Another failed Darwinian prediction XIII

Gene and host phylogenies are congruent

Evolution predicts that genetic change drives evolutionary change. Genetic changes that confer improved fitness are more likely to be selected and passed on. All of this means that evolutionary trees based on comparisons of genes should be similar, or congruent, with evolutionary trees based on comparisons of the entire species. Simply put, gene trees and species trees should be congruent. But while this has often been claimed to be a successful prediction, it is now known to be false. As one study explained, “Perhaps most unexpected of all is the substantial decoupling, now known in most, although not all, branches of organismal life, between the phylogenetic histories of individual gene families and what has generally been accepted to be the history of genomes and/or their cellular or organismal host lineages.” (Ragan, McInerney and Lake)   The molecular and the visible (morphological) features often indicate “strikingly different” evolutionary trees that cannot be explained as due to different methods being used. (Lockhart and Cameron) Making sense of these differences between the molecular and the morphological features has become a major task, (Gura) so common that it now has its own name: reconciliation. (Stolzer, et. al.)   The growing gap between molecular analyses and the fossil record, concluded one researcher, “is astounding.” (Feduccia) Instead of a single evolutionary tree emerging from the data, there is a wealth of competing evolutionary trees. (de Jong) And while the inconsistencies between molecular and fossil data were, if anything, expected to be worse with the more ancient, lower, parts of the evolutionary tree, the opposite pattern is observed. As one study explained, “discord between molecular divergence estimates and the fossil record is pervasive across clades and of consistently higher magnitude for younger clades.” (Ksepka, Ware and Lamm)   One interesting example is the Orangutans which share many similarities with humans. These “people of the forest,” as they have been called, have more in common with humans than do the other great apes. This includes features of anatomy, reproductive biology and behavior. But there is one feature in which orangutans are not the closest species to humans: the genome. The chimpanzee has the closest genome to the human genome, so it is thought to be our closest relative. The molecular and morphological comparisons point to incongruent phylogenies. As one paper concluded:   There remains, however, a paradoxical problem lurking within the wealth of DNA data: our morphology and physiology have very little, if anything, uniquely in common with chimpanzees to corroborate a unique common ancestor. Most of the characters we do share with chimpanzees also occur in other primates, and in sexual biology and reproduction we could hardly be more different. It would be an understatement to think of this as an evolutionary puzzle. (Grehan)   If it weren’t for DNA, it would be the orangutan rather than the chimp pictured next to the human in the evolutionary tree.   References   de Jong, W. 1998. “Molecules remodel the mammalian tree.”Trends in Ecology & Evolution, 13:270-275.   Feduccia, A. 2003. “‘Big bang’ for tertiary birds?.” Trends in Ecology & Evolution 18:175.   Gura, T. 2000. “Bones, molecules...or both?.” Nature 406:230-233.   Grehan J. 2006. “Mona Lisa smile: the morphological enigma of human and great ape evolution.” The Anatomical Record Part B: The New Anatomist 289B:139-157.   Ksepka, D. T., J. L. Ware, K. S. Lamm. 2014. “Flying rocks and flying clocks: disparity in fossil and molecular dates for birds.” Proceedings of the Royal Society B 281: 20140677.   Lockhart, P., S. Cameron. 2001 “Trees for bees.” Trends in Ecology and Evolution 16:84-88.   Ragan, M., J. McInerney, J. Lake. 2009. “The network of life: genome beginnings and evolution.” Philosophical Transactions of the Royal Society B 364:2169-2175. Stolzer, M., et. al. 2012. “Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees.” Bioinformatics 28 ECCB:i409–i415.

On newly discovered Japanese plant species' surprising survival strategy.

New underground plant hides from the sun and parasitises fungi:

It’s a low-down, dirty cheat. A newly discovered Japanese plant spends most of its life hidden underground and steals nutrients from fungi rather than getting its energy from the sun.

Kenji Suetsugu of Kobe University came across the previously unknown plant in an evergreen forest on the subtropical Japanese island of Yakushima while documenting other fungi-parasitising – mycoheterotrophic – plants in Japan.

The plant’s stem is about 3-9 centimetres long and has between nine and 15 purple star-shaped flowers, which push up above the ground. Suetsugu has named it Sciaphila yakushimensis after the island.

