On categorizing information.

A Taxonomy of Information
Casey Luskin November 24, 2015 12:02 PM

Note: I've gotten a few requests for notes or a handout from my recent talk at the Christian Scientific Society meeting, "A Taxonomy of Information and the Design Inference." The talk should be available online eventually, but for the time being below is a condensed and reader-friendly reformatted version of my notes from the talk.

The question I want to address is this: What are some common definitions of information, and which definition is most useful for making the design inference? To answer this question, let's review several different definitions of information.

What Is Information?

Information is not always easy to define, but it often involves a measure of degree of randomness. The fundamental intuition behind information is a reduction in possibilities. The more possibilities you rule out, the more information you've conveyed.

Nature can produce "information" under certain definitions. Intelligent agents also produce information (certain types, at least). As Henry Quastler observed, "The creation of new information is habitually associated with conscious activity."

To put it another way: The reduction in uncertainty could occur by an intelligent agent, or through a physical occurrence. For example:

Nature: Blue sky reduces uncertainty about whether it is raining.
Intelligent agents: 18 people playing baseball outdoors reduces uncertainty about whether it is raining.
Syntactic Information
Syntactic information is information that often (though not always) involves a sequence of symbols. Syntactic information uses a set of characters or symbols, or some other set of items. Symbols put into a sequence, where symbols are drawn from a fixed symbol set, with one symbol at each position.


Examples include: written language, binary code, computer language. But must syntactic information be an alphabet? Would a color count? How about a nucleotide base, like TGA?
Shannon Information:
Shannon information always pertains to syntactic information, using a fixed character set, with characters in a sequence. It's based upon the probability of a sequence occurring. Once you have that fixed character set, you can start asking about probabilities. For example, in calculating probabilities, some letters appear more than others -- i.e., "e" appears 13 percent of the time, or "q" is followed by "u" nearly 100 percent of the time.

Shannon information is measured in bits. Bits = I = - Log2 (p) (where p = probability). How do you calculate in Log2? It's easy!

Loga (x) = Logb (x) / Logb (a)
Loga (p) = Logb (p) / Logb (a)
So we can calculate bits as follows: - Log2 (p) = - Log10 (p) / Log10 (2)
Here's a little tutorial on Shannon information, using binary code as an example:

In binary code, each character has 2 possibilities: 0 or 1. Thus, the probability of any character = 0.5. So how much information does each binary digit convey? Here's the equation:

- Log2 (0.5) = - Log10 (0.5) / Log10 (2) = 1

In binary code, each binary digit conveys 1 bit of information. Thus, a string like "00110" contains 5 bits. But here's a key point: "5 bits" doesn't tell you anything about the content or meaning of the string!

Shannon information is thus only concerned with reduction in uncertainty. It is not concerned with the content or "meaning" of the string. A random string might have the same Shannon information as a meaningful string. Thus, the purpose of Shannon information is to help measure fidelity of transmission of information. What the transmission says doesn't matter.

For example, consider this 22-character string (generated by Random.org/strings):

IOAPWYDJNDGAJFLEBRSNYN
The string has 103 bits of Shannon information (using only capital letters; assuming equal probability of all letters).
Now consider this 22-character string (only upper case letters):

THISISANONRANDOMSTRING
This string likewise has 103 bits of Shannon information.
The random and non-random strings have the same amount of Shannon information! Shannon information does not help you distinguish between functional and non-functional information. Thus Shannon information doesn't quite capture the special nature of living organisms and other designed structures:

[C]lassical information theory [i.e., Shannon information] ... does not consider the meaning of a message, defining the information content of a string of symbols as simply that required to specify, store or transmit the string. ... A new measure of information -- functional information -- is required to account for all possible sequences that could potentially carry out an equivalent biochemical function, independent of the structure or mechanism used."
(Nobel Prize winner Jack W. Szostak, "Molecular messages," Nature, 423: 689 (June 12, 2003).)

Kolmogorov Information
Kolmogorov complexity is a form of algorithmic information theory. Andrey Kolmogorov sought to understand randomness. His definition of information pertained to compressibility of a string, and compressibility assumes a computer environment. We can thus express Kolmogorov complexity in terms of computer programming commands. Winston Ewert's definitions are very good: "Length of the smallest program that produces a given output" or "The number of symbols required to describe the object."

Under Kolmogorov complexity, compressibility ~ 1/randomness. If it's compressible, it's NOT random (and it's not complex). If it's not compressible it's random (and it's very complex).

For example, assume we have the string 000,111,000. We could compress it to "0,1,0." It's highly compressible with, therefore, low Kolmogorov complexity.

How many 1-bit programs are possible? Two: 0 and 1. How many programs with 100 bits? 2100. Very few 100-bit sequences would be compressible.

As another example, consider this string:

111111111111111111111111111111111111111111111111111111111
It's very compressible: "Repeat '1' 57 times." It has low Kolmogorov complexity.
Now consider this string (From Random.org):

4858686631031287008016234687093634769523
This one is much harder to describe, and it's not compressible. It has much higher Kolmogorov complexity.
How about this example:

KOMOLGOROVINFORMATIONISAPOORMEASUREOFBIOLOGICALCOMPLEXITY
How might we compress it? By removing its vowels?
How about this one:

JLNNUKFPDARKSWUVWEYTYKARRBVCLTLOPDOUUMUEVCRLQTSFFWKJDXS
It's a random string -- not compressible.
Here's the point: Kolmogorov information is not necessarily tied to likelihood. In fact, higher Kolmogorov bits could mean more randomness. In that regard, it's not useful for distinguishing functional information from non-functional.

