Tag Archives: Sequence

William Dembski discusses irreducible complexity and co-option

William Dembski explains what the debate on origins is really about.

About the speaker:

Dr. Dembski has taught at Northwestern University, the University of Notre Dame, and the University of Dallas. He has done postdoctoral work in mathematics at MIT, in physics at the University of Chicago, and in computer science at Princeton University. A graduate of the University of Illinois at Chicago where he earned a B.A. in psychology, an M.S. in statistics, and a Ph.D. in philosophy, he also received a doctorate in mathematics from the University of Chicago in 1988 and a master of divinity degree from Princeton Theological Seminary in 1996. He has held National Science Foundation graduate and postdoctoral fellowships.

The lecture:

Part 1:

Part 2:

Part 3:

Summary (snark is in italics)

What is evolution:

  • Is it enough for Christian students to just retain their faith in college?
  • Or should Christian students seek to transform their universities?
  • The word “evolution” refers to a unguided, purposeless, undirected process
  • Living organisms are not designed, they just appear to be designed
  • Therefore, it is an atheistic theory – there is NO ROOM for God
  • Random variations and natural selection can do the creating of life without God
  • Nothing about evolution suggest that God had anything to do with it

The appearance of design:

  • The cell is a nano-engineered information processing system.
  • The cell has engineering, e.g. – signal transduction, message passing, etc.
  • There are molecular machines similar to man-made machines, but less efficient
  • E.g. – the bacterial flagellum which has 40 parts
  • These molecular machines have minimal complexity – all the parts are needed
  • can’t build a molecular machine step-by-step – all the parts must be present and integrated

How does evolution try to explain molecular machines:

  • The standard naturalistic response is “co-option”
  • Each intermediate step has pieces that are used for other purposes
  • I.e. – Subsets of the parts can have different functions
  • For example, a subset of the bacterial flagellum can be used as a syringe
  • The subset, called the Type-3 secretory system, has only 13 parts
  • The problem is that evolutionists don’t show all the steps, and all the functions
  • For this to be a good response, you need a smooth path from 1 part up to 40
  • Each step of the path has to have a working system with a different function
  • But the atheists don’t have the path, or the intermediate functions
  • It’s like arguing that you can walk from Seattle to Tokyo via the Hawaiian islands

Is the bacterial flagellum a cherry-picked example?

  • There are no detailed molecular pathways for any biochemical systems in the cell
  • The atheistic response is to speculate that pathways will be found as science progresses
  • The pathways are unobservable entities, just like the multiverse and the Cambrian precursors

Where does the machinery to create proteins come from?

  • The molecular machines are composed of proteins
  • The proteins are manufactured by copying protein-building instructions from the DNA
  • The instructions are carried to the build site by messenger RNA
  • The build site is called a ribosome
  • The DNA requires proteins to build, so there is a chicken-and-egg problem
  • The problem is that protein transcription systems require everything in place
  • There is no materialistic theory about how to build this step-by-step

So what do the molecular machines tell us about how life began?

  • The problem of the origin of life is the problem of the origin of information
  • What needs to be explained are the functional sequences of parts
  • The sequences are identical to sequences of letters that make sense
  • The atheist has to say that material processes can create the information
  • The problem of finding sequences of amino acids or proteins is a search problem
  • A blind search of the space of possible sequences is not efficient
  • even with lots time, parts and trials, you can’t converge on functional proteins
  • information is required and the only known producer of information is a mind

Bill is one of my favorite people. He’s smarter than practically all of the atheists who dominate the universities. But because he is an outspoken Christian, he never gets the recognition he deserves. He just keeps plugging away on his research. He doesn’t make excuses.

What is intelligent design?

Related DVDs

Illustra also made two other great DVDs on intelligent design. The first two DVDs “Unlocking the Mystery of Life” and “The Privileged Planet” are must-buys, but you can watch them on youtube if you want, for free.

Here are the 2 playlists:

I also recommend Coldwater Media’s “Icons of Evolution”. All three of these are on sale from Amazon.com.

Related posts

William Dembski debates Lewis Wolpert about intelligent design

It’s the latest debate from Unbelievable, courtesy of Justin Brierley!

The MP3 file is here.

