The watchtower Society's commentary on the 'ecclesia'

CONGREGATION;

A group of people gathered together for a particular purpose or activity. The Hebrew word usually rendered “congregation” in the New World Translation is qa·halʹ, which is from a root meaning “call together; congregate.” (Nu 20:8; De 4:10) It is frequently used for an organized body, being found in the expressions “congregation of Israel” (Le 16:17; Jos 8:35; 1Ki 8:14), “congregation of the true God” (Ne 13:1), “congregation of Jehovah” (De 23:2, 3; Mic 2:5), and “Jehovah’s congregation” (Nu 20:4; 1Ch 28:8). Qa·halʹ designates various kinds of human gatherings, as for religious purposes (De 9:10; 18:16; 1Ki 8:65; Ps 22:25; 107:32), for dealing with civil affairs (1Ki 12:3), and for warfare (1Sa 17:47; Eze 16:40). In the book of Ecclesiastes, Solomon is identified as “the congregator” (Heb., qo·heʹleth). (Ec 1:1, 12) As the king, he congregated or assembled the people to the worship of Jehovah, one notable instance being when he gathered his subjects to the newly constructed temple in Jerusalem.—1Ki 8:1-5; 2Ch 5:2-6.

In the Christian Greek Scriptures the Greek word rendered “congregation” is ek·kle·siʹa, from which the English word “ecclesia” is derived. Ek·kle·siʹa comes from two Greek words, ek, meaning “out,” and ka·leʹo, meaning “call.” Hence, it pertains to a group of persons called out or called together, either officially or unofficially. It is the word used with reference to the congregation of Israel at Acts 7:38 and is also employed for the “assembly” stirred up by the silversmith Demetrius against Paul and his associates in Ephesus. (Ac 19:23, 24, 29, 32, 41) Most often, however, it is used with reference to the Christian congregation. It is applied to the Christian congregation in general (1Co 12:28); to a congregation in some city such as Jerusalem (Ac 8:1), Antioch (Ac 13:1), or Corinth (2Co 1:1); or to a specific group meeting in someone’s home (Ro 16:5; Phm 2). Accordingly, individual Christian congregations or “congregations of God” are also mentioned. (Ac 15:41; 1Co 11:16) Some English versions use “church” in texts pertaining to the Christian congregation, as at 1 Corinthians 16:19. (AS; KJ) Since many persons think of a church as a building for religious services rather than a congregation engaging in worship, the rendering “church” can be misleading.

The Greek word ek·kle·siʹa is usually employed in the Septuagint to translate the Hebrew word qa·halʹ, as at Psalm 22:22 (21:23, LXX).—Compare NW ftn.

The Congregation of Israel. From the time of Moses onward, the nation of Israel was referred to as a congregation. Jehovah arranged for the congregation to be ruled, not democratically by the people, but theocratically, by God himself. To that end the nation was taken into the Law covenant. (Ex 19:3-9; 24:6-8) As Moses was the mediator of that covenant, it could be said: “Moses laid as a command upon us a law, a possession of the congregation of Jacob.” (De 33:4) Jehovah was their Judge, Statute-Giver, and King. (Isa 33:22) Thus, the nation was a congregation of God and could be referred to as “the congregation of Jehovah” and “Jehovah’s congregation.”—Nu 16:3; 1Ch 28:8.

At times, the Hebrew word qa·halʹ (congregation) is used in conjunction with the Hebrew word ʽe·dhahʹ (assembly). (Le 4:13; Nu 20:8, 10) ʽE·dhahʹ is from a root meaning “appoint,” thus signifying a group assembled by appointment, and is frequently applied to the community of Israel, as in the expression “assembly of Israel.” (Ex 12:3) In the nation of Israel those who actually constituted the Hebrew population made up the congregation (qa·halʹ; Nu 15:15), whereas the assembly (ʽe·dhahʹ) seems to have embraced both the Israelites and alien residents associated with them. (Ex 12:19) So membership in the congregation, in an extended general application, seems to have included circumcised alien residents.—Nu 15:14-16.

However, there were exceptions as to membership in “the congregation of Jehovah.” No castrated man or one “having his male member cut off” could enter it; illegitimate sons, male Ammonites, and male Moabites were barred therefrom “even to the tenth generation.” But sons born to Edomites and Egyptians “as the third generation” could “come for themselves into the congregation of Jehovah.” (De 23:1-8) The exclusion “to the tenth generation” of the sons of one who was illegitimate upheld Jehovah’s law against adultery. (Ex 20:14) And though the sexually mutilated were excluded from “the congregation of Jehovah,” such ones could draw comfort from words recorded by Isaiah, as found at Isaiah 56:1-7. Of course, individuals excluded from “the congregation of Jehovah” in ancient Israel had the possibility of coming under provisions and blessings Jehovah made for people of the nations in general.—Ge 22:15-18.

Persons who were members of the congregation of Israel were shown mercy if they sinned by mistake. But they were cut off in death for doing something wrong deliberately. (Nu 15:27-31) For instance, an individual would be cut off from the congregation, and from life itself, for refusing to purify himself when he was ceremonially unclean, for eating some of the flesh of the communion sacrifice while in that condition, for partaking of fat of offerings or blood, or for eating holy things while unclean. (Nu 19:20; Le 7:21-27; 17:10, 14; 22:3) Persons were also cut off for working on the Sabbath day (Ex 31:14), for giving their offspring to Molech, for turning to spirit mediums and professional foretellers of events, for certain kinds of sexual immorality, and for not ‘afflicting’ themselves on the annual Atonement Day.—Le 20:1-6, 17, 18; 23:27-30; see also Ex 30:31-33; Le 17:3, 4, 8, 9; 18:29; 19:5-8.

While individuals made up the congregation of Israel, the nation itself was comprised of tribes, families, and households. The incident involving Achan seems to show this organizational arrangement, for in this case Israel came forward, first tribe by tribe, then family by family, next household by household, and finally able-bodied man by able-bodied man, until Achan was picked as the wrongdoer.—Jos 7:10-19.

In Israel responsible representatives often acted in behalf of the people. (Ezr 10:14) Thus, “chieftains of the tribes” made presentations after the setting up of the tabernacle. (Nu 7:1-11) Also, representatively attesting by seal the “trustworthy arrangement” of Nehemiah’s day were priests, Levites, and “the heads of the people.” (Ne 9:38–10:27) During Israel’s wilderness trek, there were “chieftains of the assembly, summoned ones of the meeting, men of fame,” 250 of whom joined Korah, Dathan, Abiram, and On in congregating themselves against Moses and Aaron. (Nu 16:1-3) In keeping with divine direction, Moses selected 70 of the older men of Israel who were officers to help him carry “the load of the people” that he was unable to bear alone. (Nu 11:16, 17, 24, 25) Leviticus 4:15 mentions “the older men of the assembly,” and it appears that the representatives of the people were the nation’s older men, its heads, its judges, and its officers.—Nu 1:4, 16; Jos 23:2; 24:1.

In the wilderness, two silver trumpets were used to convene the assembly and to break up the camp. The assembly would keep their appointment with Moses at the entrance of the tent of meeting if blasts were blown on both of these trumpets. If just one was sounded, “the chieftains as heads of the thousands of Israel” would put in an appearance there. (Nu 10:1-4) Sometimes kings convened gatherings (1Ki 8:5; 2Ch 20:4, 5), Hezekiah using runners to summon the people to Jerusalem for the grand Passover celebration of his day.—2Ch 30:1, 2, 10-13.

In later times, considerable power was wielded by the judicial body known as the Sanhedrin, composed of 71 members—the high priest and 70 other principal men of the nation, “the assembly of older men.”—Mt 26:59; Lu 22:66.

During the Jews’ Babylonian exile, or shortly thereafter, synagogues came into general use as buildings where the Jews congregated. In time, synagogues were established in various places; Jesus imparted instruction at the synagogue in Nazareth, for example. (Lu 4:16-21) Synagogues were actually schools where the Scriptures were read and taught, and they were places of prayer and for the giving of praise to God.—Ac 15:21; see SYNAGOGUE.

The congregation of Israel was in a unique position. Moses reminded them: “You are a holy people to Jehovah your God. It is you Jehovah your God has chosen to become his people, a special property, out of all the peoples that are on the surface of the ground.” (De 7:6) But the Jewish congregation ceased to be the congregation of God, being cast off because of rejecting his Son.—Ac 4:24-28; 13:23-29; Mt 21:43; 23:37, 38; Lu 19:41-44.

