Start communicating
ID
Recent Village Updates
Login to find out
has added a new journalLeaping into Trouble
Douglas Axe
Perspectives (April 3, 2008)
Biologic Institute
Proceedings of the National Academy of Sciences USA, Journal of Molecular Biology, and Biochemistry, among others, and has been reviewed in Nature and featured in a number of books, magazines and newspaper articles, including Life?s Solution by Simon Conway Morris and The Edge of Evolution by Michael Behe.]
Darwinists have always recognized the existence of an intuitive barrier that prevents many of us from joining them. Human understanding of complex things is strongly shaped by our experiences with human technology. You don?t have to be an engineer to appreciate in some way the extraordinary difficulty of getting physical systems to perform extraordinary tasks. Technology doesn?t just happen. It only comes with sizable investments of genius and diligence, along with more than a little patience.
So Darwin?s suggestion that genius and diligence are optional if patience is plentiful is a stretch for most of us. Richard Dawkins put it this way:
?It took a very large leap of imagination for Darwin and Wallace to see that, contrary to all intuition, there is another way and, once you have understood it, a far more plausible way, for complex ?design? to arise out of primeval simplicity. A leap of the imagination so large that, to this day, many people seem unwilling to make it.?
I doubt anyone, Dawkins included, would generally recommend sweeping aside all intuition to accommodate leaps of imagination, particularly when the intuition is your own and the leap is not. If Darwinism really is plausible, it must instead be the case that Darwin leapt to something of substance?something that really explains how, contrary to our intuitions, the remarkable gadgets we see in biology can be chalked up to mindless inevitability. What exactly is this explanation? It needs to be compelling, whatever it is, since the intuition we?re being asked to abandon is so tied to real-world experience?the very stuff of science.
About forty years ago, plant physiologist Frank Salisbury posed the question in terms of the origin of enzymes, the intricately folded protein chains that do all of life?s chemistry. Appearing in thousands of distinct natural forms, each form suited to a well-defined function or set of functions, these tiny workhorses have proven to be technological wonders not just inside cells but in laboratories as well. Much of today?s advanced technology for manipulating and analyzing DNA depends on them. Genomes don?t get sequenced without them. Whole companies are devoted to purifying them and selling them. Do little marvels like that really just happen if we wait long enough? Long before the age of genomics, Salisbury put the question this way:
?In reasonable time intervals, is mutation by random rearrangement of nucleotides likely to produce an enzyme? Will there be an enzyme (gene) for selection to act on??
Here?s the problem. Enzymes, like all proteins, are built within cells by linking amino acids together into long chains. There are 20 different amino acids, any one of which could potentially be placed at any position along the chain. But the actual chain sequences are anything but arbitrary. Rather, cells use elaborate machinery to link the amino acids according to the precise sequence specifications contained in genes. And because the protein chains are typically hundreds of amino acids long, the cellular machinery is hitting a very tight design specification every time a protein is made. So, even if we grant that some changes to these specifications are tolerable, the mere existence of a production line tuned to such precision implies that the precision is needed. If so, enzymes are much more complicated than they should be if they just happened. A short word might surface in your alphabet soup by chance, but a paragraph won?t.
In response to Salisbury, eminent British biologist John Maynard Smith offered an analogy along the lines of alphabet soup, starting with this succession of words:
WORD -> WORE -> GORE -> GONE -> GENE.
?This is an analogue of evolution,? he wrote, ?in which the words represent proteins; the letters represent amino acids; the alteration of a single letter corresponds to the simplest evolutionary step, the substitution of one amino-acid for another; and the requirement of meaning corresponds to the requirement that each unit step in evolution should be from one functional protein to another.? It?s an analogy worth considering because, despite its simplicity, it does capture the crucial aspect of different functions arising from different sequences.
Maynard Smith reasoned that for evolution to work, all functional proteins must be interconnected by stepwise changes in a manner analogous to four-letter words. But does his succession of words really illustrate Darwinian evolution? And is it really reasonable to think that proteins are analogous to four-letter words in this respect?
