The inner workings of a supposedly simple bacterial cell have turned out to be much more sophisticated than expected.

An in-depth “blueprint” of an apparently minimalist species has revealed details that challenge preconceptions about how genes operate. It also brings closer the day when it may be possible to create artificial life.

Mycoplasma pneumoniae, which causes a form of pneumonia in people, has just 689 genes, compared with 25,000 in humans and 4000 or more in most other bacteria. Now a study of its inner workings has revealed that the bacterium has uncanny flexibility and sophistication, allowing it to react fast to changes in its diet and environment.

“There were a lot of surprises,” says Peer Bork, joint head of the structural and computational biology unit at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany. “Although it’s a very tiny genome, it’s much more complicated than we thought.”
…
The biggest shock was that the organism gets by with just eight gene “switches”, or transcription factors, compared with more than 50 in other bacteria such as Escherichia coli. Transcription factors are generally thought of as the key components enabling living things to respond to environmental conditions by switching genes on and off.
…
Another unexpected discovery was that bacterial genes grouped together in clumps or families called “operons” don’t work as had been thought. The assumption was that if there are four genes in an operon they always work in unison, but the new analyses show that only one, or perhaps two, operate at any one time.

Even more surprising, the proteins the genes make don’t necessarily always couple with their nearest neighbours – again contrary to previous assumptions. Instead, they often join up with proteins originating from other, distant operons, vastly increasing the bacterium’s flexibility and versatility when faced with a changed environment.

Reference:
(1). ‘Simple’ bacterium shows surprising complexity, NewScientist, 11/26/09.

During 15 years of excavation they have uncovered not some monumental temple but evidence of a critical transition in religious behavior. The record begins with a simple dancing floor, the arena for the communal religious dances held by hunter-gatherers in about 7,000 B.C. It moves to the ancestor-cult shrines that appeared after the beginning of corn-based agriculture around 1,500 B.C., and ends in A.D. 30 with the sophisticated, astronomically oriented temples of an early archaic state.

This and other research is pointing to a new perspective on religion, one that seeks to explain why religious behavior has occurred in societies at every stage of development and in every region of the world. Religion has the hallmarks of an evolved behavior, meaning that it exists because it was favored by natural selection. It is universal because it was wired into our neural circuitry before the ancestral human population dispersed from its African homeland.

For atheists, it is not a particularly welcome thought that religion evolved because it conferred essential benefits on early human societies and their successors. If religion is a lifebelt, it is hard to portray it as useless.

For believers, it may seem threatening to think that the mind has been shaped to believe in gods, since the actual existence of the divine may then seem less likely.

In case you missed it before, I think John Cleese’s work in this area is as good or better than any other Darwinist speculating in this area.

Reference:
1. http://www.nytimes.com/2009/11/15/weekinreview/12wade.html

Of course critics of ID (like the folks at the NCSE) should have every right to publish their views within academic circles and should have the full protection of academic freedom. But academic freedom doesn’t just mean the freedom to agree with the predominant viewpoint. Academic freedom in science means nothing if it doesn’t include the right to hold legitimate minority scientific viewpoints. ID proponents have published serious scientific research in mainstream, credible academic venues. Many of them have sterling academic qualifications and accomplishments. They have earned the right to freely express their views without fear of intimidation or discrimination.

But free expression of pro-ID views in the academy is exactly what the NCSE doesn’t want. “Expelled Exposed” is now exposed for what it really is: it’s not just a website making the case against ID (which is perfectly fine if that’s what ID critics want to do)—it’s a website attempting to convince people that ID deserves no academic freedom. In other words, “Expelled Exposed” is an effort to encourage the further persecution of ID-proponents.

Ironically, by denying that professionally qualified ID proponents have a right to “a place in academia,” “Expelled Exposed” has justified the central thesis of the documentary Expelled, namely that qualified ID proponents do not receive academic freedom to hold, discuss, and promote their views within the academy.

I like the Discovery Institute more all the time based in part on the rabid hatred that many Darwinists have for this tiny organization. Can such intense fear and hatred come from a defense of “science” or is there something deeper going on?

