Now junk DNA "assists" evolution

Some excerpts from a recent Science Alert:

"Current theory doesn't tally with fossil evidence"

"Dr Greene, a Senior Lecturer in Molecular Genetics, said current evolutionary theory, which assumed biological lineages evolved by the slow accumulation of adaptive mutations, did not tally with the fossil record.

"However, the “Genomic Drive” theory provided a significant explanation for the way new species arose abruptly and periodically.

"The theory also fitted with fossil records which showed intermittent and long periods of stasis – where many species stood still or remained the same."

Here's Princeton:

Now researchers from Princeton University and Indiana University who have been studying the genome of a pond organism have found that junk DNA may not be so junky after all. They have discovered that DNA sequences from regions of what had been viewed as the "dispensable genome" are actually performing functions that are central for the organism. They have concluded that the genes spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow.

Remember when junk DNA "proved" Darwin's theory by being junk? It's not safe to forget that, because you have to believe two contradictory things at once for now.

More stories here at the Post-Darwinist on junk DNA.

See especially:

Junk DNA: Sorting through the trash

Junk DNA: I told you, keep those documents in the packaging ... are you listening NOW?

Junk RNA just like junk DNA? Stuff you should NOT have thrown out with the packaging?

Intelligent design vs. Darwinism: Junk DNA as the genes' antique shop?

By the way, junk DNA is the new vestigial organs - the ones you supposedly didn't need, but actually do.

"Junk DNA" now rehabilitated as "dark matter"

Slowly, but surely, the junk DNA creeps down from the attic, up from the basement, and in from the shed:

Shining a Light on the Genome's 'Dark Matter'

Elizabeth Pennisi

Science 17 December 2010: Vol. 330 no. 6011 p. 1614 | DOI: 10.1126/science.330.6011.1614 (paywall)

It used to seem so straightforward. DNA told the body how to build proteins. The instructions came in chapters called genes. Strands of DNA's chemical cousin RNA served as molecular messengers, carrying orders to the cells' protein factories and translating them into action. Between the genes lay long stretches of “junk DNA,” incoherent, useless, and inert.

That was then. In fact, gene regulation has turned out to be a surprisingly complex process governed by various types of regulatory DNA, which may lie deep in the wilderness of supposed “junk.” Far from being humble messengers, RNAs of all shapes and sizes are actually powerful players in how genomes operate. Finally, there's been increasing recognition of the widespread role of chemical alterations called epigenetic factors that can influence the genome across generations without changing the DNA sequence itself.

The scope of this “dark genome” became apparent in 2001, ...

So the ID guys were right ... oh, wait, they can't be right. It's not in the script.

Heard a rumour that one of the ID theorists is writing a book on the uses of junk DNA. Can't be true, of course.

See also: Junk DNA: Darwinism's last stand?

Now junk DNA assists evolution

Hat tip: David Tyler

Junk RNA just like junk DNA? Stuff you should NOT have thrown out with the packaging?

Casey Luskin of the Discovery Institute, writes:

When large-scale function was detected for non-coding DNA (once called "junk" DNA) Darwinists, knowing that their viewpoint had long boasted that junk-DNA was evidence for common ancestry and that they were losing that argument, responded in one of two ways: Some sought to rewrite history by claiming that evolutionary biology predicted all along that we'd find function for junk-DNA. Others, however, pushed the "junk" back to RNA. They effectively argued, "Sure, we know that most of the genome is being transcribed into RNA, but that doesn't mean that the RNAs have function. Much of the transcriptome might in fact be junk."

Evolutionist biochemist Larry Moran, for example, argued that either "[t]he so-called transcripts are just noise from accidental transcription" or "[t]he regions of junk DNA could be transcribed regularly but the transcripts are rapidly degraded. They do not have a biological function. They are junk RNA." Intelligent design (ID) proponents were quick to predict the demise of that argument, and if a recent paper in Nature is any indication, "junk RNA" may have the same fate as "junk DNA."

Larry Moran? Sounds vaguely familiar. A biochem prof at the University of Toronto. Now and then he mentions me in his online gossip column.