Semantic Information

The definition of semantic information is information that has meaning. As Dr. Randy Isaac explains, semantic information indicates "the significance of a message, whether or not an intelligent agent was involved." ("Information, Intelligence and the Origins of Life," PSCF 63(4):219-230 (Dec. 2011).) Is this the best way to detect design?

Well, where does meaning come from? We assign it. This is not what Shannon had in mind, and it's really not what's at stake with complex and specified information (CSI), as I'll explain below.

CSI identifies some subset within a reference class of possibilities. Semantic information looks at subjective meaning. But CSI isn't about subjective meaning. It's objective.

Dr. Isaac writes: "In abstract symbolism, the symbol has a meaning assigned to it which does not necessarily derive from its physical properties." I agree. Semantic information could occur by a natural cause, or by intelligence. For example:

Human intelligence creates stop signs to tell car drivers to stop.
Nature uses TGA in the genetic code to tell translation to stop.
In the genetic code, any other codon would serve to signify "stop." Does TGA then possess abstract meaning assigned to it that doesn't derive from its physical properties? Yes, it does. Why, then, should the genetic code be considered anything but intelligently designed, semantic information?
Randy Isaac further writes: "Coding in and of itself does not necessitate intelligence unless the coding represents abstract symbolic meaning," and "Abstract symbolism is a hallmark of intelligence, especially as manifest in language and communication techniques." Yes -- I agree! So again, why should the genetic code be excluded from examples of abstract symbolism? It too carries semantic information that, presumably, we can use to detect design.

Complex and Specified Information (CSI) and the Design Inference

Complex and specified information can be understood as follows:

Complexity is related to unlikelihood. Information is "complex" if it is unlikely.
Specification is present if an event or string or scenario or object matches an independent pattern.
Stephen Meyer gives these examples of CSI:
Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source -- from a mind or personal agent.
(Stephen C. Meyer, "The origin of biological information and the higher taxonomic categories," Proceedings of the Biological Society of Washington, 117(2):213-239 (2004).)

It's important to understand that the idea of complex and specified information is NOT an invention of ID proponents. The first use I'm aware of comes from origin-of-life theorist Leslie Orgel in the 1970s:
[L]iving organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple, well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures which are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity.
(Leslie E. Orgel, The Origins of Life: Molecules and Natural Selection, p. 189 (Chapman & Hall: London, 1973).)

Between CSI and Semantic Information, Which Is the Better Indicator of Design?
There are many examples where CSI helps us detect design in objects that clearly carry no semantic information. This shows that CSI is a superior method of detecting design, and we don't need to necessarily find semantic information to detect design.

First, consider Mount Rushmore: This mountain has an unlikely shape that matches an independent pattern. We find high CSI, and detect design, without finding semantic information!

Or consider the life-friendly fine-tuning of the physical laws and constants of the universe. Here, we have very unlikely values of laws and constants that match a narrow pattern of settings that is required for life. This is high CSI, but not semantic information.

Or consider a car engine: There's no abstract "message" here, but there certainly is high CSI, and a designed system.

The same goes for the bacterial flagellum. It has a complex pattern that existed before we observed it, and it matches many aspects of designed systems. It has high CSI, but carries no semantic information.


I would describe the relationship between CSI and semantic information as follows:Again, semantic information is useful for detecting design -- but it's not the only way to detect design. Semantic information is a subset of CSI, which is a more generally useful definition of information for detecting design. The genetic code is a form of semantic information and is high in CSI.

Conclusion

To summarize, Information can be understood and defined in different ways. Some are useful for detecting design and/or measuring bioinformation. Some are not. Semantic information is useful for detecting design, but it's not the only way to detect design. It's a special case of design, not the general case. Semantic information as a class falls within complex and specified information, which is a more general mode of design detection. The genetic code is a form of syntactic, semantic, and complex specified information.
Acknowledgments:
I would like to thank William Dembski and Stephen Meyer for their insights and thoughts in preparation of this talk and material.

Ever a cause for gratitude

What to Feel Thankful for on Thanksgiving? How About a Universe Minutely Tailored for You
David Klinghoffer November 25, 2015 12:40 PM

It's a Thanksgiving custom with many families to go around the table and everyone has to say what he or she is especially thankful for. This puts everyone on the spot -- perhaps that's the point -- and can be an occasion for awkwardness since some may feel more or less "blessed" than their dining companions.

But how about this? A reason to be thankful that equally encompasses every human being that has ever existed and will ever exist.

That's the thesis advanced by biologist Michael Denton in the 33-mintue Discovery Institute documentary Privileged Species: The extraordinary fine-tuning of biology, chemistry, and physics powerfully testifies that the cosmos saw us coming from the beginning. Somehow, everything was set in place for creatures very much like ourselves.


Rather than argue about politics or sports -- two other Thanksgiving staples -- why not share Privileged Species with your friends and loved ones this holiday? There couldn't be a more a persuasive case than the one Dr. Denton makes that human life is special and meaningful, and that its remarkable status in the universe is not just a matter of assertion but compelled by objective scientific evidence.

Frequently asked question.

