Which came first...?

What Chaperone Proteins Know

Evolution News & Views September 7, 2012 5:28 A.M

 

Here's a riddle for you: Proteins are used to make proteins, so if we assume a purely naturalistic origin of life, where did the first proteins come from?

If a cell is a factory, proteins are the factory workers. Proteins conduct most of the necessary functions in a cell. Proteins are made up of amino acid building blocks. A chain of amino acids must fold into the appropriate three-dimensional structure so that the protein can function properly. Within cells are proteins known as chaperones that help fold the amino acid chain into its proper three-dimensional structure. If the amino acid chain folds improperly, then this could wreak havoc on the cell and potentially the entire organism. The chaperone works to prevent folding defects and is a key player in the final steps of protein synthesis.

However, as important as chaperones are, there are still many questions as to how exactly they work. For example, do the chaperones fold the amino acid chain while it is still being constructed (during translation), or is the amino acid chain first put together, and then the folding beings? Or, is it some combination of both? Studies indicate that it is indeed a combination of both. There are two different kinds of chaperone proteins within the cell, one for translation and one for post-translation. With these two different kinds of chaperones, where and how does regulation happen to prevent misfolds?

Recent research on bacterial cells sheds light on the chaperones' important function. One chaperone in particular, Trigger Factor, plays a key role in correcting misfolds that may occur early on in the translational process. Trigger Factor can slow down improper amino acid folding, and it can even unfold amino acid chains that have already folded up incorrectly.

Here are some of the neat features of Trigger Factor:

• Trigger Factor actually constrains protein folding more than the ribosome does. It doesn't just "get in the way" like the ribosome. It also regulates the folding.
• Trigger Factor's function is specific to the particular region of the amino acid chain. It does not just perform one function no matter what the composition of the amino acid chain. It changes based on the region of the chain it is working with.
• Trigger Factor also changes its activity based on where the protein is in the translation process.
• Trigger Factor's process depends on how the amino acid chain is bound to the ribosome, and can even unfold parts of the chain that were misfolded in the translation process.

An additional factor that regulates when amino acid chains fold into proteins is its distance from the ribosome (the place where the amino acid chain is made). The closer the chain is to the ribosome, the less room it has to fold into a three-dimensional protein. Trigger Factor works with this spatial hindrance, making an interesting and complex regulation system.

Trigger Factor is only called into the game once the amino acid chain is a certain length (around 100 amino acids long) and when the chain has certain features, such as hydrophobicity. As the authors state it, Trigger Factor keeps the protein from folding into its three-dimensional structure until the amino acid chain has all of the information it needs to fold properly:

In summary, we show that the ribosome and TF each uniquely affect the folding landscape of nascent polypeptides to prevent or reverse early misfolds as long as important folding information is still missing and the nascent chain is not released from the ribosome.

So we have a protein that is able to perform various functions that inhibit or slow protein folding until the amino acid has the right chemical information for folding to occur.

This does not solve the riddle about proteins being made from proteins (otherwise known as the chicken-and-the-egg problem). It actually adds another twist to the riddle: How does one protein know how much information a completely different protein needs to fold into a three dimensional structure? How does a protein evolve the ability to "know" how to respond to specific translational circumstances as Trigger Factor does?

Why the search for a simple lifeform is a fool's errand.

Ciliate Organism Undergoes "Scrambled Genome" and "Massive...Rearrangement"

Casey Luskin October 14, 2014 3:39 A.M

 

 

 A fascinating new paper in the journal Cell, "The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development," describes how a unique single-celled eukaryotic organism, Oxytricha trifallax, scrambles and then reassembles its own genome as the organism reproduces. According to a story about the paper over at Princeton University's news desk:

The pond-dwelling, single-celled organism Oxytricha trifallax has the remarkable ability to break its own DNA into nearly a quarter-million pieces and rapidly reassemble those pieces when it's time to mate... The organism internally stores its genome as thousands of scrambled, encrypted gene pieces. Upon mating with another of its kind, the organism rummages through these jumbled genes and DNA segments to piece together more than 225,000 tiny strands of DNA. This all happens in about 60 hours.

One of the paper's lead researchers points out something that would occur to most any reader: "People might think that pond-dwelling organisms would be simple, but this shows how complex life can be, that it can reassemble all the building blocks of chromosomes." That kind of changes the meaning of the insult "Pond-scum"!

This ciliate organism is strange in other ways, as its cell contains two nuclei. One, called the somatic macronucleus (MAC), is used like a typical eukaryotic cell's functioning nucleus -- to generate proteins and function kind of like a CPU. But the second nucleus, called the germline micronucleus (MIC), is used to store genetic material that will be passed on to offspring during reproduction. And it's in the second nucleus that all the rearrangement and scrambling of the genome takes place.

