he says there weren’t any scientific papers on this subject, this does not mean it is so!
The intracellular transport systems in plant and animal cells are also extremely complicated. Cellular components including proteins and enzymes have to be transported between various cellular compartments. Some components are packaged into molecular “trucks”, and each truck has its own unique “key” that can only fit the “lock” of its cellular destination. Other types of proteins act like loading docks -- opening and dumping the contents into the compartment once the transport system has reached its destination. Of course, I’m simplifying this and am speaking in lay terms. It reality, it is all much more complex than this.
` Yes, I am not ignorant of these facts. Are you suggesting that this is too complicated to have evolved, just because you cannot imagine this happening? A few IDists have written on such subjects, suggesting that it cannot. For example, Lee Spetner has written all about how ligands and receptors could not possibly evolve because, he says, evolution cannot produce new information. It sounds like you are familiar with his work.
` Sadly for Spetner, it turns out that his work is (unsurprisingly) not based on reality. For example, Ian Musgrave has much to say on the subject. (And what does Ian Musgrave do? According to the Panda's Thumb: His current area of research is into a protein so obscure that only four other people actually belive it exists. He is also researching Alzheimer’s disease, for reasons he can’t currently remember.)
` This biomedical researcher has has written a most illuminating article on this subject, and I think you will find it quite comprehensive. (Comprehensible is another matter, however....)
` Not certain that you will bother, however, I have pasted here the more intriguing parts. First of all, it would appear that Spetner is using an inappropriate method for his work:

It is interesting that in a book supposedly about information theory, the classic formulation of information theory of Shannon and Weaver (2) does not get mentioned.
` Yes, quite interesting! It turns out that most people who are attempting to discredit evolution also ignore this most important tool.
` Besides this, what does Musgrave promise to deliver in this paper? (Emphases mine.)
In this review I will consider if Spetner's metrics can be validly applied to biology, and how Spetner actually applies them to real world examples. Although his arguments are superficially plausible, a closer look with some knowledge of biochemistry shows significant flaws. I will first briefly describe Spetner's metric of information, I will then show that 1) Spetner's metrics depend on a binding mechanism that does not occur in nature, 2) that Spetner's metrics require that substances bind to enzymes in an all or nothing fashion, whereas real substrates do not bind in this way. Furthermore, I will show that Spetner himself is inconsistent in his application of his metrics. In his Xylitol example he does not actually use the measure he develops, and in the streptomycin example he swaps to a different metric, when his original metric would show increased information. Finally, I will show that his "directed evolution" model is based on a misunderstanding of one form of random mutation.
` So, first of all, Spetner’s binding mechanism that he says must be designed does not actually exist.
...[I]t might seem intuitively obvious that a more specific lock accepting only one key has more information a less specific lock which accepts many keys. This is actually incorrect, but rather than go into this here see this paper on cryptography and master keys.... For the moment we will accept this though.
` Analogously we might expect an enzyme is more specific because it has more binding points than an enzyme that is less specific (and there is also the unstated assumption that single substrate enzymes are more important than multi substrate enzymes. They are not).
For example we might imagine an active site that uses 4 binding points has more information than one with two binding points.... Unfortunately, biology doesn't work that way.
` And, of course, he goes on to explain in what way biology does work, if you would be so interested to learn.
` Second of all, he demonstrates that; the real world the binding of a ligand to a protein is not an all or nothing affair, substrates have varying degrees of "stickyness", which is not addressed by Spetner's metric. Even a very specific enzyme will bind one ligand very tightly, a few not so tightly, and a great number very weakly. One cannot simply say that only very strongly bound ligands will be considered, as very weak ligands may be of great physiological importance, if they are present in a high enough concentration.... This has a theoretical and a practical implication....
` Which Musgrave then explains, if you should be so curious.
` Also:
Note that the amino [acids] are in different positions in the different receptors... partly because the AT2 receptor has a longer C-terminus, and also due to an insertion into the sequence between N and K and between K and H in the AT2 receptor. [There are illustrations here to help people from getting lost.] Thus the concept of "precise sequence" is not exactly applicable to receptor binding. The amino acids are [brought] close (but not into a linear sequence, more like a ring) by the three dimensional folding of the proteins, and this three dimensional folding is [brought] about by very different sequences.
` This is problematic for Spetner's claims, as the sequence DNKH depends on a number of factors that are NOT dependent on that sequence, thus the "true" information content is not reflected by the binding sequence alone. Again note that the three dimensional folding is not rigid, and flips between a number of different states (Protein chains are somewhat flexible, more like a ball of semi-cooked spaghetti than the rigid shapes they are sometimes drawn as, thus enzymes and receptors are "floppy" locks and ligands are "floppy" keys: this is relevant to Spetner's claims, more later)
` Again, what Spetner says might make intuitive sense, but it does not match up to the real world. Indeed, modeling proteins after words is not a very accurate way to describe them:
Broadly analogous to ghtshi-lightship "binding". F actually binds to both K and H. This is mostly electrostatic interactions rather than the physical "bumps and hollows" Spetner uses in his (incorrect) analogy for streptomycin binding. The basic amino acid R binds electrostatically to the acidic amino acid D, Y and N form hydrogen bonds and F forms a pi bond with H, and a hydrogen bond with Y. (In SarAsp, the acidic D interacts with the acidic D, but dipole charge distribution means that they bind rather than repel. Chemistry and common sense do NOT go well together. (5,6))
` But as we look at SarIle and SarAsp, we can see Spetner's model of binding is going badly wrong....
` After this, he then goes on to address the fact that the length of the binding string is not actually related to the number of ligands.
So, what happens when we shorten the binding string DNKH. According to Spetner's model, you should increase the number of ligands bound. We can mutate the amino acid H to A (alanine), Q (glutamine) or R (arginine). The Q mutation keeps charge and size, but loses the pi bonding, the R mutation keeps the charge, the A mutation loses charge and size, thus mutations from H to R and A are like truncating the binding string to DNK. In the AT1 receptor, the binding doesn't change with any of these mutations. When we mutate H to Q or R in the AT2 receptor, all binding is lost (7,8). Either way, Spetner's model is dead wrong about what happens when the "string length" of a ligand binding string is shortened (and this again invalidates his measure).
` Even worse, what happens when you mutate N in DNKH (Asparagine at position 111 in the AT1 receptor and position 126 in the AT2 receptor)? If you mutate N to G (glycine) a very short neutral amino acid, unlike the longer charged asparagine, there is no contact with the ligand and the G, so the binding sitestring becomes DKH. Despite this truncation, you still bind AII, AIII, etc., but AIV has become "stickier"(something which Spetner doesn't actually address in his metric). As I mentioned before, the AT receptors flop between several conformational shapes. The N->G mutation restricts the receptor to fewer conformational shapes, making it MORE specific....
` Thus binding is a critical function of 3D shape, not covered by Spetner's metric, and a single mutation can increase specificity (as according to Spetner's criteria, a protein that has one conformational shape has more specificity than one with multiple conformational shapes).
` What is going on here is that Spetner has insisted that the substrate number corresponds to the amount of information in the proteins. Musgrave is explaining that nature does not function in this way.
` Furthermore, he shows that Spetner is using measuring systems that are utterly inappropriate as to what he is trying to show.
He does consider a biochemical measure called specificity, but this is not Spetner's specificity measure.... Critically, two substrates can have the same binding specificity, but different catalytic efficacy which confounds the information analysis.
` He goes on and on and on about everything in this experiment, from Spetner’s irrelevant measuring practices to filling in information that was completely glossed over – in light of which Spetner’s arguments make no sense.
...If you exclude a lock and key binding allosteric modulator of enzyme action like streptomycin from consideration, then you are ignoring biology.
` Indeed; Spetner seems unusually fond of doing that....
