On the supposed common ancestry of man and ape.

Do Shared ERVs Support Common Ancestry?
Jonathan M. May 26, 2011 10:52 AM

In my  previous article, I discussed the background of one of the most commonly made arguments for primate common ancestry. In this article, I want to examine the first of the three layers of evidence offered by a popular-level article written about this subject.

The author of the article under discussion tells us,
When we examine the collective genome of Homo sapiens, we find that a portion of it consists of ERVs (IHGS Consortium, 2001). We also find that humans share most of them with Chimpanzees, as well as the other members of Hominidae (great apes), the members of Hylobatidae (gibbons), and even the members of Cercopitheciodae (old world monkeys) (Kurdyukov et al., 2001; Lebedev et al., 2000; Medstrand and Mager, 1998; Anderssen et al., 1997; Steinhuber et al., 1995). Since humans don't and/or can't regularly procreate and have fertile offspring with members of these species, and thus don't make sizable contributions to their gene pools, and vice versa, their inheritance cannot have resulted from unions of modern species. As previously mentioned, parallel integration is ruled out by the highly random target selection of integrase. And even if it was far more target-specific than observed, it would require so many simultaneous insertion and endogenizations that the evolutionary model would still be tremendously more parsimonious. This leaves only one way an ERV could have been inherited: via sexual reproduction of organisms of a species that later diverged into the one the organisms that share the ERV belong to, i.e. an ancestral species--simply put, humans and the other primates must share common ancestry.
Just how target-specific are these ERV integrations? In the portion of the article headed "common creationist responses," we are told that,
...while proviral insertion is not purely random, it is also not locus specific; due to the way it directly attacks the 5' and 3' phosphodiester bonds, with no need to ligate (Skinner et al., 2001). So relative to pure randomness, insertion is non-random, but relative to locus specificity, insertion is highly random.
Really?

Let's take a few moments to do what any good student of biology would do -- and briefly survey some of the literature.

In one relevant study, Barbulescu et al. (2001) report that,
We identified a human endogenous retrovirus K (HERV-K) provirus that is present at the orthologous position in the gorilla and chimpanzee genomes, but not in the human genome. Humans contain an intact preintegration site at this locus. [emphasis added]
It seems that the most plausible explanation for this is an independent insert in the gorilla and chimpanzee lineages. Notice that the intact preintegration site at the pertinent locus in humans precludes the possibility of the HERV-K provirus having been inserted into the genome of the common ancestor of humans, chimpanzees and gorillas, and subsequently lost from the human genome by processes of genetic recombination. Though there are other possible candidate hypotheses for this observation (such as incomplete lineage sorting), in the context of other indications of locus-specific site preference, this data is, at the very least, suggestive that these inserts may in fact be independent events.

But there's more.

Another study, by Sverdlov (1998) reports,

But although this concept of retrovirus selectivity is currently prevailing, practically all genomic regions were reported to be used as primary integration targets, however, with different preferences. There were identified 'hot spots' containing integration sites used up to 280 times more frequently than predicted mathematically. [emphasis added]
In addition,Yohn et al. (2005) report that,

Horizontal transmissions between species have been proposed, but little evidence exists for such events in the human/great ape lineage of evolution. Based on analysis of finished BAC chimpanzee genome sequence, we characterize a retroviral element (Pan troglodytes endogenous retrovirus 1 [PTERV1]) that has become integrated in the germline of African great ape and Old World monkey species but is absent from humans and Asian ape genomes.
I could continue in a similar vein for some time. Other classes of retroelement also show fairly specific target-site preferences. For example, Levy et al. (2009) report that Alu retroelements routinely preferentially insert into certain classes of already-present transposable elements, and do so with a specific orientation and at specific locations within the mobile element sequence. Moreover, a study published in Science by Li et al.(2009) found that, in the waterflea genome, introns routinely insert into the same loci, leading the internationally-acclaimed evolutionary biologist Michael Lynch to note,

Remarkably, we have found many cases of parallel intron gains at essentially the same sites in independent genotypes. This strongly argues against the common assumption that when two species share introns at the same site, it is always due to inheritance from a common ancestor.
Finally, Daniels and Deininger (1985) suggest that,

...a common mechanism exists for the insertion of many repetitive DNA families into new genomic sites. A modified mechanism for site-specific integration of primate repetitive DNA sequences is provided which requires insertion into dA-rich sequences in the genome. This model is consistent with the observed relationship between galago Type II subfamilies suggesting that they have arisen not by mere mutation but by independent integration events.
Such target-site preferences are also documented here, here, and here.

Why might these ERV site-preferences exist? Presumably because these sites are most conducive to their successful reproduction (e.g. the necessitude for expression of the ERV's regulatory elements; the activity of the host's DNA correction system, etc). Mitchell et al. (2004) suggest "that virus-specific binding of integration complexes to chromatin features likely guides site selection."

Out of tens of thousands of ERV elements in the human genome, roughly how many are known to occupy the same sites in humans and chimpanzees? According to this Talk-Origins article, at least seven. Let's call it less than a dozen. Given the sheer number of these retroviruses in our genome (literally tens of thousands), and accounting for the evidence of integration preferences and site biases which I have documented above, what are the odds of finding a handful of ERV elements which have independently inserted themselves into the same locus?

A Nested Hierarchy?
What about this "nested hierarchy" of which we are told?

We are (incorrectly) told that "There is only one, solitary known deviation of the distributional nested hierarchy; a relatively recently endogenized/fixed ERV called HERV-K-GC1."

This claim, however, is false.

In addition to the case mentioned, Yohn et al. (2005) report:
We performed two analyses to determine whether these 12 shared map intervals might indeed be orthologous. First, we examined the distribution of shared sites between species (Table S3). We found that the distribution is inconsistent with the generally accepted phylogeny of catarrhine primates. This is particularly relevant for the human/great ape lineage. For example, only one interval is shared by gorilla and chimpanzee; however, two intervals are shared by gorilla and baboon; while three intervals are apparently shared by macaque and chimpanzee. Our Southern analysis shows that human and orangutan completely lack PTERV1 sequence (see Figure 2A). If these sites were truly orthologous and, thus, ancestral in the human/ape ancestor, it would require that at least six of these sites were deleted in the human lineage. Moreover, the same exact six sites would also have had to have been deleted in the orangutan lineage if the generally accepted phylogeny is correct. Such a series of independent deletion events at the same precise locations in the genome is unlikely (Figure S3).

[...]

Several lines of evidence indicate that chimpanzee and gorilla PTERV1 copies arose from an exogenous source. First, there is virtually no overlap (less than 4%) between the location of insertions among chimpanzee, gorilla, macaque, and baboon, making it unlikely that endogenous copies existed in a common ancestor and then became subsequently deleted in the human lineage and orangutan lineage. Second, the PTERV1 phylogenetic tree is inconsistent with the generally accepted species tree for primates, suggesting a horizontal transmission as opposed to a vertical transmission from a common ape ancestor. An alternative explanation may be that the primate phylogeny is grossly incorrect, as has been proposed by a minority of anthropologists.