The reproductive process of these organisms is also very strange. They don't use sex to reproduce, whether by binary fission or by creating a "new" organism. Rather, when two members of this species have "sex," they only exchange DNA for the purpose of replacing old, broken down genes. This allows them to "replace aging genes with new genes and DNA parts from its partner." Though the genome of the organism is reborn with each new generation, the organism itself is essentially immortal. The process goes approximately like this:

First the information in the second nucleus (the germline micronucleus) is broken into about 225,000 small fragments. Next, the organism swaps about half of that DNA with its mate. Then, the organism reassembles its thousands of chromosomes in the germline micronucleus. And this reassembly process shows the important functionality of non-coding DNA: "millions of noncoding RNA molecules from the previous generation direct this undertaking by marking and sorting the DNA pieces in the correct order." After sex, the old somatic macronucleus disintegrates, and a new somatic micronucleus is created from a copy of the newly assembled germline micronucleus. The paper describes the process:

In the micronucleus (MIC), macronuclear destined sequences (MDSs) are interrupted by internal eliminated sequences (IESs); MDSs may be disordered (e.g., MDS 3, 4, and 5) or inverted (e.g., MDS 4). During development after conjugation [sex], IESs, as well as other MIC-limited DNA, are removed. MDSs are stitched together, some requiring inversion and/or unscrambling. Pointers are short identical sequences at consecutive MDS-IES junctions. One copy of the pointer is retained in the new macronucleus (MAC). The old macronuclear genome degrades. Micronuclear chromosome fragmentation produces genesized nanochromosomes (capped by telomeres) in the new macronuclear genome. DNA amplification brings nanochromosomes to a high copy number.

Obviously this is an incredibly complex process, which requires numerous carefully orchestrated cellular subroutines. In fact, don't miss the paper's reference to the term "pointer." That's a term from computer science, where a pointer is a computer programming element that tells a computer where to put some piece of information. In a similar way, these ciliate organisms use pointers tell the organism where to put some piece of DNA information when it reassembles the genome.

"Radical Genome Architecture"

If that sounds complicated, consider some of the details reported in the paper about the germline micronucleus (MIC). In fact, the big story here is that this research represents the first attempt to decipher what's going on in the germline micronucleus. According to the paper, the MIC contains "over 225,000 [DNA] segments, tens of thousands of which are complexly scrambled and interwoven," where, "Gene segments from neighboring loci are located in extreme proximity to each other, often overlapping." The paper puts it this way:

The germline genome is fragmented into over 225,000 precursor DNA segments (MDSs) that massively rearrange during development to produce nanochromosomes containing approximately one gene each.

These nanochromosomes come in two types: scrambled and unscrambled. They thus further find:

In addition to the intense dispersal of all somatic coding information into >225,000 DNA fragments in the germline, a second unprecedented feature of the Oxytricha MIC genome is its remarkable level of scrambling (disordered or inverted MDSs). The germline maps of at least 3,593 genes, encoded on 2,818 nanochromosomes, are scrambled. No other sequenced genome bears zthis level of structural complexity.

They describe a striking example of scrambling: "The most scrambled gene is a 22 kb MIC locus fragmented into 245 precursor segments that assemble to produce a 13 kb nanochromosome encoding a dynein heavy chain family protein." But the complexity of the germline micronucleus goes even deeper, as some of the scrambled genes entail genes encoded within genes:

A third exceptional feature we noted is 1,537 cases (1,043 of which are scrambled) of nested genes, with the precursor MDS segments for multiple different MAC chromosomes interwoven on the same germline locus, such that IESs for one gene contain MDSs for another.

Additionally, these precursor DNA sequences may encode multiple chromosomes in the somatic macronucleus, which are shuffled and spliced back together during the reassembly process:

A fourth notable feature arising from this radical genome architecture is that a single MDS in the MIC may contribute to multiple, distinct MAC chromosomes. Like alternative splicing, this modular mechanism of "MDS shuffling" ... can be a source of genetic variation, producing different nanochromosomes and even new genes and scrambled patterns. At least 1,267 MDSs from 105 MIC loci are reused, contributing to 240 distinct MAC chromosomes. A single MDS can contribute to the assembly of as many as five different nanochromosomes.

There's a lot more in this paper discussing the complexity of these processes that deconstruct and reassemble the genome of Oxytricha trifallax. The natural question that arises is "How did this evolve?" The paper doesn't even attempt to offer an answer -- it's simply descriptive.

In a way, the degradation and reassembly of the genome brings to mind the liquidation and rebuilding of an insect's body during holometabolism. For more on that, see the Illustra film Metamorphosis. Holometabolism has also baffled evolutionary biologists since the programming for the entire process must be fully in place before it occurs, or you end up with a dead organism. Given the importance of a genome to an organism's survival, one would expect the same to be true of the processes involved in the degradation and reassembly of the Oxytricha trifallax genome.
From the perspective of intelligent design, these complex processes are more readily accounted for. They require a cause capable of thinking ahead, with planning and foresight. Intelligent agency is capable of doing that. An intelligent agent could produce the information to program the process of deconstructing and reassembling the Oxytricha trifallax genome from the beginning.

A goal-directed creative process like ID can shed light on the mystery of the Oxytricha trifallax genome. Obviously this paper in no way suggests that ID is the answer. But something tells me that unguided evolutionary explanations of the genomic complexity reported by these researchers won't be forthcoming.

 

Things that make you say "hmmm."