The plant can’t photosynthesise and, like other mycoheterotrophs, steals the carbon it needs from a fungal host. The parasitic plant attracts strands of mycorrhizal fungus into its many hairy roots and then feeds off fungus growing inside the roots.

Life in the dark
Its parasitic lifestyle is an adaptation to the forest understorey, where the sun’s rays struggle to penetrate and so photosynthetic plants are rare, says Suetsugu.

Because it doesn’t rely on photosynthesising the sun’s light for its energy, it can stay underground, reducing the risk of being eaten by aboveground herbivores. It only pokes through the leaf litter to flower and fruit.

Vast fungal networks in the forest soil are linked up with plant roots and usually get their carbon from trees, in exchange for water and minerals that their tiny hairs extract from soil.

But mycoheterotrophs taps into this network and get the carbon from fungi, which got it from other plants to start with.

“These mycoheterotrophs are extremely rare and could not survive without a flourishing forest, sustained by species-rich underground fungal networks,” says Suetsugu.

Rare but not protected
Given that it only seems to have two small populations, the new species can be considered critically endangered, Suetsugu says. Other mycoheterotrophic plant species have recently been found in the area, but many are not yet officially protected.

Such plants are dependent on their host fungi, so Suetsugu says it will be necessary to conserve entire ecosystems to protect these rare plants. He recommends that regulators should restrict logging and construction to preserve these and other endemic species in the forest habitats of Yakushima.

Constantijn Mennes at the Naturalis Biodiversity Center in Leiden, the Netherlands, says there is still a substantial amount of undescribed biodiversity, even in flowering plants.

“This observation adds to a large list of critically endangered mycoheterotrophic species, like species of Kupea and Kihansia in Africa,” he says.


Journal reference: Journal of Japanese Botany, Vol. 91 No. 1

On theistic naturalism's false dichotomy

The False Dichotomy Between Intelligent Design and Natural Causes
Casey Luskin 

In a previous article in this series, we saw that a self-described theistic evolutionist had left the BioLogos camp because he was concerned about the way BioLogos writers treat Darwin-critics:
I have got used to the vituperative and often incoherent level of discussion about faith and evolution in the last year or so. Generally speaking, as one would now expect, Gnus attempting to savage anything they can identify as a theist are the greatest offenders. But on BioLogos, a frighteningly similar kind of abuse, if usually expressed with more gentility, is directed not back at non-theists, nor even YECs, but at ID sympathisers....I think I can draw two tentative conclusions about the reasons for this degree of passion, which is clearly far more than an opinion that ID arguments are wrong. In my opinion, although BioLogos is quite a diverse forum, its "ruling spirit" is fundamentally committed to (a) methodological naturalism and (b) theological naturalism.
How does the "theological naturalism" of BioLogos influence its perspective on intelligent design (ID)? Unfortunately, for one, it seems to lead some ID-critics to wrongly think that ID denies that God can use natural causes.

For example, in his series on "Evolution and the Origin of Biological Information," Dennis Venema sets up a false dichotomy between intelligent design (ID) and natural causes, wrongly claiming ID that creates a "'natural versus God' dichotomy" or alternatively claiming that ID tries to "eliminate the possibility of divine action" when "we use science to understand natural cause and effect." Venema also states:
[D]escribing how specified information can arise through natural means does not in any way imply God's absence from the process. After all, natural processes are equally a manifestation of God's activity as what one would call supernatural events. So-called "natural" laws are what Christians understand to be a description of the ongoing, regular and repeatable activity of God. As such, the dichotomy presented in ID writings of "naturalism" versus theism is a false one: is not God the Author of nature, after all?
While defending naturalism, Venema has badly misstated the claims of ID: there is no false dichotomy in intelligent design that says God is never allowed to use natural causes. The only party who's setting up a false dichotomy here is Dennis Venema, in suggesting that if one accepts ID then God is no longer allowed to use "natural laws." 

Venema seeks to paint ID as bad theology which somehow denies that God is the author of all nature when God uses secondary material or "natural" causes. ID is a scientific theory and doesn't make such theological claims. Thus, as a science, ID never claims that if we observe the "ongoing, regular and repeatable activity" of "natural laws" then somehow God is absent from the process.