As irritating to the evolutionary model as it might be, there are, in fact, a significant number of deviations from the orthodox phylogeny.


In the final part of this blog series, I will discuss the argument based on "shared mistakes" in these ERV elements, as well as the argument based on degrees of mutational divergence between the retroviral 5' and 3' long terminal repeats (LTRs).

Mindless intelligence? or Darwinists' claim to have finally got that free lunch they've been seeking.

You Can't Ascribe Intelligence to an Unguided Process
Evolution News & Views February 4, 2016 3:55 AM

There's a new movement afoot among some evolutionary biologists to co-opt the term "intelligent design" for Darwin. It's not the same as Dawkins's famous line that "Biology is the study of complicated things that give the appearance of having been designed for a purpose." In this newer view, it's not just an appearance; it's a reality. The process of evolution itself is learning how to get smarter as it goes.

Richard A. Watson at the University of Southampton proposes this idea at The Conversation in a piece titled, "Intelligent design without a creator? Why evolution may be smarter than we thought." This is not your grandfather's Darwinism:

Charles Darwin's theory of evolution offers an explanation for why biological organisms seem so well designed to live on our planet. This process is typically described as "unintelligent" -- based on random variations with no direction. But despite its success, some oppose this theory because they don't believe living things can evolve in increments. Something as complex as the eye of an animal, they argue, must be the product of an intelligent creator.

I don't think invoking a supernatural creator can ever be a scientifically useful explanation. But what about intelligence that isn't supernatural? Our new results, based on computer modelling, link evolutionary processes to the principles of learning and intelligent problem solving -- without involving any higher powers. This suggests that, although evolution may have started off blind, with a couple of billion years of experience it has got smarter. [Emphasis added.]

With its provocative title, the article mischaracterizes intelligent design as a supernatural explanation involving "higher powers." In reality, ID is a scientific theory that only appeals to types of causes now known to be in operation, based on our uniform experience with causes that can produce complex specified information. Inferences to design can be made without any appeal to the "supernatural," as in the case of inferring intelligence as the cause of Mt. Rushmore.

That said, Watson does seem to have looked into ID, or at least the scholarship of our colleague, the science historian Michael Flannery. Watson writes:

Alfred Russel Wallace (who suggested a theory of natural selection at the same time as Darwin) later used the term "intelligent evolution" to argue for divine intervention in the trajectory of evolutionary processes. If the formal link between learning and evolution continues to expand, the same term could become used to imply the opposite.

That's an interesting connection, but as far as we're aware, it wasn't Wallace who introduced the term "intelligent evolution" in this context. Professor Flannery did so in the title of a book, seeking in a brief phrase to summarize Wallace's thinking and what it implies. Still, it's commendable that Watson appears to have done some extra reading to broaden his horizon.

What about the contention the evolution gets smarter over time? Watson's argument begins with the analogy of neural networks that "learn" to make connections that lead to greater rewards. Those, needless to say, are designed (see "Designless Logic: Is a Neural Net a Budding Brain?"). Can he make the transition to mindless processes, or is this another case of Darwin comparing artificial selection to natural selection?

But what about evolution, can it get better at evolving over time? The idea is known as the evolution of evolvability. Evolvability, simply the ability to evolve, depends on appropriate variation, selection and heredity -- Darwin's cornerstones. Interestingly, all of these components can be altered by past evolution, meaning past evolution can change the way that future evolution operates.

The notion of evolvability has been around for some time, Watson notes. In fact, Michael Behe has given a more rigorous definition of it in an article here at Evolution News. What's new in the notion of evolvability is the application of learning theory. Watson hopes this will give it a "much needed theoretical foundation." In his research, he has worked to compare genes in regulatory networks with synapses in neural networks.

Our work shows that the evolution of regulatory connections between genes, which govern how genes are expressed in our cells, has the same learning capabilities as neural networks. In other words, gene networks evolve like neural networks learn. While connections in neural networks change in the direction that maximises rewards, natural selection changes genetic connections in the direction that increases fitness. The ability to learn is not itself something that needs to be designed -- it is an inevitable product of random variation and selection when acting on connections.

The exciting implication of this is that evolution can evolve to get better at evolving in exactly the same way that a neural network can learn to be a better problem solver with experience. The intelligent bit is not explicit "thinking ahead" (or anything else un-Darwinian); it is the evolution of connections that allow it to solve new problems without looking ahead.

As an example of what he means, he discusses limbs. Random variation might change each limb separately, but if a regulatory network changed them all together, the next solution would be easier. Say, for instance, height would increase fitness. Having an upstream regulator change all four limbs together is an easier problem than changing them separately. This is how evolution could evolve to "learn" better ways to solve problems over time.

Watson is now ready to show how this kind of "intelligent design" is purely natural and requires no "divine intervention."

So, when an evolutionary task we guessed would be difficult (such as producing the eye) turns out to be possible with incremental improvement, instead of concluding that dumb evolution was sufficient after all, we might recognise that evolution was very smart to have found building blocks that make the problem look so easy.

To recap, Watson says that evolution is "smarter than we thought." It's not a clunky, blind opportunist tinkering at random. It can learn. It can find easier ways to increase fitness, and therefore get better at evolving over time. No intervening intelligence is required; as evolution learns, the organism becomes more evolvable. The more difficult problems (like arriving at an eye) are bound to be solved.

Notice, however, that Watson's "neural networks" are already designed entities. Once again, a Darwinian evolutionist has snuck information in the side door while talking about the magical power of material forces to produce rabbits from hats (see "Arrival of the Fittest: Natural Selection as an Incantation"). Gene regulatory networks, Stephen Meyer has shown, require more information to rewire. As for Watson's example of synchronized limb evolution, that's a post-hoc rationalization. If animals had four very different limbs, it's likely he would be ready with a good story about how evolution "learned" to do that.

If "learning" was a law of nature for material phenomena, we should expect to find all kinds of nonliving systems acting similarly. Picture a flow of water on a mildly sloping plain. The water will find the easiest way down, and will "learn" to flow that way, carving a channel deeper over time. But does that increase its "fitness"? Are the limestone terraces we discussed here more fit than random limestone blocks? Is wind that "learns" to drop sand grains on a dune more fit than wind that scatters sand across a beach? Intuitively, something seems amiss. This kind of thinking would make Mars more fit because of its canyons and dunes.

Information is a concept unfortunately lacking in Watson's proposal. Clearly, to build an animal from matter would require vast increases in information. The genome of a Cambrian body plan is extraordinarily more information-rich than that of amino acids in a primordial soup. A human brain, we recently pointed out, has the memory capacity of the World Wide Web. Can material substances "learn" to build libraries of complex specified information? Only in a Darwinist's dreams. Our uniform experience locates that ability in free-acting minds with real intelligence, not in material forces.