The Christian Congregation of God. Prior to the rejection of the Jewish nation and the end of its position as the congregation of God, Jesus Christ identified himself as the “rock-mass” upon which he would build what he termed “my congregation.” (Mt 16:18) This is as Peter, to whom he spoke, understood matters, for the apostle later identified Jesus as the figurative “stone” that was rejected by men but was “chosen, precious, with God” and as the “foundation cornerstone” on which a person could rest his faith without disappointment. (1Pe 2:4-6; Ps 118:22; Isa 28:16) Paul also definitely identified Jesus Christ as the foundation upon which the Christian congregation is built. (Eph 2:19-22; 1Co 3:11) And, belonging to Jehovah as it does, it is appropriately referred to as “the congregation of God.”—Ac 20:28; Ga 1:13.

This Christian congregation (Gr., ek·kle·siʹa), founded on Christ, also has him as its head. Thus it is stated: “He [God] also subjected all things under his feet, and made him head over all things to the congregation, which is his body, the fullness of him who fills up all things in all.”—Eph 1:22, 23; see also Col 1:18.

The Christian congregation of God took the place of the congregation of Israel at Pentecost of 33 C.E., when holy spirit was poured out on Jesus’ followers in Jerusalem. The first prospective members of that congregation were chosen shortly after Jesus’ baptism, at the beginning of his ministry on earth. (Ac 2:1-4; Joh 1:35-43) From among his early followers Jesus selected 12 apostles (Lu 6:12-16), and later he chose Saul of Tarsus, who became “an apostle to the nations.” (Ac 9:1-19; Ro 11:13) The 12 faithful apostles of the Lamb Jesus Christ, including Matthias who replaced Judas, constitute secondary foundations of the Christian congregation.—Ac 1:23-26; Re 21:1, 2, 14.

This congregation is referred to as “the congregation of the firstborn who have been enrolled in the heavens,” the full number of which, under Christ the head, is 144,000. (Heb 12:23; Re 7:4) These called-out ones are “bought from among mankind” to carry out a special work here on earth and then to be with Christ in heaven as his bride. As there were requirements for membership in the Hebrew congregation of God, so there are requisites for membership in the Christian “congregation of God.” Those making it up are spiritual virgins who keep following the Lamb, Jesus Christ, no matter where he goes, “and no falsehood was found in their mouths; they are without blemish.”—Re 14:1-5.

The members of the Christian congregation of God are selected by Jehovah. (Ro 8:30; 2Th 2:13) The first members thereof were called out from the rejected Jewish congregation, which had not accepted God’s Son as their Messiah. However, beginning with Cornelius in 36 C.E., members of the Christian congregation were also called out from the nations in general, so that Paul could say: “There is neither Jew nor Greek, there is neither slave nor freeman, there is neither male nor female; for you are all one person in union with Christ Jesus.” (Ga 3:28; Ac 10:34, 35; Ro 10:12; Eph 2:11-16) Whereas the Law covenant mediated by Moses and under which the congregation of Israel was regulated was fulfilled by Christ and was taken out of the way by Jehovah God (Mt 5:17; 2Co 3:14; Col 2:13, 14), members of the Christian congregation of God partake of the benefits of the new covenant mediated by the Greater Moses, Jesus Christ. (Mt 26:28; Heb 12:22-24; Ac 3:19-23) Also, while the priests and kings of Israel were anointed with oil (Ex 30:22-30; 2Ki 9:6), those chosen by God to be members of the Christian congregation are anointed with holy spirit (2Co 1:21, 22; 1Jo 2:20) and are adopted by Jehovah God as his sons.—Eph 1:5.

Basically the Hebrew congregation was composed of natural Israelites. Persons comprising the anointed Christian congregation of God are spiritual Israelites, forming the tribes of spiritual Israel. (Re 7:4-8) Inasmuch as the majority of the natural Israelites rejected Jesus Christ, “not all who spring from Israel are really ‘Israel,’” that is, spiritual Israel. (Ro 9:6-9) And, regarding the Christian congregation of God comprised of spiritual Jews, Paul stated: “He is not a Jew who is one on the outside, nor is circumcision that which is on the outside upon the flesh. But he is a Jew who is one on the inside, and his circumcision is that of the heart by spirit.”—Ro 2:28, 29.

Usually when the Christian Greek Scriptures mention “the congregation” in a general sense, reference is being made to the 144,000 members thereof, the anointed followers of Christ exclusive of Jesus himself. (Eph 5:32; Heb 12:23, 24) However, the inspired application of David’s words recorded at Psalm 22:22 to Jesus Christ at Hebrews 2:12 shows that the term “congregation” can be applied to include the head thereof, Jesus Christ. Partly quoting David, the writer to the Hebrews stated: “For both he who is sanctifying and those who are being sanctified all stem from one, and for this cause he [Jesus Christ] is not ashamed to call them ‘brothers,’ as he says: ‘I will declare your name to my brothers; in the middle of the congregation I will praise you with song.’” (Heb 2:11, 12) Like David, who was a member of the congregation of Israel in the middle of which he praised Jehovah, Jesus Christ can, in this instance, be viewed as one of the spiritual congregation, the others in it being called his “brothers.” (Compare Mt 25:39, 40.) David belonged to the Israelite congregation of Jehovah God, and Jesus Christ was also a member of it while on earth, preaching amidst its members. A remnant of that congregation became part of Jesus’ congregation.

Organization of the Christian Congregation. While Christian congregations of God were established in various places, they did not function independently of one another. Instead, they all recognized the authority of the Christian governing body at Jerusalem. This governing body was comprised of the apostles and older men of the Jerusalem congregation, there being no rival bodies elsewhere seeking to supervise the congregation. It was to the faithful Christian governing body of the first century C.E. that the issue of circumcision was submitted for consideration. When the governing body made its decision, as directed by the holy spirit, that decision was accepted and became binding upon all Christian congregations, these willingly submitting to it.—Ac 15:22-31.

The Christian body in Jerusalem sent out traveling representatives. Thus, Paul and others delivered the governing body’s decision just mentioned, it being stated: “Now as they traveled on through the cities they would deliver to those there for observance the decrees that had been decided upon by the apostles and older men who were in Jerusalem.” Concerning the effects produced, it is said: “Therefore, indeed, the congregations continued to be made firm in the faith and to increase in number from day to day.” (Ac 16:4, 5) Earlier, when the apostles in Jerusalem “heard that Samaria had accepted the word of God, they dispatched Peter and John to them; and these went down and prayed for them to get holy spirit.”—Ac 8:14, 15.

The individual congregations adhered closely to the direction of the Christian governing body, which supervised the appointment of older men. (Tit 1:1, 5) So it was that, as directed by the Christian governing body under the influence of the holy spirit, overseers as well as assistants, ministerial servants, were appointed for each congregation. The men placed in these positions of trust and responsibility had to meet specific qualifications. (1Ti 3:1-13; Tit 1:5-9) Traveling representatives of the governing body, such as Paul, followed Christ and set a fine example to be imitated. (1Co 11:1; Php 4:9) In fact, all of those in the position of spiritual shepherds were to become “examples to the flock” (1Pe 5:2, 3), were to show loving concern for individuals within the congregation (1Th 2:5-12), and were to be of real assistance to those spiritually sick.—Ga 6:1; Jas 5:13-16; see OLDER MAN; OVERSEER; MINISTER.

Hence, just as Jehovah organized the congregation of Israel under older men, heads, judges, and officers (Jos 23:2), He saw to the supervision of the Christian congregation by having older men appointed to positions of trust therein. (Ac 14:23) And, as responsible men sometimes acted representatively for the entire congregation of Israel, as in judicial matters (De 16:18), God arranged for each individual Christian congregation to be similarly represented in such matters by responsible men placed in positions of authority by the holy spirit. (Ac 20:28; 1Co 5:1-5) However, should difficulties develop between members of the Christian congregation of God, the words of Jesus Christ recorded at Matthew 18:15-17 (spoken before the Jewish congregation of God had been rejected by Jehovah and thus initially applicable to it) served as a basis for settling or handling such problems.

Jehovah God has set the members in the spiritual “body” of Christ “just as he pleased.” And Paul stated: “God has set the respective ones in the congregation, first, apostles; second, prophets; third, teachers; then powerful works; then gifts of healings; helpful services, abilities to direct, different tongues.” Not all performed the same functions, but all were needed by the Christian congregation. (1Co 12:12-31) Paul explained that the supplying of apostles, prophets, evangelizers, shepherds, and teachers for the Christian congregation was “with a view to the readjustment of the holy ones, for ministerial work, for the building up of the body of the Christ, until we all attain to the oneness in the faith and in the accurate knowledge of the Son of God, to a full-grown man, to the measure of stature that belongs to the fullness of the Christ.”—Eph 4:11-16.

The congregation of Israel was provided with the laws of God and was made to appreciate that “not by bread alone does man live but by every expression of Jehovah’s mouth does man live.” (De 8:1-3) Jesus Christ also recognized that man could not live on bread alone “but on every utterance coming forth through Jehovah’s mouth.” (Mt 4:1-4) Hence, adequate provision has been made for the Christian congregation to have needed spiritual food, Christ himself mentioning the “slave” through whom such food is dispensed to Christian “domestics.” Jesus, as part of his prophecy concerning his own presence and “the conclusion of the system of things,” showed that, on arriving, the “master” would appoint this “faithful and discreet slave” “over all his belongings.”—Mt 24:3, 45-47.