Do Jehovah’s Witnesses Have a Paid Clergy

Following the model of first-century Christianity, Jehovah’s Witnesses have no clergy-laity division. All baptized members are ordained ministers and share in the preaching and teaching work. Witnesses are organized into congregations of about 100 members. Spiritually mature men in each congregation serve as “older men,” or elders. (Titus 1:5) They do so without being paid for their services.

The Junk DNA meme continues to take flak

Stanford U: Ancient viruses are part of us and we need them
November 25, 2015 Posted by News under Genomics, Human evolution, News


From The Telegraph:

The human genome is littered with sequences left behind from long-ago viral infections but now scientists have found the code is still active

Now researchers at Stanford University School of Medicine have found that genetic material from a retrovirus called HERV-H is not only active, but is crucial in allowing a fertilised human egg to grow into an embryo.

…

“What’s really interesting is that these sequences are found only in primates, raising the possibility that their function may have contributed to unique characteristics that distinguish humans from other animals.

Let’s back up and be cautious here. For one thing, many primates are not particularly clever, so we need to be much more specific about why it worked (if it did) so well in the human, and not especially in the tarsier. And the way things have been going, the same sequence or a very similar one could turn up in the opossum, but no one has looked. Who knew the water bear shared so many genes with unrelated life forms?

“We’re starting to accumulate evidence that these viral sequences, which originally may have threatened the survival of our species, were co-opted by our genomes for their own benefit.” More.

But we don’t know that either, do we? HERV-H could once have been a useless or even useful parasite that somehow got incorporated into the system.

Question: What were fertilised human eggs doing, to grow into embryos, before HERV-H was available? Or are we to assume it always was available, for all humans? Stay tuned.

See also: Horizontal gene transfer: Sorry, Darwin, it’s not your evolution any more


and This just in: One sixth of water bear’s genes are from microbes Researcher: More than 90 percent of these come from bacteria, but others come from archaea (a distinct group of microbes), fungi, and even plants. “The number of them is pretty staggering,” he says.

An unmistakable signature IV

Denying the Signature: More on Substance Dualism
Stephen C. Meyer November 25, 2015 4:43 AM

Editor's note: Readers of Evolution News likely know the central thesis of Stephen Meyer's bestseller, Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design. Meyer argues that the functional biological information necessary to build the Cambrian animals is best explained by the activity of a designing intelligence, rather than an undirected, materialistic evolutionary process. Most reviews of Darwin's Doubt curiously omitted to address or even to accurately report this central claim. However, a review by philosophers Robert Bishop and Robert O'Connor in Books & Culture was a welcome exception. In this 6-part series, adapted from Debating Darwin's Doubt, edited by ENV's David Klinghoffer, Dr. Meyer responds to their critiques. 

Though I don't need to justify substance dualism as a condition of making design inferences, it doesn't follow that there are not good justifications either for (a) presupposing some form of minimalist pre-theoretic form of dualism or (b) for the philosophical position of substance dualism itself.

In the first place, some form of dualism may well be a properly basic belief, justified by the universal human experience of being aware of ourselves as simple, conscious subjects or "I's" distinct from our physical bodies. Since we have a similar awareness of our mind's causal powers (and their ability to exercise "downward" causation on the physical world as opposed to being a mere epiphenomenon resting inertly atop a neurophysiological substrate) our pre-theoretic awareness of these powers may well implicitly constitute a dualist understanding of mind. Yet, it does not follow from this fact that our pre-theoretic conceptions of mind need explicit philosophical justification. Instead, assuming a (minimally dualistic) conception of mind may well be a properly basic belief.

Indeed, virtually everyone accepts the belief that their minds have causal powers, including powers that material objects and process do not. Moreover, even those few materialist scientists or philosophers who deny this belief in their explicit philosophical or scientific statements betray a commitment to it in many ways as they go about their daily lives. Materialists cannot live consistently with their own denial of the causal powers of their own minds. Instead, their actions betray their belief in those powers.

In addition, virtually no one gives arguments for -- or, more importantly, feels the need to give arguments for -- their belief in the causal powers of their own mind. And almost no one (save for a few ideologically-zealous physicalist philosophers) thinks there are defeaters for this belief. For all these reasons, it seems the common belief that our minds have causal powers, including causal powers that material objects and processes do not, seems to qualify as properly basic.

In any case, there are also good explicit scientific and philosophical arguments justifying substance dualism as a theory of mind-body interaction. See, for example, The Mysterious Matter of Mind, by Arthur Custance, which summarizes the many neurophysiological experiments that led neuro-scientists such as Wilder Penfield and Sir John Eccles to adopt a "dualist interactionist" view of mind and brain.1 See also Angus Menuge's Agents Under Fire for a good philosophical defense of substance dualism.2 Just as there are good philosophical arguments showing that a minimalist pre-theoretic form of dualism does not need justification (i.e., is properly basic), there are also good scientific and philosophical arguments justifying substance dualism as a good theory of mind-body interaction.

Nevertheless, Bishop and O'Connor think that because mind-body dualism requires a philosophical justification, intelligent design does not qualify as a scientific theory, but instead "looks more like philosophy than science." But that doesn't follow for several reasons already discussed: The case for intelligent design does not depend upon substance dualism; a more minimalist pre-theoretic form of dualism doesn't necessarily require any justification (and may be regarded as properly basic); and there are scientific, as well as philosophical, justifications for substance dualism (or the closely related position of dualist interactionism).