The only way Watson can tell his story is by personifying evolution, endowing it with learning ability. This is equivalent to calling a canyon smarter as it gets deeper, or the wind intelligent as it learns to pile sand higher. In all out experience, though, whenever we find a material entity employing complex specified information to act in an intelligent way (as in a computer or robot), we know that intelligence was its ultimate cause. It is a logical inference to ascribe an intelligent cause to intelligence in animals as well.


Unless they are willing to relegate their own intelligence to mindless material forces, advocates of the "evolvability" theory are well advised to avoid shooting themselves in the foot. How can Watson trust his own mind, if it is the product of mindless matter? Particles and forces are dumb. They do not act with goals, thinking through concepts to arrive at logical conclusions. They do not learn things. The concept of learning implies pre-existing intelligence.

Well past the slippery slope.

Brave New World, Here We Come
Wesley J. Smith February 2, 2016 10:17 AM

The West seems congenitally incapable of restraining Brave New World. In the cause of eliminating suffering by any means necessary, no technology -- including lethal -- is apparently off limits.

Now, the we-never-say-no UK Embryo Authority -- which once approved attempts at human cloning with cow eggs -- has told CRISPR gene editors to feel free to edit away. From the BBC story:

It is the first time a country has considered the DNA-altering technique in embryos and approved it.

The research will take place at the Francis Crick Institute in London and aims to provide a deeper understanding of the earliest moments of human life. It will be illegal for the scientists to implant the modified embryos into a woman.

But the field is attracting controversy over concerns it is opening the door to designer -- or GM -- babies.

"Concerns"? That is the ultimate point!

Nascent human life is considered so much clay to be researched upon and destroyed. That will lead to fetal farming one day, in which fetuses will be similarly treated and destroyed.


This is 21st-century eugenics -- and it will, in the end, become just as oppressive and anti-human equality as the original version.

  Ps. Dismaying but not surprising,the logic is that it is better to go light on the morals lest the money and brainpower gravitate to the competition.

File under "Well said" XX

I hate war as only a soldier who has lived it can, only as one who has seen its brutality, its futility, its stupidity.
Dwight D. Eisenhower

The debate is done?: Pros and cons.

Is I.D true science?: Pros and Cons

The thumb print of Jehovah V

Poll shows teaching pros and cons of evolution uncontroversial with public.

For Darwin's Birthday, Poll Shows Broad Support for Teaching Evidence For and Against Darwin's Theory

 Evolution News & Views February 1, 2016 3:31 AM

 

 

Just in time for Charles Darwin's birthday on February 12, a new nationwide survey reveals that 81 percent of American adults believe that "when teaching Darwin's theory of evolution, biology teachers should cover both scientific evidence that supports the theory and scientific evidence critical of the theory."

Only 19 percent of Americans believe that "biology teachers should cover only scientific evidence that supports the theory."

"Americans agree by an overwhelming margin that students should learn about all of the scientific evidence relating to Darwinian evolution, pro and con," said Dr. John West, Vice President of Discovery Institute. "This is a common-sense approach. Most people understand that it's not good education to present a one-sided review of the data, especially in science."

"There is growing peer-reviewed research that questions the adequacy of the Darwinian mechanism of random mutation and natural selection," added Discovery Institute biologist Ann Gauger. Gauger holds a PhD in developmental biology from the University of Washington, and she has served in the past as a post-doctoral Fellow at Harvard University.

Support for teaching the scientific evidence for and against Darwin's theory is overwhelming regardless of age, gender, religious affiliation, geography, party affiliation, and household income.

• 79 percent of men and 83 percent of women support teaching the evidence for and against Darwin's theory.


• 85 percent of theists, 65 percent of atheists, and 79 percent of agnostics support this approach.


• 79 percent of Democrats support teaching the evidence for and against Darwin's theory, and so do 82 percent of independents and 85 percent of Republicans.


• 85 percent of middle-aged Americans (ages 45-59) support teaching the evidence for and against Darwin's theory, and so do 81 percent of young adults (ages 18-29) and senior citizens (ages 60 and older).

The poll was conducted by Discovery Institute using SurveyMonkey Audience, which randomly sampled the adult members of its nationally representative panel of more than 6 million U.S. residents. Survey responses were collected from January 5-9, 2016, and the survey included 2,117 completed responses for this question.

The SurveyMonkey platform has been utilized for public opinion surveys by NBC News, the Los Angeles Times, and other media organizations. More information on how SurveyMonkey Audience recruits respondents is available here.

Darwinism Vs. the real world XXVII

The Body as a Battlefield: Proteins of the Innate Immune System

Howard Glicksman February 3, 2016 5:07 AM

 

Editor's note: Physicians have a special place among the thinkers who have elaborated the argument for intelligent design. Perhaps that's because, more than evolutionary biologists, they are familiar with the challenges of maintaining a functioning complex system, the human body. With that in mind, Evolution News is delighted to offer this series, "The Designed Body." For the complete series, see here. Dr. Glicksman practices palliative medicine for a hospice organization.

 Since life takes place in the context of nature, it must not only exist in accordance with physical and chemical laws, but must also protect itself from many of the organisms in its environment. There are a wide variety of microbes that our senses cannot detect and that are always trying to enter our body so they can multiply.

The first line of defense against infection by these microorganisms is the skin and the epithelial tissues that line the respiratory, gastrointestinal, and genitourinary tracts. Without any one of them, our earliest ancestors could not have survived long enough to reproduce. However, if by injury to the body or functional ability of the microorganism, the microbes penetrate into the tissues below, then they come up against the second line of defense: the immune system.

As we've seen already in this series, the immune system can be divided into two parts: the innate immune system that each of us is born with and the adaptive immune system that develops over time as we are exposed to the environment. Each of these systems has its unique cells and proteins, needed for the body to defend against microbial invasion. In my last two articles we looked at some of the more important immune cells of the innate system: the mast cells, macrophages, and dendritic cells, which are the first responders in the tissues, and the neutrophils that travel in the blood and respond to the signal to come to the battlefield. Now we will look at the proteins of the innate immune system and how they work to bring other immune cells to the field of battle, make neutrophils and macrophages more effective, and fight invading microbes.

The plasma proteins of innate immunity, which leak into the tissues when inflammation takes place, are collectively known as the complement system, or sometimes simply the complement, because they complement (complete) the function of its cellular components. The complement system consists of thirty or more proteins that, like the clotting factors, are mostly produced in the liver and enter the blood in an inactive form.

Also, just as with clotting, there is more than one pathway for activation and once it begins, it progresses quickly in a cascading fashion, like falling dominoes. Finally, just as with the coagulation cascade, activation of the complement system requires that two key enzymatic steps take place to unleash its power. Since inappropriate activation of the complement can result in significant injury, the body must make sure that it only turns on when it's needed and stays or turns off when it's not.

Just as the final common pathway for coagulation involves mainly two clotting factors (prothrombin and fibrinogen), so too, activation of the complement system involves mainly two complement proteins called C3 and C5. There are thought to be three chemical pathways by which foreign molecules on the surface of invading microbes triggers complement activation.