Gatherings for the worship of Jehovah and a consideration of his law were important in the congregation of Israel. (De 31:12; Ne 8:1-8) Similarly, meetings for the worship of Jehovah and a study of the Scriptures are an essential feature of the Christian congregation of God, the writer to the Hebrews admonishing the recipients of his letter not to be forsaking such gathering of themselves together. (Heb 10:24, 25) Activities in the synagogues of later Jewish history included the reading and teaching of the Scriptures, the offering of prayers, and the giving of praise to God. Such features were carried over into places of Christian assembly, though without the ritualistic accretions that had eventually developed in synagogue services. In the synagogue no sacerdotal class was set apart, sharing in Scripture reading and exposition being open to any devout male Jew. Comparably, no clergy-laity or similar division existed within the early Christian congregation. Of course, neither therein nor in the synagogue did the women teach or exercise authority over the men.—1Ti 2:11, 12.

The maintaining of proper order at meetings of the Christian congregation of God harmonized with the fact that Jehovah, who made provision for the congregational arrangement among Christ’s followers, is a “God, not of disorder, but of peace.” This orderliness also worked to the great spiritual benefit of all in attendance.—1Co 14:26-35,

On I.D and the limits of science

Undesirable Intelligent Design is Still Intelligent Design
Casey Luskin February 29, 2012 6:01 AM

I thought I would add a few thoughts to David Klinghoffer's insightful comments on the "Centre for Unintelligent Design." Its proprietor, Keith Gilmour, offers a list of features from life and nature that he says show "unintelligent design" but in fact are best classified as illustrating "undesirable design." Looking at the website, I also noticed that Gilmour misunderstood and/or misrepresented an email exchange with University of Warwick sociologist Steve Fuller. Because this is a challenge that comes up often, it's worth clarifying.

Fuller wrote, apparently in response to Gilmour's sending him a link to the website:

Dear Keith,
Thanks for this. You might perhaps make more headway with ID people if you understood the position better. The problem of apparent "unintelligent design" in nature is one that people with ID sympathies have long tackled. Simply look up the literature on "theodicy."

Steve Fuller

To which Gilmour replies:
Dear Prof Fuller,
I am immensely grateful to you for your "stunning" reply to my recent email. In just one line, you inadvertently "destroy" the notion that ID is science:

"The problem of apparent 'unintelligent design' in nature is one that people with ID sympathies have long tackled. Simply look up the literature on 'theodicy.'"

By admitting that "unintelligent design" is a branch of theology, you necessarily admit that "Intelligent" Design is also a branch of theology.

Not quite what I was expecting, but absolutely priceless!

Many thanks again,

Keith Gilmour

The response from the "ID people" that Fuller mentioned is as follows: Those who cite alleged examples of undesirable design are making a theological argument, and since ID is a scientific argument, those theological arguments don't refute ID. Contrary to Gilmour's claims, "By admitting that '[undesirable] design' is a branch of theology," Fuller did NOT "admit that 'Intelligent' Design is also a branch of theology." That's because, if you take the time to read ID responses on this topic, they point out that "undesirable design" arguments do not refute ID arguments precisely because "undesirable design" arguments are theologically based, whereas ID is NOT!
As a science, ID doesn't address theological questions about whether the design is "desirable," "undesirable," "perfect," or "imperfect." Undesirable design is still design. Gilmour just doesn't like it because (in his own subjective view) it's undesirable. Here's a quick illustration of what I mean:

I'm writing this on a PC using Windows; this PC has crashed probably a dozen times in the past two weeks. Right now, I hate my PC. I consider it poorly designed, full of imperfections, and very undesirable. Does that mean it wasn't designed by intelligent agents? No. "Undesirable design" and "intelligent design" are two different things. "Undesirable," "poor," or "imperfect" design do not refute intelligent design.

In speaking of "unintelligent design," Gilmour misuses the term "intelligent," ignoring how ID proponents use it. By the word "intelligent," ID proponents simply mean to indicate that a structure has features requiring a mind capable of forethought to design the blueprint. Thus, ID proponents test ID by looking for complex and specified information, which is an indicator that some goal-directed process, capable of acting with will, forethought, and intentionality, was involved in designing an object.

We do not test ID by looking for "perfect design" or "undesirable design," because minds don't always make things that are "perfect," and sometimes they make things that are "undesirable" (to other minds, at least). Holding biological systems to some vague standard of "perfect design" where they are refuted by "undesirable design" is the wrong way to test ID. Examples like broken machinery, computer failures, and decaying buildings all show that a structure might be designed by an intelligent agent even if it subsequently breaks or shows flaws. Intelligent design does not necessarily mean "perfect design." It doesn't even require optimal design. Rather, "intelligent design" means exactly what it sounds like: design by an intelligent agent.

"Undesirable design" arguments share three general problems, some or all of which can be found in each of Gilmour's 130 examples. Here are the three main problems:
(1) An object can have imperfections and be undesirable, but still be designed.
(2) Critics' standards of perfection are often arbitrary. 
(3) "Bad design" arguments don't hold up under their own terms, as the objects often turn out to be well designed when we inspect them more closely.
Problem (1) applies to every single example Gilmour gives. Problems (2) and (3) apply to many, though not all, of his examples. In fact, some of them are legitimate examples of undesirable design. I mean, who likes "easily worn out knees" or hernias -- both examples of how our bodies break down? Objectively speaking, those are flaws or imperfections. But as much as you might not like "undesirable design," they don't refute ID because ID is a scientific argument that isn't concerned with the moral value, perfection, or desirable/undesirable quality of a structure. Computers break down but were still intelligently designed. In the same way, the fact that our bodies break down doesn't mean they weren't intelligently designed.

Gilmour's website implies designers must always design things so they NEVER break down. But I'm not aware of a single example of human-designed technology that never breaks down. Undesirable qualities, breakdowns, and imperfections are a normal part of intelligently designed objects; they don't refute intelligent design.

I would say to Keith Gilmour and the many others who adopt his approach: Stop playing games and just lay your cards on the table. You are arguing against the idea that an all-perfect, all-knowing, all-powerful God created everything, because you claim that if such a God existed then there would be no flaws in nature. In essence, you are raising the "problem of evil." So you're arguing against a different, much broader thesis than intelligent design. You are making a theological argument, not a scientific one.

For millennia, the Judeo-Christian theistic tradition has offered theological explanations for how a perfect God can exist, even as we observe undesirable and evil things in nature. But these issues are separate from ID. Oxford philosopher Richard Swinburne wrote, "It seems to be generally agreed by atheists as well as theists that what is called 'the logical problem of evil' has been eliminated, and all that remains is 'the evidential problem.'" Obviously, I don't deny that evil can be hard to cope with, which is why I like C.S. Lewis's words when he wrote in The Problem of Pain:

[T]he only purpose of the book is to solve the intellectual problem raised by suffering; for the far higher task of teaching forgiveness and patience I was never fool enough to suppose myself qualified, nor have I anything to offer my readers except my conviction that when pain is to be borne, a little courage helps more than knowledge, a little human sympathy more than much courage, and the least tincture of the love of God more than all.

So I think one can be a traditional theist and a scientific proponent of ID -- I personally fit into this category. But again, these questions are separate questions from the science of ID, as ID doesn't specify the "desirability" or "perfection" of the design. Familiarizing himself with ID arguments would help Keith Gilmour to better understand why Dr. Fuller was right to note that "You might perhaps make more headway with ID people if you understood the position better." I hope Gilmour and other likeminded folks take that piece of good advice and come to understood the ID position a bit better.

Another failed Darwinian prediction XII

Genomic features are not sporadically distributed:

A fundamental concept in evolutionary theory is the inheritance of genetic variations via blood lines. (Forbes) This so-called vertical transmission of heritable material means that genes, and genomes in general, should fall into a common descent pattern, consistent with the evolutionary tree. Indeed, such genes are often cited as a confirmation of evolution. But as more genomic data have become available, an ever increasing number of genes have been discovered that do not fit the common descent pattern because they are missing from so many intermediate species. (Andersson and Roger 2002; Andersson and Roger 2003; Andersson 2005; Andersson, Sarchfield and Roger 2005; Andersson 2006; Andersson et. al. 2006; Andersson 2009; Andersson 2011; Haegeman, Jones and Danchin; Katz; Keeling and Palmer; Richards et. al 2006a; Richards et. al 2006b; Takishita et. al.; Wolf et. al.)