ID proponents who believe in God never deny that God can use secondary material "natural" causes to achieve his will. In those instances, ID would simply say that material causes are the best explanation. ID does not "eliminate the possibility of divine action" when "we use science to understand natural cause and effect." To wit: ID proponents have often inferred design from the fine-tuning of the laws that govern the universe and make it friendly for life. Indeed, this is an area where BioLogos supposedly agrees with intelligent design. In any event, Venema's description of ID is backwards: in contexts of physics and cosmology, the actions of natural laws themselves can trigger a design inference.

Remember, ID is a cautious scientific theory and not a theological doctrine. When ID theorists look for scientifically detectable design at the biological level, they often treat natural causes as background. So the biological design that's detected normally involves features that (1) go well beyond the capacities of natural causes, and (2) exhibit telltale signs of intelligent agency (such as being the product of foresight). On the other hand, when ID infers a natural cause, pro-ID theists would simply say God used a natural cause, and would not say that God is somehow "absent."

All theists who support ID affirm that God is behind, in some sense, every event. "Natural cause" never means (for theists anyway) "not caused by God." I'm not aware of any ID theorist who is also a theist who has ever claimed otherwise.

This leads us to the question, why does ID critique theistic naturalism, and how does ID contrast with theistic evolution?

Theistic naturalism isn't merely the view that God at times (or even most of the time) works through natural causes. Rather, it is the view that assumes that God must only use natural causes and is never allowed to work in other ways that might break the "ongoing, regular and repeatable activity" of "natural laws." 

ID rejects such assumption-based views. ID is entirely compatible with the view that God at times (or even most of the time) works through natural causes. But ID isn't precommitted to answers about how God must have acted, and leaves open the possibility that sometimes God doesn't use "natural" causes. ID simply wants to follow the evidence where it leads. 

Thus, theistic naturalism is the wholesale assumption that if God exists, He must always use secondary material causes, and is never allowed to act in nature in a scientifically detectable way. The reason ID proponents critique naturalism is because it tends to presuppose materialistic answers to all questions about how life arose and diversified.

There are thus two potential extreme positions in this debate: (A) Everything is detectably designed and God never uses natural causes, or (B) Nothing is detectably designed and God always uses natural causes. 

Ironically, though ID critics (wrongly) accuse ID proponents of adopting extreme position (A), it is ID-critics themselves, including many theistic evolutionist proponents of theistic naturalism, who seem to adopt extreme position (B). This makes for bad science because it presupposes the scientific answers, and bad theology because it tries to dictate to God what He ought to do. 


In contrast, ID rejects both extreme positions, and uses this motto: let's not presuppose answers, but let's follow the evidence where it leads.

From the Cambrian era,further reason to doubt Darwin.

From the Cambrian Explosion, a Remarkably Preserved Image of a Nervous System
David Klinghoffer March 2, 2016 3:54 AM

Quite beautiful, isn't it? Like a dragon float from a Chinese New Year parade. The Washington Post calls it an "ugly arthropod." Are they blind?

News from Cambridge University of an unprecedented Cambrian find from, in fact, China:

A 520 million-year-old fossilised nervous system -- so well-preserved that individually fossilised nerves are visible -- is the most complete and best example yet found, and could help unravel how the nervous system evolved in early animals.

How did this arthropod's nervous system "evolve"? Suddenly, it seems, all but out of a clear blue sky, as far as we have any reason to say. What's striking about the new images of Chengjiangocaris kunmingensisis, a product of the Cambrian explosion, is the remarkable detail preserved from soft tissue. The difficulty of preserving soft tissue was once given as a reason that the Cambrian animals' precursors seem not appear in the fossil record.

At some earlier stage of life's history, these features were not there -- then they were. This is said to help "unravel" the mystery of evolution. More:

Researchers have found one of the oldest and most detailed fossils of the central nervous system yet identified, from a crustacean-like animal that lived more than 500 million years ago. The fossil, from southern China, has been so well preserved that individual nerves are visible, the first time this level of detail has been observed in a fossil of this age.

The findings, published in the Proceedings of the National Academy of Sciences, are helping researchers understand how the nervous system of arthropods -- creepy crawlies with jointed legs -- evolved. Finding any fossilised soft tissue is rare, but this particular find, by researchers in the UK, China and Germany, represents the most detailed example of a preserved nervous system yet discovered.