All three of these pathways converge to form an enzyme called C3 convertase. C3 convertase, as its name implies, is an enzyme that breaks specific bonds within hundreds of molecules of C3 and converts them into two fragments called C3a and C3b. (It sounds like the scientists who came up with these names must have been brought up on Dr. Seuss's book The Cat in the Hat Comes Back. Remember Little Cats C, D, E, et al.?)

The smaller fragment, C3a, binds to specific receptors on mast cells, which trigger them to release histamine to bring about inflammation and call more immune cells and proteins to the battlefield. The larger fragment, C3b, usually does one of two things. It can attach to foreign proteins on microbes, allowing neutrophils and macrophages to better identify and attach to them by using specific complement receptors. Then they can engulf and digest them or it can join with C3 convertase to form another enzyme called C5 convertase, which breaks C5 into two fragments called C5a and C5b.

Like C3a, C5a, the smaller fragment, triggers inflammation by attaching to complement receptors on mast cells to release chemicals like histamine. C5a also helps neutrophils and monocytes (macrophages), pass through the capillaries and attracts them to the field of battle by chemotaxis. The larger fragment, C5b, acts as an anchor to which several specific complement proteins attach to form what is called the Membrane Attack Complex (MAC). The MAC is a weapon made up of these complement proteins that literally drills a hole through the cell membrane of the microbe to kill it.

However, just as in clotting, where inappropriate activation of the system is very problematic, so too the body must be able to control the explosive power of the complement system. To control hemostasis, the body has to have enough anti-clotting factors that can resist coagulation unless significant injury and bleeding takes place. Here as well, to control the activation of the complement, the body has to have enough inhibiting proteins to resist the formation of both C3 and C5 convertase unless a significant infection is present.

When activated, the proteins of the complement system provide the body's immune defense with significant assistance and firepower to fight against resistant pathogenic microbes. Activated complement proteins increase inflammation (C3a, C5a), attract phagocytes to the battlefield (C5a), help them attach to microbes for phagocytosis (C3b), and directly kill microbes (C5b, MAC).

In addition, to prevent tissue damage, the body must have enough inhibiting proteins so that the complement only turns on when it's needed and stays or turns off when it's not. Deficiency of a specific complement protein or one of their inhibitors is rare and usually manifests as either recurrent infection or serious allergic or autoimmune disease. This means that if our earliest ancestors hadn't had enough of most of the proteins that make up the complement system, they never could have survived long enough to reproduce.

Evolutionary biologists observe that certain of the components of the complement system are present in some earlier forms of life and they conclude that its development can be explained by gene duplication. However, not only is the system irreducibly complex, requiring all of the parts to work properly, but there has to be enough of each of the components and their inhibitors as well.

In other words, the body requires a natural survival capacity to produce enough of each component, the control of which evolutionary biologists can't explain and neither can medical science. Now that you know the components of the innate immune system and how they work together to help defend the body from infection, we'll look at the adaptive immune system.

Using design to debunk design?

Intelligent Design Lab is Going Where no Evolution Simulation has Gone Before:
Robert Crowther June 10, 2008 8:46 AM |

Over the past decade or so there has been much hype about computer simulations of Darwinian evolution. The most hyped is Avida at the MSU Digital Evolution Laboratory. Avida researchers claim their work is not a simulation, but actually is Darwinian evolution in action. They describe it like this:

In Avida, a population of self-replicating computer programs is subjected to external pressures (such as mutations and limited resources) and allowed to evolve subject to natural selection. This is not a mere simulation of evolution -- digital organisms in Avida evolve to survive in a complex computational environment and will adapt to perform entirely new traits in ways never expected by the researchers, some of which seem highly creative.
According to MSU's Robert Pennock: "Avida is not a simulation of evolution; it is an instance of it."
You can't ignore the fact that ...

... previous computer simulations of evolution, such as Avida, were carefully proscribed and tightly constrained by the environment created by its programmers. For example Avida shows how organisms can advance in an environment where they are solving problems, but problems that were set up for them to solve. The digital organisms produced there can only do so much or go so far as they are constrained by the environment the programmer has designed.

Should the Avida team be working in quarantine? Lenski argues that Avida itself acts as a quarantine, because its organisms can exist only in its computer language. "They're living in an alien world," Lenski says. "They may be nasty predators from Mars, but they'd drop dead here." Life is a different environment than that programmed for Avida's digital organisms.
Enter the new evolution computational software just released by Biologic Institute. The program, Stylus, was developed by molecular biologist Douglas Axe and software engineer Brendan Dixon, and announced last week in a peer-reviewed publication at PLos One.

Stylus however goes way beyond previous computer simulations. Axe describes it this way:

Like the structures of life, the structures of language are used to solve real problems at a high level. And the high level solutions in both worlds depend on a succession of solutions at lower levels.
In life, body plans serve the needs of particular modes of life, organs serve the needs of particular body plans, tissues serve the needs of particular organs, cells serve the needs of particular tissues, protein functions serve the needs of particular cells, protein structures serve the needs of particular protein functions, protein sequences serve the needs of particular structures, and genes serve the needs of these particular protein sequence requirements.


In a similarly hierarchical way, texts of various kinds serve the needs of particular communication objectives, sections serve the needs of particular texts, paragraphs serve the needs of particular sections, sentences serve the needs of particular paragraphs, phrases serve the needs of particular sentences, and words serve the needs of particular phrases.

What about letters serving the needs of words? Well, the problem with letter-based texts is that they are only sequences, whereas structures figure prominently in the functions of proteins. Protein sequences must form functional three-dimensional structures in order to work, whereas alphabetic sequences function directly as sequences.

But not all written languages are alphabetic. Chinese writing, in particular, employs structural characters that are analogous in some interesting ways to protein structures. Like folded proteins, these written characters perform the low level functions from which higher functions can be achieved.

Why is this important? Well, for one thing, if realism is important it shows how far Avida falls short as an "instance of evolution." And for another thing, it is going to open new avenues of research into how much or how little organisms can evolve and whether it really is possible to go from the simplest building blocks of life to the more complex and necessary functions of life without any guiding intelligence at all.

Avida, Stylus. Stylus, Avida. Out with the old, in with the new.

A clash of titans VI

I.D,the limits of science and the nature of design opponents' propaganda.