This type of pattern is also found for genome architecture features which are sporadically distributed and then strikingly similar in distant species. In fact these similarities do not merely occur twice, in two distant species. They often occur repeatedly in a variety of otherwise distant species. This is so widespread that evolutionists have named the phenomenon “recurrent evolution.” As one paper explains, the recent explosion of genome data reveals “strikingly similar genomic features in different lineages.” Furthermore, there are “traits whose distribution is ‘scattered’ across the evolutionary tree, indicating repeated independent evolution of similar genomic features in different lineages.” (Maeso, Roy and Irimia)

One example is the uncanny similarity between the kangaroo and human genomes. As one evolutionist explained: “There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order. We thought they’d be completely scrambled, but they’re not.” (Taylor)

It is now well recognized that this prediction has failed: “Vertical transmission of heritable material, a cornerstone of the Darwinian theory of evolution, is inadequate to describe the evolution of eukaryotes, particularly microbial eukaryotes.” (Katz) And these sporadic, patchy patterns require complicated and ad hoc scenarios to explain their origin. As one paper explained, the evolution of a particular set of genes “reveals a complex history of horizontal gene transfer events.” (Wolf et. al.) The result is that any pattern can be explained by arranging the right mechanisms. Features that are shared between similar species can be interpreted as “the result of a common evolutionary history,” and features that are not can be interpreted as “the result of common evolutionary forces.” (Maeso, Roy and Irimia)

These common evolutionary forces are complex and must have been created by evolution. They can include horizontal (or lateral) gene transfer, gene loss, gene fusion, and even unknown forces. For instance, one study concluded that the best explanation for the pattern of a particular gene was that it “has been laterally transferred among phylogenetically diverged eukaryotes through an unknown mechanism.” (Takishita et. al.) Even with the great variety of mechanisms available, there still remains the unknown mechanism.

References

Andersson, J., A. Roger. 2002. “Evolutionary analyses of the small subunit of glutamate synthase: gene order conservation, gene fusions, and prokaryote-to-eukaryote lateral gene transfers.” Eukaryotic Cell 1:304-310.

Andersson, J., A. Roger. 2003. “Evolution of glutamate dehydrogenase genes: evidence for lateral gene transfer within and between prokaryotes and eukaryotes.” BMC Evolutionary Biology 3:14.

Andersson, J. 2005. “Lateral gene transfer in eukaryotes.” Cellular and Molecular Life Sciences 62:1182-97.

Andersson, J., S. Sarchfield, A Roger. 2005. “Gene transfers from nanoarchaeota to an ancestor of diplomonads and parabasalids.” Molecular Biology and Evolution 22:85-90.

Andersson, J. 2006. “Convergent evolution: gene sharing by eukaryotic plant pathogens.” Current Biology 16:R804-R806.

Andersson, J., R. Hirt, P. Foster, A. Roger. 2006. “Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes.” BMC Evolutionary Biology 6:27.

Andersson, J. 2009. “Horizontal gene transfer between microbial eukaryotes.” Methods in Molecular Biology 532:473-487.

Andersson, J. 2011. “Evolution of patchily distributed proteins shared between eukaryotes and prokaryotes: Dictyostelium as a case study.” J Molecular Microbiology and Biotechnology 20:83-95.

Haegeman, A., J. Jones, E. Danchin. 2011. “Horizontal gene transfer in nematodes: a catalyst for plant parasitism?.” Molecular Plant-Microbe Interactions 24:879-87.

Katz, L. 2002. “Lateral gene transfers and the evolution of eukaryotes: theories and data.” International J. Systematic and Evolutionary Microbiology 52:1893-1900.

Keeling, P., J. Palmer. 2008. “Horizontal gene transfer in eukaryotic evolution,” Nature Reviews Genetics 9:605-18.

Maeso, I, S. Roy, M. Irimia. 2012. “Widespread Recurrent Evolution of Genomic Features.” Genome Biology and Evolution 4:486-500.

Richards, T., J. Dacks, J. Jenkinson, C. Thornton, N. Talbot. 2006. “Evolution of filamentous plant pathogens: gene exchange across eukaryotic kingdoms.” Current Biology 16:1857-1864.

Richards, T., J. Dacks, S. Campbell, J. Blanchard, P. Foster, R. McLeod, C. Roberts. 2006. “Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements.” Eukaryotic Cell 5:1517-31.

Takishita, K., Y. Chikaraishi, M. Leger, E. Kim, A. Yabuki, N. Ohkouchi, A. Roger. 2012. “Lateral transfer of tetrahymanol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen.” Biology Direct 7:5.

Taylor, R. 2008. “Kangaroo genes close to humans,” Reuters, Canberra, Nov 18.

Wolf, Y., L. Aravind, N. Grishin, E. Koonin. 1999. “Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events.” Genome Research 9:689-710.

Another failed Darwinian prediction XI

             MicroRNA:


Genes hold information that is used to construct protein and RNA molecules which do various tasks in the cell. A gene is copied in a process known as transcription. In the case of a protein-coding gene the transcript is edited and converted into a protein in a process known as translation. All of this is guided by elaborate regulatory processes that occur before, during and after this sequence of transcription, editing and translation.

For instance, some of our DNA which was thought to be of little use actually has a key regulatory role. This DNA is transcribed into strands of about 20 nucleotides, known as microRNA. These short snippets bind and interfere with RNA transcripts—copies of DNA genes—when the production of the gene needs to be slowed.

MicroRNAs can also help to modify the translation process by stimulating programmed ribosomal frameshifting. Two microRNAs attach to the RNA transcript resulting in a pseudoknot, or triplex, RNA structure form which causes the reading frameshift to occur. (Belew)

MicroRNAs do not only come from a cell’s DNA. MicroRNAs can also be imported from nearby cells, thus allowing cells to communicate and influence each other. This helps to explain how cells can differentiate in a growing embryo according to their position within the embryo. (Carlsbecker)

MicroRNAs can also come from the food we eat. In other words, food not only contains carbohydrates, proteins, fat, minerals, vitamins and so forth, it also contains information—in the form of these regulatory snippets of microRNA—which regulate our gene production. (Zhang)

While microRNAs regulate the production of proteins, the microRNAs themselves also need to be regulated. So there is a network of proteins that tightly control microRNA production as well as their removal. “Just the sheer existence of these exotic regulators,” explained one scientist, “suggests that our understanding about the most basic things—such as how a cell turns on and off—is incredibly naïve.” (Hayden)

Two basic predictions that evolutionary theory makes regarding microRNAs are that (i) like all of biology, they arose gradually via randomly occurring biological variation (such as mutations) and (ii) as a consequence of this evolutionary origin, microRNAs should approximately form evolution’s common descent pattern. Today’s science has falsified both of these predictions.

MicroRNAs are unlikely to have gradually evolved via random mutations, for too many mutations are required. Without the prior existence of genes and the protein synthesis process microRNAs would be useless. And without the prior existence of their regulatory processes, microRNAs would wreak havoc.

Given the failure of the first prediction, it is not surprising that the second prediction has also failed. The microRNA genetic sequences do not fall into the expected common descent pattern. That is, when compared across different species, microRNAs do not align with the evolutionary tree. As one scientist explained, “I've looked at thousands of microRNA genes and I can't find a single example that would support the traditional [evolutionary] tree.” (Dolgin)

While there remain questions about these new phylogenetic data, “What we know at this stage,” explained another evolutionist, “is that we do have a very serious incongruence.” In other words, different types of data report very different evolutionary trees. The conflict is much greater than normal statistical variations.

“There have to be,” added another evolutionist, “other explanations.” One explanation is that microRNAs evolve in some unexpected way. Another is that the traditional evolutionary tree is all wrong. Or evolutionists may consider other explanations. But in any case, microRNAs are yet another example of evidence that does not fit evolutionary expectations. Once again, the theory will need to be modified in complex ways to fit the new findings.

In the meantime, scientists are finding that imposing the common descent pattern, where microRNAs must be conserved across species, is hampering scientific research:

These results highlight the limitations that can result from imposing the requirement that miRNAs be conserved across organisms. Such requirements will in turn result in our missing bona fide organism-specific miRNAs and could perhaps explain why many of these novel miRNAs have not been previously identified. (Londin)

Evolutionary theory has been limiting the science. While the common descent pattern has been the guide since the initial microRNA studies, these researchers “liberated” themselves from that constraint, and this is leading to good scientific progress:

In the early days of the miRNA field, there was an emphasis on identifying miRNAs that are conserved across organisms … Nonetheless, species-specific miRNAs have also been described and characterized as have been miRNAs that are present only in one or a few species of the same genus. Therefore, enforcing an organism-conservation requirement during miRNA searches is bound to limit the number of potential miRNAs that can be discovered, leaving organism- and lineage-specific miRNAs undiscovered. In our effort to further characterize the human miRNA repertoire, we liberated ourselves from the conservation requirement … These findings strongly suggest the possibility of a wide-ranging species-specific miRNA-ome that has yet to be characterized. (Londin)

The two microRNA predictions have been falsified and, not surprisingly, the evolutionary assumption has hampered the scientific research of how microRNAs work.