Again, the question of what this means for evolution:

For [Javier Ortega-Hernández, of the University of Cambridge's Department of Zoology,] and his colleagues, a key question is what this discovery tells us about the evolution of early animals, since the nervous system contains so much information. Further analysis revealed that some aspects of the nervous system in C. kunmingensis appear to be structured similar to that of modern priapulids (penis worms) and onychophorans (velvet worms), with regularly-spaced nerves coming out from the ventral nerve cord.

In contrast, these dozens of nerves have been lost independently in the tardigrades (water bears) and modern arthropods, suggesting that simplification played an important role in the evolution of the nervous system.


The nervous system is information rich, and "these dozens of nerves" were lost by tardigrades and today's arthropods. These latter creatures evolved in part by losing information, not gaining it -- becoming simpler, not more complex. So where did the information come from in the first place? They don't say. They can't say.

Darwinism vs. the real world XXXII

Absorbing and Storing Energy: How the Body Controls Glucose
Howard Glicksman March 2, 2016 4:44 PM 


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


Just like a car needs the energy, in the form of gasoline, to run properly, the body needs the energy in glucose to survive. When we haven't eaten for a while, our blood glucose level drops and our stomach is empty, causing the hunger center in our brain to tell us to eat or drink something with calories. As I have explained in my last couple of articles, the complex molecules that are in what we eat and drink enter the gastrointestinal system, where digestive enzymes break them down into simpler molecules so the body can absorb them. Carbohydrates are broken down into simple sugars, like glucose, which are then absorbed into the blood. Tissues, such as the brain and other organs, rapidly absorb some of this glucose, to be used for their immediate energy needs.

However, the amount of glucose absorbed after a meal is usually much more than what the tissues can use right away, causing excess. The body is able to chemically link these excess glucose molecules together to form a carbohydrate called glycogen. Most of the glycogen in the body is made and stored in the liver, with smaller amounts in the muscles, kidneys, and other tissues. Once the liver and other tissues have filled up their glycogen stores, any excess glucose is stored as fat, apparently without limit. These tissues can use this stored energy in between meals, during exercise, and fasting overnight, when there aren't any new supplies of glucose coming into the body. However, the brain cannot store glucose and is mostly dependent on the glucose in the blood for all of its energy needs.

One way the body makes sure the brain receives enough glucose during fasting is to have the liver release glucose from its glycogen stores into circulation. The liver has the capacity to store enough glucose to meet all of the body's energy needs for about 24 hours. In addition, when necessary, the liver can take certain proteins and fats and convert them into glucose and other molecules, called ketones, that the brain can use for energy as well. This is partly why we don't have to eat food as often as we have to breathe or drink water. But clinical experience teaches that not just any blood level of glucose will do for human survival. Real numbers have real consequences and the brain always needs a certain amount of glucose. Even though the body may be physically at rest, the brain is always working hard. It must keep us awake, monitor what's going on inside and around us, and control vital functions like breathing and circulation.

Between meals, the blood glucose level usually runs between 70-90 units. Several hours after we eat, when the blood glucose level starts to drop towards 70 units, our hunger center warns us to eat something. If the blood glucose drops below 50 units, symptoms of brain malfunction, like weakness, dizziness, and problems with concentration occur. If it drops below 40 units, you'll probably start experiencing problems speaking, confusion, and drowsiness. Below 30 units, seizures and coma result, and below 20 units, brain death is certain. Being able to control the blood glucose is important for human survival and it doesn't just happen because we eat and drink things that have sugar in them. It requires the body to know when to store glucose and when to release it so the brain is always receiving what it needs. Here's how the body does it.

As we've seen in this series, the first thing you need to take control is a sensor that can detect what needs to be controlled. The pancreas is not only an exocrine gland that, as noted in the previous articles, sends fluid containing various chemicals and enzymes into the intestine to help digest food. It is also an endocrine gland that sends hormones into the blood to help control the blood glucose. Scattered throughout the pancreas are small clumps of cells that make up what is called the islets of Langerhanswhich perform this endocrine function. These cells have glucosensors,allowing them to detect the blood level of glucose.