The Darwinist Misinformation Train:
Casey Luskin September 7, 2005 12:55 PM:

A good friend of mine getting his teaching credential to teach public high school called me this weekend to converse about his professor’s response to a paper he wrote supporting the teaching of ID. Apparently his professor disapproved of teaching ID because he felt that ID was untestable science. The professor’s criticism went something like this:

“My main problem with ID is that it purports to not identify the designer when everyone knows it's really just God. Intelligent design thus shouldn’t be taught because it is essentially creation science repackaged. Thus, it’s just an untestable appeal to the supernatural. However, if I had to choose, I would actually prefer creation science to ID because at least creation scientists are up-front about who they think the designer is.”
This view was also echoed recently in the Seattle Weekly, where a commentator threw in a not-so-subtle, below-the-belt criticism about ID:
“[ID is] the notion … that an unspecified creator (who sounds an awful lot like the Christian notion of God) is responsible for the creation and development of everything, including human beings.”
Without nitpicking over the many inaccurate details of this description, here again we see the same implicit criticism of ID: "ID proponents say it doesn’t identify the designer, but everybody knows the designer is “God” [at this point, Eugenie Scott adds in her famous “wink wink, nudge nudge” line], therefore it isn’t science."
I found this criticism interesting, because a different article on the same day made the exact opposite criticism against intelligent design: ID isn’t science because it supposedly DOES identify the designer as a supernatural deity. This very point was argued recently by University of Utah bioengineering professor Gregory Clark before the Utah State Board of Education:
“Intelligent design fails as science because it does exactly that - it posits that life is too complex to have arisen from natural causes, and instead requires the intervention of an intelligent designer who is beyond natural explanation. Invoking the supernatural can explain anything, and hence explains nothing.”

These misconstruals are not mere trivialities. In fact, they form the basis for the ACLU's lawsuit against teaching intelligent design in Dover, Pennsylvania (Kitzmiller et al. v. Dover Area School District). As read in their complaint:

"Intelligent design is a non-scientific argument or assertion, made in opposition to the scientific theory of evolution, that an intelligent, supernatural actor has intervened in the history of life..."

So on the one hand, intelligent design fails as science because it does identify the designer as supernatural. On the other hand, intelligent design fails because it doesn’t identify the designer. Both positions can’t be right. But what does intelligent design really say, and can it overcome these criticisms?
The truth about ID:
Had my friend’s professor, or Dr. Clark, bothered to actually read (and / or choose to accurately represent) the writings of ID proponents, they would have found this matter of the designer’s identity to be crystal clear:

"Intelligent design is modest in what it attributes to the designing intelligence responsible for the specified complexity in nature. For instance, design theorists recognize that the nature, moral character and purposes of this intelligence lie beyond the competence of science and must be left to religion and philosophy." (William Dembski, The Design Revolution, pg. 42)
"Although intelligent design fits comfortably with a belief in God, it doesn't require it, because the scientific theory doesn't tell you who the designer is. While most people - including myself - will think the designer is God, some people might think that the designer was a space alien or something odd like that." (Michael Behe, Pittsburgh Post-Gazette, 02/08/01).

"[T]the place of intelligent design in science has been troubling for more than a century. That is because on the whole, scientists from within Western culture failed to distinguish between intelligence, which can be recognized by uniform sensory experience, and the supernatural, which cannot. Today we recognize that appeals to intelligent design may be considered in science, as illustrated by current NASA search for extraterrestrial intelligence (SETI). Archaeology has pioneered the development of methods for distinguishing the effects of natural and intelligent causes. We should recognize, however, that if we go further, and conclude that the intelligence responsible for biological origins is outside the universe (supernatural) or within it, we do so without the help of science." (Of Pandas and People, a pro-ID textbook, pg. 126-127, emphasis added)

Reading these quotes from leading ID theorists makes it completely clear that ID theory does not identify the designer, and cannot even really get very far into elaborating upon the nature of the designer. The reason for this is also clear: there are natural empirical limitations to what science can study. If we can’t study the identity of the designer, that’s not ID’s fault, that’s just the nature of the limits of science.
Why then do so many Darwinists publicly criticize ID as if it has the very weakness (i.e. advocating for an explicitly supernatural creator) which it goes out of its way to clearly avoid? The answer is simple: mischaracterizing ID as an appeal to the supernatural places it both outside the scope of science, and also outside legal rules laid down in Edwards v. Aguillard for legitimate origins ideas. But the whole notion that ID does identify the designer as supernatural is false.

The Darwinist Misinformation Train:
I have a 3 step theory for how it comes to pass that many people come to believe that intelligent design is an appeal to the supernatural:

Type I Darwinists critics: It starts with these Darwinist critics who correctly understand ID and realize that it respects the limits of science and doesn’t try to identify the designer. Yet, Type I Critics then purposefully misrepresent ID to the public (and particularly to scientists) as an untestable and unscientific appeal to the supernatural. This is despite the fact that ID proponents understand the nature of scientific inquiry and have formulated their theory to respect its boundaries. The dubious tactics of Type I critics are effective because it results in many people thinking that ID cannot be science because it makes claims about the supernatural -- beyond the scope of what can be studied using the scientific method.
Type II Darwinist critics: These are the people created by the activities of Type I critics. Type II critics misunderstand ID because they have been told by Type I critics that ID is an untestable appeal to the supernatural. This causes them to think it is makes exclusively religious claims, is not scientific, not empirically based, and not appropriate for the laboratory or the classroom. Type II Critics aren’t necessarily to blame for their misapprehensions because they have been misled. Nonetheless, it would behoove them to pick up some of the scholarship of ID proponents they are criticizing before they speak about it publicly. If they did so, they would realize their misunderstandings.
The Public: The Public consists of the people out there who are trying to figure out ID. Some of them may have read books or other literature by ID proponents and know the truth. But, for the most part, the public has been misled by Type I and Type II critics who are telling them that ID is an unscientific appeal to the supernatural, and shouldn’t be studied in labs or taught in science classes.


Though Type II critics are more honest and genuine than Type I critics, both have a common goal: make sure that ID gets construed such that the designer turns out to be a supernatural deity, because then it’s very easy to argue that it isn’t science (and isn’t constitutional to teach). This results in momentum for the Darwinist misinformation train:Some Darwinists critics want to get the ID train from Point A (reality) to Point B (fiction).

Point A represents the actual nature of intelligent design theory, where ID respects the limits of scientific inquiry and cannot identify the designer. At point A, ID relies upon the scientific method and makes no faith-based appeals to God. Here, it is pure science.

Point B represents where Darwinists would like to take ID theory: where it is an explicit appeal to the supernatural, and thus does not respect the inherent limitations of the scientific method. At point B, ID would have a clearly religious component as it identifies the designer as God. This would make it both unscientific and unconstitutional. Point B is fiction, because, of course, ID respects science and is ultra clear that the theory cannot identify the designer and avoids such religious claims.

Type I critics provide momentum for the train by misinforming the other scientists about intelligent design theory. Having spawned many genuinely believing (but ultimately wrong) Type II critics, both Type I and Type II critics go out to the public to press the case that ID shouldn’t be taught because it is an unscientific appeal to the supernatural.This is another way of representing the misinformation about intelligent design theory: The Misinformation Pyramid Scheme which makes use of the “Trickle Down Theory” of misinformation. Under their model, Type I Critics at the top purposefully misinform scientists and others about the nature of ID theory. Type I critics and their followers (Type II critics) then, relying upon a false understanding of intelligent design (some realizing that falsity, some not), go out and tell the public that ID is supposedly not science and should not be taught in schools, because they wrongly state is an unscientific appeal to the supernatural. In the end, the public is the real loser because they miss out on an accurate understanding of a new and potent scientific theory: ID.