Actually, there appears to be a significant problem with the illustration itself. For a succession of changes to illustrate an adaptive process, each one has to provide not just function but function that is helpful in the sense of advancing a principal objective. For Darwinism, the principal objective is reproductive success. New functions are only adaptive if they advance that objective. Language has communication as a principal objective. While these objectives are very different, both imply that functions are very unlikely to be helpful simply by virtue of being new.
For example, imagine needing to communicate something with a vocabulary restricted to four-letter English words. ?NEED HELP CALL COPS?, might be the desired message. As a further restriction, suppose you?re granted your first word but have to construct the rest of your message from single-letter variants of that word or subsequent ones. Suppose also that adding a word is permissible only if it advances your communication objective as is. It becomes apparent that your objective needs to be met with your first word?the one given to you?because these constraints virtually preclude adding anything to it. ?HELP? on its own is much better than ?HELP KELP? or ?HEAP HELP?.
Furthermore, if letters correspond to amino acids, as Maynard Smith suggested, then biological functions that require several protein chains, each consisting of hundreds of amino acids, are more like lengthy messages than short words. If Darwin?s approach has trouble finding the words to summon the police, just imagine how much trouble it would have dispatching the police?to a particular location, prepared to deal with particular circumstances.
Of course, we should keep in mind that the exchange between Salisbury and Maynard Smith took place in 1969, when molecular biology was in its infancy. The genetic code, used by cells to build proteins according to the sequence information in genes, had just been cracked; only a few protein structures were known ; and the beginnings of the boom in DNA technology were still years away. But did the huge scientific discoveries of the subsequent decades strengthen Maynard Smith?s case? Have we found that protein structures, and therefore sequences, are mostly accretions of junk, with just a handful of amino-acid residues forming the equivalent of his four-letter words?
Quite the opposite. I was present in 1997 when the champagne was uncorked at the MRC Centre in Cambridge in honor of John Walker. He was to share the Nobel Prize in chemistry that year with Paul Boyer and Jens Christian Skou for his work on the structure of the enzyme complex that uses pH gradients to drive ATP synthesis. Known as F-type ATPase, this molecular machine is built of dozens of protein chains of seven specialized types. Boyer was not exaggerating when he described it as ?aF-type ATPase image splendid molecular machine?. With design elegance and miniaturization wholly unrivaled in human technology, the F-type ATPase is a double energy transducer, first converting gradient energy into rotational energy, and then using the rotational energy to make ATP, the chemical energy currency used in all life?all in a package 1/500 the size of a small pollen grain.
There is no junk here. The ATPase is made not of four amino acids but four thousand?more like an essay than a paragraph (much less a word). Could it have started out much smaller? Not much, in view of the two sections that have to be coupled for it to work. Like an essay, it might withstand trimming in some places, and some of the parts might be reworded if we knew the rules of composition for proteins. Typos can be tolerated to an extent, as with essays. But none of this explains how random single-letter changes can produce new essays, whether from scratch or from existing essays on other subjects. According to intuition, there?s only one way to get an essay.
So, Maynard Smith?s beautiful analogy ends up supporting the design intuition that troubles Darwinism so. And the funny thing is, it?s awfully hard to find an analogy that doesn?t do that. Maybe that?s why so many people are unwilling to leap along with Darwin?s imagination. And maybe that?s why the leapers keep resorting to the same arguments, long after their flaws are known.
The year that we toasted Walker?s achievements, geneticist Graham Bell?s excellent monograph on natural selection came out. Upon receiving my copy and glancing at the contents, I immediately turned to section 10, titled: ?Very improbable structures readily arise through the cumulation of small alterations.? That would certainly solve the problem, if structural innovations could morph themselves into existence, one adaptive frame at a time. So, was Bell going to deliver the goods that no one else seemed to be able to deliver? Was the long awaited violation of the design intuition finally going to be revealed?
I?m afraid not. Bell took his argument straight from Maynard Smith:
WORD -> WORE -> GORE -> GONE -> GENE.
Evidently three decades of huge advances in molecular biology hadn?t improved the case for the leap.
What about the design intuition, though? If proposed justifications for the leap always come up short, often validating the design intuition instead, doesn?t that indicate something more substantive than an intuition? Many would argue that it does, and you have to admit that their position has something potent in its favor. It?s called common sense. No leap required.