Details:

William (Bill) Dembski is an American mathematician, theologian and professor of Theology at Southwestern Baptist Theological Seminary, TX. He debates the issue of ID with atheist Lewis Wolpert, Emeritus Professor of Biology at University College London.

For Bill Dembski see http://www.designinference.com/ or his blog http://www.uncommondescent.com/

For Lewis Wolpert’s Wikipedia profile see http://en.wikipedia.org/wiki/Lewis_Wolpert

Intro:

  • Bill Dembski’s religious background (Catholic-raised atheist/agnostic, later Protestant)
  • Dembski’s view of the interface between science and religion
  • Lewis Wolpert’s religious background (Jewish-raised atheist)
  • Wolpert’s view of whether God exists

First half:

  • Dembski explains the mathematical foundations for detecting design
  • Wolpert asks whether designs can emerge without intelligence
  • Dembski asks whether anything in biology could be like SETI signals
  • Wolpert says that it is impossible to recognize design in biology
  • Dembski asks whether the Darwinian hypothesis is falsifiable
  • Wolpert says that it is never warranted to rule out chance as an explanation
  • Dembski says that you can set limits on what chance can do within a certain time
  • Wolpert says that chance can do anything regardless of time, etc.
  • Dembski says, what about the work of Doug Axe published in the peer-reviewed JMB?
  • Wolpert says those calculations must be wrong!
  • Dembski says then you’re just a dogmatic reductionist
  • Wolpert agrees that he is a dogmatic reductionist

Second half:

  • Dembski explains why intelligent is not repackaged creationism
  • Dembski explains why intelligent design isn’t an argument from ignorance
  • Dembski talks about whether evolutionary mechanisms can create more information
  • Wolpert asks whether chemistry requires intelligent design too
  • Dembski says that there is a fine-tuning argument for cosmological constants too
  • Wolpert agrees that the origin of life is unexplained naturalistically
  • Wolpert asks if everything after the origin of life is explained
  • Dembski says that there are still problems like the Cambrian explosion
  • Wolpert asks Dembski if anything could falsify intelligent design
  • Dembski gives an example of something that could falsify intelligent design
  • Dembski asks whether naturalistic explanations of life are falsifiable
  • Wolpert asks whether intelligent design affects the way that people do science
  • Dembski asks whether it is possible that the resources of naturalism are adequate to explain life
  • Wolpert says that you can’t explain anything in nature as the result of intelligence
  • Dembski says that it happens all the time in other sciences like engineering
  • Wolpert says that he doesn’t want a Designer
  • Dembski says we should just follow the evidence and who cares what people on either side want

And then there are closing speeches.

I am not sure if I had anything to do with this, but I did send Justin Bill’s e-mail address recently. I’m pretty happy that Justin managed to get Bill and Lewis to debate on this topic. Justin says that Bill will be back next week! He’ll be discussing his new book “The End of Christianity” which is about the problem of evil.

Did you miss Lewis Wolpert’s last debate with the professor of nanotechnology?

UPDATE: Justin says that it was indeed my e-mail that helped him to contact Bill, and what’s more we should expect a show that features Stephen C. Meyer soon, too!

MUST-READ: Doug Axe defends intelligent design at science conference in Germany

Doug Axe got his Ph.D from Caltech and did post-doc research at Cambridge University, and published some of his findings in the peer-reviewed Journal of Molecular Biology. He was trying to see whether it is easy or hard to shuffle amino acids randomly in order to make functional proteins. Those JMB publications show that the number of functional amino acid sequences is tiny, compared to the number of possible sequences.

Doug Axe’s research likewise studies genes that it turns out show great evidence of design. Axe studied the sensitivities of protein function to mutations. In these “mutational sensitivity” tests, Dr. Axe mutated certain amino acids in various proteins, or studied the differences between similar proteins, to see how mutations or changes affected their ability to function properly. He found that protein function was highly sensitive to mutation, and that proteins are not very tolerant to changes in their amino acid sequences. In other words, when you mutate, tweak, or change these proteins slightly, they stopped working. In one of his papers, he thus concludes that “functional folds require highly extraordinary sequences,” and that functional protein folds “may be as low as 1 in 10^77.”

And now let’s see what he was up to in Stuttgart, Germany.

Story here from Evolution News.

Excerpt:

While there have been many events to discuss intelligent design sponsored by the scientific establishment this year, few have dared to invite an actual design proponent.