As a case in point, consider the recent study, Musical Aptitude Is Associated with AVPR1A-Haplotypes.¹

NewScientist² reports on the study:

MUSICAL ability is linked to gene variants that help control social bonding. The finding adds weight to the notion that music developed to cement human relationships.

…

Järvelä thinks musical aptitude evolved because musical people were better at forming attachments to others: “Think of lullabies, which increase social bonding and possibly the survival of the baby.”

And from the original source:

Interestingly, AVPR1A has been known to modulate social cognition and behavior (see the recent review by Donaldson and Young [55]) making it a strong candidate gene for music perception and production. Several features in perceiving and practicing music, a multi-sensory process, are closely related to attachment [56]. Based on animal studies Darwin proposed in 1871 that singing is used to attract the opposite sex. Furthermore, lullabies are implied to attach infant to a parent and singing or playing music together may add group cohesion [57]. Thus, it is justified to hypothesize that music perception and creativity in music are linked to the same phenotypic spectrum of human cognitive social skills, like human bonding [13] and altruism [17] both associated with AVPR1A. It is of notice that both altruism (also called pathological trusting), and intense interest towards music and relatively sparse language skills are the characteristic features of Williams-Beuren syndrome (WBS), a neurodevelopmental syndrome with elfin facial features, supravalvular aortic stenosis, hypercalcemia and scoliosis [55], [58]. AVPR1A is also associated with autism, an opposite phenotype with poor social communication skills [14], [46], [59].

The source article is actually titled appropriately. In other words, it suggests the mere genetic association (correlation). The authors seem to want us to believe that since Darwin proposed studies in 1871 about the singing behavior of animals and reproduction, it is reasonable to think that evolution is the hidden causal variable in the mix.

References:
1. Ukkola LT, Onkamo P, Raijas P, Karma K, Järvelä I, 2009 Musical Aptitude Is Associated with AVPR1A-Haplotypes. PLoS ONE 4(5): e5534. doi:10.1371/journal.pone.0005534
2. Genes help us make sweet music together, NewScientist, 6/2/09

And biologist Kenneth Miller of Brown University, author of the popular book Finding Darwin’s God (which is used in many Christian colleges), insists that evolution is an undirected process, flatly denying that God guided the evolutionary process to achieve any particular result—including the development of human beings. Indeed, Miller insists that “mankind’s appearance on this planet was not preordained, that we are here… as an afterthought, a minor detail, a happenstance in a history that might just as well have left us out.” [Finding Darwin’s God (1999), p. 272]

Miller does say that God knew that the undirected process of evolution was so wonderful it would create some sort of rational creature capable of praising Him eventually. But what that something would be was radically undetermined. How undetermined? At a 2007 conference, Miller admitted that evolution could have produced “a big-brained dinosaur” or a “mollusk with exceptional mental capabilities” rather than human beings. [Quoted in Darwin Day, p. 226]

The Outsider, DB, would call this type of thinking, making it up as we go.  Essentially, that appears to be the approach of most theistic evolutionists. Unfortunately, they seem to apply a similar process to theology that many Darwinists apply to history. In other words, they imagine God to be whatever they want (e.g., a powerless cosmic puppy dog who loves you perhaps). Basically, they often seem to be worshiping science first and God second. But the God they worship (second to science) appears to be one of their own making.

Reference:
According to theistic evolution, did God direct evolution and know its outcome?

So, it is in this sense that life can very minimally be considered to be beyond natural (i.e., supernatural).  It is beyond natural in that it transcends laws of nature and what can be accomplished by natural forces alone.  Therefore, this argues powerfully for a supernatural (beyond natural law) origin of life.

(1). “Life’s Conservation Law: Why Darwinian Evolution Cannot Create Biological Information”

“Idiocricy:” A Bad Comedy or Covert Eugenics (Genetics) Propaganda?

H₀: Two simultaneous mutations are the upper limit for providing any functional advantage by evolutionary processes.
H₁: Evolutionary processes may result in three or more simultaneous mutations conferring a functional advantage to an organism.