I'd rather he didn't, really, but I am glad to say that the Internet is - with all its faults - a free country. That part I like.

Here's a podcast on the new "junque RNA."

Junk DNA: Sorting through the trash

From the evil Discos:

When "Junk DNA" Isn't Junk: Farewell to a Darwinist Standard Response
Richard Sternberg, research scientist at the Biologic Institute supported by the Center for Science and Culture, is now blogging at Evolution News & Views, weighing in on the latest research showing that so-called “Junk DNA,” which Darwinists have discounted as “rubbish,” are actually “anything but that.”

Sternberg writes:

In the Darwinist repertoire, a standard response to evidence of design in the genome is to point to the existence of “junk DNA.” What is it doing there, if purposeful design really is detectable in the history of life’s development? Of course this assumes that the “junk” really is junk. That assumption has been cast increasingly into doubt. New research just out in the journal Nature Genetics finds evidence that genetic elements previously thought of as rubbish are anything but that. The research describes tiny strands of RNA, previously thought to be junk, that now turn out to play a role in gene expression. Another finding by Dr. Geoff Faulkner shows that “retrotransposons,” a further variety of “junk” as the dogma previously taught, play a similar role.

Click here to read more

See also these stories abut supposed "junk" DNA.

Find out why there is an intelligent design controversy:

Junk DNA: I told you, keep those documents in the packaging ... are you listening NOW?

Commenting, I gather on this post, a reader writes,

This morning I had a guest speaker giving a run down on DNA diagnostic technology to a Medical Science class and almost as a throw-away line he commented on part of the DNA which doesn't code for proteins and virtually dismissed the use of the term Junk DNA and confirmed it afterwards in a brief conversation.

See also:

Junk RNA just like junk DNA? Stuff you should NOT have thrown out with the packaging?

Intelligent design vs. Darwinism: Junk DNA as the genes' antique shop? Find out who honestly believed it was junk and went on record ...

Find out why there is an intelligent design controversy:

Intelligent design vs. Darwinism: Junk DNA as the genes' antique shop?

Scene: The antiques road show: "You're telling me this old book is worth $10 000 to a collector?" (Faints)

One often hears the claim that researchers' belief in the myth of junk DNA (the garbage heap of evolution that most of our genes supposedly are, because they do not apparently code for anything) did not retard scientific progress.

Usually, the claim shores up Darwinism (or neo-Darwinism), which the junk factor was said to demonstrate. Devout Catholic Darwinist Kenneth Miller, for example, called it "a sea of nonsense."

From a design perspective, that idea is highly suspect.

Richard Dawkins has also called it that.

A friend points me to this startling admission:

“Although catchy, the term ‘junk DNA’ for many years repelled mainstream researchers from studying noncoding DNA. Who, except a small number of genomic clochards, would like to dig through genomic garbage? However, in science as in normal life, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. Because of them, the view of junk DNA, especially repetitive elements, began to change in the early 1990s. Now, more and more biologists regard repetitive elements as a genomic treasure ( 4, 5).” (Wojciech Makalowski, “Not Junk After All,” Science, Vol. 300(5623): (May 23, 2003). )

So swearing allegiance to Darwin, vs. design, wasted a lot of time.

Here's an explanation of how junk became junque.

Now, can anyone point to ID-friendly or non-Darwinian scientists who had the confidence to make this prediction before it was confirmed? If they didn't, it shows how lack of confidence can lead to lost opportunities.

Find out why there is an intelligent design controversy:

Junk reclaimed: Junk DNA now hailed as "powerful regulator"

Yes! See here:

Large swaths of garbled human DNA once dismissed as junk appear to contain some valuable sections, according to a new study by researchers at the Stanford University School of Medicine and the University of California-Santa Cruz. The scientists propose that this redeemed DNA plays a role in controlling when genes turn on and off.

...

It turns out that most of the segments described in the research paper cluster near genes that play a carefully orchestrated role during an animal's first few weeks after conception. Bejerano and his colleagues think that these sequences help in the intricate choreography of when and where those genes flip on as the animal lays out its body plan. In particular, the group found the sequences to be especially abundant near genes that help cells stick together. These genes play a crucial role early in an animal's life, helping cells migrate to the correct location or form into organs and tissues of the correct shape.