But on the 150th anniversary of On the Origin of Species, Biologic Institute Director Douglas Axe was invited to the National Museum of Natural History in Stuttgart, Germany, for a panel discussion titled Design without a Designer? where “the ‘bold generation’ of young thinkers turned up in droves, listening intently as the discussion went well beyond its advertised ninety minutes.”

Here’s the official description of the event (in German), and a translated excerpt:

On the occasion of the 150th anniversary of the first publication of Darwin’s theory, this high-caliber panel discussion between evolutionists and Darwin critics will consider the question of whether the evolution of life on Earth is based solely on blind and unguided natural processes, or whether there is non-religiously based, verifiable evidence of meaningful and purposeful acts of creative intelligence in the natural world. This meeting at the Stuttgart Museum of Natural History aims to contribute constructively and with clarity and objectivity to this important debate. A public debate between evolutionary biologists and evolutionary critics at this high level is very rare in Germany, and therefore can be expected to be a very exciting evening.

You can read more at the Biologic Institute. They even have excerpts from Doug’s opening statement. It’s short and to the point.

Excerpt:

William Dembski and Stephen Meyer have both framed the design argument in terms of functional information, meaning information that specifies a significant functional outcome.  Since this fits well with my own understanding, I offer the following three-statement summary of the design argument:

First: Living things contain within their genomes large amounts of functional information.

Second: The only cause known to be capable of generating large amounts of functional information is intelligence.

And third: It is therefore reasonable to infer that the functional information in living things must have an intelligent source.

Here we have not a pronouncement but an argument based on evidence and logic.  It is perfectly fair to argue against it, of course, but it is hardly fair to dismiss it as dogma.

I like this, because I am a software engineer. This is what we do.

How long will it take to sort a deck of cards by trial and error?

Inside the cell, things like proteins and DNA are formed by sequencing parts together in just the right way so that the sequence will have biological function. If the sequence is wrong, because some component of the sequence is the wrong piece or is in the wrong place, the sequence has no function. It’s just like writing English or computer instructions.

To calculate the probabilities, you have to use a rule called “The Product Rule”, because the order of the parts in the sequence (“permutation”) is important. For example, the odds of getting the sequence “ABC” just by choosing three random letters is 1/26 x 1/26 x 1/26 = 1/17576. Things get very unlikely quite quickly, don’t they?

So, take a look at Neil Simpson’s latest post, where he uses cards instead of letters or amino acids, but the principle is exactly the same. His calculation is a little different because the odds actually go down a little each time you choose a card. So, for the first card, it’s 1/52, but the second card is only 1/51, and so on…

Excerpt:

This is by no means a definitive argument against evolution, but I offer it to put the “time, chance and random mutation” theory in perspective.

Everyone knows that micro-evolution occurs, such as dog breeding and bacteria becoming resistant to antibiotics.  But macro-evolutionists believe that with enough time an amazingly complex single cell of unknown origin could make lots and lots of small changes, develop reproductive capacities and eventually become humans, elephants, caterpillar/butterflies, chameleons and so much more.

Let’s consider something very simple.  Imagine that you shuffle a deck of cards.  If you shuffled it one time per second, how often would all the cards go back into their original order? (Ace of spades, King of spades, etc.)  The math is simply 1/52 (the odds of the Ace of spades being on top) times 1/51 times 1/50, etc. I left out the Jokers to make it easier.

Guess how many years it takes?

Click through to see his calculations, or do them yourself! It’s easy and fun! Neil has a pretty fun discussion going on with the angry atheists who frequent his site, too.

This is everyone should learn probabilities in school, because then we can really talk about these things with our neighbor. Shalini can even do biochemistry, so she can actually explain it even better than I can!

Remember, we are looking for a specific sequence of cards – the sequence that the cards originally came in. In this example, it’s that sequence and that sequence alone that has biological function. The other sequences are just junk – they have no biological function. And most importantly, you don’t get to save any of the cards that are in the right spots because the sequence as a whole has no present function that would allow it to be “saved” for later. You have to re-select all 52 cards each time at random!

A typical protein isn’t made of 52 parts, it’s made of around 200, and there are 80 possible amino acids, not just 26! And in the case of proteins,the vast majority of the possible sequences that you can make won’t have any biological function at all! (And there are many more problems besides, such as chirality, cross reactions, and bonding type). Even if you filled the whole universe with reactants and reacted it all at Planck time, for the entire history of the universe, you still wouldn’t be likely to get even one protein!