In the example above, H₀ is the null hypothesis, and H₁ is the experimental hypothesis. When an experiment is conducted, a finding of 3 or more simultaneous mutations resulting in a functional advantage would be said to falsify the null hypothesis.

The final writeup would go something like, “Our experiments demonstrated that 3 simultaneous mutations occurred resulting in a functional advantage for the organism. Therefore, we reject H₀ in favor of H₁.” The trouble in evolutionary biology is that there often is no H₀. There is no formal null hypothesis. Evolution is considered to be a fact, and the null hypothesis is not addressed or tested.

Consider a recent peer-reviewed article that provides a null hypothesis that has not been falsified by Darwinist researchers:

The theme of this paper is the active pursuit of falsification of the following null hypothesis:
“Physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” At first glance the falsification of this hypothesis might seem like a daunting task. But a single exception of non trivial, unaided, spontaneous optimization of formal function by truly natural process would quickly falsify this null hypothesis.⁽¹⁾

Again, the trouble with most Darwinists is that they would not even consider testing this null hypothesis, because “evolution is a fact.” It is my opinion, that the metaphysical worldview of these scientists (i.e., philosophical naturalism), prevents them from doing real science. Without testing their theories against ID hypotheses, they are failing to conduct valid research, and are engaging in little more than materialistic apologetics.

It is also possible to use a null hypothesis as an experimental hypothesis. Extra safeguards are needed with an experiment of this nature. Specifically, what is needed is more experimental power. This translates essentially to a larger subject pool or number of trials. The experimental power required varies based on the field of study and what is being studied. The level required is based on a scientific consensus. In other words, scientists may agree in a given area of study that the power must be 95%. This translates essentially to “The probability that a true experimental hypothesis will be supported by our methods.” The 5% in this case is considered to be an acceptable risk for the given field of study. In other words, 5% of the time in similarly conducted studies, we would find results that do not support the experimental hypothesis when the experimental hypothesis is in fact true.

In psychology, the level of power needed is often considered 80%. When a null hypothesis is used as an experimental hypothesis, the power needed may be set at 90 to 95%. There are other technical and statistical aspects of determining the number of trials or subjects needed, but I won’t get into that.

Suffice it to say, that properly conducted research may state as an experimental hypothesis: “Two mutations are the maximum number of simultaneous mutations that can occur in a population of X size and given Y generations which would confer a functional advantage.” This is one reason that part of the work done by Michael Behe in the Edge of Evolution is valid science. Hypotheses stated in this way are not arguments from ignorance, but valid scientific hypotheses that lend themselves to scientific investigation.

I don’t know if Dr. Abel, who published the article, The Capabilities of Chaos and Complexity, is an IDist or a Darwinist. That doesn’t really matter much to me, but what does matter is that he has given a fair treatment to the issue in a way that advances science.

Dr. Abel writes:

While proof may be evasive, science has an obligation to be honest about what the entire body of evidence clearly suggests. We cannot just keep endlessly labeling abundant evidence of formal prescription in nature “apparent.” The fact of purposeful programming at multiple layers gets more “apparent” with each new issue of virtually every molecular biology journal [179-181]. Says de Silva
and Uchiyama:

Molecular substrates can be viewed as computational devices that process physical or chemical ‘inputs’ to generate ‘outputs’ based on a set of logical operators. By recognizing this conceptual crossover between chemistry and computation, it can be argued that the success of life itself is founded on a much longer-term revolution in information handling when compared with the modern semiconductor computing industry. Many of the simpler logic operations can be identified within chemical reactions and phenomena, as well as being produced in specifically designed systems. Some degree of integration can also be arranged, leading, in some instances, to arithmetic processing. These molecular logic systems can also end themselves to convenient reconfiguring. Their clearest application area is in the life sciences, where their small size is a distinct advantage over conventional semiconductor counterparts. Molecular logic designs aid chemical (especially intracellular) sensing, small object recognition and intelligent diagnostics [181].