The second thing you need to take control is something to integrate the data, decide what needs to be done, and then send out a message. There are two different types of gland cells in the islets of Langerhans that together control the blood glucose. One is the beta cell,which sends out a hormone called insulin,made up of 51 amino acids joined together in a specific order. After a meal, the more the blood glucose rises above 70 units (it normally peaks at about 110 units), the more insulin the beta cells release into the blood. However, several hours after eating, as the blood glucose drops toward 70 units and below, the beta cells reduce the levels of insulin they send out. The other cell is the alpha cell, which sends out a hormone called glucagon,made up of 29 amino acids joined together in a specific order. Several hours after a meal, when the blood glucose drops toward 70 units and below, the more glucagon the alpha cells send out and after a meal, the more the blood glucose rises above 70 units, the less glucagon the alpha cells send out.

As you can see, both the beta and alpha cells have glucosensors, but they respond to changes in blood glucose in opposite ways. Normally, the higher the blood glucose rises above 70 units, the more insulin the beta cells send out and the less glucagon the alpha cells send out. And when the blood glucose drops toward 70 units and below, the less insulin the beta cells send out and the more glucagon the alpha cells send out.

The third thing you need to take control is an effector that can do something about the situation. After a meal, the blood glucose rises because the amount of glucose brought into the blood is more than what the body can use right away. As noted above, the beta cells react to this rise in blood glucose by sending out more insulin. Insulin travels in the blood and locks onto specific receptors within target organs, especially the liver, and tells them to absorb glucose for energy and store what is left over. In general, insulin is an anabolic hormone, e.g. it promotes the formation of more complex molecules from simpler ones. Not only does insulin promote the formation of glycogen from glucose in the liver and muscles, it also tells some cells to take in amino acids to form proteins and others to take in fatty acids to form fats. In other words, insulin tells the body "We've just been fed and we've got more than we need right now. Store up the excess for later use."

In contrast, several hours after a meal, the blood glucose falls as the body takes glucose out of the blood and uses it for its energy needs without new supplies coming in through the gastrointestinal system. As I noted, the alpha cells react to this drop in blood glucose by sending out more glucagon. Glucagon travels in the blood where it locks onto specific receptors on target cells, mainly in the liver, and tells them to release the glucose from within glycogen and other forms of stored energy. In general, glucagon is a catabolic hormone, which promotes the breakdown of more complex molecules into simpler ones. Not only does glucagon cause glucose to be released from the glycogen stores, it also tells cells to break down certain proteins and fats into glucose and ketones, so the brain can be use them for energy. In other words, glucagon tells the body "We haven't been fed for a while. Release the energy we stored up before."

Once again, you can see that insulin and glucagon order the liver and other cells to do things that are opposed to each other. Insulin tells the body when it is fed and must take glucose out of the blood and store it in the liver and fat cells for later use. Glucagon tells the body when it is in starvation mode and must release glucose and other chemicals from the liver and fat cells into the blood so the brain will have enough energy. It is important to note that due to the breakdown by enzymes, the metabolic effect of a given amount of insulin or glucagon only lasts a few minutes and along with the ratio of insulin and glucagon this allows for moment-to-moment blood glucose control within the body.

There are twenty different amino acids that make up the proteins in the body. Since insulin consists of 51, and glucagon, 29 amino acids arranged in a specific order, this means that the chances of one molecule of each of them coming into being at random is one in 1066 for insulin and one in 1038 for glucagon. It was this extremely high improbability of any one of the thousands of biologically significant molecules, such as insulin and glucagon, being formed by chance and the laws of nature, which alerted scientists that the cells must have an intelligent agent telling them how to make them.

This is what first motivated scientists to search for and find the DNA molecule. However, paradoxically, evolutionary biologists see all of the information packed into the DNA molecule and still conclude that it all came about by chance and the laws of nature alone rather than through a mind at work. In other words, scientists, using their ability to detect intelligence, recognized that there had to be an intelligent agent inside the cell instructing it on how and when to produce these complex and vital molecules, but after finding it, concluded that this intelligent agent itself had come about by chance and the laws of nature alone.

Alternatively, many people now believe nature itself was the intelligent agent that, through evolution, brought about DNA and all of the innovations needed for life, because that was what was needed. They seem to forget that, by definition, evolution, as defined by its modern Darwinist proponents, is a blind process that has no goals.

