Casey Luskin and Stephen C. Meyer discuss information outside the genome

This episode of ID the Future is 20 minutes long and it’s a follow up to a previous podcast I posted.

Details:

On this episode of ID the Future, hear the second part of Casey Luskin’s interview with Dr. Stephen C. Meyer, author of the forthcoming book Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design. Dr. Meyer discusses how the origin of information in the Cambrian explosion poses a problem for evolutionary biology.

Special limited time offer: Save 43% and get 4 free digital books when you pre-order Darwin’s Doubt.

You can grab the MP3 here.

Topics:

• Last time, they discussed how the sudden origin of animal body plans requires an infusion of new information
• Also, the sudden origin of animal forms is inexplicable naturalistically, because there are no transitional forms
• New body plans require new genetic information
• The Cambrian explosion involve a sudden increase of body plans, which means a sudden increase of information
• For example, a new body plan requires dozens of new cell types
• Each cell type will be composed of new proteins and enzymes
• Proteins are composed of functional sequences of amino acids – genetic information
• Can the neo-Darwinian mechanisms generate new functional sequences?
• The problem with making functional sequences by chance: Product Rule
• When calculating probabilities of forming a functional sequence, you multiply to calculate probabilities
• A bike lock with 4 dials and 10 possibilities has 10 x 10 x 10 x 10 = 10,000 possibilities
• Each sequence is equally likely to get by random guesses
• But it’s far more likely that any random attempt will NOT work
• Getting one or two settings right has no value to opening the lock, and will not be saved for later attempts
• There is no credit for partial success: you have to get the whole combination right the first time
• In addition, there are other sources of information other than DNA that are required for new body plans
  
• For example, there is information in cell membranes, cytoskeletons, etc. which is also needed
• Neo-Darwinism can only work on mutating genes – even in the best case it would just give you new proteins
• Neo-Darwinism cannot add information in non-genome areas, which are required for new animal forms
• The information in these non-genome areas are required to arrange the proteins to make new body pans
• Genetic inofrmation = information in the genome, Epigenetic information = information outside the genome
• This problem of information outside the genome is called “the problem of the origin of form”

So those last few points are, I think, a sneak peek into the contents of the new “Darwin’s Doubt” book.

If you haven’t yet read Meyer’s first book, “Signature in the Cell”, you should probably grab that one. It’s the best book on intelligent design that’s out right now. It talks about the origin of the first living cell, surveying all naturalistic explanations for it, and concluding that the best explanation – the one most consistent with what we know now – is intelligent design.

Filed under: Podcasts, Biological Information, Body Plan, Charles Darwin, Darwinism, Epigenetic, Evolution, Genetic, Information, Mutation, Origin of Life, Protein, Selection, Specified Complexity, Stephen C. Meyer

Can Darwinian evolution create new functional biological information?

Here’s a great article from Evolution News that explains the trouble that Darwinian evolution has in building up to functional new biological information by using a process of random mutation and natural selection.

Casey Luskin takes a look at a peer-reviewed paper that claims that Darwinian evolution can do the job of creating new information, then he explains what’s wrong with the paper.

Excerpt:

In Wilf and Ewens’s evolutionary scheme there is a smooth fitness function. Under this view, there is no epistasis, where one mutation can effectively interact with another to affect (whether positively or negatively) fitness. As a result, any mutations that move the search toward its “target” are assumed to provide an immediate and irrevocable advantage, and are thus highly likely to become fixed. Ewert et al. compare the model to playing Wheel of Fortune:

The evolutionary model that Wilf and Ewens have chosen is similar to the problem of guessing letters in a word or phrase, as on the television game show Wheel of Fortune. They specify a phrase 20,000 letters long, with each letter in the phrase corresponding to a gene locus that can be transformed from its initial “primitive” state to a more advanced state. Finding the correct letter for a particular position in the target phrase roughly corresponds to finding a beneficial mutation in the corresponding gene. During each round of mutation all positions in the phrase are subject to mutation, and the results are selected based on whether the individual positions match the final target phrase. Those that match are preserved for the next round. … After each round, all “advanced” alleles in the population are treated as fixed, and therefore preserved in the next round. Evolution to the fully “advanced” state is complete when all 20,000 positions match the target phrase.

The problem with this approach is that a string of biological information that has only some letters that are part of a useful sequence has no present function, and therefore cannot survive and reproduce.