Doctor Doom, Eric Pianka, Receives Standing Ovation from Texas Academy of Science

Jonathan Witt April 3, 2006 3:15 P 

 

 

The following is excerpted from "Meeting Doctor Doom" by Forrest Mims, Chairman of the Environmental Science Section of the Texas Academy of Science:

... I watched in amazement as a few hundred members of the Texas Academy of Science rose to their feet and gave a standing ovation to a speech that enthusiastically advocated the elimination of 90 percent of Earth's population by airborne Ebola. The speech was given by Dr. Eric R. Pianka (Fig. 1), the University of Texas evolutionary ecologist and lizard expert who the Academy named the 2006 Distinguished Texas Scientist. Something curious occurred a minute before Pianka began speaking. An official of the Academy approached a video camera operator at the front of the auditorium and engaged him in animated conversation. The camera operator did not look pleased as he pointed the lens of the big camera to the ceiling and slowly walked away.
This curious incident came to mind a few minutes later when Professor Pianka began his speech by explaining that the general public is not yet ready to hear what he was about to tell us.

Because of many years of experience as a writer and editor, Pianka's strange introduction and the TV camera incident raised a red flag in my mind. Suddenly I forgot that I was a member of the Texas Academy of Science and chairman of its Environmental Science Section. Instead, I grabbed a notepad so I could take on the role of science reporter. One of Pianka's earliest points was a condemnation of anthropocentrism, or the idea that humankind occupies a privileged position in the Universe. He told a story about how a neighbor asked him what good the lizards are that he studies. He answered, "What good are you?"
Pianka hammered his point home by exclaiming, "We're no better than bacteria!"
Pianka then began laying out his concerns about how human overpopulation is ruining the Earth. He presented a doomsday scenario in which he claimed that the sharp increase in human population since the beginning of the industrial age is devastating the planet. He warned that quick steps must be taken to restore the planet before it's too late.
Saving the Earth with Ebola
Professor Pianka said the Earth as we know it will not survive without drastic measures. Then, and without presenting any data to justify this number, he asserted that the only feasible solution to saving the Earth is to reduce the population to 10 percent of the present number.
He then showed solutions for reducing the world's population in the form of a slide depicting the Four Horsemen of the Apocalypse. War and famine would not do, he explained. Instead, disease offered the most efficient and fastest way to kill the billions that must soon die if the population crisis is to be solved.
Pianka then displayed a slide showing rows of human skulls, one of which had red lights flashing from its eye sockets.
AIDS is not an efficient killer, he explained, because it is too slow. His favorite candidate for eliminating 90 percent of the world's population is airborne Ebola ( Ebola Reston ), because it is both highly lethal and it kills in days, instead of years. However, Professor Pianka did not mention that Ebola victims die a slow and torturous death as the virus initiates a cascade of biological calamities inside the victim that eventually liquefy the internal organs.
After praising the Ebola virus for its efficiency at killing, Pianka paused, leaned over the lectern, looked at us and carefully said, "We've got airborne 90 percent mortality in humans. Killing humans. Think about that."
With his slide of human skulls towering on the screen behind him, Professor Pianka was deadly serious. The audience that had been applauding some of his statements now sat silent.
After a dramatic pause, Pianka returned to politics and environmentalism. But he revisited his call for mass death when he reflected on the oil situation.
"And the fossil fuels are running out," he said, "so I think we may have to cut back to two billion, which would be about one-third as many people." So the oil crisis alone may require eliminating two-third's of the world's population.
How soon must the mass dying begin if Earth is to be saved? Apparently fairly soon, for Pianka suggested he might be around when the killer disease goes to work. He was born in 1939, and his lengthy obituary appears on his web site.
When Pianka finished his remarks, the audience applauded. It wasn't merely a smattering of polite clapping that audiences diplomatically reserve for poor or boring speakers. It was a loud, vigorous and enthusiastic applause.
Questions for Dr. Doom
Then came the question and answer session, in which Professor Pianka stated that other diseases are also efficient killers.
The audience laughed when he said, "You know, the bird flu's good, too." They laughed again when he proposed, with a discernable note of glee in his voice that, "We need to sterilize everybody on the Earth."
After noting that the audience did not represent the general population, a questioner asked, "What kind of reception have you received as you have presented these ideas to other audiences that are not representative of us?"
Pianka replied, "I speak to the converted!"
Pianka responded to more questions by condemning politicians in general and Al Gore by name, because they do not address the population problem and "...because they deceive the public in every way they can to stay in power."
He spoke glowingly of the police state in China that enforces their one-child policy. He said, "Smarter people have fewer kids." ...
With this, the questioning was over. Immediately almost every scientist, professor and college student present stood to their feet and vigorously applauded the man who had enthusiastically endorsed the elimination of 90 percent of the human population. Some even cheered. Dozens then mobbed the professor at the lectern to extend greetings and ask questions. It was necessary to wait a while before I could get close enough to take some photographs (Fig. 1).
I was assigned to judge a paper in a grad student competition after the speech. On the way, three professors dismissed Pianka as a crank. While waiting to enter the competition room, a group of a dozen Lamar University students expressed outrage over the Pianka speech.
Yet five hours later, the distinguished leaders of the Texas Academy of Science presented Pianka with a plaque in recognition of his being named 2006 Distinguished Texas Scientist. When the banquet hall filled with more than 400 people responded with enthusiastic applause, I walked out in protest.
Corresponding with Dr. Doom
Recently I exchanged a number of e-mails with Pianka. I pointed out to him that one might infer his death wish was really aimed at Africans, for Ebola is found only in Central Africa. He replied that Ebola does not discriminate, kills everyone and could spread to Europe and the the Americas by a single infected airplane passenger.
In his last e-mail, Pianka wrote that I completely fail to understand his arguments. So I did a check and found verification of my interpretation of his remarks on his own web site. In a student evaluation of a 2004 course he taught, one of Professor Pianka's students wrote, "Though I agree that convervation [sic] biology is of utmost importance to the world, I do not think that preaching that 90% of the human population should die of ebola [sic] is the most effective means of encouraging conservation awareness." (Go here and scroll down to just before the Fall 2005 evaluation section near the end.)
Yet the majority of his student reviews were favorable, with one even saying, " I worship Dr. Pianka."
The 45-minute lecture before the Texas Academy of Science converted a university biology senior into a Pianka disciple, who then published a blog that seriously supports Pianka's mass death wish.
Dangerous Times
Let me now remove my reporter's hat for a moment and tell you what I think. We live in dangerous times. The national security of many countries is at risk. Science has become tainted by highly publicized cases of misconduct and fraud.
Must now we worry that a Pianka-worshipping former student might someday become a professional biologist or physician with access to the most deadly strains of viruses and bacteria? I believe that airborne Ebola is unlikely to threaten the world outside of Central Africa. But scientists have regenerated the 1918 Spanish flu virus that killed 50 million people. There is concern that small pox might someday return. And what other terrible plagues are waiting out there in the natural world to cross the species barrier and to which scientists will one day have access?
Meanwhile, I still can't get out of my mind the pleasant spring day in Texas when a few hundred scientists of the Texas Academy of Science gave a standing ovation for a speaker who they heard advocate for the slow and torturous death of over five billion human beings. ...