In any case, many scientific theories -- Einstein's theory of general relativity, Newton's theory of universal gravitation, and Darwin's theory of evolution, to cite just a few examples -- are, arguably, based upon deeper philosophical premises, presuppositions, and concepts, which either can be, or need to be, justified by philosophical lines of argument. Despite their background in the philosophy of science, Bishop and O'Connor seem to assume the ability to make strict demarcations between science and philosophy in a way that philosophers of science have now almost universally repudiated (for reasons that I explain in both my books). Besides, as I argue in both books, what matters is not how we classify a theory, but whether a theory is true or warranted by the evidence.

One final point is worth making. Though I'm not obligated to justify substance dualism as a theory of the mind, I would certainly concede that offering a robust philosophical and/or scientific justification for such a theory would enhance the philosophical importance of the case I make for intelligent design.

If mind cannot be adequately accounted for by reference to materialistic processes, then any evidence of mind acting in the history of life would pose a more explicit challenge to the philosophy of scientific materialism than I develop in my books. It would provide evidence of an immaterial agency acting in the history of life. If, in addition, there is strong evidence for the activity of a designing agent establishing the finely tuned conditions of the universe present from its beginning, as I believe there is, then the conjunctions of these considerations would provide strong grounds for theistic belief.

References:

(1) Arthur C. Custance, The Mysterious Matter of Mind (second online edition, 2001; originally published by Probe Ministries and Zondervan Publishing, 1980).


(2) Angus Menuge, Agents Under Fire: Materialism and the Rationality of Science (Lanham, MD: Rowman & Littlefield, 2004)

Google loves Lucy.

Honoring the 41st Anniversary of the Discovery of "Lucy," Google Offers a Misleading Doodle:
Evolution News & Views November 24, 2015 11:12 AM


Yes, it's the 41st anniversary of the discovery of "Lucy." Google has a cute Doodle in her honor:However, back in 2009, Casey Luskin made a pilgrimage to see the lady's bones, then on display at the Seattle Science Center. He wrote here at Evolution News:

The whole experience seeing Lucy was enlightening, though probably not in the way its creators intended. In short, I left the exhibit struck by the paucity of actual hard evidence for human evolution from ape-like species, and the amount of subjective, contradictory interpretation that goes into fossil hominid reconstructions.

"Lucy" was discovered by paleoanthropologist Donald Johansen and his team in Ethiopia in 1974. The first half (or more!) of the exhibit was actually quite fascinating as it told the cultural and political history of the Ethiopian people and the Aksumite Empire. This history seemed well-documented by facts and evidence, replete with coins, weapons, religious artifacts, and art, which inform us about this rich and beautiful culture. And when the evidence was thin, the exhibit acknowledged that there are aspects of the Aksumite people where we know very little. This high standard of evidential documentation and appropriate tentativeness disappeared, however, as soon as we entered the section of the exhibit dealing with human evolution.

Lucy in the Dirt with Rock Rubble

The first thing my friends and I noticed when seeing Lucy's bones was the incompleteness of her skeleton. Only 40 percent was found, and a significant percentage of the known bones are rib fragments. Very little useful material from Lucy's skull was recovered. (This seems to be common: many of the replica skulls of early hominids at the exhibit were clearly based upon extremely fragmentary pieces.) And yet, according to the exhibit, Lucy still represents the most complete pre-Homo known hominid skeleton to date.

Not only was I underwhelmed by the incompleteness of Lucy's skeleton, but I was also struck by admissions at the exhibit that, in my mind, cast serious doubt on whether we know for certain that Lucy's bones are from a single individual from a single species.

On the issue of whether Lucy walked upright, as the Google Doodle misleadingly implies:

As noted, the most interesting part of Lucy's skeleton is her half-pelvis and half-femur that were discovered, which are said to indicate that she walked upright. Thus, despite these nagging questions about the integrity of Lucy's skeleton, the exhibit boldly states that "Lucy's species walked bipedally, in much the same way as we do," at one point saying Lucy's skeleton "approximate[s] a chimpanzee-like head perched atop a human-like body." Of course, this is a gross oversimplification of the data and a poor reflection of the sharply contradicting opinions of many learned paleoanthropologists.

Lucy did have a small, chimp-like head, but as Mark Collard and Leslie Aiello observe in Nature, much of the rest of the body of Lucy's species, Australopithecus afarensis, was also "quite ape-like" with respect to its "relatively long and curved fingers, relatively long arms, and funnel-shaped chest." (Nature, Vol 404:339-340, 3-23-00.)

Collard and Aiello's article also reports that we now have "good evidence" that A. afarensis (including Lucy) "'knuckle-walked,' as chimps and gorillas do today." Due to their evolutionary preconception that Lucy was a bipedal precursor to our genus Homo, they call this plain evidence that Lucy knuckled-walked "counterintuitive." They suggest the possibility that "the locomotor repertoire of A. afarensis included forms of bipedalism, climbing and knuckle-walking." This is a tenuous proposal, however, as knuckle-walking is obviously very different from bipedal locomotion. Collard and Aiello suggest avoiding the "counterintuitive" evidence that Lucy climbed and knuckle-walked by discarding it as unused "primitive retentions" from her ancestors.

By ignoring the skeletal evidence that Lucy didn't walk "bipedally, in much the same way as we do," I'm sure these Darwinists are pleased that Lucy can retain her prized position as our alleged bipedal ape-like ancestor.

Read the rest. As a monument to human evolution, clarifying the mystery of our origins, Lucy falls well short.