Look:

Thus, Wilf and Ewens ignore the problem of non-functional intermediates. They assume that all intermediate stages will be functional, or lead to some functional advantage. But is this how all fitness functions look? Not necessarily. It’s well known that in many instances, no benefit is derived until multiple mutations are present all at once. In such a case, there’s no evolutionary advantage until multiple mutations are present. The “correct” mutations might occur in parallel, but the odds of this happening are extremely low. Ewert et al. illustrate this problem in the model by using the example of the difficulty of one phrase evolving into another:

Suppose it would be beneficial for the phrase

“all_the_world_is_a_stage___”

to evolve into the phrase

“methinks_it_is_like_a_weasel.”

What phrase do we get if we simply alternate letters from the two phrases?

“mlt_ihk__otli__siaesaaw_a_e_.”

Under the assumptions in the Wilf and Ewens model, the “fitness” of this nonsense phrase ought to be exactly half-way between the fitnesses of “all the world is a stage” and “methinks it is like a weasel.” Such a result only makes sense if we are measuring the fitness of the current phrase by its proximity to the target phrase.

But the gibberish of the intermediate phrase doesn’t cause any problem under Wilf and Ewens’s model. Not unlikeRichard Dawkins, they assume that intermediate stages will always yield some functional advantage. And as more and more characters in the phrase match the target, it becomes more and more fit. This yields a nice, smooth fitness function — rich in active information — not truly a blind search.

Not only is there that first problem, but here’s a second:

Wilf and Ewens endowed their mathematical model of evolution with foresight. It is directed toward a target — an advantage that natural selection conspicuously lacks. And what, in our experience, is the only known cause that is goal-directed and has foresight? It’s intelligence. This means that once again, the Evolutionary Informatics Lab has shown that simulations of evolution seem to work only because they’ve been intelligently designed.

This is worth the read. If Darwinian mechanisms really could generate code, then there would be no software engineers. The truth is, the mechanisms don’t work to create new information. For that, you need an intelligent designer.

Filed under: Polemics, Blind Search, Darwinism, Evolution, Feature Space, Fitness Landscape, Future Function, Genetic Algorithm, Information Technology, Intelligent Design, Letters, Mathematics, Mutation, Natural Selection, Naturalism, Origin of Life, Phase Space, Search, Search Problem, Selection, Sentences, Software Engineering, Words

How biological convergence falsifies Darwinian evolution

Cornelius Hunter, a software engineer / biologist with a Ph.D in bioinformatics from UIUC explains the latest discovery of biological convergence on his blog. (H/T Tweet from J. Warner Wallace)

Excerpt:

The theory of evolution states that the species arose spontaneously, one from another via a pattern of common descent. This means the species should form an evolutionary tree, where species that share a recent common ancestor, such as two frog species, are highly similar, and species that share a distant common ancestor, such as humans and squids, are very different. But the species do not form such an evolutionary tree pattern. In fact this expectation has been violated so many times it is difficult to keep track. These violations are not rare or occasional anomalies, they are the rule. Entire volumes have been written on them. Many examples are the repeated designs found in what, according to evolution, must be very distant species. Such evolutionary convergence is biology’s version of lightning striking twice. To explain this evolutionists must say that random mutations just happened to hit upon the same detailed, intricate design at different times, in different parts of the world, in different ecological niches, and so forth. The idea that the most complex designs we know of would spontaneously arise by themselves is, itself, not scientifically motivated and a real stretch of the imagination. But for the same intricate designs to arise independently by chance is even more of a stretch. That is why evolutionist’s claim this week that they have found evidence for convergent evolution was so intriguing.

[...]Though evolutionists sometimes deny biological convergence, it is a scientific fact. And a paper from this week added yet another example:

In mammals, hearing is dependent on three canonical processing stages: (i) an eardrum collecting sound, (ii) a middle ear impedance converter, and (iii) a cochlear frequency analyzer. Here, we show that some insects, such as rainforest katydids, possess equivalent biophysical mechanisms for auditory processing. Although katydid ears are among the smallest in all organisms, these ears perform the crucial stage of air-to-liquid impedance conversion and signal amplification, with the use of a distinct tympanal lever system. Further along the chain of hearing, spectral sound analysis is achieved through dispersive wave propagation across a fluid substrate, as in the mammalian cochlea. Thus, two phylogenetically remote organisms, katydids and mammals, have evolved a series of convergent solutions to common biophysical problems, despite their reliance on very different morphological substrates.

It is another curious example of biological convergence, so rather than attempt to deny the undeniable, evolutionists now claim it as another confirmation of evolution.