By taking control to follow the rules,the system the body uses to control its blood glucose, involving insulin and glucagon, seems to know what it's doing. But, as noted above, regarding having too low of a blood sugar, real numbers have real consequences. Next time, we'll look at what can take place when the system isn't working right and the body experiences too high a level of blood sugar instead.

What might education over indoctrination look like?

Picture This: What Teaching the Controversy over Evolution Looks Like in the Classroom
Sarah Chaffee March 4, 2016 3:22 AM 

According to Nature and Scientific American, "[S]tudents gain a much deeper understanding of science when they actively grapple with questions than when they passively listen to answers." In Nature, Jay Labov, a senior education advisor for the U.S. National Academy of Sciences, described active engagement as "learning content not as something you memorize and regurgitate, but as raw material for making connections, drawing inferences, creating new information -- learning how to learn."

Discovery Institute advocates "teaching the controversy" over evolution. But in practice what should that look like?

In general terms, as I wrote to a parent recently, we recommend that students learn more about evolution, not less, and critically evaluate both the scientific strengths and weaknesses of the theory.

Our Science Education Policy states:

Instead of mandating intelligent design, Discovery Institute seeks to increase the coverage of evolution in textbooks. It believes that evolution should be fully and completely presented to students, and they should learn more about evolutionary theory, including its unresolved issues. In other words, evolution should be taught as a scientific theory that is open to critical scrutiny, not as a sacred dogma that can't be questioned.

Discovery Institute believes that a curriculum that aims to provide students with an understanding of the strengths and weaknesses of neo-Darwinian and chemical evolutionary theories (rather than teaching an alternative theory, such as intelligent design) represents a common ground approach that all reasonable citizens can agree on.

We would normally recommend that teachers cover this material in whatever grade the curriculum covers evolution. Typically, the most extended discussions of neo-Darwinism come in high school biology courses. From our Educators' Briefing Packet:

Suggested Plan for Teaching Unit on Neo-Darwinian Evolution

Objectivity also means that students must be allowed to form and express their own opinions. An objective unit covering neo-Darwinian evolution might look something like this:

First, cover the required curriculum by teaching the material in the textbook. Ensure that students understand the scientific arguments for neo-Darwinian evolution. (1-2 weeks)

Next, spend a few days discussing scientific criticisms of neo-Darwinian evolution. The DVD Investigating Evolution, the DVD Icons of Evolution, and the Icons of Evolution Study Guide are potential resources. Encourage students to think critically. (2-3 days)

Finally, consider allowing students to spend a couple days wrestling with the data and forming their own opinions. This could include in-class debates, or an assignment where students write a position statement on neo-Darwinian evolution. In these exercises, students may defend whatever position they wish, but must justify it using only scientific evidence and scientific arguments. (1-2 days)

Most public school curricula stop after step 1, missing out on the benefits from steps 2 and 3.

Some might claim those extra steps would take too much time. But teaching the modern neo-Darwinian theory of evolution in an objective fashion need not take any more time than the 2-3 weeks typically spent on an evolution unit.

More importantly, any extra time taken to teach this topic objectively is not wasted -- it will help students better understand the evidence, better appreciate scientific reasoning, and fulfill standards requiring critical thinking and use of the inquiry method. Finally, this approach will be welcomed by students who find this topic engages their interest in science.

There are several areas in which teachers can engage students with this fascinating scientific controversy.

First, one may cover the primary mechanism of evolution -- natural selection acting on random mutations. Does the evidence demonstrate that this mechanism is able to account for the complexity of life? Most biology textbooks claim that it does, but many scientists disagree. Over 950 PhD scientists have signed a Dissent from Darwinism list agreeing they are "skeptical of claims for the ability of random mutations and natural selection to account for the complexity of life." Common textbook examples of natural selection like the changes within the Galápagos finches or the peppered moth, or antibiotic resistance, demonstrate only small-scale evolution. They do not show how new species emerge.

Second, a teacher may discuss the concept of universal common ancestry -- helping students to analyze whether vertebrate embryos are or are not similar in their earliest stages, whether the fossil record shows intermediate links, and whether DNA evidence points to a grand "tree of life."