What scientific evidence exists of physicodynamics ever having programmed a single purposeful configurable switch-setting? If we cannot present any such evidence, we should be self-honest enough to start asking ourselves, “How long are we going to try to maintain this ruse that the cybernetic programming we repeatedly observe is only ‘apparent’ rather than real?”

Indeed, if you want to start conducting real science in evolutionary biology, then it is time to start including ID notions as null or experimental hypotheses. However, the Darwinists are likely to continue their metaphysical pursuits at the sacrifice of properly conducted scientific investigation.

References:
(1). Abel, D. L. (2009). The Capabilities of Chaos and Complexity, International Journal of Molecular Sciences.

Hat Tip: scordova @ Uncommon Descent

Regardless of age assumptions, it is clear that the theory of evolution requires deep time to work it’s magic. So, for the sake of argument, we will grant the Darwinists deep time and use their own dating assumptions to discuss the problems with their theory. When a fossil is discovered much earlier than previously thought, it gives the purported gradualism or slow process of evolution less time to work its magic.

Stephen J. Gould postulated ‘punctuated equilibrium’ to attempt to fit the theory of evolution with the evident discontinuity of the fossil record. In other words, creatures appear in the fossil record with no evident precursors, and other fossils exhibit little differences from current species despite hundreds of millions of years of time that has purportedly passed. This can be thought of as the “naturalism of the gaps” hypothesis. The trend in paleontology is that these gaps are decreasing with each fossil find of a species that remains unchanged in the fossil record and appears earlier than previously thought.

As Cornelius Hunter, author of DarwinsPredictions.com notes:

It is now known that evolution has nowhere near the eons of time predicted and required by Darwin. Indeed, the time windows available are even less than those allowed by William Thomson, which themselves were unacceptable to the evolutionists. This falsification of evolution’s prediction does not derive from the age of the earth, but rather from the fossil record. We now know that, even with billions of years of earth history, the major events in the fossil record take place in time windows that are no longer than a few tens of millions of years or even less.⁽²⁾

It is with these facts in mind that I start this series to illustrate yet another glaring problem for naturalistic evolution.

References

(1). On Christian Views of Creationism–Part IV (Continued: Young Earth Creationism)
(2). On Christian Views of Creationism–Part III (Continued: Young Earth Creationism)
(2). Evolution has hundreds of millions of years available, Darwin’s Predictions, Cornelius Hunter

Notes:

I would like to thank my coauthor mynym for suggesting the idea for this series.

Two points:

1- Gene duplication, in order to do something, also requires all the meta-information- a binding site, a promoter, an enhancer and a repressor. Otherwise all the gene duplication in the world will not do anything except add more DNA to the existing genome.

2- In his book “Why is a Fly Not a Horse?” Giuseppe Sermonti has a chapter (VIII) titled “I Can Only Tell You What You Already Know”, which examines this very thing- how do organisms “know” to migrate and to where?

An experiment was conducted on birds-blackcaps, in this case. These are diurnal Silviidae that become nocturnal at migration time. When the moment for the departure comes, they become agitated and must take off and fly in a south-south-westerly direction. In the experiment, individuals were raised in isolation from the time of hatching. In September or October the sky was revealed to them for the first time. Up there in speldid array were stars of Cassiopeia, of Lyra (with Vega) and Cygnus (with Deneb). The blacktops became agitated and, without hesitation, set off flying south-south-west. If the stars became hidden, the blackcaps calmed down and lost their impatience to fly off in the direction characteristic of their species. The experiment was repeated in the Spring, with the new season’s stars, and the blackcaps left in the opposite direction- north-north-east! Were they then acquainted with the heavens when no one had taught them?

The experiment was repeated in a planetarium, under an artificial sky, with the same results!

The bottom-line is there is much more going on than just chemical reactions caused by genetic material. But that reduction is all the evolutionists have and I say it hampers investigations by preventing us from seeking answers outside of the genome.

So did God design the ability to read the stars into these birds, or was this a result of blind necessity?