I’m a software engineer, and we re-use components all the time for different programs that have no “common ancestor”. E.g. – I can develop my String function library and use it in my web application and my Eclipse IDE plug-in, and those two Java programs have no common ancestry, but they do have a common designer. So you find the same bits in two different programs because I am the developer of both programs.

Previously, I blogged about another example of convergence reported by Science Daily. One of the predictions of intelligent design theory is that examples of convergence, which is really just re-use of common code by the designer, will be everywhere in nature. And that predictions just keeps getting confirmed as science marches forward, and the primitive religion of naturalism retreats.

Filed under: News, Ancestor, Ancestry, Bioinformatics, Biological Convergence, Biology, Common Ancestry, Common Design, Common Designer, Computer Science, Convergence, Convergent Evolution, Convergent Trait, Darwinism, Design, Design Patterns, Designer, DNA, Evolution, Feature, Gene, Genetics, Information Theory, Intelligent Design, Mutation, Phenotype, Phylogeny, Selection, Structure, Trait

List of peer-reviewed papers supporting intelligent design now up to 50

Molecular biologist Ann Gauger working in her lab

From Evolution News.

Excerpt: (links removed)

While intelligent design research is a new scientific field, recent years have been a period of encouraging growth, producing a strong record of peer-reviewed scientific publications. New publications continue to appear, now listed at our updated page.

The current boom goes back to 2004, when Discovery Institute senior fellow Stephen Meyer published a groundbreaking paper advocating ID in the journal Proceedings of the Biological Society of Washington. There are multiple hubs of ID-related research.

Biologic Institute, led by molecular biologists Doug Axe and Ann Gauger, is “developing and testing the scientific case for intelligent design in biology.” Biologic conducts laboratory and theoretical research on the origin and role of information in biology, the fine-tuning of the universe for life, and methods of detecting design in nature. That’s Dr. Gauger at the Biologic lab pictured above.

Another ID research group is the Evolutionary Informatics Lab, founded by senior Discovery Institute fellow William Dembski along with Robert Marks, Distinguished Professor of Electrical and Computer Engineering at Baylor University. Their lab has attracted graduate-student researchers and published multiple peer-reviewed articles in technical science and engineering journals showing that computer programming “points to the need for an ultimate information source qua intelligent designer.”

Other pro-ID scientists around the world are publishing peer-reviewed pro-ID scientific papers. These include biologist Ralph Seelke at the University of Wisconsin Superior, Wolf-Ekkehard Lönnig who recently retired from the Max Planck Institute for Plant Breeding Research in Germany, and Lehigh University biochemist Michael Behe.

Researchers have published their work in a variety of relevant technical venues, including peer-reviewed scientific journals, peer-reviewed scientific books from mainstream university presses, trade-press books, peer-edited scientific anthologies, peer-edited scientific conference proceedings and peer-reviewed philosophy of science journals and books.

These papers have appeared in scientific journals such as Protein Science, Journal of Molecular Biology, Theoretical Biology and Medical Modelling, Journal of Advanced Computational Intelligence and Intelligent Informatics, Quarterly Review of Biology, Cell Biology International, Rivista di Biologia/Biology Forum, Physics of Life Reviews, Annual Review of Genetics, and many others. At the same time, pro-ID scientists have presented their research at conferences worldwide in fields such as genetics, biochemistry, engineering, and computer science.

This body of research is converging on a consensus: complex biological features cannot arise by unguided Darwinian mechanisms, but require an intelligent cause.

My favorite area of ID research is the area of protein formation. I like to read about the research done by Doug Axe and Ann Gauger in that area. 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 (ones that can form functioning proteins) 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. I think that this very valuable research, indeed.

You can read more about the problem of protein synthesis in this previous post.

Filed under: News, Amino Acid, Ann Gauger, Biochemistry, Biologic Institute, Biology, Charles Darwin, Darwin Day, Design, Discovery, Discovery Institute, Doug Axe, Experiment, Experiments, Fine Tuning, Information, Intelligent Cause, Intelligent Design, Irreducible COmplexity, Lab, Molecular Biology, Mutation, Naturalism, Nature, Origin of Life, Paper, Peer-Review, Progress of Science, Protein, Publication, Research, Science, Selection, Sequence, Specified Complexity, Study

Peer-reviewed paper in medical journal challenges Darwinian evolution

Casey Luskin explains over at Evolution News.