Streptomycin-binding ribosomes turn out garbage proteins because streptomycin messes up the proof-reading centre (which is how streptomycin kills bacteria). The mutant version which doesn't bind streptomycin is actually MORE accurate, i.e. more SPECIFIC, than the wild type. The wild-type proof reading centre makes a few mistakes even in the absence of streptomycin, and the mutant forms make even fewer mistakes than the wild type( roughly 85% fewer; 12).
This is a clear increase in Spetner's binding specificity:
1 - The mutant gene product doesn't bind streptomycin at all (it has one ligand rather than two)
2 - It binds the substrate peptidyl tRNA more accurately
3 - It catalyses more accurate peptide synthesis.
Does Spetner acknowledge this? No, Spetner now swaps to the expectation measure and claims (without evidence) that since there must be more S12 sequences that don't bind streptomycin than those that do, information must have decreased (why didn't he do this analysis on the ribulose enzyme?).
However, he is dead wrong....
` Does this not sound the least bit intriguing to you? And, as for mutations which supposedly imply a driving force behind them:
The apparent existence of "directed" mutations was based on some early work by Barry Hall. However, Spetner did not follow up the more recent research on this work, and misunderstands the origin and significance of "directed" mutations.
` Which are henceforth known as “Fred.”
"Fred" occurs only under non-lethal selection in non-dividing cells, and has been suggested to be a neo-Lamarkian mechanism for getting environmental information into the genes. However, "Fred" is no such thing (16,17,18), and is not directed in the sense that Spetner suggests....
` ...So the following model shows how "adaptive" mutations occur. Nutritionally deprived non-growing cells are under stress, stress leads to double stranded breaks in the DNA, recombination vis RecBCD primes the DNA synthesis, DNA PolIII finishes the job but makes mistakes, which slip through because starvation has largely turned off mismatch repair. This results in genome wide mutation at a faster rate than normal, and the occasional mutant that can utilize the "selective" substrate (16,17,18).
` Indeed, he goes right ahead and shows a real-world instance of this. If you'd like to actually read this article, it is here for the viewing! And, if you take issue with Musgrave, go complain to him on his blog! (Actually, a much more constructive place to get his attention is The Panda's Thumb. It's fun!)
` Anyhow, the idea that these cellular receptors cannot evolve due to their supposed inability to increase in information is but one example of research done by a creationist with the preconceived, dogmatic notion in mind that something is too complex to have evolved. Like other such research of this type, however, it is massively flawed to the point where it bears no resemblance to reality.
` Of course, I am not a scientist like Miller or Musgrave; I merely understand how it works. And, I am knowledgeable in many broad fields of biology. Despite my non-professionality, it is still easy for me to see blatant discrepancies with scientific facts and concepts while reading ID material, so much so that I could make a hundred posts, each about a different IDist distortion! (And I probably will, eventually, so please be patient.)
A wide variety of other examples could be cited, but this isn’t MY blog.
` And, so far as I have seen, those are also just as easily refuted.
What is boils down to is that even cells -- the most basic ingredient in life -- are breathtakingly complex.
` Biologists are well aware of this breathtaking complexity, as well as the fact that cells are also assembled rather haphazardly, full of closely-related structural ‘copies’ that do different things, other parts that are atrophied into uselessness, and generally full of lots of little extraneous molecular bits which do not inhibit functioning when removed from the system. (In fact, they only seem to get in the way!)
` That is not something that Intelligent Design proponents are wont to mention, as they apparently know very little of these things; they mainly listen to each other’s ‘findings’ and then cry “bigots!” whenever scientists tell them that their arguments are based on something that has little basis on the real world.
James Shapiro, a professor of biochemistry at the University of Chicago, once wrote, "There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system, only a variety of wishful speculations." I would have to agree with him.
` True, he says this although did you know that he does not find any evidence for Intelligent Design, either? Besides, the fact that he’s a scientist is no reason to take him seriously. That’s what objectivity is needed for!
Scientists have on occasion suggested non-Darwinian theories to account for the origins of the cell, but I don't find any of them the least bit convincing. Instead, I find it most likely that the complex systems were in fact deliberately designed. I’ve seen no evidence of another mechanism aside from deliberate design, including Darwin's theory of evolution, which is capable of producing that kind of complexity.
` Non-Darwinian accounts of the cell? I'm not even going to get into that. So far as I see, you are so completely hung up on complexity even though you do not seem to know what it is. High levels of complexity do not necessitate a designer in many cases; an overly-simple example is the fact that a naturally-forming crystal is a much more complex structure than a crystal ball that has been ground and polished by humans; yet, which was constructed with an intent?
` Did you also know that randomness can be very complex? I am not suggesting that evolution is random, however. Indeed, mutations are random, and they are many and varied. Natural selection is by definition not random.
If scientists demonstrated that bacteria without a flagellum could systematically evolve such a feature, or evolve any new structure of comparative complexity, my system of thought would be called into question. But so far, this hasn’t happened, and I doubt that it ever will.
` And of course, I have directed you to a few articles which do indeed demonstrate both the scientific principles behind flagellum evolution as well as at least one possible way it could have come about: Just because Behe is ignorant of such research does not mean that you have to be.
` So, what say you?
But, I AM open-minded, and my belief in a creator doesn’t mean that I am unable to consider that this creator might have used mechanisms that I hadn’t considered to do the creating.
` Here is one thing I hope you are willing to consider: Intelligent Design proponents don’t care about scientific accuracy as long as they succeed in making Christianity a part of science in the public eye.


Galtron said...

Um, Quine..... I'm fairly sure the ID people have already convinced this Dawn-person of their scientific legitimacy. (And, apparently that Steve-person as well.) What on earth makes you think she will even listen to you?
I know your post makes 100% sense, but how could she judge that when the ID people have taught her that following ancient scriptures is just another way of knowing that is completely equal with science?

S E E Quine said...

` Quiet, you!!!

` ...Ohhh, I guess you're right. Especially since you evidently weren't pulverized by the impact: From this evidence, I hypothesize that it would not make so much as a dent in the psyche of a person so influenced.

` Grah.

Galtron said...

Also, I just thought of something..... what Dawn called 'natural laws' are probably not supposed to be 'laws of nature', but some kind of Darwninan thing she is refferring to.

S E E Quine said...

` D'oh!! I think you're right!

Galtron said...

I wonder if our candid, arrogant-sounding exchanges have pissed her off?

S E E Quine said...

` Yes, we do sound like bastardly, exclusionary people in here, don't we?
` Well, hey, it's only because we happen to be on the same level.