You can read more about the origin of life in this post.

Is the presupposition of naturalism a science stopper?

UPDATE: Welcome readers from 4Simpsons! Thanks for the link Neil!

In cosmology, we had to wait decades for the theism-friendly big bang theory to beat out atheism-friendly theories like the eternal universe model, the steady-state model, the oscillating model, etc. Piles of taxpayer money wasted trying to prove atheistic flights of fancy. But in the end, the evidence for the big bang was too much for the atheistic theories, and we beat them out.

Junk DNA

And here is another example of how atheism is bad for scientific inquiry: “Junk DNA”.

The purpose of the genome is to contain the instructions that allow the cell to build functional sequences of smaller components. If the sequences are done right, you get a folded-up protein that can be used for all kinds of things.

But what those parts of the genome that don’t code for proteins? Well, atheists have been calling them “Junk DNA” and hailing it as proof that there is no designer to life. I can remember Christian groups like Reasons to Believe predicting that a purpose for “Junk DNA” would be found. But atheists pooh-pooh’d that idea. Gee, I wonder who was right? The same people who are always right: THEISTS.

Denyse O’Leary cites this Princeton University press release on Post-Darwinist:

Now researchers from Princeton University and Indiana University who have been studying the genome of a pond organism have found that junk DNA may not be so junky after all. They have discovered that DNA sequences from regions of what had been viewed as the “dispensable genome” are actually performing functions that are central for the organism. They have concluded that the genes spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow.

…The term “junk DNA” was originally coined to refer to a region of DNA that contained no genetic information. Scientists are beginning to find, however, that much of this so-called junk plays important roles in the regulation of gene activity. No one yet knows how extensive that role may be.

She’s got a stack of other related links at the bottom of the post.

Commenter ECM also sent me this story from Cornelius Hunter’s new blog.

Excerpt:

One problem with evolution is its strong bias toward viewing everything in biology as a kludge. When a newly discovered structure is examined, evolutionists take one look and conclude it is leftover junk. After all, blind, unguided mutations and other processes just happened to produce everything we see. The evolutionist’s going in position is that biology is a fluke. We’re lucky anything works.

Hunter then cites this passage from some naturalist researchers who study “junk DNA”:

Here we have a molecule that serves an important role in how cells function and survive, but it contains these puzzling ‘junk’ sequences that don’t seem to have any apparent purpose. Our work suggests that this disorder is really a way of creating flexibility, allowing the protein to function as a molecular switch, a process that is thought to go wrong in certain diseases.

Evolution has provided researchers with convenient modular structures, areas that are repeated over and over again to make up proteins, and so we tend to dismiss the interspersed disordered sequences that don’t seem to have any definable structure. Here we show that the weak molecular interactions in a disorganized protein sequence are essential in giving this protein its unique attributes.

Know what? If you substitute “Flying Spaghetti Monster” in there for “Evolution”, it makes just as much sense! Try it! Evolution causes toothpaste to come out of the toothpaste tube when you squeeze it, and Shakespearean rhyming couplets to rhyme, and my Java code to compile. It’s all evolution!

Conclusion

Atheists, always remember this quote from agnostic NASA astronomer Robert Jastrow, regarding the progress of science:

For the scientist who has lived by his faith in the power of reason, the story ends like a bad dream. He has scaled the mountains of ignorance; he is about to conquer the highest peak; as he pulls himself over the final rock, he is greeted by a band of theologians who have been sitting there for centuries.

In the 1920s, there was no theory about a universe that begins to exist out of nothing, no fine-tuning, no DNA, no Cambrian explosion, nothing. Then science progressed, reducing atheism to a kind of childish delusion, still believed by ignorant snake-handlers and people with certain persistent moral, … ah… issues. But that’s what psychiatrists are for!

Science is always for us, it’s never for you. You have faith. Blind faith. We have all the evidence. We invented science, and every new discovery makes your materialism look more silly and naive… you bravely hold out hope for some hopeful Flying Spaghetti Monster to swoop in and rescue your atheism from the big, bad mind-independent reality. When will you grow up?

There is no Flying Spaghetti Monster!