References

Belew, Ashton T., et. al. 2014. “Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway.” Nature 512:265-9.

Carlsbecker, Annelie, et. al. 2010. “Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate.” Nature 465:316-21.

Dolgin, Elie. 2012. “Phylogeny: Rewriting evolution.” Nature 486:460-2.

Hayden, Erika Check. 2010. “Human genome at ten: Life is complicated.” Nature 464:664-7.

Londin, Eric, et. al. 2015. “Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs.” Proc Natl Acad Sci USA 112:E1106-15.

Zhang, L., et. al. 2012. “Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA.” Cell Research 22:107-26.

The brand of the beast.

If Patients Were Pets
Wesley J. Smith February 29, 2016 2:44 PM

A Canadian government panel -- charged with recommending terms for the Supreme Court-imposed right to euthanasia -- wants MDs (and nurses) to have lower conscience rights than veterinarians. What do I mean? If someone presents a pet to be euthanized, the veterinarian can say no if she thinks the condition of the animal does not warrant that extreme action.

But if the panel gets its way, not so with doctors. It wants all MDs required by law to either kill the legally qualified patient or -- if they have a religious or other predicated conscience objection to committing homicide -- to provide an "effective referral" to a colleague to perform the lethal injection.

"Effective referral" will likely mean procuring a death doctor they know will be willing to do the deed, which is the law in Victoria, Australia, around abortion. From the report:

RECOMMENDATION 10 That the Government of Canada work with the provinces and territories and their medical regulatory bodies to establish a process that respects a health care practitioner's freedom of conscience while at the same time respecting the needs of a patient who seeks medical assistance in dying. At a minimum, the objecting practitioner must provide an effective referral for the patient.

Some objecting doctors might try to get around the effective referral requirement by claiming they didn't find the patient legally qualified medically. But conscientiously, religiously, or morally objecting nurses would have no such wiggle room.

The panel wants nurses to be allowed to kill. But since they wouldn't be the ones determining whether a patient was qualified legally for euthanasia, nurses would face the stark choice of administering the lethal injection when directed by a doctor, or being insubordinate and losing their livelihood. The same would no doubt apply to pharmacists who would concoct the death brew.

Not only that, but religious medical institutions will be required to permit euthanasia in their facilities if the panel has its way. This includes Catholic nursing homes if they receive government funding, which, I am told, is how Canada's system works. Again, from the report:

RECOMMENDATION 11 That the Government of Canada work with the provinces and territories to ensure that all publicly funded health care institutions provide medical assistance in dying.

Here's the bottom line: If the panel's recommendations are enacted, to practice medicine, nursing, pharmacy, or run a nursing home or hospice in Canada will require participation or complicity in the killing of sick, disabled, and mentally ill patients.


There's a word for that. Hint: It is the antithesis of liberty.

The case for design is as plain as nose on your face.

The Physics and Biology of Olfaction
Evolution News & Views March 1, 2016 3:26 AM 

If you've seen Living Waters, you were undoubtedly amazed at the complexity of operations going on inside a salmon's nose. Yet that animation vastly oversimplifies the olfactory sense. New findings continue to bring scientists closer to understanding how it works, adding to what we previously reported in September.

Last time we focused on the olfactory epithelium, the tissue that receives the odor molecules. We saw how it is organized into a hierarchical pattern that provides the best possible reception for different kinds of odorants. Each nostril's epithelium contains half a million olfactory sensory neurons (OSNs), long cells with cilia at one end and an axon at the other end. The cilia are where the odor molecules make contact with olfactory receptors (ORs). When a molecule "fits" just right, the receptor responds, triggering a cascade of activity. But what makes a good fit?

Vibrating Locks and Keys

There's been a lively debate about that. The leading view was that the molecule's shape fits the shape of the receptor like a "lock and key." In the 1990s, however, Luca Turin and others proposed a "vibrational" theory to account for shortcomings in the shape model. Why, for instance, do different shapes produce similar smell sensations in some cases, and similar shapes produce different sensations in others? Because the debate between the "shapists" and "vibrationists" has remained unsettled, the animators at Illustra alluded to both possibilities, showing the molecule fitting like a glove but also vibrating. (It's possible, too, that both theories are partly right.)

The vibration theory was thought to be down for the count last year when a team failed to find evidence for it in an experiment with mouse olfactory receptors in a petri dish. The receptors didn't react differently to two molecules with the same shape but different vibration frequencies. Now, though, the vibration theorists are back with a vengeance. John Hewitt tells about this at PhysOrg. A team from Italy, publishing in Scientific Reports, found evidence for discrimination between molecules with identical shapes but different vibrations. Four pairs of odorant molecules were carefully designed to be identical except that some hydrogen atoms were replaced with deuterium (heavy hydrogen, containing an extra neutron). The slight mass difference in these "isotopomers" ("same topology") alters the vibration frequency of the molecule. These same-shaped odorants were wafted into the noses of honeybees while the scientists monitored their brains in real time.

Sure enough, the bees appeared able to discriminate them, showing very different responses to the same-shaped pairs. "Considering the close structural correspondence between isotopomers," Hewitt writes, "the experimental truths observed here would be difficult for even the most ardent adherent to the shapist receptor philosophy to sweep under the rug." The implications are interesting for design theorists. Hewitt continues:

The authors observe that the shape-independent discrimination capabilities they found can not be dismissed as idiosyncratic to a few peculiar olfactory receptors, rather, they are a more general feature of ligand-receptor interaction. Much of the palpable in-house derision that members of the larger olfactory and neuroscience communities routine reserve for the vibrational theory might be traced to a deeper, more insidious fear: despite exhaustively focused efforts, they have no idea how receptors actually work. [Emphasis added.]

Hewitt sees a possible overarching principle at work in biological sensing. How did living things apply themselves to the task of "quickly (in evolutionary time) coming up with and artfully deploying 'universal detectors'" that are applied for diverse inputs, in everything from olfaction to vision to touch? Even the suntan response to UV light deploys this strategy. "Nature has unleashed her unbridled imagination," he quips -- and artfully so.

Score one for the vibrationists. The debate will continue, undoubtedly, but more to our interest, it illustrates the complexity of the olfactory sense and its extreme precision that has baffled scientists for decades. Imagine a honeybee, fruit fly, or salmon being able to discriminate twin molecules that differ only by one or two atomic mass units. Design doesn't get better than that.

Dynamic Switchboard

Meanwhile, a recent paper in Nature Communications takes us down the other end of the olfactory neuron to the tip of the axon. As shown in the Illustra animation, the nerve endings of a million OSNs converge on a remarkable organ, the olfactory bulb (OB), which is studded with connection points called glomeruli. In an amazing example of preprogrammed networking, these axons "know" during development somehow which glomerulus to attach to, depending on the type of odorant receptor they express (and there are hundreds of those). Axons for one receptor might grow toward a glomerulus on top of the bulb; axons for another to the backside. Between top-bottom, front-back, and left-right, the OB has three axes by which to discriminate connections coming from different classes of receptors. This is the first stage of sorting and classifying odorant types. (Note: it gets even more complicated from there.)

These scientists from the NIH and Carnegie Mellon University wanted to find out how malleable the olfactory inputs are. Once set up, is the olfactory tissue set for life? Can the olfactory bulb be rewired as conditions change or the fish grows older? When a new neuron replaces an old one, does it wire up the same way? The short answer is that rewiring is not only possible, but it occurs throughout adult life. Why might that be?

Incorporation of new neurons enables plasticity and repair of circuits in the adult brain. Adult neurogenesis is a key feature of the mammalian olfactory system, with new olfactory sensory neurons (OSNs) wiring into highly organized olfactory bulb (OB) circuits throughout life. However, neither when new postnatally generated OSNs first form synapses nor whether OSNs retain the capacity for synaptogenesis once mature, is known. Therefore, how integration of adult-born OSNs may contribute to lifelong OB plasticity is unclear. Here, we use a combination of electron microscopy, optogenetic activation and in vivo time-lapse imaging to show that newly generated OSNs form highly dynamic synapses and are capable of eliciting robust stimulus-locked firing of neurons in the mouse OB. Furthermore, we demonstrate that mature OSN axons undergo continuous activity-dependent synaptic remodelling that persists into adulthood. OSN synaptogenesis, therefore, provides a sustained potential for OB plasticity and repair that is much faster than OSN replacement alone.

Notice that reference to the "highly organized olfactory bulb circuits." Unlike Hewitt, who verged off into evolutionary speculations in his article after describing those "artfully deployed" sensors, these scientists didn't go the storytelling route. Their approach was to observe a phenomenon and find a purpose for it.