Dawkins R (1986). The Blind Watchmaker. Penguin Books.
www.neb.com
Salisbury FB (1969). Natural selection and the complexity of the gene. Nature 224: 342-343.
Maynard Smith J (1970). Natural selection and the concept of a protein space. Nature 225: 563-564.
pdbbeta.rcsb.org
www.ncbi.nlm.nih.gov
Bell G (1997). Selection - The Mechanism of Evolution. Chapman & Hall.
Login to find out
has added a new journalMystery of the origin of life and machines cracked! Important message from the Ministry of Science, Technology, and Education (recorded video broadcast: vatul.net).
Cast of Characters
- Richard Dawkins: well known atheist, initial MC, and rapper
- Daniel Dennett: zombie philosopher, and author of Darwin?s Dangerous Idea: Evolution and the Meanings of Life
- Eugenie Scott: NCSE cheerleader
- Christopher Hitchens: with ?I ?love? booze? sweatband and spliff
- Paul Z. Myers: associate professor at podunk UMM
- Sam Harris: atheist who wrote The End of Faith
- William Paley: who in his book Natural Theology popularized the analogy that upon finding a watch, you would assume it was made by a watchmaker
- Samuel Wilberforce: Bishop of Oxford who debated evolution with Thomas Huxley in 1860
- Charles Darwin: invented the Theory of Evolution
- Thomas Huxley: Charles Darwin?s Bulldog
runner_forever
Just for fun - the official transcript.Opening credits: Ministry of Science Propaganda. BEWARE THE BELIEVERS. THEY ARE AMONG US! Reporting Idiocy isn?t really squealing.
Richard Dawkins as MC: Ladies and gentleman, we are on the cusp of a glorious age. The age of the machine.
Crowd gasps at sight of machine.
Richard Dawkins: We appreciate your concern. It is noted, and stupid. After all, we are scientists; much, much smarter than you. But perhaps, a little demonstration will set your minds at ease.
Fades to laboratory.
A Scientist peering into a microscope: Hey, Wallace, take a look at this.
Darwinist pops up from behind lab bench, looks into microscope: Big deal. Natural selection creates that sort of thing every day.
Scientist, as Darwinist walks away: Natural selection? I think there is something else going on here.
Darwinist furtively radios back to PT-mafia: Big gadget, little tool. We?ve got ourself a situation.
The Machine busts through laboratory wall, snatches first scientist with lobster like claw, and throws him from an university tower after stamping ?Expelled? on his head. The Expelled scientist?s head crashes into and cracks lens for effect.
Fade to Richard Dawkins as MC: I wish I could take full credit for the machine?s development. For its efficient expulsion of so-called scientists, its unwavering rejection of your quaint but ludicrous notions about the origins of life. But the story of the machine began well before I arrived on the scene. For that, we present this little diddy:
Richard Dawkins snaps his finger, and is transformed into Eminem.
Richard Dawkins, with PZ Myers providing backup: My name is D to the I to C to the K, Yeah I?m the Dickie D, I got my Ph.D. and coming your way on the Youtube to bust your world view so just listen to me and don?t you argue.
You see, this battle?s been raging since Zeus was on the bottle, between Science like Democritus and Faith like Aristotle, who said the mover was unmoving like some magic trick but that?s no good logic, my posse is far too quick for this religious shtick.
cause science is the only way to know y?all, you stand with me y?all, or you can fall y?all. So go ahead and take your pick?
Eugenie Scott: Yeah you tell him Rick ?
Charles Darwin: cause if you don?t know me ?
Richard Dawkins: You don?t know dick!!!
PZ Myers leading the chorus : Yeah he?s the Dick to the Dawk to the Ph.D.,
he?s smarter than you he?s got a science degree!
Yeah he?s the Dick to the Dawk to the Ph.D.,
he?s smarter than you he?s got a science degree!
Unknown: On the shoulders of midgets we built up this machine,
Daniel Dennett: Yeah!!!
Richard Dawkins: Science silenced that watchdog wingnut Paley growing stronger and harder almost daily, storming Wilber by force as we framed the discourse that faith and science are split in schismatic divorce.