Aristotle Vs.Dualism

Aristotelian Anti-Dualism:
Aristotle, thus, opposes Platonic or Cartesian dualism. Body and soul together make up one substance. A major problem that Aristotle and Aquinas see with dualism is that it cannot explain why the soul, if it essentially different from and superior to the body, should be united to the body. For Aristotle and Aquinas, however, it is for the good of the soul (or rather, it is for the good of the composite which has its vital activities in virtue of its soul) that the soul is united to the body; a body is necessary for a soul to exercise all vital capacities, since (almost) all vital functions are the functions of body and soul together. The sensitive soul requires a body, since the acts of sensation, of seeing, for example, require bodily organs. Similarly, the act of intellection, which is proper to humans alone, requires sensation, and sensation in turn requires a body. Thus, if human beings are to exercise their proper functions, they necessarily must have a body.

Aquinas, interestingly, appeals to personal experience in his claim that a person is not his soul, or his intellect, alone, as Plato and Descartes claim. A man cannot be merely a mind without a body

because it is one and the same man who is conscious both that he understands and that he senses. But one cannot sense without a body, and therefore the body must be some part of man.(Summa Theologiae Ia 76, 1).

If a man were just a mind, essentially unrelated to the body, he would not directly experience things that happen to the body, as he clearly does when he senses. Therefore, the human soul is in essence the substantial form of a human body, and body and soul together make up one substance.

The favored place:The Watchtower Society's Commentary

BOSOM POSITION:
In an illustration, Jesus spoke of a beggar named Lazarus who was carried at his death to “the bosom position of Abraham,” and John refers to Jesus as being in “the bosom position with the Father.” (Lu 16:22, 23; Joh 1:18) The expression “bosom position” alludes to one’s reclining in front of another person on the same couch at a meal.

Guests reclined on their left side with a pillow supporting their left elbow, leaving the right arm free. Usually three persons occupied each couch, but there could be as many as five. The head of each one would be on or near the breast, or bosom, as it were, of the person behind him. The person with no one at his back was considered in the highest position and the one next to him in the second place of honor. In view of the nearness of the guests to one another, it was the custom that friend be placed next to friend, which made it rather easy to engage in confidential conversation if desired. To be in such a bosom position of another at a banquet was indeed to occupy a special place of favor with that one. So the apostle John, whom Jesus dearly loved, “was reclining in front of Jesus’ bosom,” and in such a position he “leaned back upon the breast of Jesus” and privately asked him a question at the celebration of the last Passover.—Joh 13:23, 25; 21:20.


For these reasons John, in describing the very special position of favor enjoyed by Jesus, said that he was in “the bosom position” of his Father Jehovah. Likewise, in Jesus’ illustration, Lazarus was carried to “the bosom position” of Abraham, denoting that this beggar finally came into a position of special favor with one who was his superior.

For Darwinism:Danger from the dark.

The Dark Proteome and Dark Evolution
Evolution Did It

A new PNAS paper published last week on the dark proteome has some interesting implications for the theory of evolution. The paper presents a survey of protein sequences, focusing on the many sequences for which the corresponding three dimensional protein structure is not known, and cannot be inferred from any remotely similar sequence. Why is this so-called “dark proteome” is so large? The survey finds that the various hypotheses to explain this—that the dark proteins are intrinsically disordered, or their sequences are compositionally biased, or they are transmembrane proteins, all reasons that can confound structure determination—don’t work very well. The paper concludes that “a surprisingly large fraction of dark proteins … cannot be easily accounted for by these conventional explanations.” And not surprisingly, these dark proteins are less common across the species. So where did all these dark protein sequences come from? Well evolution did it. As the paper explains, “dark proteins may be newly evolved proteins or rare proteins adapted to specific functional niches.”

We might call this dark evolution. Once again, the pattern is not one of common descent, but of unique structures.

The results also have implications for the so-called orphans, open reading frames found only in a particular species. Such genetic sequences contradict evolution and when they were first discovered evolutionists predicted they would be found in other species as more genomes were decoded. Instead the number of orphans just continued to grow.

Evolutionists next predicted that orphan sequences were probably not part of a mature protein coding gene and did not form functional proteins. That has not been found to be true, and this new survey provides further evidence for this. As the authors conclude, “Thus, our results suggest that many of the uncharacterized orphan sequences … are indeed real proteins.”

Protein science, however, is clear that blind mutations cannot form real proteins this fast from scratch (or at all for that matter). Hence we must believe that built-in cellular processes must have created these proteins—processes that are complex and require, among other things, proteins.

Real ones.

Posted by Cornelius Hunter at Monday, November 23, 2015 

Ezekiel1-7 New Jerusalem Bible

1)1 In the thirtieth year, on the fifth day of the fourth month, as I was among the exiles by the River Chebar, heaven opened and I saw visions from God.

2 On the fifth of the month -- it was the fifth year of exile for King Jehoiachin-

3 the word of Yahweh was addressed to the priest Ezekiel son of Buzi, in Chaldaea by the River Chebar. There the hand of Yahweh came on him.

4 I looked; a stormy wind blew from the north, a great cloud with flashing fire and brilliant light round it, and in the middle, in the heart of the fire, a brilliance like that of amber,

5 and in the middle what seemed to be four living creatures. They looked like this: They were of human form.