 

Chance and necessity of the gaps.

Alister McGrath Mistakes Intelligent Design for a God-of-the-Gaps Argument

Casey Luskin October 15, 2014 11:04 AM 

BioLogos's concluding article in its series responding to Darwin's Doubt is by theologian and philosopher Alister McGrath, recently installed as the Andreas Idreos Professor at Harris Manchester College, University of Oxford. I'm a fan of much of McGrath's writings, but when it comes to intelligent design, there are problems. He has made a long series of inaccurate chargesthat ID is a "God of the gaps" argument. Oddly, McGrath's piece at BioLogos isn't about Darwin's Doubt at all. In fact, it doesn't mention intelligent design. Rather, it's a transcript from a talk he gave, and someone apparently added the title, "Big Picture or Big Gaps? Why Natural Theology is Better than Intelligent Design," to the speech. However BioLogos evidently intends McGrath's piece as a response to intelligent design, so I'll treat the criticisms there accordingly.

McGrath frames his critique as follows:

My own approach is not to retreat into explanatory gaps. There are those who say (and perhaps I caricature or mis-say what they say), "Well, you know, science can't explain that. But if there were a god, he could. Therefore, what science can't explain -- that is a good reason for believing in God." And part of me wants to say, "Yes!" to that. But part of me also wants to say, well, this is not a very good idea, and leaves us bereft of the richness of a vision of God. It kind of implies that you believe in God because of the tiny little holes in somebody else's explanation, which you think you can explain better in brackets -- at least for the time being. For me, it's not about saying, "Oh look! There's a gap there, and that's where God comes in!" No, no, no, it's about the big picture. That is what makes us think that the Christian faith makes sense of things.

Before we get into this discussion too much, it's helpful to understand what an early "coiner" of the phrase "God of the gaps," Dietrich Bonhoeffer, wrote in defining the concept:

...[H]ow wrong it is to use God as a stop-gap for the incompleteness of our knowledge. If in fact the frontiers of knowledge are being pushed further and further back (and that is bound to be the case), then God is being pushed back with them, and is therefore continually in retreat. We are to find God in what we know, not in what we don't know; God wants us to realize his presence, not in unsolved problems but in those that are solved.

(Dietrich Bonhoeffer, May 30, 1944, Letters and Papers from Prison, edited by Eberhard Bethge, translated by Reginald H. Fuller, Touchstone, 1997.)

By that measure, intelligent design is not in fact a "God of the gaps" argument! I first encountered this comment from Bonhoeffer in Douglas Ell's book Counting to God, which rightly praised Bonhoeffer's reasonable argument. ID does not find God, or evidence of design by any intelligent being, in "what we don't know" but rather "in what we know." The design inference is fundamentally grounded in our experience-based observations that high levels of complex and specified (CSI) information come only from intelligence. We find evidence for design in what we know about the causes of new information. Intelligent design is a solution to the question of the origin of information.

Well, what if ID were a "gaps"-based argument? What might it look like? Something like this:

To put it another way, a gaps-based argument for design would say, "Natural selection and random mutation cannot produce new information, therefore intelligent design is correct."