So what is the purpose of rapid structural remodelling of OSN synapses? Synapse turnover clearly plays an essential role during circuit formation (and in the case of the OB, incorporation of newborn neurons into existing circuits) by enabling selection, refinement and error correction. Hence, transient pre- or post-synaptic structures may represent those that fail to locate a synaptic partner, or form inappropriate connections that are rapidly eliminated. This may explain why immature OSN presynaptic terminals are formed and eliminated more rapidly than their mature counterparts (Figs 4, 5). Alternatively, these transient synaptic structures may represent short-lived synaptic contacts that temporarily contribute to network function, or play other roles such as promoting axon branch stabilization. Whatever the role of transient synaptic structures, ongoing synapse formation and elimination endows OB circuits with a plasticity potential that can be harnessed when needed, such as during learning or in response to altered experience.

That's the spirit. There must be a role, a purpose, a potential. At first, it would appear startling that so much rewiring takes place. What chip manufacturer would alter integrated circuits while they are in use? Maybe manufacturers could learn something from the way life does things.

Clearly a salmon is undergoing a lot of "learning" and "altered experience" as it grows from fingerling to adult, swimming downstream through a welter of new sensory experiences, memorizing hundreds of new odors and mapping them into its memory. It's possible that the brain and the olfactory bulb are triggering some of that rewiring in elaborate feedback loops, strengthening the connections to weak signals or reducing the connections to overpowering signals. It brings to mind a skilled technician on a sound board turning knobs and moving sliders to get the ideal overall experience in auditory space. In olfactory space, though, the salmon's sliders are automated. "Whatever the role" of these transient connections, we can infer from the results -- such as that a salmon can detect odorants at parts per trillion -- that they contribute to the spectacular performance of the olfactory system.

We've discussed "plasticity" before as a challenge to Darwinism. Why would a blind evolutionary process create "plasticity potential" that can be "harnessed when needed" in case of an altered experience? Darwinian evolution has no foresight. Plasticity makes perfect sense, though, from a design-based perspective on biology. There's no better example than right there in a salmon's nose, where the olfactory system will be encountering numerous new environments over a period of years. The scientists' expectations of roles for synaptic plasticity were confirmed in their conclusions (readers can find the details in the open-access paper).

One more thing. The scientists found that rewiring is "much faster" than replacement. While OSNs are replaced throughout life, the rewiring "plasticity potential" provides a more rapid response, giving the animal both high-speed (transient) and low-speed (permanent) fine tuning of its olfactory system. Since this is true of mice, it's undoubtedly true for us as well.


Now go out and smell the roses.

Homology vs. Darwin

The Types: Why Shared Characteristics Are Bad News for Darwinism
Michael Denton February 29, 2016 3:28 AM 

Editor's note: In his new book Evolution: Still a Theory in Crisis, Michael Denton not only updates the argument from his groundbreaking Evolution: A Theory in Crisis (1985) but also presents a powerful new critique of Darwinian evolution. This article is one in a series in which Dr. Denton summarizes some of the most important points of the new book. For the full story, get your copy of Evolution: Still a Theory in Crisis. For a limited time, you'll enjoy a 30 percent discount at  CreateSpace by using the discount code QBDHMYJH.

One of the major achievements of pre-Darwinian biology was the discovery that the living world is organized into a hierarchy of ever more inclusive classes or Types, each clearly defined by a unique homolog or suite of homologs possessed by all the members of the Type and which in many cases have remained invariant in divergent phylogenetic lines for tens or hundreds of millions of years.

Seeking an explanation for the distinctness of the Types and determining their ontological status was seen to be one of the major tasks of 19th-century biology. Virtually all pre-Darwinian biologists, and many after Darwin, saw the Types as immanent and invariant parts of the world-order, no less than crystals or atoms.

There is currently a widespread impression that pre-Darwinian biologists derived their discontinuous-typological conception of nature from all sorts of discredited metaphysical beliefs. This view has been severely criticized by recent researchers and shown to be largely a myth created by twentieth-century advocates of the neo-Darwinian evolutionary synthesis1 -- what Ron Amundson calls "Synthesis Historiography."2 As Amundson shows, whatever their metaphysical leaning, pre-Darwinian biologists did not derive their view of the Types as changeless components of the world order from any a priori metaphysics but from solid empirical observations.

The 19th-century structuralist conception of the Type, and of an ascending hierarchy of taxa or Types of ever-widening comprehensiveness as immanent features of nature, was close to the classic Aristotelian worldview. But it was based on the facts of biology, not on a philosophical a priori assumption -- Aristotelian, Platonic, or otherwise.

Today, 150 years after Darwin, Owen's "biological atoms" are as distinct as ever. The vast majority of all organisms can be assigned to unique classes based on their possession of particular defining homologs or novelties that are not led up to via Darwin's "innumerable transitional forms."

For readers subjected to popular and pervasive claims by evolutionary biologists that there are innumerable transitional forms of organisms, it might come as something of a surprise that there are unique taxon-defining novelties not led up to gradually from some antecedent form, and that remain invariant after their actualization for vast periods of time.

There is indeed something incongruous about the very notion of distinct taxa and genuine immutable "taxon-defining novelties" in the context of the functionalist Darwinian framework, which implies that all taxa-defining traits should be led up to via long series of adaptive transitional forms! On such a Darwinian model, taxa-defining novelties should not exist; neither should distinct Types in which all members possess unique defining novelties not shared by the members of any other taxa.

Let me reiterate: If evolution has occurred as conceived of by Darwin, invariant taxa-defining novelties, not led up to via long sequences of transitional forms from some antecedent structure, should not exist.

Ironically, it is only because organisms can be classified into distinct groups on the basis of their possession of invariant unique homologs that descent with modification can be inferred in the first place. If it was not for the invariance of the homologs and the Types they define, the common descent of all the members of a particular clade from a common ancestor would be in serious doubt. The living realm would conform to a chaotic network rather than an orderly branching tree.

Types are still as distinct today as they were for Richard Owen, Agassiz, and the other typologists and structuralists in the pre-Darwinian era and even for Darwin himself.3 They are still clearly defined by homologs or synapomorphies that are true evolutionary novelties without antecedent in earlier putative ancestral forms.

References:

(1) Mary Winsor, "The Creation of the Essentialism Story: An Exercise in Metahistory," History and Philosophy of the Life Sciences 28 (2006): 149-174.

(2) Amundson, The Changing Role of the Embryo in Evolutionary Thought, 11.


(3) Charles Darwin, Origin of Species, 6th ed. (London: John Murray 1872), 264 (Chapter 10): "The distinctness of specific forms, and their not being blended together by innumerable transitional links, is a very obvious difficulty."

Another failed Darwinian prediction X

Similar species share similar genes:

The only figure in Darwin’s book, The Origin of Species, showed how he envisioned species branching off of one another. Similar species have a relatively recent common ancestor and have had limited time to diverge from each other. This means that their genes should be similar. Entirely new genes, for instance, would not have enough time to evolve. As François Jacob explained in an influential paper from 1977, “The probability that a functional protein would appear de novo by random association of amino acids is practically zero.” (Jacob) Any newly created gene would have to arise from a duplication and modification of a pre-existing gene. (Zhou et. al.; Ohno) But such a new gene would retain significant similarity to its progenitor gene. Indeed, for decades evolutionists have cited minor genetic differences between similar species as a confirmation of this important prediction. (Berra, 20; Futuyma, 50; Johnson and Raven, 287; Jukes, 120; Mayr, 35)

But this prediction has been falsified as many unexpected genetic differences have been discovered amongst a wide range of allied species. (Pilcher) As much as a third of the genes in a given species may be unique, and even different variants within the same species have large numbers of genes unique to each variant. Different variants of the Escherichia coli bacteria, for instance, each have hundreds of unique genes. (Daubin and Ochman)

Significant genetic differences were also found between different fruit fly species. Thousands of genes showed up missing in many of the species, and some genes showed up in only a single species. (Levine et. al.) As one science writer put it, “an astonishing 12 per cent of recently evolved genes in fruit flies appear to have evolved from scratch.” (Le Page) These novel genes must have evolved over a few million years, a time period previously considered to allow only for minor genetic changes. (Begun et. al.; Chen et. al., 2007)

Initially some evolutionists thought these surprising results would be resolved when more genomes were analyzed. They predicted that similar copies of these genes would be found in other species. But instead each new genome has revealed yet more novel genes. (Curtis et. al.; Marsden et. al.; Pilcher)

Next evolutionists thought that these rapidly-evolving unique genes must not code for functional or important proteins. But again, many of the unique proteins were in fact found to play essential roles. (Chen, Zhang and Long 1010; Daubin and Ochman; Pilcher) As one researcher explained, “This goes against the textbooks, which say the genes encoding essential functions were created in ancient times.” (Pilcher)

References

Begun, D., H. Lindfors, A. Kern, C. Jones. 2007. “Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade.” Genetics 176:1131-1137.

Berra, Tim. 1990. Evolution and the Myth of Creationism. Stanford: Stanford University Press.