The intelligent design advocates have long maintained that junk DNA would not turn out to be junk, so this should be a score for their side, but watch fora ll sorts of people to deny that. For an interesting discussion of that problem, go here, but you have to hunt and peck on "junk" DNA.

Why is there an intelligent design controversy? Read By Design or by Chance?, my overview of the intelligent design controversy.

Coffee!! Found: A use for junk DNA

Cosmologist Paul Davies suggested, in a recent essay ("Is Anybody Out There?" Wall Street Journal (April 10, 2010), another way of finding space aliens:

Another physical object with enormous longevity is DNA. Our bodies contain some genes that have remained little changed in 100 million years. An alien expedition to Earth might have used biotechnology to assist with mineral processing, agriculture or environmental projects. If they modified the genomes of some terrestrial organisms for this purpose, or created their own micro-organisms from scratch, the legacy of this tampering might endure to this day, hidden in the biological record.

Which leads to an even more radical proposal. Life on Earth stores genetic information in DNA. A lot of DNA seems to be junk, however. If aliens, or their robotic surrogates, long ago wanted to leave us a message, they need not have used radio waves. They could have uploaded the data into the junk DNA of terrestrial organisms. It would be the modern equivalent of a message in a bottle, with the message being encoded digitally in nucleic acid and the bottle being a living, replicating cell. (It is possible—scientists today have successfully implanted messages of as many as 100 words into the genome of bacteria.) A systematic search for gerrymandered genomes would be relatively cheap and simple. Incredibly, a handful of (unsuccessful) computer searches have already been made for the tell-tale signs of an alien greeting.

But what if, as scientists are increasingly finding out, the so-called junk is actually functional.

That would increase the aliens' difficulty because they would need to use an existing useful structure to encode "Take me to your leader?" or "We are the voice of Unity". I wonder how they would do that.

Richard Sternberg, vindicated, publishes paper on "junk DNA"

Well, as you've probably heard, Richard Sternberg wasn't wrong when he figured his bosses at the Smithsonian were out to get him, after he permitted the publication of a peer-reviewed ID-friendly paper in a Smithsonian journal. As David Klinghoffer recounts in National Review, Office of Special Counsel attorney James McVay has found that (August 5, 2005):

Our preliminary investigation indicates that retaliation [against Sternberg by his colleagues] came in many forms. It came in the form of attempts to change your working conditions...During the process you were personally investigated and your professional competence was attacked. Misinformation was disseminated throughout the SI [Smithsonian Institution] and to outside sources. The allegations against you were later determined to be false. It is also clear that a hostile work environment was created with the ultimate goal of forcing you out of the SI.

Klinghoffer's piece is a well-written summary of a persecution campaign that should embarrass the scientists involved.

Interestingly, Sternberg has never claimed to be an ID supporter, but he enjoys considering new ideas. As he told Michael Powell of the Washington Post, ""I loathe careerism and the herd mentality," he said. "I really think that objective truth can be discovered and that popular opinion and consensus thinking does more to obscure than to reveal." Powell's excellent piece on Sternberg reveals the shameful role that National Center for Science Education, a seriously mission-challenged organization, played in promoting the persecution. NCSE's alleged purpose is to promote Darwinism in the public school system, not hound a productive scientist at a research institution. (Note: For an interview with Sternberg, go here.)