6 Each had four faces, each had four wings.

7 Their legs were straight; they had hooves like calves, glittering like polished brass.

8 Below their wings, they had human hands on all four sides corresponding to their four faces and four wings.

9 They touched one another with their wings; they did not turn as they moved; each one moved straight forward.

10 As to the appearance of their faces, all four had a human face, and a lion's face to the right, and all four had a bull's face to the left, and all four had an eagle's face.

11 Their wings were spread upwards, each had one pair touching its neighbour's, and the other pair covering its body.

12 And each one moved straight forward; they went where the spirit urged them, they did not turn as they moved.

13 Between these living creatures were what looked like blazing coals, like torches, darting backwards and forwards between the living creatures; the fire gave a brilliant light, and lightning flashed from the fire,

14 and the living creatures kept disappearing and reappearing like flashes of lightning.

15 Now, as I looked at the living creatures, I saw a wheel touching the ground beside each of the four-faced living creatures.

16 The appearance and structure of the wheels were like glittering chrysolite. All four looked alike, and their appearance and structure were such that each wheel seemed to have another wheel inside it.

17 In whichever of the four directions they moved, they did not need to turn as they moved.

18 Their circumference was of awe-inspiring size, and the rims of all four sparkled all the way round.

19 When the living creatures moved, the wheels moved beside them; and when the living creatures left the ground, the wheels too left the ground.

20 They moved in whichever direction the spirit chose to go, and the wheels rose with them, since the wheels shared the spirit of the animals.

21 When the living creatures moved on, they moved on; when the former halted, the latter halted; when the former left the ground, the wheels too left the ground, since the wheels shared the spirit of the animals.

22 Over the heads of the living creatures was what looked like a solid surface glittering like crystal, spread out over their heads, above them,

23 and under the solid surface, their wings were spread out straight, touching one another, and each had a pair covering its body.

24 I also heard the noise of their wings; when they moved, it was like the noise of flood-waters, like the voice of Shaddai, like the noise of a storm, like the noise of an armed camp; and when they halted, they lowered their wings;

25 there was a noise too.

26 Beyond the solid surface above their heads, there was what seemed like a sapphire, in the form of a throne. High above on the form of a throne was a form with the appearance of a human being.

27 I saw a brilliance like amber, like fire, radiating from what appeared to be the waist upwards; and from what appeared to be the waist downwards, I saw what looked like fire, giving a brilliant light all round.

28 The radiance of the encircling light was like the radiance of the bow in the clouds on rainy days. The sight was like the glory of Yahweh. I looked and fell to the ground, and I heard the voice of someone speaking to me.
2)1 He said, 'Son of man, get to your feet; I will speak to you.'

2 As he said these words the spirit came into me and put me on my feet, and I heard him speaking to me.

3 He said, 'Son of man, I am sending you to the Israelites, to the rebels who have rebelled against me. They and their ancestors have been in revolt against me up to the present day.

4 Because they are stubborn and obstinate children, I am sending you to them, to say, "Lord Yahweh says this."

5 Whether they listen or not, this tribe of rebels will know there is a prophet among them.

6 And you, son of man, do not be afraid of them or of what they say, though you find yourself surrounded with brambles and sitting on scorpions. Do not be afraid of their words or alarmed by their looks, for they are a tribe of rebels.

7 You are to deliver my words to them whether they listen or not, for they are a tribe of rebels.

8 But you, son of man, are to listen to what I say to you; do not be a rebel like that rebellious tribe. Open your mouth and eat what I am about to give you.'

9 When I looked, there was a hand stretch- ing out to me, holding a scroll.

10 He un- rolled it in front of me; it was written on, front and back; on it was written 'Lamentations, dirges and cries of grief '.
3)1 He then said, 'Son of man, eat what you see; eat this scroll, then go and speak to the House of Israel.'

2 I opened my mouth; he gave me the scroll to eat

3 and then said, 'Son of man, feed on this scroll which I am giving you and eat your fill.' So I ate it, and it tasted sweet as honey.

4 He then said, 'Son of man, go to the House of Israel and tell them what I have said.

5 You are not being sent to a nation that speaks a difficult foreign language; you are being sent to the House of Israel.

6 Not to big nations that speak difficult foreign languages, and whose words you would not understand -- if I sent you to them, they would listen to you;

7 but the House of Israel will not listen to you because it will not listen to me. The whole House of Israel is defiant and obstinate.

8 But now, I am making you as defiant as they are, and as obstinate as they are;

9 I am making your resolution as hard as a diamond, harder than flint. So do not be afraid of them, do not be overawed by them, for they are a tribe of rebels.'

10 Then he said, 'Son of man, take to heart everything I say to you, listen carefully,

11 then go to your exiled countrymen and talk to them. Say to them, "Lord Yahweh says this," whether they listen or not.'

12 The spirit lifted me up, and behind me I heard a great vibrating sound, 'Blessed be the glory of Yahweh in his dwelling-place!'

13 This was the sound of the living creatures' wings beating against each other, and the sound of the wheels beside them: a great vibrating sound.

14 The spirit lifted me up and took me, and I went, bitter and angry, and the hand of Yahweh lay heavy on me.

15 I came to Tel Abib, to the exiles beside the River Chebar where they were living, and there I stayed with them in a stupor for seven days.

16 After seven days the word of Yahweh was addressed to me as follows,

17 'Son of man, I have appointed you as watchman for the House of Israel. When you hear a word from my mouth, warn them from me.

18 If I say to someone wicked, "You will die," and you do not warn this person; if you do not speak to warn someone wicked to renounce evil and so save his life, it is the wicked person who will die for the guilt, but I shall hold you responsible for that death.