Then Darwin took to the seas to see what no one had seen, and ever since then we?ve been increasingly keen, they may never adore us, but they?ll no longer ignore us, give it to them PZ hit these with the chorus!!!
Chorus: Yeah he?s the Dick to the Dawk to the Ph.D.,
he?s smarter than you he?s got a science degree!
The Dick to the Dawk to the Ph.D.,
he?s still smarter than you he studied biology!
Richard Dawkins: Then there was Darrow dukin? it out with the straight and the narrow, a raging bull in the ring, he did his thing, and took it on the chin like he was Bobby De Niro.
We might have lost at Scopes, beaten down by the dopes, and the stooges of popes, but in losin? we coped, becoming more than we hoped, creationists slipped on the soap of their own slippery slope.
What was impossible, improbable, is now wholly unstoppable untoppleable, the Dick Doc?ll roll up as you creationists foldup
you haters talkin? bull, don?t you know that this Dick is un-cock-frickin? blockable ?
Chorus: Yeah he?s the Dick to the Dawk to the Ph.D.,
he?s smarter than you he?s got a science degree!
The Dick to the Dawk to the Ph.D.,
he?s still smarter than you he studied biology!
Richard Dawkins: Now the machine of our making, sees culture ripe for the taking,
cause I?m the rappinest, rabidest atheist who unlike the Catholic, Muslim or even the Jew, believes that no God but science could ever be true, hell if I was dyslexic I?d even hate Dog too.
Time to open your eyes, get yourself wise, the age of science will rise to be religion?s demise, and while you churchies all cry, shouting ?why God oh why,? I?ll still be popping my collar earning more dollars than Allah.
Hollah!
Chorus: Yeah he?s the Dick to the Dawk to the Ph.D.,
he?s smarter than you he?s got a science degree!
The Dick to the Dawk to the Ph.D.,
he?s still smarter than you he studied biology!
Login to find out
has added a new journalDarwinism is part of the theology of many theistic or deistic evolutionists because they apparently cannot conceive of any other way that God would run the world or they do not believe that God would create any other way, and thus Darwinism becomes their theological supposition. Then there are atheists who must have some naturalistic mechanism for evolution because they cannot admit that God exists and directs the world. It is not easy to tell the difference between the theistic or the deistic evolutionist and the atheist strictly on the grounds of evolutionary theory because they both see the same world in terms of life forms and their materialistic history, and they both seem chained to their theistic and atheistic beliefs as opposed to the empirical framework of science.
There is a third group, however, which does not allow predetermined beliefs to impinge on empiricism and theory. Whatever science reveals for them is how the world works. So they could believe in Darwinism if the evidence pointed that way, or they could accept intelligent intervention. The distinguishing feature of this group is that it remains free to accept whatever science shows. ID squarely falls into this third camp, and science leads the way for ID.
Nadeem
runner_forever
Thank you too for engaging me in an interesting dialogue.The so-called ?inferior? design sometimes turns out to be a misinterpretation due to human ignorance or incompetence. Let us review one recent case.
Darwinists used to claim that the inverted retina of vertebrates is bad design and that a designer would not have created the eye that way. The thing is that light has to pass through several retinal layers to get to the photosensitive cells at the back of the retina. And this is considered ?bad? design, for why were the photosensitive cells, it is asked, not placed at the front of the retina so that light did not have to travel all the way to the back of the retina through several retinal layers before the visual signal is transmitted to the brain? Dawkins protested:
?Any engineer would naturally assume that the photocells would point towards the light, with their wires leading backwards towards the brain. He would laugh at any suggestion that the photocells might point away from the light, with their wires departing on the side nearest the light. Yet this is exactly what happens in all vertebrate eyes. Each photocell is, in effect, wired in backwards, with its wires sticking out on the side nearest to the light. This means that the light, instead of being granted an unrestricted passage to the photocells, has to pass through a forest of connecting wires, presumably suffering at least some attenuation and distortion (actually probably not much but, still, it is the principle of the thing that would offend any tidy-minded engineer!)? (Richard Dawkins (1986). The Blind Watchmaker. London: Penguin Books, pp. 93-94.)
The eccentric arrangement of retinal wiring and photocells is, by the way, what causes the blind spot in human vision.