Being Honest
But there are many honest Darwinists out there, like my friend’s professor, who acknowledges that ID does not identify the designer. However, my friend's professor still misunderstands ID because he then turned this strength of ID into a criticism by saying that it doesn’t matter what ID theory says, because we know the designer must be God, therefore ID isn't science. This argument makes no sense: if ID doesn't identify the designer, then how can one claim that ID theory says designer is God? It requires a misconstrual of ID theory which probably stems from critics mistaking some religious beliefs of ID proponents for the conclusions of ID theory.

For example, William Dembski, who in the above quote makes it ultra-clear that ID theory can’t identify the designer, is also clear elsewhere that he believes the designer is indeed God. In fact, when Dembski talks about the identity of the designer, he is often misquoted (the “Logos quote” comes to mind) by reporters and Darwinists who try to twist Dembski’s words into saying that it is ID theory which says the designer is God. This is unfortunate because Dembski makes it clear that he does not derive his beliefs about the identity of the designer from ID theory. Rather, when he identifies the designer, he does so not from ID theory, but from out of his own Christian religious faith.

Darwinists who think that they can misconstrue ID as if it identifies the designer as God simply because they can point to the beliefs of some ID proponents, are using a specious argument. To be accurate and truthful, one has to accept the way ID has been formulated by its proponents. And given the above quotes, there is little doubt as to how ID theory actually works: it can’t identify the designer.

(Besides, if the critics are right and ID theory mandates that the designer is God, then what about those ID sympathizers who aren’t religious—like the agnostic philosopher Antony Flew?)

The moral of this story is that you can’t go from Point A to Point B by going in opposite directions. Darwinists can’t criticize ID on the one-hand because it does identify the designer as supernatural, and then on the other-hand because it doesn’t, and then both claim that ID isn’t science. For those interested, the truth is that ID theory does not identify the designer, doesn’t even focus on studying the designer. While ID proponents may have beliefs about the designer, those beliefs are not derived from ID theory.

Of course, in the end, for all the Type I Critics out there, it doesn’t really matter what I write or whether or not I show clear documentation about how ID theory cannot identify the designer. But for those who are interested in taking ID seriously, I hope they will echo my desire that this Misinformation Train gets stuck at the reality station.

Thanks for reading.

Another failed Darwinian prediction IV

Mutations are not adaptive:

In the twentieth century, the theory of evolution predicted that mutations are not adaptive or directed. In other words, mutations were believed to be random with respect to the needs of the individual. As Julian Huxley put it, “Mutation merely provides the raw material of evolution; it is a random affair, and takes place in all directions. … in all cases they are random in relation to evolution. Their effects are not related to the needs of the organisms.” (Huxley, 36) Or as Jacques Monod explained:

chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, at the very root of the stupendous edifice of evolution: this central concept of modern biology is no longer one among other possible or even conceivable hypotheses. It is today the sole conceivable hypothesis, the only one that squares with observed and tested fact. And nothing warrants the supposition—or the hope—that on this score our position is likely ever to be revised. (Monod, 112)

Ronald Fisher wrote that mutations are “random with respect to the organism’s need” (Orr). This fundamental prediction persisted for decades as a recent paper explained: “mutation is assumed to create heritable variation that is random and undirected.” (Chen, Lowenfeld and Cullis)

But that assumption is now known to be false. The first problem is that the mutation rate is adaptive. For instance, when a population of bacteria is subjected to harsh conditions it tends to increase its mutation rate. It is as though a signal has been sent saying, “It is time to adapt.” Also, a small fraction of the population increases its mutation rates even higher yet. These hypermutators ensure that an even greater variety of adaptive change is explored. (Foster) Experiments have also discovered that duplicated DNA segments may be subject to higher mutation rates. Since the segment is a duplicate it is less important to preserve and, like a test bed, appears to be used to experiment with new designs. (Wright)

The second problem is that organisms use strategies to direct the mutations according to the threat. Adaptive mutations have been extensively studied in bacteria. Experiments typically alter the bacteria food supply or apply some other environmental stress causing mutations that target the specific environmental stress. (Burkala, et. al.; Moxon, et. al; Wright) Adaptive mutations have also been observed in yeast (Fidalgo, et. al.; David, et. al.) and flax plants. (Johnson, Moss and Cullis) One experiment found repeatable mutations in flax in response to fertilizer levels. (Chen, Schneeberger and Cullis) Another exposed the flax to four different growth conditions and found that environmental stress can induce mutations that result in “sizeable, rapid, adaptive evolutionary responses.” (Chen, Lowenfeld and Cullis) In response to this failed prediction some evolutionists now are saying that evolution somehow created the mechanisms that cause mutations to be adaptive.

References

Burkala, E., et. al. 2007. “Secondary structures as predictors of mutation potential in the lacZ gene of Escherichia coli.” Microbiology 153:2180-2189.

Chen, Y., R. Lowenfeld, C. Cullis. 2009. “An environmentally induced adaptive (?) insertion event in flax.” International Journal of Genetics and Molecular Biology 1:38-47.

Chen, Y., R. Schneeberger, C. Cullis. 2005. “A site-specific insertion sequence in flax genotrophs induced by environment.” New Phytologist 167:171-180.

David, L., et. al. 2010. “Inherited adaptation of genome-rewired cells in response to a challenging environment.” HFSP Journal 4:131–141.

Fidalgo, M., et. al. 2006. “Adaptive evolution by mutations in the FLO11 gene.” Proceedings of the National Academy of Sciences 103:11228-11233.

Foster, P. 2005. “Stress responses and genetic variation in bacteria.” Mutation Research / Fundamental and Molecular Mechanisms of Mutagenesis 569:3-11.

Huxley, Julian. 1953. Evolution in Action. New York: Signet Science Library Book.

Johnson, C., T. Moss, C. Cullis. 2011. “Environmentally induced heritable changes in flax.” J Visualized Experiments 47:2332.

Monod, Jacques. 1971. Chance & Necessity. New York: Vintage Books.

Moxon, E., et. al. 1994. “Adaptive evolution of highly mutable loci in pathogenic bacteria.” Current Biology 4:24-33.

Orr, H. 2005. “The genetic theory of adaptation: a brief history.” Nature Review Genetics 6:119-127.

Wright, B. 2000. “A biochemical mechanism for nonrandom mutations and evolution.” J Bacteriology 182:2993-3001.

The Watchtower Society's commentary on Mildness

MILDNESS:
A New Testament Wordbook, by William Barclay, says of the adjective pra·ysʹ: “In classical Greek this is a lovely word. Of things it means ‘gentle’. It is used, for instance, of a gentle breeze or a gentle voice. Of persons it means ‘mild’ or ‘gracious’. . . . There is gentleness in praus but behind the gentleness there is the strength of steel . . . It is not a spineless gentleness, a sentimental fondness, a passive quietism.” (London, 1956, pp. 103, 104) Vine’s Expository Dictionary of Old and New Testament Words states that the noun form pra·yʹtes “consists not in a person’s ‘outward behaviour only; nor yet in his relations to his fellow-men; as little in his mere natural disposition. Rather it is an inwrought grace of the soul; and the exercises of it are first and chiefly towards God. It is that temper of spirit in which we accept His dealings with us as good, and therefore without disputing or resisting; it is closely linked with the word tapeinophrosunē [humility], and follows directly upon it.’”—1981, Vol. 3, pp. 55, 56.