Chen, S., H. Cheng, D. Barbash, H. Yang. 2007. “Evolution of hydra, a recently evolved testis-expressed gene with nine alternative first exons in Drosophila melanogaster.” PLoS Genetics 3.

Chen, S., Y. Zhang, M. Long. 2010. “New Genes in Drosophila Quickly Become Essential.” Science 330:1682-1685.

Curtis, B., et. al. 2012. “Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs.” Nature 492:59-65.

Daubin, V., H. Ochman. 2004. “Bacterial genomes as new gene homes: The genealogy of ORFans in E. coli.” Genome Research 14:1036-1042.

Futuyma, Douglas. 1982. Science on Trial: The Case for Evolution. New York: Pantheon Books.

Jacob, François. 1977. “Evolution and tinkering.” Science 196:1161-1166.

Johnson, G., P. Raven. 2004. Biology. New York: Holt, Rinehart and Winston.

Jukes, Thomas. 1983. “Molecular evidence for evolution” in: Scientists Confront Creationism, ed. Laurie Godfrey. New York: W. W. Norton.

Le Page, M. 2008. “Recipes for life: How genes evolve.” New Scientist, November 24.

Levine, M., C. Jones, A. Kern, H. Lindfors, D. Begun. 2006. “Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression.” Proceedings of the National Academy of Sciences 103: 9935-9939.

Marsden, R. et. al. 2006. “Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.” Nucleic Acids Research 34:1066-1080.

Mayr, Ernst. 2001. What Evolution Is. New York: Basic Books.

Ohno, Susumu. 1970. Evolution by Gene Duplication. Heidelberg: Springer.

Pilcher, Helen. 2013. “All Alone.” NewScientist January 19.

Zhou, Q., G. Zhang, Y. Zhang, et. al. 2008. “On the origin of new genes in Drosophila.” Genome Research 18:1446-1455.

The first protein vs. Darwin

Yockey and a Calculator Versus Evolutionists

Zero Probability is Not a Problem

In a 1977 paper published in the Journal of Theoretical Biology, Hubert Yockey used information theory to evaluate the likelihood of the evolution of a relatively simple protein. Yockey’s model system was cytochrome c, a protein consisting of about one hundred amino acids. Cytochrome c plays an important role in the mitochondria’s electron transport chain (ETC) which helps to convert the chemical energy in carbon-carbon and carbon-hydrogen bonds, in the food we eat, to an electrochemical potential energy in the form of hydrogen ions (or protons) stored within the mitochondria’s inner membrane. Like water pressing against a dam and turning its turbines to generate electricity, the high-concentration hydrogen ions drive the ATP synthase “turbine” to create the high-energy ATP molecule. Like the electrical outlets in your house, the ATP molecule provides a standardized form of energy that is used for a wide range of applications in your body, such as muscle contraction and nerve signals. There is no scientific explanation for how the ETC evolved. There also is no scientific explanation for how a single protein, such as cytochrome c, evolved. Yockey explained this in 1977, and since then the problem has only gotten worse.

Given 20 different amino acids to choose from, then for a protein with a sequence of 101 amino acids, such as cytochrome c, there are 20 raised to the power of 101, or 20^101, different possible amino acid sequences. That represents an astronomically (and impossible) number of sequences for evolution to search through to find a functional cytochrome c protein.

The problem is more complicated than this, however, since the different amino acids are not equally likely and there are many different sequences that will form a functional cytochrome c protein.

Yockey accounts for these factors to determine the effective number of sequences evolution would have to search through to find cytochrome c. For instance, Yockey uses the known cytochrome c proteins at the time, from many different species, to get an idea of the different amino acids that are possible at each position, within the sequence of 101 residues. Some residues allow for quite a few different amino acids while others seem to be more stringent.

This approach is reasonable, but by no means the only way of estimating the number of different amino acid sequences that could work. One way or another, the bottom line is this: while the number of different sequences that could form a successful type of protein, such as cytochrome c, is a pretty big number, it doesn’t solve the problem.

Yockey found that the probability of evolution finding the cytochrome c protein sequence is about one in 10^64. That is a one followed by 64 zeros—an astronomically large number. He concluded in the peer-reviewed paper that the belief that proteins appeared spontaneously “is based on faith.”

Indeed, Yockey’s early findings are in line with, though a bit more conservative than, later findings. A 1990 study of a small, simple protein found that 10^63 attempts would be required for evolution to find the protein.

A 2004 study found that 10^64 to 10^77 attempts are required, and a 2006 study concluded that 10^70 attempts would be required.

These requirements dwarf the resources evolution has at its disposal. Even evolutionists have had to admit that evolution could only have a maximum of 10^43 such experiments. It is important to understand how tiny this number is compared to 10^70. 10^43 is not more than half of 10^70. It is not even close to half. 10^43 is an astronomically tiny sliver of 10^70.

Furthermore, the estimate of 10^43 is, itself, entirely unrealistic. For instance, it assumes the entire history of the Earth is available, rather than the limited time window that evolution actually would have had. And it assumes the pre existence of bacteria and, yes, proteins. In fact, the evolutionists assumed the earth was covered with bacteria, and each bacteria was full of proteins. That of course is not an appropriate assumption for the question of how proteins could have evolved in the first place. In fact, it is circular.

Of course the evolution of a single protein is only one of many problems for evolution. Consider, for example, the cellular apparatus that constructs proteins—the protein synthesis machinery. One paper used a back-of-the-envelope, simple and conservative calculation to show that the probability of such an apparatus evolving by chance is one in 10^1018. That’s a one followed by 1,018 zeros. Normally in science this would be considered far beyond impossible, so therefore evolutionists are considering an infinite universe, or multiverse, to solve the problem. In such a universe, it does not matter how improbable any event is, it will eventually occur:

Origin of life is a chicken and egg problem: for biological evolution that is governed, primarily, by natural selection, to take off, efficient systems for replication and translation are required, but even barebones cores of these systems appear to be products of extensive selection. The currently favored (partial) solution is an RNA world without proteins in which replication is catalyzed by ribozymes and which serves as the cradle for the translation system. However, the RNA world faces its own hard problems as ribozyme-catalyzed RNA replication remains a hypothesis and the selective pressures behind the origin of translation remain mysterious. Eternal inflation offers a viable alternative that is untenable in a finite universe … In an infinite universe (multiverse), emergence of highly complex systems by chance is inevitable. Therefore, under this cosmology, an entity as complex as a coupled translation-replication system should be considered a viable breakthrough stage for the onset of biological evolution.

There you have it. Probabilities don’t matter. You can point out how unlikely evolution is, and evolution remains a fact. Science is done by people, and people seek certain answers, regardless of the data.

Religion drives science, and it matters.

Posted by Cornelius Hunter 

Gilded smoke

Recession proof.

The invincible enemy?:A prequel

Extreme poverty the invincible enemy?

A clash of Titans X

Another failed Darwinian prediction IX

Biology is not lineage specific:

Evolution expects the species to fall into a common descent pattern. Therefore a particular lineage should not have highly differentiated, unique and complex designs, when compared to neighboring species. But this has been increasingly found to be the case, so much so that this pattern now has its own name—lineage-specific biology.

For example, transcription factors are proteins that bind to DNA and regulate which genes are expressed. Yet despite the importance of these proteins, their DNA binding sites vary dramatically across different species. As one report explained, “It was widely assumed that, like the sequences of the genes themselves, these transcription factor binding sites would be highly conserved throughout evolution. However, this turns out not to be the case in mammals.” (Rewiring of gene regulation across 300 million years of evolution) Evolutionists were surprised when transcription factor binding sites were found to be not conserved between mice and men, (Kunarso et. al.) between various other vertebrates, and even between different species of yeast. So now evolution is believed to have performed a massive, lineage-specific “rewiring” of cellular regulatory networks. (Pennacchio and Visel)

There are many more such examples of lineage-specific biology. Although flowers have four basic parts: sepals, petals, stamens and carpels, the daffodil’s trumpet is fundamentally different and must be an evolutionary “novelty.” (Oxford scientists say trumpets in daffodils are ‘new organ’) Out of the thousands of cockroach species, Saltoblattella montistabularis from South Africa is the only one that leaps. With its spring-loaded hind legs it accelerates at 23 g’s and out jumps even grass hoppers. (Picker, Colville and Burrows) An important immune system component, which is highly conserved across the vertebrates, is mysteriously absent in the Atlantic cod, Gadus morhua. (Star, et. al.) The brown algae, Ectocarpus siliculosus, has unique enzymes for biosynthesis and other tasks. (Cock) And the algae Bigelowiella natans has ten thousand unique genes and highly complex gene splicing machinery never before seen in a unicellular organism. It is, as one evolutionist explained, “unprecedented and truly remarkable for a unicellular organism.” (Tiny algae shed light on photosynthesis as a dynamic property)

Another fascinating example of lineage-specific biology are the many peculiar morphological and molecular novelties found in disparate, unrelated unicellular protists. As one study concluded, “Both euglenozoans and alveolates have a reputation for ‘doing things their own way,’ which is to say that they have developed seemingly unique ways to build important cellular structures or carry out molecular tasks critical for their survival. Why such hotspots for the evolution of novel solutions to problems should exist in the tree of life is not entirely clear.” (Lukes, Leander and Keeling, 2009a) Or as one evolutionist exclaimed, “this is totally crazy.” (Lukes, Leander and Keeling, 2009b)

References

Cock, J., et al. 2010. “The Ectocarpus genome and the independent evolution of multicellularity in brown algae.” Nature 465:617-621.