Now, a study published last year in the scientific journal PNAS shows that the wiring in the eye is cleverly set up this way for a good reason (press release: www.theregister.co.uk). The researcher remarked, ?Nature is so clever. This means there is enough room in the eye for all the neurons and synapses and so on, but still the Muller cells can capture and transmit as much light as possible.? The Muller cells ?work almost exactly like a fibre optic plate: a ?zero-length window? that optical engineers can use to transmit an image without using a lens.? There could be even more reasons for this peculiar design.
Darwinists interpreted the backward wiring of the retina (again, based on the predetermined philosophical constraint) as evidence for the purposeless process of evolution, which must produce a lot of trash. Darwinists claimed that no designer in his right mind would have muddled up the cells in such an eccentric way and that there is no good reason for the cells to be muddled up that way. Today, the creative arrangement of cells in the eye is inspiring engineers in the design of optics, sensors, and computers. Now that it is found that backward wiring is there for a good reason, is Darwinism?s claim that it is not there for a reason falsified? No, Darwinism will simply invent another speculative story to support how ?nature is so clever? that it produced the newly discovered arrangement through the purposeless process of mutation and selection. This is one of the ways that Darwinism seems immune to scientific falsification and seems more like a religious belief. Sounds like another Darwinian just-so story.
runner_forever
>> To add flavour to the discussion dna replication is sometimes not fault free also, is this also as per ID stance.The video is worth a clarification. Intelligent design does not require that all designed objects be necessarily optimized or always perform well. Indeed, a flaw in design does not refute design. Genetic abnormalities and diseases do not refute the design inference. A common objection against ID is that ?inferior design or flaw in design or sub-optimal design or painful design or abnormal design = no design.? Perhaps the confusion arises from the word ?intelligent,? which in design theory actually could refer to an intelligent agent who may even act stupidly (as long as the agent designs something). Dembski explained this point further in his writings.
In any case, first, no one, I think, would claim that the Toyota Camry was not designed if inferior design of the vehicle?s exhaust intake manifold leads to product recall or that the space shuttle was not designed since due to inferior design of the o-ring in the external fuel tank and the subsequent gas leak the shuttle exploded in mid-air shortly after lift-off. The objection against design in natural systems is theological in that God would not create inferior design or that God would create a perfect world or that God would not create genetic abnormalities and disease. ?How could God be evil or uncaring or incompetent?? we hear. Such objections, some of which were raised in the video, are not science (although theology offers clarification for theists). Interestingly, even some atheists raise similar objections even though they do not believe that God exists.
Second, engineers know that design can involve trade-offs, a phenomenon that occurs due to the laws of physics that govern the universe. That is why design cannot always be optimized across all engineering parameters. For instance, a robotics engineer may have to sacrifice one parameter (material strength) in order to optimize another parameter (weight) in a complex design that is intended to perform a specified function (e.g., robot should run the hilly Boston marathon with human-like biomechanics) with some acceptable level of quality, reliability, and designer satisfaction (finish the marathon within 2 hours and 45 minutes on a 72F day with light rain and 25mph winds out of the north-east, for instance).
Admittedly, the DNA replication process is not completely without faults, but the extreme precision with which the process normally takes place most of the time, not to mention the genome?s informational codes which are now being more fully appreciated, must also be taken into account. Dr. James Shapiro (Division of Biological Sciences, University of Chicago) explains the DNA replication process in the E. coli bacteria this way (emphasis mine):
?When an E. coli cell divides every 20 minutes, exquisitely reliable coordination has been achieved for hundreds of millions of biochemical reactions and biomechanical events. E. coli cells replicate their DNA at almost 4000 base-pairs per second but have an error frequency of far less than one nucleotide misincorporation per every genome duplication (2 X 4.6 million base pairs duplicated every 40 minutes; Cooper & Helmstetter, 1968; www.genome.wisc.edu). This incredible precision is accomplished not by rigid mechanical precision but rather by using two layers of expert error monitoring and correction systems: (1) exonuclease proofreading in the polymerase itself, which catches and corrects over 99.9% of all mistakes as soon as they are made (Kunkel & Bebenek, 2000), and (2) the methyl-directed mismatch repair (MMR) system, which subsequently detects and fixes over 99% of any errors that escaped the exonuclease (Modrich, 1991). Together, this multilayered proofreading system boosts the 99.999% precision of the polymerase to over 99.99999999%. At both stages of the error correction process, detailed molecular analysis has clarified the distinct roles of sensory and repair components. In the case of the MMR system, the sophistication is even more impressive because the molecules discriminate newly replicated from old DNA so that they only correct the newly synthesized strand (Radman & Wagner, 1988).? (?Bacteria Are Small But Not Stupid: Cognition, Natural Genetic Engineering, and Sociobacteriology,? Studies in History and Philosophy of Biological and Biomedical Sciences )
We must consider: what is the typical first time through (FTT) and parts per million (PPM) quality of a human-made product manufacturing facility and how does that compare to the E. coli?s DNA replication precision rate? Although design is not necessarily without flaw, biological nanomachinery generally far surpasses human-engineered products in terms of quality and efficiency.