The word pra·ysʹ is variously translated in Bible versions “meek,” “mild,” “mild-tempered,” and “gentle.” (KJ, AS, NW, NE) However, as expressed in Barclay’s work quoted in the foregoing, pra·ysʹ goes somewhat deeper than gentleness and, when used of persons, means mild, gracious.

Although Jehovah is one who will not tolerate sin and badness, he has lovingly provided the way of approach to himself through the ransom sacrifice and priestly services of Jesus Christ. Jehovah’s worshipers and servants can therefore seek his face without any feeling of morbid fear and dread. (Heb 4:16; 10:19-22; 1Jo 4:17, 18) Jesus represented Jehovah God so perfectly that he could say: “He that has seen me has seen the Father also.” He also said: “Come to me, all you who are toiling and loaded down, and I will refresh you. Take my yoke upon you and learn from me, for I am mild-tempered [Gr., pra·ysʹ] and lowly in heart, and you will find refreshment for your souls. For my yoke is kindly and my load is light.” (Joh 14:9; Mt 11:28-30) Accordingly, Jehovah God is fully approachable by those who love him, and he generates mildness, great confidence, and strength in those appealing to him.

A Trait of Strength. Mildness of temper or of spirit is not an attribute of one weak in character. Jesus Christ said: “I am mild-tempered and lowly in heart.” (Mt 11:29; 2Co 10:1) Yet Jesus had the full power of his Father backing him, and he was firm for what is right; he used great freeness of speech and action when such was called for.—Mt 23:13-39; compare 21:5.

The mild-tempered person is such because he has faith and a source of strength. He is not easily unbalanced or caused to lose his good sense. Lack of mildness of temper is the result of insecurity, frustration, lack of faith and hope, and even desperation. A person who is not mild-tempered is described by the proverb: “As a city broken through, without a wall, is the man that has no restraint for his spirit.” (Pr 25:28) He is open and vulnerable to the invasion of any and all improper thoughts, which may motivate him to improper actions.

A Fruit of the Spirit. Mildness is a fruit of God’s holy spirit, his active force. (Ga 5:22, 23) God is therefore the Source of mildness, and one must apply to him for his spirit and must cultivate this fruit of the spirit to have genuine mildness of temper. Hence, it is not acquired by the exercise of sheer willpower, but results from drawing close to God.

Lack of mildness results in undue excitability, harshness, lack of self-control, and fights. On the other hand, the Christian is counseled to preserve unity and peace by “lowliness of mind and mildness.”—Eph 4:1-3.

Jealousy and contention, if allowed to take root and grow, will lead to disorders of every sort. Mildness, on the other hand, will prevent such conditions from developing among the followers of Christ. Hence, the Bible writer James urges those who are wise and understanding in the congregation to display “fine conduct” in the form of “mildness that belongs to wisdom,” “the wisdom from above.”—Jas 3:13, 17.

“Mildness,” in the Bible, is frequently coupled with “spirit,” for example, “mildness of spirit,” or “mild spirit.” Genuine mildness is, accordingly, something that is more than an outward, transitory or occasional quality; rather, it is a part of one’s makeup, or temperament. The apostle Peter points out this fact when he says: “And do not let your adornment be that of the external braiding of the hair and of the putting on of gold ornaments or the wearing of outer garments, but let it be the secret person of the heart in the incorruptible apparel of the quiet and mild spirit, which is of great value in the eyes of God.”—1Pe 3:3, 4.

The apostle Paul writes: “Clothe yourselves with . . . mildness,” which, superficially read, might seem to indicate that it is somewhat of a veneer for mere outward appearance; but in the same context he admonishes: “Clothe yourselves with the new personality, which through accurate knowledge is being made new according to the image of the One who created it.” (Col 3:10, 12; Eph 4:22-24) This shows that mildness is indeed a personality trait, primarily gained as a fruit of God’s spirit through accurate knowledge and application thereof, rather than just naturally inherited.

Essential for Those Having Oversight. In his letter of instructions to young Timothy on proper care of the congregation, Paul commanded him as to handling difficult matters, saying: “A slave of the Lord does not need to fight, but needs to be gentle toward all, qualified to teach, keeping himself restrained under evil, instructing with mildness those not favorably disposed; as perhaps God may give them repentance.” (2Ti 2:24, 25) Here we see a similarity between mildness and long-suffering. The individual realizes why he has to deal with the difficulty: God has permitted it, and as an overseer he must handle it in the best interests of the individual(s) involved. He must put up with the difficulty until it is settled, without getting overwrought.

Titus, another overseer, residing in Crete, was likewise counseled to remind his Christian brothers “to be reasonable, exhibiting all mildness toward all men.” To impress upon Titus the need for mildness, Paul calls attention to the unsurpassed love and mercy of God as manifested through his Son, calling for a forsaking of the old ways of maliciousness and hatred and following the new way leading to everlasting life.—Tit 3:1-7.

Again, Paul addresses those who are spiritually mature ones in the congregation, outlining the responsibility upon them: “Even though a man takes some false step before he is aware of it, you who have spiritual qualifications try to readjust such a man in a spirit of mildness, as you each keep an eye on yourself, for fear you also may be tempted.” (Ga 6:1) They should keep in mind how God has dealt with them. Doing so, they should not give the erring man a harsh reprimand but should try to readjust him in a spirit of mildness. This will prove to be far more effective and beneficial to all concerned.

Mildness will accomplish good when dealing with a difficult situation or an angry person, breaking down difficulty, whereas harshness would magnify the bad situation. The proverb says: “An answer, when mild, turns away rage, but a word causing pain makes anger to come up.” (Pr 15:1) Mildness can have great force. “By patience a commander is induced, and a mild tongue itself can break a bone.”—Pr 25:15.

Essential When Under Discipline. Another fine principle involving mildness or calmness is set forth by Solomon. It concerns the tendency we may have to show a rebellious spirit when corrected or chastised by one in authority. We may get so indignant as to leave our place of proper submission, hastily giving up our assigned position. But Solomon warns: “If the spirit of a ruler should mount up against you, do not leave your own place, for calmness itself allays great sins.” (Ec 10:4; compare Tit 3:2.) The proper attitude of calmness and mildness under discipline not only avoids further anger from the authority but also enables us to improve our personality through keeping our temper and our assigned place, or position, and applying the discipline.


This is especially true when the ruler is Jehovah God and when discipline comes through those set in authority by him. (Heb 12:7-11; 13:17) It also applies in our relationship to those permitted by God to wield worldly governing authority. (Ro 13:1-7) Even when such a ruler may make a harsh demand of the Christian as to the reason for the hope he has, the Christian, while firmly putting obedience to God first, should answer “with a mild temper and deep respect.”—1Pe 3:15.