Kunarso G., et. al. 2010. “Transposable elements have rewired the core regulatory network of human embryonic stem cells.” Nature Genetics 42:631-634.

Lukes, J., B. Leander, P. Keeling. 2009. “Cascades of convergent evolution: the corresponding evolutionary histories of euglenozoans and dinoflagellates.” Proceedings of the National Academy of Sciences 106 Suppl 1:9963-9970.

Lukes, J., B. Leander, P. Keeling. 2009. “The corresponding evolutionary histories of euglenozoans and dinoflagellates: cascades of convergent evolution or accumulation of oddities?.” The National Academies. http://sackler.nasmediaonline.org/2009/darwin/julius_lukes/julius_lukes.html

“Oxford scientists say trumpets in daffodils are ‘new organ’.” 2011. BBC News February 28. http://www.bbc.co.uk/news/uk-england-oxfordshire-12598054

Pennacchio, L., A. Visel. 2010. “Limits of sequence and functional conservation.” Nature Genetics 42:557-558.

Picker, M., J. Colville, M. Burrows. 2012. “A cockroach that jumps.” Biology Letters 8:390-392.

“Rewiring of gene regulation across 300 million years of evolution.” 2010. ScienceDaily April 12. http://www.sciencedaily.com/releases/2010/04/100409093211.htm

Star, B., et. al. 2011. “The genome sequence of Atlantic cod reveals a unique immune system.” Nature 477:207–210.

“Tiny algae shed light on photosynthesis as a dynamic property.” 2012. ScienceDaily November 28. http://www.sciencedaily.com­ /releases/2012/11/121128132253.htm

Another failed Darwinian prediction VIII

Serological tests reveal evolutionary relationships:

Early in the twentieth century scientists studied blood immunity and how immune reaction could be used to compare species. The blood studies tended to produce results that parallel the more obvious indicators such as body plan. For example, humans were found to be more closely related to apes than to fish or rabbits. These findings were said to be strong confirmations of evolution. In 1923 H. H. Lane cited this evidence as supporting “the fact of evolution.” (Lane, 47) Later in the century these findings continued to be cited in support of evolution. (Berra, 19; Dodson and Dodson, 65)

But even by mid century contradictions to evolutionary expectations were becoming obvious in serological tests. As J.B.S.Haldane explained in 1949, “Now every species of mammal and bird so far investigated has shown quite a surprising biochemical diversity by serological tests. The antigens concerned seem to be proteins to which polysaccharides are attached.” (quoted in Gagneux and Varki)

Indeed these polysaccharides, or glycans, did not fulfill evolutionary expectations. As one paper explained, glycans show “remarkably discontinuous distribution across evolutionary lineages,” for they “occur in a discontinuous and puzzling distribution across evolutionary lineages.” (Bishop and Gagneux) These glycans can be (i) specific to a particular lineage, (i) similar in very distant lineages, (iii) and conspicuously absent from very restricted taxa only.

Here is how another paper described glycan findings: “There is also no clear explanation for the extreme complexity and diversity of glycans that can be found on a given glycoconjugate or cell type. Based on the limited information available about the scope and distribution of this diversity among taxonomic groups, it is difficult to see clear trends or patterns consistent with different evolutionary lineages.” (Gagneux and Varki)

References

Berra, Tim. 1990. Evolution and the Myth of Creationism. Stanford: Stanford University Press.

Bishop J., P. Gagneux. 2007. “Evolution of carbohydrate antigens--microbial forces shaping host glycomes?.” Glycobiology 17:23R-34R.

Dodson, Edward, Peter Dodson. 1976. Evolution: Process and Product. New York: D. Van Nostrand Company.

Gagneux, P., A. Varki. 1999. “Evolutionary considerations in relating oligosaccharide diversity to biological function.” Glycobiology 9:747-755.

Lane, H. 1923. Evolution and Christian Faith. Princeton: Princeton University Press.

On the limits of intelligent design theory

Good Questions on the Nature of Intelligent Design
Ann Gauger February 25, 2016 6:01 AM

Earlier, Evolution News responded helpfully to a question from an email correspondent. Here are more questions and answers. A reader writes with a few good queries on the nature of ID theory.

Question:

On the complexity and specificity arguments, I've read that there are two arguments used as evidence for a designer's existence. However, do such arguments entail that the designer is still intervening in the ongoing development of the universe and of life within it? Or does ID only state that there was a designer at least at the very beginning, and ID as a theory does not categorically state (or necessarily entail) that this designer is still interested in making changes? Thus, are the complexity and specificity arguments examples rather than actual requirements?

Answer: ID is about design detection, and makes no statements about ongoing design or a design mechanism. We simply say that there are elements in the universe that give evidence of being designed. Anything further goes beyond what we can say. For example, we can say nothing about how (by what mechanism) design is instantiated. As for specified complexity and irreducible complexity, they are methods of design detection. I see irreducible complexity as a special case of specified complexity. There are probably other valid arguments for design, such as the fact that the universe is intelligible to us when there is no logical requirement that it be so.

Question:

Does ID associate any particular attributes with this "designer"? I am aware that various prominent ID proponents have said, on different occasions, yes and no -- and I do see a difference between a) ID theory itself, and b) personal opinion on aspects of the theory. The first is a necessary contingent on the theory itself. The second is not. My analogy for this is -- Christians believe certain things. Catholics accept the main Christian belief, plus a few other things.

Answer: ID posits nothing about the attributes of this designer, other than the fact that the designer must be capable of carrying out design at the appropriate scale. Anything more is personal opinion. As one leading ID scientist has written:

I myself do believe in a benevolent God, and I recognize that philosophy and theology may be able to extend the argument. But a scientific argument for design in biology does not reach that far. Thus while I argue for design, the question of the identity of the designer is left open. Possible candidates for the role of designer include: the God of Christianity; an angel -- fallen or not; Plato's demiurge; some mystical New Age force; space aliens from Alpha Centauri; time travelers; or some utterly unknown intelligent being. Of course, some of these possibilities may seem more plausible than others based on information from fields other than science. Nonetheless, as regards the identity of the designer, modern ID theory happily echoes Isaac Newton's phrase "Hypothesis non fingo"(I make no hypothesis).

(Michael Behe, "The Modern Intelligent Design Hypothesis," Philosophia Christi, Series 2, Vol. 3, No. 1 (2001), pg. 165)

Question:

Inherent in ID theory, is there the idea that there was purpose in the design? And, if so, what specific purposes?

Answer: ID also does not say anything about purpose, aside from the fact that things, especially biological things, look like they were made to carry out some particular function. They work together as a whole to make a functional organism. That functional organism is part of an ecosystem, and contributes to the functioning of that system. But is there an overall purpose to that system? To make a biosphere? This can be pushed out only so far; as to the reason for the existence of all of this -- why there should be such a planet, or the reason for our existence on the planet -- that goes beyond what ID can say. Final ends belong in the realms of philosophy and theology.

Question:

A personal question regarding how the ID debate has been fought. Why oh why was it based on biology??? IMHO, that was a terrible starting point! I would suggest later iterations and discussions focus on even more fundamental aspects of the universe. Time (apparently) is constant and measurable (not random and chaotic); the universal constant is just that -- a constant -- and without such a very, very limited range of variation, we could not exist (at least, not as we do now). Mathematics works -- again, in my thinking, a sign that this universe is rational; and if rational, designed (rationality and order from chaos...???). I know Plato et al. discussed this, but it seems to have been ignored in the ID debate. As I hope I have clearly indicated, I'm after answers that clearly differentiate ID as a theory in general from any personal takes on it (e.g., characteristics of the designer).

Answer: ID is not based purely on biology, though it may appear to be sometimes. The extreme fine-tuning of the universe for life; the fact that mathematics is rational and elegant, and fits the needs of science; the fact that chemistry is ordered so as to make its discovery possible, and that the planet is ordered so as to permit intelligent life to discover science at all (see The Privileged Planet) -- all these are arguments for design, design that is detectable by minds such as ours. I suggest reading A Meaningful World, by Benjamin Wiker and Jonathan Witt.

The reason it often appears that the argument is all about biology is because it is from there that the majority of pushback comes.


Thanks for your questions, and I hope my response helps.