But the most encouraging news is, Sternberg has just co-authored a paper. (Note: If you click this link, you may not be able to get back using the back browser button. ) So they didn't ruin his career after all. Here's the abstract:

Why repetitive DNA is essential to genome function
Biol. Rev. (2005), 80, pp. 227–250. f 2005 Cambridge Philosophical Society 227 doi:10.1017/S1464793104006657

James A. Shapiro 1,* and Richard von Sternberg 2,3

There are clear theoretical reasons and many well-documented examples which show that repetitive DNA is essential for genome function. Generic repeated signals in the DNA are necessary to format expression of unique coding sequence files and to organise additional functions essential for genome replication and accurate transmission to progeny cells. Repetitive DNA sequence elements are also fundamental to the cooperative molecular interactions forming nucleoprotein complexes. Here, we review the surprising abundance of repetitive DNA in many genomes, describe its structural diversity, and discuss dozens of cases where the functional importance of repetitive elements has been studied in molecular detail. In particular, the fact that repeat elements serve either as initiators or boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the repetitive component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the ‘functionalist ’ perspective on repetitive DNA leads to new ways of thinking about the systemic organisation of cellular genomes and provides several novel possibilities involving repeat elements in evolutionarily significant genome reorganisation. These ideas may facilitate the interpretation of comparisons between sequenced genomes, where the repetitive DNA component is often greater than the coding sequence component.

While we are at it, what about the ID-friendly paper that NCSE and the Smithsonian boffins tried to ruin his career over?

Apparently, it has received way more publicity than it ever would have otherwise.

Good thing, too. Now that the bullies are (we hope) leaving town by a slow train, maybe we can start to have reasonable discussions about the way in which the Cambrian explosion fails to support the predictions of classical Darwinism.

Junk DNA - oops, non-coding DNA - less junky than ever but still expected to fit the "frame"

Junk DNA has sure come up in the world: From Dawkins's "sea of nonsense" to increasingly biologically important - but somehow it is still supposed to support the conventional explanations.

One consequence of growing efforts to "frame" science is that readers of reports on new research must be skilled at seeing past elaborate frames, in order to discern findings. For more, go here.

Recent podcasts in the intelligent design controversy

Brought to you by the evil Discos:

1. Dr. Jonathan Wells on The Language of God

Click here to listen.

On this episode of ID the Future Logan Gage interviews Dr. Jonathan Wells on his recent review of Francis Collins' The Language of God, addressing questions of common ancestry, mistaken definitions of intelligent design, and Collins' use of so-called "junk"-DNA to advance a "Darwin-of-the-gaps" argument.

[Collins is a curious figure, in my view - a well meaning non-denominational (?) Christian who seems to think that Christians who insist that the universe and life forms show evidence of design are creating conflict in society. Well, ... a conflict with whom, exactly? Who is supporting the other side? The new atheists, basically. A far cry from the old atheists, who just didn't believe in God, the new atheists want power. It'll be a bad time for anyone who questins their views. Of course, there are a few useful idiots on the Christian side, including one entire organization of Christians in science, but we would expect that. It doesn't change anything; it just makes the problem worse.]

2. Exposing Darwinist Ronald Wetherington’s Bluffs About Human Evolution

Click here to listen.

This episode of ID the Future explores the many holes in SMU professor Ronald Wetherington's testimony before the Texas State Board of Education. Listen in as Casey Luskin explains why Wetherington -- and anyone else who claims that there are "no gaps" in the fossil record or "no lack of transitional fossils" in human evolution -- overstates his case.

For more rebutting Ronald Wetherington's testimony, click here.

[It's not so much that there are no gaps (there are plenty of those), but the Darwinist explanation doesn't make sense of the evidence, and never has and never will.]

3. Calling Darwinist David Hillis' Bluffs Before the Texas State Board of Education

Click here to listen.

On this episode of ID the Future Casey Luskin exposes the many bluffs and blunders of Darwinist David Hillis, who testified before the Texas State Board of Education with the outlandish claim that there's "overwhelming agreement" on the Tree of Life -- the same day that New Scientist published "Why Darwin was wrong about the tree of life." Listen is as IDTF calls Hillis' bluff.

Click here to read more

[Remember, these guys have been screwing dollars out of the taxpayer for years to fund a basically dead idea. They will say whatever they need to, to keep the spout open.]

4. Predictions from an Intelligent Design Perspective Conversation with Biologist Luman Wing, Part 3

Click here to listen.

On this episode of ID the Future, biologist Luman Wing explains to Casey Luskin about the predictions of an intelligent design perspective in biology. Wing discusses junk-DNA, the irreducible complexity of the blood clotting cascade, and the implications of ID and Darwinism on personalized medicine.