Third, a teacher could address chemical evolution. A teacher could ask the question, "Has science come up with a plausible explanation for the origin of the first life?" While few textbooks will admit that no such answer exists, leading biologists like Eugene Koonin have stated, among other things, that "the origin of life field is a failure -- we still do not have even a plausible coherent model, let alone a validated scenario, for the emergence of life on Earth."

An instructor using the 2014 Miller-Levine biology textbook would cover the Galápagos finches as evidence for natural selection. After completing the unit on evolution, she could show the class the section of the DVD Investigating Evolution on the Galápagos finches, presenting a different view. Finally, students could be asked to form their own opinions on the Galápagos finches and their significance for natural selection.

As our factsheet "Tips for Teaching Evolution Objectively" notes:

Teachers who personally support the standard neo-Darwinian view should not refuse to cover scientific criticisms of that position. In fact, what the teacher personally thinks doesn't matter. If taught properly, students may not even know exactly where the teacher stands on this topic.

Nothing above references intelligent design or creationism. This is purely a discussion of the theory of evolution -- its scientific strengths, presented in mainstream textbooks, and objections raised in recent scientific research.

This kind of objective science instruction paves the way for high-level learning. And it's time for a change. Carl Wieman, a physicist at Stanford who won the 2001 Nobel Prize in his field, began advocating for science education reform after interacting with newly graduated scientists who "had done really well as undergraduates, but couldn't do research." Today, along with prominent journals such as Nature, Scientific American, and Science, he promotes active engagement in the classroom.

Nature concludes its keynote editorial, "But change is essential.... In an era when more of us now work with our heads, rather than our hands, the world can no longer afford to support poor learning systems that allow too few people to achieve their goals."


These advocates of critical thinking in science education are right. Unfortunately, most of them probably don't apply their advice to the teaching of Darwinian evolution. They should reconsider.

On Christ's redeeming sacrifice:A commentary by the Watchtower society

How Is Jesus’ Sacrifice “a Ransom for Many”?:

The Bible’s answer:

Jesus’ sacrifice is the means by which God delivers, or saves, humankind from sin and death. The Bible refers to the shed blood of Jesus as a ransom price. (Ephesians 1:7; 1 Peter 1:18, 19) Thus, Jesus said that he came “to give his life a ransom for many.”—Matthew 20:28, King James Version.

Why was “a ransom for many” needed?:

The first man, Adam, was created perfect, or without sin. He had the prospect of living forever but lost it by choosing to disobey God. (Genesis 3:17-19) When he had children, he passed on to them the defect of sin. (Romans 5:12) For this reason, the Bible indicates that Adam “sold” himself and his children into slavery to sin and death. (Romans 7:14) Being imperfect, none of them could buy back what Adam lost.—Psalm 49:7, 8.


God felt compassion for Adam’s descendants in their hopeless situation. (John 3:16) However, God’s standard of justice required that he not simply overlook or excuse their sins without a valid basis. (Psalm 89:14; Romans 3:23-26) God loves mankind, so he provided the necessary legal means for their sins to be not only forgiven but also eliminated. (Romans 5:6-8) The ransom is that legal basis.

How does the ransom work?:

In the Bible, the term “ransom” involves the following three elements:

It is a payment.—Numbers 3:46, 47.
It brings about a release, or redemption.—Exodus 21:30.
It corresponds to the value of what is paid for, or covers it. *
Consider how these elements apply to the ransom sacrifice of Jesus Christ.

Payment. The Bible says that Christians were “bought with a price.” (1 Corinthians 6:20; 7:23) That price is the blood of Jesus, with which he “bought people for God out of every tribe and tongue and people and nation.”—Revelation 5:8, 9.
Release. Jesus’ sacrifice provides a “release by ransom” from sin.—1 Corinthians 1:30; Colossians 1:14; Hebrews 9:15.
Correspondence. Jesus’ sacrifice corresponds exactly to what Adam lost—one perfect human life. (1 Corinthians 15:21, 22, 45, 46) The Bible says: “Just as through the disobedience of the one man [Adam] many were made sinners, so also through the obedience of the one person [Jesus Christ] many will be made righteous.” (Romans 5:19) This explains how the death of one man can pay the ransom for many sinners. In fact, Jesus’ sacrifice is “a corresponding ransom for all” those who take the steps necessary to benefit from it.—1 Timothy 2:5, 6.

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.