runner_forever
In my opinion, it would be an impressive achievement far surpassing most of the other scientific or technological achievements of the human race if it is ever demonstrated that life came from non-life by purely naturalistic means and then replicated by the Darwinian mechanism, eventually producing the human machine and its conscious mind. If it is ever demonstrated that mud led to mind without intervention, the ID camp would be effectively wiped out (falsified), leaving no proverbial ID campers alive or the ID camp itself to embrace anything. This potential for falsfication is a key criterion of science.When I said that ID does not ?allow predetermined beliefs to impinge on empiricism and theory,? I mean that prior to the investigation ID as an epistemological framework does not rule out or forbid, based on some predetermined philosophical premise, any particular cause (law, chance, or agency) in the explanation of the natural world. However, if and only if the investigation shows that certain features of living things are most likely the product of intelligent cause and that natural processes are fundamentally incapable of producing those features, then ID would indefinitely hold on to those falsifiable hypotheses (as it currently does) until demonstrated otherwise, at which point ID itself would be falsified and would not exist as a viable theory to embrace anything. If the rival naturalistic or Darwinian theory ever demonstrates otherwise, then ID would no longer remain a viable theory to embrace the findings of the naturalistic theory, because ID?s aforesaid hypotheses would have been toppled (falsified). The theory itself would be dead, so to speak. Following the scientific investigation that probes both nature and agency as potential causes, the agnostic third camp proposes that natural processes alone cannot produce life from non-life (amino acids) or certain features of a conscious human machine from a single-celled bacterial machine and that some engineer?s plan and foresight are required. If a naturalistic theory demonstrates how such a complex-specified transformation (even one) could occur in the complete absence of intervention, the third camp would be wiped out (falsified) and would not exist to embrace anything.
Login to find out
has added a new journal"Do you not see that God made subservient to you all that is in the earth and the ships that sail in the sea by His command? And He withholds the sky from falling on the earth except by His leave. Surely, God is Compassionate, Merciful to humankind." -Quran 22:65
On the Universality and Other Attributes of the God of Nature
By Philip Freneau
All that we see, about, abroad,
What is it all, but nature's God?
In meaner works discovered here
No less than in the starry sphere.
In seas, on earth, this God is seen;
All that exist, upon Him lean;
He lives in all, and never strayed
A moment from the works He made:
His system fixed on general laws
Bespeaks a wise creating cause;
Impartially He rules mankind
And all that on this globe we find.
Unchanged in all that seems to change,
Unbounded space is His great range;
To one vast purpose always true,
No time, with Him, is old or new.
In all the attributes divine
Unlimited perfectings shine;
In these enwrapt, in these complete,
All virtues in that centre meet.
This power doth all powers transcend,
To all intelligence a friend,
Exists, the greatest and the best
Throughout all the worlds, to make them blest.
All that He did He first approved,
He all things into being loved;
O'er all He made He still presides,
For them in life, or death provides.
Login to find out
has added a new journalKnock out the human appendix. No effect observed on the body. Therefore, the appendix is vestigial or useless. What's wrong with this reasoning? Hint www.cnn.com).
Knock out a gene. No effect observed on the cell. Therefore, the gene performs no function. What's wrong with this reasoning? Hint: Cherished files on a computer.