19 If, however, you do warn someone wicked who then fails to renounce wickedness and evil ways, the wicked person will die for the guilt, but you yourself will have saved your life.

20 When someone upright renounces uprightness to do evil and I set a trap for him, it is he who will die; since you failed to warn him, he will die for his guilt, and the uprightness he practised will no longer be remembered; but I shall hold you responsible for his death.

21 If, however, you warn someone upright not to sin and this person does not sin, such a one will live, thanks to your warning, and you too will have saved your life.'

22 While I was there the hand of Yahweh came on me; he said, 'Get up, go out into the valley, and there I shall speak to you.'

23 I got up and went out into the valley; the glory of Yahweh was resting there, like the glory I had seen by the River Chebar, and I fell to the ground.

24 The spirit of Yahweh then entered me and put me on my feet and spoke to me. He said, 'Go and shut yourself in your house.

25 Son of man, you are about to be tied and bound, and unable to mix with other people.

26 I am going to make your tongue stick to the roof of your mouth; you will be dumb, and no longer able to reprove them, for they are a tribe of rebels.

27 When I speak to you, however, I shall open your mouth and then you will say to them, "Lord Yahweh says this: Let anyone prepared to listen, listen; let anyone who refuses, refuse!"-for they are a tribe of rebels.'
4)1 'For your part, son of man, take a brick and lay it in front of you; on it scratch a city, Jerusalem.

2 You are then to besiege it, trench round it, build earthworks, pitch camps and bring up battering-rams all round.

3 Then take an iron pan and place it as though it were an iron wall between you and the city. Then fix your gaze on it; it is being besieged and you are besieging it. This is a sign for the House of Israel.

4 'Lie down on your left side and take the guilt of the House of Israel on yourself. You will bear their guilt for as many days as you lie on that side.

5 Allowing one day for every year of their guilt, I ordain that you bear it for three hundred and ninety days; this is how you will bear the House of Israel's guilt.

6 And when you have finished doing this, you are to lie down again, on your right side, and bear the guilt of the House of Judah for forty days. I have set the length for you as one day for one year.

7 Then fix your gaze on the siege of Jerusalem, raise your bared arm and prophesy against her.

8 Look, I am going to tie you up and you will not be able to turn over from one side to the other until the period of your seclusion is over.

9 'Now take wheat, barley, beans, lentils, millet and spelt; put them all in the same pot and make them into bread for yourself. You are to eat it for as many days as you are lying on your side -- three hundred and ninety days.

10 Of this food, you are to weigh out a daily portion of twenty shekels and eat it a little piece at a time.

11 And you are to ration the water you drink -- a sixth of a hin -- drinking that a little at a time.

12 You are to eat this in the form of a barley cake baked where they can see you, on human dung.'

13 And Yahweh said, 'This is how the Israelites will have to eat their defiled food, wherever I disperse them among the nations.'

14 I then said, 'Lord Yahweh, my soul is not defiled. From my childhood until now, I have never eaten an animal that has died a natural death or been savaged; no tainted meat has ever entered my mouth.'

15 'Very well,' he said, 'I grant you cow-dung instead of human dung; you are to bake your bread on that.'

16 He then said, 'Son of man, I am going to cut off Jerusalem's food supply; in their extremity, the food they eat will be weighed out; to their horror, the water they drink will be rationed,

17 until there is no food or water left, and they fall into a stupor and waste away because of their guilt.'
5)1 'Son of man, take a sharp sword, use it like a barber's razor and run it over your head and beard. Then take scales and divide the hair you have cut off.

2 Burn one-third inside the city, while the days of the siege are working themselves out. Then take another third and chop it up with the sword all round the city. The last third you are to scatter to the wind, while I unsheathe the sword behind them.

3 Also take a few hairs and tie them up in the folds of your cloak;

4 and of these again take a few, and throw them on the fire and burn them. From them fire will come on the whole House of Israel.

5 'The Lord Yahweh says this, "This is Jerusalem, which I have placed in the middle of the nations, surrounded with foreign countries.

6 She has rebelled more perversely against my observances than the nations have, and against my laws than the surrounding countries have; for they have rejected my observances and not kept my laws."

7 'Therefore, the Lord Yahweh says this, "Because your disorders are worse than those of the nations round you, since you do not keep my laws or respect my observances, and since you do not respect even the observances of the surrounding nations,

8 very well, the Lord Yahweh says this: I, too, am against you and shall execute my judgements on you for the nations to see.

9 Because of all your loathsome practices I shall do such things as I have never done before, nor shall ever do again.

10 Those of you who are parents will eat their children, and children will eat their parents. I shall execute judgement on you and disperse what remains of you to the winds.

11 For, as I live -- declares Lord Yahweh -- as sure as you have defiled my sanctuary with all your horrors and all your loathsome practices, so I too shall reject you without a glance of pity, I shall not spare you.

12 A third of your citizens will die of plague or starve to death inside you; a third will fall by the sword round you; and a third I shall scatter to the winds, unsheathing the sword behind them.

13 I shall sate my anger and bring my fury to rest on them until I am avenged; and when I have sated my fury on them, then they will know that I, Yahweh, spoke out of jealousy for you.

14 Yes, I shall reduce you to a ruin, an object of derision to the surrounding nations, in the eyes of all who pass by.

15 You will be an object of derision and insults, an example, an object of amazement to the surrounding nations, when I execute judgement on you in furious anger and furious punishments. I, Yahweh, have spoken.

