Tag Archives: Amino Acid

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

Doug Axe explains the chances of getting a functional protein by chance

I’ve talked about Doug Axe before when I described how to calculate the odds of getting functional proteins by chance.

Let’s calculate the odds of building a protein composed of a functional chain of 100 amino acids, by chance. (Think of a meaningful English sentence built with 100 scrabble letters, held together with glue)

Sub-problems:

  • BONDING: You need 99 peptide bonds between the 100 amino acids. The odds of getting a peptide bond is 50%. The probability of building a chain of one hundred amino acids in which all linkages involve peptide bonds is roughly (1/2)^99 or 1 chance in 10^30.
  • CHIRALITY: You need 100 left-handed amino acids. The odds of getting a left-handed amino acid is 50%. The probability of attaining at random only L–amino acids in a hypothetical peptide chain one hundred amino acids long is (1/2)^100 or again roughly 1 chance in 10^30.
  • SEQUENCE: You need to choose the correct amino acid for each of the 100 links. The odds of getting the right one are 1 in 20. Even if you allow for some variation, the odds of getting a functional sequence is (1/20)^100 or 1 in 10^65.

The final probability of getting a functional protein composed of 100 amino acids is 1 in 10^125. Even if you fill the universe with pre-biotic soup, and react amino acids at Planck time (very fast!) for 14 billion years, you are probably not going to get even 1 such protein. And you need at least 100 of them for minimal life functions, plus DNA and RNA.

Research performed by Doug Axe at Cambridge University, and published in the peer-reviewed Journal of Molecular Biology, has shown that the number of functional amino acid sequences is tiny:

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.”

The problem of forming DNA by sequencing nucleotides faces similar difficulties. And remember, mutation and selection cannot explain the origin of the first sequence, because mutation and selection require replication, which does not exist until that first living cell is already in place.

But you can’t show that to your friends, you need to send them a video. And I have a video!

A video of Doug Axe explaining the calculation

Here’s a clip from Illustra Media’s new ID DVD “Darwin’s Dilemma”, which features Doug Axe and Stephen Meyer (both with Ph.Ds from Cambridge University).

I hope you all read Brian Auten’s review of Darwin’s Dilemma! It was awesome.

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.

New video takes you inside the cell to see how DNA is replicated

Wow, this is pretty! (H/T Uncommon Descent via ECM)

If you need to understand how to explain this video in the context of intelligent design, see my previous posts on the building blocks of life and the origin of biological information. I find it useful to draw up the probability calculations for your friends. It’s all explained in the latter article. Fun!