But there's a big and crucial difference between that argument and the actual case for intelligent design made by ID proponents. An actual argument for intelligent design might be logically portrayed as follows:

In other words, "Natural selection and random mutation cannot produce new information. Intelligent agency, uniquely in our experience, can produce new information. Therefore intelligent design is the better explanation for the information we see in life." This is not a gaps-based argument. Rather, it's a positive argument for design, based upon finding in nature the type of information that in our experience only comes from intelligence. Stephen Meyer frames the basic logic of the positive argument this way in Darwin's Doubt (p. 351):

Major premise: If intelligent design played a role in the Cambrian explosion, then feature (X) known to be produced by intelligent activity would be expected as a matter of course.

Minor premise: Feature (X) is observed in the Cambrian explosion of animal life.

Conclusion: Hence, there is reason to suspect that an intelligent cause played a role in the Cambrian explosion.

You'd never find that in a "gaps-based" argument, and thus, there's a big difference between ID and a "God of the gaps" argument because ID has the necessary positive argument -- that intelligence causes high produce CSI -- which remove ID from being a "gaps-based" argument.

McGrath's Odd Formulation of a "Gaps-Based" Argument

McGrath describes a "gaps-based" argument a bit differently from the classical formulation. In the classical criticism, "god" has no positive explanatory value whatsoever, other than to fill in and make up for the failure of some scientific explanation. But McGrath is attacking a slightly different formulation, which, in his description, says "science can't explain that. But if there were a god, he could." In saying that a "god ... could" explain something, McGrath apparently tries to add a positive component to what he still labels a "gaps-based" argument." Adding the "god ... could" component, changes the dynamic of the case. Now, McGrath is no longer attacking a strictly negative "gaps-based" argument with no explanatory value. Instead he is attacking an argument with some positive explanatory value (though the mere addition of the word "could" doesn't give us much in the way of positive explanatory value). Is McGrath necessarily justified in rejecting this sort of "gaps-based" argument?

No, not necessarily. Given that BioLogos frames McGrath's article as a broadside against Meyer's arguments for intelligent design, let's say that he's rejecting the following argument: "Science can't explain that. But intelligent agency could. Therefore, what science can't explain -- that is a good reason for believing in intelligent design." This argument, which I am not making, dramatically understates the explanatory power of intelligent design. But insofar as it does resemble the argument for ID, McGrath is unjustified in rejecting it. Here's why.

McGrath dramatically understates the explanatory power of intelligent design. In Darwin's Doubt, Stephen Meyer doesn't just say that intelligent design "could" explain the information in life, but he describes many specific properties of life and the Cambrian explosion which require an explanation that could only be intelligent design. Meyer looks at both the nature of the Cambrian animals themselves, and the nature of their appearance in the fossil record, and finds a whole array of specific features which are only explained by intelligent design. Specifically, Meyer finds that "the cause of the origin of the new animal forms in the Cambrian explosion must be capable of:

• "generating new form rapidly
• generating a top-down pattern of appearance
• constructing, not merely modifying, complex integrated circuits" (p. 357)

He goes on to say that "any explanation for the origin of the Cambrian animals must identify a cause capable of generating:

• "digital information
• structural (epigenetic) information
• functionally integrated and hierarchically organized layers of Information" (p. 358)

Let's see how Meyer provides positive evidence showing that intelligent agents produce those features:

Generating New Form Rapidly:

Intelligent agents have foresight. Such agents can determine or select functional goals before they are physically instantiated. They can devise or select material means to accomplish those ends from among an array of possibilities. They can then actualize those goals in accord with a preconceived design plan or set of functional requirements. Rational agents can constrain combinatorial space with distant information-rich outcomes in mind. (pp. 362-363)

Intelligent agents sometimes produce material entities through a series of gradual modifications (as when a sculptor shapes a sculpture over time). Nevertheless, intelligent agents also have the capacity to introduce complex technological systems into the world fully formed. Often such systems bear no resemblance to earlier technological systems -- their invention occurs without a material connection to earlier, more rudimentary technologies. When the radio was first invented, it was unlike anything that had come before, even other forms of communication technology. For this reason, although intelligent agents need not generate novel structures abruptly, they can do so. Thus, invoking the activity of a mind provides a causally adequate explanation for the pattern of abrupt appearance in the Cambrian fossil record. (pp. 373, 375)

Generating a Top-down Pattern of Appearance:

"Top-down" causation begins with a basic architecture, blueprint, or plan and then proceeds to assemble parts in accord with it. The blueprint stands causally prior to the assembly and arrangement of the parts. But where could such a blueprint come from? One possibility involves a mental mode of causation. Intelligent agents often conceive of plans prior to their material instantiation -- that is, the preconceived design of a blueprint often precedes the assembly of parts in accord with it. An observer touring the parts section of a General Motors plant will see no direct evidence of a prior blueprint for GM's new models, but will perceive the basic design plan immediately upon observing the finished product at the end of the assembly line. Designed systems, whether automobiles, airplanes, or computers, invariably manifest a design plan that preceded their first material instantiation. But the parts do not generate the whole. Rather, an idea of the whole directed the assembly of the parts. (pp. 371-372)

Constructing, Not Merely Modifying, Complex Integrated Circuits:

Integrated circuits in electronics are systems of individually functional components such as transistors, resistors, and capacitors that are connected together to perform an overarching function. ... [I]n our experience, complex integrated circuits -- and the functional integration of parts in complex systems generally -- are known to be produced by intelligent agents -- specifically, by engineers. Moreover, intelligence is the only known cause of such effects. Since developing animals employ a form of integrated circuitry, and certainly one manifesting a tightly and functionally integrated system of parts and subsystems, and since intelligence is the only known cause of these features, the necessary presence of these features in developing Cambrian animals would seem to indicate that intelligent agency played a role in their origin. (p. 364)

Generating New Digital Information:

Intelligent agents, due to their rationality and consciousness, have demonstrated the power to produce specified or functional information in the form of linear sequence-specific arrangements of characters. Digital and alphabetic forms of information routinely arise from intelligent agents. A computer user who traces the information on a screen back to its source invariably comes to a mind -- a software engineer or programmer. The information in a book or inscription ultimately derives from a writer or scribe. Our experience-based knowledge of information flow confirms that systems with large amounts of specified or functional information invariably originate from an intelligent source. The generation of functional information is "habitually associated with conscious activity." Our uniform experience confirms this obvious truth. (p. 360)

Rational agents can arrange both matter and symbols with distant goals in mind. They also routinely solve problems of combinatorial inflation. In using language, the human mind routinely "finds" or generates highly improbable linguistic sequences to convey an intended or preconceived idea. In the process of thought, functional objectives precede and constrain the selection of words, sounds, and symbols to generate functional (and meaningful) sequences from a vast ensemble of meaningless alternative possible combinations of sound or symbol. Similarly, the construction of complex technological objects and products, such as bridges, circuit boards, engines, and software, results from the application of goal-directed constraints. Indeed, in all functionally integrated complex systems where the cause is known by experience or observation, designing engineers or other intelligent agents applied constraints on the possible arrangements of matter to limit possibilities in order to produce improbable forms, sequences, or structures. Rational agents have repeatedly demonstrated the capacity to constrain possible outcomes to actualize improbable but initially unrealized future functions. Repeated experience affirms that intelligent agents (minds) uniquely possess such causal powers. (p. 362)

Generating New Structural (Epigenetic) Information and Constructing Functionally Integrated and Hierarchically Organized Layers of Information:

After noting that "the role of epigenetic information provides just one of many examples of the hierarchical arrangement (or layering) of information-rich structures, systems, and molecules within animals," Meyer writes:

The highly specified, tightly integrated, hierarchical arrangements of molecular components and systems within animal body plans also suggest intelligent design. This is, again, because of our experience with the features and systems that intelligent agents -- and only intelligent agents -- produce. Indeed, based on our experience, we know that intelligent human agents have the capacity to generate complex and functionally specified arrangements of matter -- that is, to generate specified complexity or specified information. Further, human agents often design information-rich hierarchies, in which both individual modules and the arrangement of those modules exhibit complexity and specificity -- specified information as defined in Chapter 8. Individual transistors, resistors, and capacitors in an integrated circuit exhibit considerable complexity and specificity of design. Yet at a higher level of organization, the specific arrangement and connection of these components within an integrated circuit requires additional information and reflects further design.

Conscious and rational agents have, as part of their powers of purposive intelligence, the capacity to design information-rich parts and to organize those parts into functional information- rich systems and hierarchies. (p. 366)

Meyer concludes that "both the Cambrian animal forms themselves and their pattern of appearance in the fossil record exhibit precisely those features that we should expect to see if an intelligent cause had acted to produce them" (p. 379) He sums his positive argument as follows:

When we encounter objects that manifest any of the key features present in the Cambrian animals, or events that exhibit the patterns present in the Cambrian fossil record, and we know how these features and patterns arose, invariably we find that intelligent design played a causal role in their origin. Thus, when we encounter these same features in the Cambrian event, we may infer -- based upon established cause-and-effect relationships and uniformitarian principles -- that the same kind of cause operated in the history of life. In other words, intelligent design constitutes the best, most causally adequate explanation for the origin of information and circuitry necessary to build the Cambrian animals. It also provides the best explanation for the top- down, explosive, and discontinuous pattern of appearance of the Cambrian animals in the fossil record. (p. 381)

Thus we see that Meyer identifies a large breadth of features in both biology and the fossil record that are positively and uniquely explained by intelligence. ID is not the arbitrary filling of a gap. There are specific positive reasons for inferring design, based upon our observations of intelligent agents and their products. We use those observations to generate expectations and predictions about what we should find if an intelligent agent was at work in the natural world. When we find those features in the natural world, and conclude that no other natural cause can explain then, we justifiably infer design. This makes ID the opposite of a "gaps-based" argument, because we're finding in nature specific features which we know from observation only come from intelligence. The argument has a strong positive component, and without that strong positive argument, we cannot infer design.

After seeing all of the features of the Cambrian animals and their pattern of appearance in the fossil record that intelligent design predicts and explains, it's very difficult to accept BioLogos's and McGrath's suggestion that Meyer's extensive positive argument for design is a "God of the gaps."

Materialism of the Gaps

So why, despite ID's vast positive explanatory power, does McGrath dismiss ID as an argument based on "gaps"? Because his unwavering default position is to look exclusively to unguided material causes. He assumes methodological naturalism, and privileges material explanations in all circumstances regardless of their explanatory power. In McGrath's view, even if intelligent design has vast explanatory power, we should still not infer it, because we're filling a "gap" that ought to be filled by material causes.