16 On them I shall send the deadly arrows of famine, which will destroy you -- for I shall send them to destroy you; then I shall make the famine worse and cut off your food supply.

17 I shall send famine and wild animals on you to rob you of your children; plague and bloodshed will sweep through you, and I shall bring the sword down on you. I, Yahweh, have spoken." '
6)1 The word of Yahweh was addressed to me as follows,

2 'Son of man, turn towards the mountains of Israel and prophesy against them.

3 Say, "Mountains of Israel, hear the word of the Lord Yahweh. The Lord Yahweh says this to mountains and hills and ravines and valleys: Look, I am going to summon the sword against you and destroy your high places.

4 Your altars will be wrecked, and your incense burners smashed; I shall fling your butchered inhabitants down in front of your foul idols;

5 I shall lay the corpses of the Israelites in front of their foul idols and scatter their bones all round your altars.

6 Wherever you live, the towns will be destroyed and the high places wrecked, to the ruin and wrecking of your altars, the shattering and abolition of your foul idols, the smashing of your incense burners and the utter destruction of all your works.

7 As the butchered fall about you, you will know that I am Yahweh.

8 "But I shall spare some of you to escape the sword among the nations, when you have been dispersed in their lands;

9 and your survivors will remember me among the nations where they are held captive, since I shall have broken their adulterous hearts for having deserted me, and destroyed their eyes for having turned adulterously towards their foul idols. They will loathe themselves for all the wrong they have caused by their loathsome practices.

10 Then they will know that I am Yahweh and that I was not talking lightly when I said that I would inflict these disasters on them."

11 'The Lord Yahweh says this, "Clap your hands, stamp your feet, and say: Alas for all the loathsome sins of the House of Israel, which is about to fall by sword, famine and plague!

12 Far off, they will die by plague; near at hand they will fall by the sword; and any who survive or are spared will die of famine. This is how I shall sate my fury on them.

13 Then you will know that I am Yahweh, when their butchered corpses lie among their foul idols, all round their altars, on every high hill, on every mountain top, under every green tree, under every leafy oak, wherever they offer a smell pleasing to all their idols.

14 I shall point my finger at them and reduce the country to an empty wasteland from the desert to Riblah, everywhere they live, and they will know that I am Yahweh." '
7) The word of Yahweh was addressed to me as follows,

2 'Son of man, say, "Lord Yahweh says this to the land of Israel: Finished! The end is coming for the four corners of the country.

3 This is the end for you; I shall unleash my anger on you, and judge you as your conduct deserves and call you to account for all your loathsome practices.

4 I shall show you no pity, I shall not spare you; I shall repay you for your conduct and for the loathsome practices in which you persist. Then you will know that I am Yahweh.

5 "The Lord Yahweh says this: Disaster, a unique disaster, is coming.

6 The end is coming, the end is coming, it is on the move towards you, it is coming now.

7 Now it is your turn, you who dwell in this country. Doom is coming, the day is near; no joy now, only tumult, on the mountains.

8 Now I shall soon vent my fury on you and sate my anger on you: I shall judge you as your conduct deserves and repay you for all your loathsome practices.

9 I shall show neither pity nor mercy, but shall repay you for your conduct and the loathsome practices in which you persist. Then you will know that I am Yahweh and that I strike.

10 "Now is the day, your turn has come, it has come, it appears, the sceptre has blossomed, pride is at its peak.

11 Violence has risen to become the scourge of wickedness . . .

12 Doom is coming, the day is near. Neither should buyer rejoice, nor seller regret, for the fury rests on everyone alike.

13 The seller will not be able to go back on his bargain; each persists in his sins; they take no defensive measures.

14 The trumpet sounds, all is ready, but no one goes into battle, since my fury rests on all alike.

15 "Outside, the sword; inside, plague and famine. Whoever is living in the countryside will die by the sword; whoever is living in the city will be devoured by famine and plague.

16 And those who escape will escape to the mountains and there, like doves of the valleys, I shall slaughter them all, each one for his sin.

17 Every hand will grow limp, every knee turn to water.

18 They will put on sackcloth, each one trembling. Every face will be ashamed and every head be shaved.

19 They will throw their silver away in the streets and their gold they will regard as a pollution; neither their silver nor their gold will be able to save them on the day of Yahweh's fury. Never again will they have enough to eat, never again will they fill their bellies, since that was the occasion for their guilt.

20 They used to pride themselves on the beauty of their jewellery, out of which they made their loathsome images, their horrors; so now I have made it pollute them.

21 I shall hand it over as plunder to foreigners, as loot to the most evil people on earth. They will profane it.

22 I shall turn my face away from them, while my treasure-house is profaned and robbers will force their way in and profane it.

23 "Forge yourself a chain; for the country is full of bloody executions and the city full of deeds of violence,

24 so I shall bring the cruellest of the nations to seize their houses. I shall put an end to the pride of their e'lite, and their sanctuary will be profaned.

25 Terror is on the way: they will look for peace and there will be none.

26 Disaster will follow on disaster, rumour on rumour; they will pester the prophet for a vision; the priest will be at a loss over the law and the elders on how to advise.

27 The king will go into mourning, the prince be plunged in grief, the hands of the country people tremble. I shall treat them as their conduct deserves, and judge them as their own verdicts merit. Then they will know that I am Yahweh!" '