On the British Monarchy

A whale of a challenge for Darwinism.

In search of earth 2.0

Common design vs. common descent

Modular Paint-Box Explains Butterfly Color Patterns:
Evolution News & Views January 21, 2016 12:32 AM

Butterflies of the Amazon exhibit astonishing beauty and diversity. The Heliconius genus, in particular, is striking for its examples of mimicry, where members of different species have converged on the same color patterns on their wings. Collections of these butterflies can be arranged into series where yellow and red spots grow and shrink, grading into one another. How did this diversity come about?

The usual answer is Darwinian evolution -- a mutation of a gene leading to a novelty, then common ancestry and natural selection. A new model, published in PLOS Biology, does not dispute that kind of evolution, but offers different mechanisms that fit with intelligent design. As the authors discuss in news from the University of Cambridge, it's a story of shared technology.

Research finds independent genetic switches control different splotches of colour and pattern on Heliconius butterfly wings, and that these switches have been shared between species over millions of years, becoming "jumbled up" to create new and diverse wing displays. [Emphasis added.]

Everything else about the butterflies appears normal; the body anatomy; the antennae; even the basic wing shape. It's primarily the color splotches that vary. Each one has a so-called dennis patch at the base of the wing, and red "ray" streaks that fan out across the hindwing. Within any individual, though, the patterns remain symmetrical: the left wing is a mirror image of the right wing.

The Cambridge researchers looked at the genomes of dozens of specimens.

New research on butterfly genomes has revealed that the genetic components that produce different splotches of colour on wings can be mixed up between species by interbreeding to create new patterns, like a "genetic paint box."

This is not the usual mutation-selection mechanism of Darwinian evolution, in other words. The researchers believe that existing genetic switches can be "shared" between species by interbreeding, hybridization and introgression, a process of gene flow from one species into another population that results from repeated backcrossing of an interspecific hybrid with one of its parent species.

Novelty is not originating by mutation, in short, but rather by new combinations of genetic switches that were already present. Interbreeding and hybridization shuffles these genetic switches that turn particular colors on and off in different parts of the wings. Is this type of sharing common in the world?

It has been known for some time that exchange of genes between species can be important for evolution: humans have exchanged genes with our now extinct relatives which may help survival at high altitudes, and Darwin's Finches have exchanged a gene that influences beak shape. In butterflies, the swapping of wing pattern elements allows different species to share common warning signs that ward off predators -- a phenomenon known as mimicry.

However, the new study, published today in the journal PLOS Biology, is the first to show such mixing of genetic material can produce entirely new wing patterns, by generating new combinations of genes.

One wonders if these researchers realize they have undermined Neo-Darwinism in these famous examples. Swapping of genetic elements does not require mutation and selection. Moreover, early humans, finches and butterflies had to be able to interbreed or at least hybridize to benefit from the shared information.

The authors state that these switches evolved just once, then are used in different parts of the wings. In different individuals, they can see little regions of color "jumping about all over the place." And because of pleiotropy -- the linkage of the color function to other functions on the gene -- the gene itself cannot evolve:

The key to this evolutionary butterfly painting is the independence of each genetic switch. "The gene that these switches are controlling is identical in all these butterflies, it is coding for the same protein each time. That can't change as the gene is doing other important things," said lead author Dr Richard Wallbank, also from Cambridge's Department of Zoology.

"It is the switches that are independent, which is much more subtle and powerful, allowing evolutionary tinkering with the wing pattern without affecting parts of the genetic software that control the brain or eyes.

"This modularity means switching on a tiny piece of the gene's DNA produces one piece of pattern or another on the wings -- like a genetic paint box," Wallbank said.

We must not get confused about the meaning of "evolution" in these papers. The wing patterns may vary, but all the species are members of one genus. We're looking at a mechanism for robustness and flexibility that is consistent with intelligent design. In the tropics where these butterflies live, the ability to try out new color patterns can be advantageous to attract mates and avoid predators. These are tiny changes to combinations of existing switches, not matters of great transformations, such as gaining a new organ. It's mere shuffling of what already exists.

The paper is even more emphatic about nature preventing novelty by mutation:

One of the major impediments to evolutionary innovation is the constraint on genetic change imposed by existing function. Mutations that confer advantageous phenotypic effects in a novel trait will often result in negative pleiotropic effects in other traits influenced by the same gene. Several mechanisms have been proposed by which evolution can circumvent such constraints, resulting in phenotypic diversification. In particular, the modularity of cis-regulatory elements means that novel modules can encode new expression domains and functions without disrupting existing expression patterns. This modularity underlying gene regulation has led to the assertion that much of morphological diversity has arisen through regulatory evolution.

What does this do to old-fashioned Darwinian gradualism?

This might seem to imply that the evolution of novel regulatory alleles is relatively gradual, requiring the evolution of many small effect substitutions, but recent adaptive radiations can show extremely rapid rates of morphological change. The role of regulatory modularity therefore remains to be tested in adaptive radiations in which morphological variation evolves very rapidly.

Although this paper is full of the word "evolution," it's really a different concept they are proposing.

We show that two patterning switches -- one that produces red rays on the hindwing and the other a red patch on the base of the forewing -- are located adjacent to one another in the genome. These switches have each evolved just once among a group of 16 species but have then been repeatedly shared between species by hybridisation and introgression. Despite the fact that they are now part of a common pattern in the Amazon basin, these two pattern components actually arose in completely different species before being brought together through hybridisation. In addition, recombination among these switches has produced new combinations of patterns within species. Such sharing of genetic variation is one way in which mimicry can evolve, whereby patterns are shared between species to send a common signal to predators. Our work suggests a new mechanism for generating evolutionary novelty, by shuffling these genetic switches among lineages and within species.

In addition, they appeal to "convergent evolution" to explain some spectacular cases of mimicry. But if this were all due to chance, why are the patterns symmetrical? What about Darwinian mechanisms would require the left and right wings match?

None of what they describe requires neo-Darwinism or supports macroevolution. The switches were already there. They only control how much color goes into each spot. They can be shared within and across species by shuffling mechanisms, allowing rapid changes in wing patterns. It sounds like a great way for butterflies to quickly send different signals in different situations, so that they remain viable. Think of a flagman, using the same flags but in different combinations to send different messages. The flags were already there, and the man (or a programmable robot) knows how to use them.

Evolutionists have focused long and hard on the patterns on butterfly wings, which indeed are interesting, but they need to explain the weightier matters: how an egg becomes a crawling caterpillar, enters a chrysalis, and emerges a flying butterfly. As illustrated in Metamorphosis: The Beauty and Design of Butterflies, that's like turning a Model T into a helicopter.


The very traits they have focused on (wing patterns) turn out to be non-Darwinian and restrained by pleiotropy, reliant on "switches" that look designed. How much more must the critical organs for digestion, reproduction, and flight require specific information targeted for those functions? Only intelligence creates that kind of information.