Summary: (links removed)

A new article by Dr. Joseph Kuhn of the Department of Surgery at Baylor University Medical Center, appearing in the peer-reviewed journal Baylor University Medical Center Proceedings, poses a number of challenges to both chemical and biological evolution. Titled “Dissecting Darwinism,” the paper begins by recounting some of the arguments raised during the Texas State Board of Education debate that challenged chemical and biological evolution. Those challenges include:

1. Limitations of the chemical origin of life data to explain the origin of DNA
2. Limitations of mutation and natural selection theories to address the irreducible complexity of the cell
3. Limitations of transitional species data to account for the multitude of changes involved in the transition.

(Joseph A. Kuhn, “Dissecting Darwinism,” Baylor University Medical Center Proceedings, Vol. 25(1): 41-47 (2012).)

It’s a good little introduction to where the action is on the origins debate but regular readers will have read it all before.

But there was one thing I found interesting.

The naturalistic response to this paper:  (links removed)

The journal also published a rebuttal to Dr. Kuhn by Charles Stewart Roberts, a cardiovascular surgeon in Virginia. Dr. Roberts’s rebuttal simply asserted, as if it were a truth that required no scientific backing, that all biological features could be produced by evolution:

The notion of “irreducible complexity” in a cell, as an argument against evolution, is beyond my present understanding. Knowing that life has existed on planet earth for billions of years, however, I suspect that there has been time enough for evolution, no matter how complex, with reducibility.

I was having a debate with an atheist on Facebook and this guy did nothing but duck and dodge by citations of peer-reviewed evidence, like the paper from December 2011 on the oxygen in the early Earth’s atmosphere, which destroys naturalistic origin of life scenarios. My favorite of his speculations was when he responded to the Big Bang cosmology by saying “one can easily envision a scenario in which the universe has existed eternally”. Or something like that. Atheists – always easily envisioning things that are falsified by the available experimental evidence.

Casey comments on Roberts’ “rebuttal”: (links removed)

We’ve addressed this sort of unsophisticated and poorly articulated argument in defense of defending Darwinian evolution many times. You can’t just vaguely appeal to vast and unending amounts of time (and other probabilistic resources) and assume that Darwinian evolution can produce anything “no matter how complex.” Rather, you have to demonstrate that sufficient probabilistic resources exist to produce the feature.

Rather than making assumptions, proponents of intelligent design ask what the Darwinian mechanism can, or cannot, do. For example, a 2010 peer-reviewed research paper by pro-ID scientist Doug Axe modeled a population of evolving bacteria, and found that there are severe limits on the ability of Darwinian evolution to produce multi-mutation features. (A multi-mutation feature is one that requires multiple mutations to be present before there is any advantage given to the organism.)

Axe’s research makes assumptions very generously favoring Darwinian evolution. He assumed the existence of a huge population of asexually reproducing bacteria that could replicate quickly — perhaps nearly 3 times per day — over the course of billions of years. But he found that complex adaptations requiring more than six neutral mutations would exhaust the probabilistic resources available over the entire history of the earth.

[...]Axe’s work suggests that we cannot assume, as Roberts does, that sufficient probabilistic resources exist to produce all the features we see in life, “no matter how complex.” Indeed, follow-up research by Axe and Ann Gauger suggests that many features might require more mutations before conferring an advantage than could arise in the history of the earth. Their 2011 study attempted to convert one protein into another, closely related protein — the kind of transformation that evolutionists claim happened easily in the history of life. Through mutational analysis, they found that a minimum of seven independent mutations — and probably many more — would be necessary to convert the protein and its function into that of its allegedly close relative.

Evolutionary theory certainly can explain some things. It works up to a point. But there is only so much time available, so much material to react, and so many reactions per second. Hand-waving is not going to prove the neo-Darwinian hypothesis. It’s going to take published experimental results. Like the results of Doug Axe and Ann Gauger.

Oh by the way, there’s another peer-reviewed article confirming the inability of naturalistic mechanisms to create first life discussed on Evolution News. (David L. Abel, “Is Life Unique?,” Life, Vol. 2:106-134 (2012)). I can’t blog on all of them!

Filed under: Polemics, Ann Gauger, Cambrian Explosion, Darwinism, Doug Axe, Education, Evolution, Intelligent Design, Irreducible COmplexity, Journal, Limits, Mutation, Natural Selection, Origin of Life, Peer-Reviewed, Research, Science, Selection, Teach the Controversy, Texas