In subjecting the scientific enterprise to methodological naturalism (MN), McGrath would force ID to operate under the presumption that natural causes always take precedence, regardless of whether they otherwise seem to fail. This itself is a "gaps-based" argument. McGrath assumes that material causes will eventually fill all the relevant gaps. This is not a real search for the best explanation. It's a search for the best explanation, provided that the explanation is naturalistic. It's materialism of the gaps.

ID changes our paradigm, and ID advocates take a different approach. We don't prejudge the scientific evidence, force-fitting it into the mold of methodological naturalism. Rather, using the principle of uniformitarianism, we make an "inference to the best explanation" -- even if that explanation is non-material. If natural causes are the "best explanation" than we appeal to natural causes. If intelligent causes are the "best explanation" then so be it.

This is sound scientific reasoning. I think that Meyer's inference to design in Darwin's Doubt would win Dietrich Bonhoeffer's approval.

Why I don't doubt Jehovah's promise of eternal life.

The players change but the game goes on.

Is universal common descent up a tree?

Another Look at the Latest Blow to the Darwinian Tree of Life, and the Man Who Dealt It

Evolution News & Views July 3, 2012 2:41 PM

How many times can evolutionists say everything they know is wrong before people start to really believe it?

As Casey Luskin noted here earlier, a news article in Nature tells the tree-shaking story of Kevin Peterson. This whole subject is so delightful it deserves another look.

A molecular paleobiologist at Dartmouth, Peterson never set out to disturb fellow believers in Darwinian theory. He just thought he would try a new method for constructing phylogenetic trees: tracking relationships via micro-RNAs. Peterson thought micro-RNAs would be a good marker of evolutionary relationships:

MicroRNAs, Peterson and [colleague Lorenzo] Sempere discovered, are unlike any of the other molecular metrics that biologists typically use to tease apart evolutionary relationships. DNA binding sites, for example, continuously mutate; microRNAs, by contrast, are either there or they aren't, so their interpretation doesn't require such complex sequence and alignment analyses. And once gained, microRNAs usually remain functional, which means that their signal stays intact for hundreds of millions of years.

But when Peterson tested the conventional Darwinian tree of life for rotifers, his tree didn't match the conventional one. That was only the beginning. He found tree rot all over:

But a chance investigation of microRNAs in microscopic creatures called rotifers led him to examine these regulatory molecules in everything from insects to sea urchins. And as he continues to look, he keeps uncovering problems, from the base of the animal tree all the way up to its crown.

Peterson's observations, first published in a minor journal but now getting notice in Nature andScience, are winning him some vocal critics, but mostly reluctant supporters. His work on the family tree of placental mammals will be his latest unsettling contribution. Peterson had decided to lay it all on the line by testing the family tree of mammals. "We're mammals, so this matters," he said. Sure enough, problems are surfacing there, too.

The data's refusal to cooperate with other Darwinian phylogenies has left Peterson "up a tree," asNature writer Elie Dolgin quips: "At first, Peterson was shocked by his results, which still haven't been published. But he has spent the past year validating his tree with gene-expression libraries and genomic sequences, all of which he says support his findings." He's being extra careful, because "If we get this wrong, all faith that anyone has in microRNAs [for phylogenetics] will be lost," his colleague Philip Donoghue, a palaeobiologist at the University of Bristol, said. "It could well be the end of all our careers."

The reactions of other scientists have been entertaining:

• "One of the reviewers said it was impossible, what we were describing," Peterson said.
• "He's talking about the entire genome that has to be wrong."
• "I don't give it any serious consideration. There have to be other explanations."
• "What we know at this stage is that we do have a very serious incongruence. It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong. We don't know yet."

Stirring controversy was not Peterson's intention. Dolgin describes him as a "mild-mannered but straight-talking Montanan" who "didn't set out to rewrite textbooks."

For now, he's trying to amass the best evidence he can before publishing the mammal study. Then he wants to return to the quiet life of an ancient-invertebrate biologist. But if Peterson's voyage upends the mammalian phylogeny, he'll have left a furry mess in his wake.

Why is this so surprising to anyone? In fact, it's old news. Since the first molecular studies with proteins like cytochrome C and other molecules, neo-Darwinists have repeatedly generated trees that conflict with each other depending on the marker used. Over and over, they have had to explain away these observations. There is so much wiggle room in the methods that some have invoked epicycle-style fudge factors like "rate heterogeneity" (molecular clocks ticking at different rates) to keep the data in sync with the theory.

This is a classic example of theory directing data, instead of the other way around -- a form of theplaustrum ante equum (cart before the horse) fallacy. The fallacy becomes evident when different practitioners with the same theory generate contradictory data sets and have to invoke fudge factors to avoid changing their assumptions. You notice that Nature titled its article "Phylogeny: Rewriting evolution," not "Phylogeny: Falsifying evolution."

Trying to play the unbiased scientist, Peterson said, "Ultimately, I don't really care how mammals are related to one another -- it doesn't matter to me. But what does matter is the validity of the data set." That's a commendable attitude, but would he be equally comfortable questioning neo-Darwinian theory itself?

Intelligent-design advocates are unsurprised by any of this, because their focus is on the origins of functional information, not unobservable prehistories imagined by assuming that a universal common ancestor gave birth to a family tree via random mutation and natural selection. Design theorists also believe in following the evidence where it leads.

Just a name? II

On irreducible complexity and oversimplification.

Has Ken Miller Refuted Irreducible Complexity with a Tie Clip?

Michael Flannery October 6, 2014 4:53 AM |

At a recent meeting of the student apologetics group Ratio Christi an acquaintance suggested to me that biologist Ken Miller's use of a mousetrap as a tie clip -- with the catch and the hold-down bar removed -- was somewhat cheesy but had "made its point." Really?

What exactly was Ken Miller's point? Well, the idea is that Miller's tie clip purportedly demonstrates that Michael Behe's example of the mouse trap as an irreducibly complex (IR) apparatus (comparable in this respect to the bacterial flagellum with its own IR design) fails by a simple analogy. In other words, what we see now as a complete bacterial flagellum might well have served a different function in an earlier form. The degree to which this kind of theatrics has lodged itself in the public mind as a "refutation" of IR caught me by surprise, especially because it came from someone from whom I would have least expected it.

My first inclination was to respond, "The tie clip demonstration doesn't address the essential point, namely, that ALL parts of the mouse trap are necessary to make it function as intended. Now if by removing a part of the mouse trap the mechanism could still function in the same capacity, then I think a valid point would be made. But Behe's whole point is that ALL parts of the mouse trap are needed to function as a mouse trap."

My off-the-cuff answer is valid, I think, but it seemed to me a simpler explanation was likely available. So I e-mailed some friends for their thoughts, and to my satisfaction a great many responses poured in. I will paraphrase the two best, which can be posed as plain rhetorical questions, as follows. First, did the tie clip spontaneously assemble or did it require some intentional, purposeful design? Second, could the selective pressures that led the tie clip to morph into an apparatus for catching mice be explained?

Those simple questions show Miller's complete misunderstanding of IR and ID. Behe has addressed this directly himself (for the complete chapter go here):

Finally, rather than showing how their theory could handle the obstacle, some Darwinists are hoping to get around irreducible complexity by verbal tap dancing. At a debate between proponents and opponents of intelligent design sponsored by the American Museum of Natural History in April 2002, Kenneth Miller actually claimed (the transcript is available at the website of the National Center for Science Education) that a mousetrap isn't irreducibly complex because subsets of a mousetrap, and even each individual part, could still "function" on their own. The holding bar of a mousetrap, Miller observed, could be used as a toothpick, so it still had a "function" outside the mousetrap. Any of the parts of the trap could be used as a paperweight, he continued, so they all had "functions." And since any object that has mass can be a paperweight, then any part of anything has a function of its own. Presto, there is no such thing as irreducible complexity! Thus the acute problem for gradualism that any child can see in systems like the mousetrap is smoothly explained away.

Of course the facile explanation rests on a transparent fallacy, a brazen equivocation. Miller uses the word "function" in two different senses. Recall that the definition of irreducible complexity notes that removal of a part "causes the system to effectively cease functioning." Without saying so, in his exposition Miller shifts the focus from the separate function of the intact system itself to the question of whether we can find a different use (or "function") for some of the parts. However, if one removes a part from the mousetrap I pictured, it can no longer catch mice. The system has indeed effectively ceased functioning, so the system is irreducibly complex, just as I had written. What's more, the functions that Miller glibly assigns to the parts -- paperweight, toothpick, key chain, [tie clip,] etc. -- have little or nothing to do with the function of the system of catching mice (unlike the mousetrap series proposed by John McDonald, discussed below), so they give us no clue as to how the system's function could arise gradually. Miller explained precisely nothing.

With the problem of the mousetrap behind him, Miller moved on to the bacterial flagellum -- and again resorted to the same fallacy. If nothing else, one has to admire the breathtaking audacity of verbally trying to turn another severe problem for Darwinism into an advantage. In recent years it has been shown that the bacterial flagellum is an even more sophisticated system than had been thought. Not only does it act as a rotary propulsion device, it also contains within itself an elegant mechanism to transport the proteins that make up the outer portion of the machine, from the inside of the cell to the outside. (Aizawa 1996) Without blinking, Miller asserted that the flagellum is not irreducibly complex because some proteins of the flagellum could be missing and the remainder could still transport proteins, perhaps independently. (Proteins similar -- but not identical -- to some found in the flagellum occur in the type III secretory system of some bacteria. See Hueck 1998.) Again he was equivocating, switching the focus from the function of the system to act as a rotary propulsion machine to the ability of a subset of the system to transport proteins across a membrane. However, taking away the parts of the flagellum certainly destroys the ability of the system to act as a rotary propulsion machine, as I have argued. Thus, contra Miller, the flagellum is indeed irreducibly complex. What's more, the function of transporting proteins has as little directly to do with the function of rotary propulsion as a toothpick has to do with a mousetrap. So discovering the supportive function of transporting proteins tells us precisely nothing about how Darwinian processes might have put together a rotary propulsion machine.

I suppose what disturbs me most is how Miller gets away with such shenanigans. When antics replace analysis and stunts substitute for serious discussion, the only purpose served is the expansion of Miller's calendar of speaking engagements and his honoraria.