Dr. Luman Wing is a signer of A Scientific Dissent From Darwinism. [I just hope he keeps his job.]

“Junk” DNA: Darwinism’s Last Stand?

Here Jonathan Wells writes about the junk that turned out not to be.

Suppose your genome was your late great aunt's attic. You think the stuff in her attic is all just a load of junk. But unknown to you, her great-great grandma's Georgian dressing table is worth US$50 000 on the museum market, and archivists would kill for her great-grandpa's letters from the front.

Darwinists assumed that everything that wasn't being used now was junk, but apparently they were wrong - because they neglected the value of information generally, and stored information in particular. They truly believe in randomness, not information. Anyway, here's Wells:

We are often told that the evidence for evolution is “overwhelming.” If “evolution” is defined as “change over time” or “minor changes within existing species,” this is a truism. But what if “evolution” means Charles Darwin’s theory? According to Darwin, all living things are descendants of a common ancestor that have been modified by unguided processes such as random variation and natural selection.

Despite the hype from Darwin’s followers, the evidence for his theory is underwhelming, at best.

Natural selection—like artificial selection—can produce minor changes within existing species. But in the 150 years since the publication of Darwin’s Origin of Species by Means of Natural Selection, no one has ever observed the origin of a new species by natural selection—much less the origin of new organs and body plans.

As a result, the only evidence that all living things are biologically descended from a common ancestor comes from comparisons of the similarities and differences among fossil and living species. When making such comparisons, however, Darwinists start by assuming common ancestry. Then they try to fit similarities and differences into the branching-tree pattern that would result from it, and they ignore the glaring inconsistencies that often remain.

Read the rest here at Evolution News and Views

See also Wells's book Politically Incorrect Guide to Darwinism and Intelligent Design (Regnery, 2006)

Find out why there is an intelligent design controversy:

Pond scum: Two genomes and as many genes as humans

A recent story, from Science Daily features a pond scum organism called thermophila with as many genes as a human, and no so-called “junk DNA.”

I think it mainly shows that we do not know how much of what we need to know about an organism is even in its DNA. The organism actually has two genomes. Check it out.

I am woman? I am invincible?: I am having a hard time keeping a straight face, actually

Regular readers with the time to spare for this space may recall that we had a little ID conference at the University of Toronto a couple of weekends ago, and there I ran into an interesting biochem textbook author named Larry Moran, an evolutionary biologist who does not seem to be a Darwinist or a Darwinian evolutionist. (See below.)

He wants to be called an evolutionary biologist , which is fair enough to describe what he does for a living, but virtually every colleague who is a fanatical Darwinist on the issues under discussion will want the same thing.

Larry thinks (see the Comments box) that I somehow benefit from the busload of cranks prophesying in Darwin's name because I want to impugn "real scientists":

With all due respect, I think you're getting a lot of mileage out of lumping the kooks in with real scientists and covering them all with the "Darwinist" label. It allows you to attack and make fun of the kooky non-science in "The Universal Darwinism" while impugning real scientists by implication.

Well, of course, blowing off silliness about the infidelity genes or the God meme is certainly easier than slogging through actual news but - call me unlucky, I've always preferred the news beat. I send up the folly in my spare time, of course, but there would still be plenty of folly if the Darwin cranks packed themselves off to Quaoar for a very long vacation, and I'd still have to make a living on the side.

Larry, who apparently believes that all things work together for good for me, has sent me a link to one of his essays "Evolution by Accident", and I have now read it. He seems to be far more of a Gouldian than a Dawkins-ite.

He writes, in part,

Excellent arguments have been advanced to prove that most of evolution is due to random genetic drift and that's the position I take. Thus, in a discussion about the role of chance and accident in evolution I would say that most of evolution is accidental because of the frequency of drift vs. selection. Note that this says nothing about the perceived importance of these mechanisms. That's a value judgement. Some evolutionists think that adaptation, or evolution by natural selection, is the only interesting part of evolution. These evolutionists don't deny that random genetic drift occurs; instead, they simply relegate it to the category of uninteresting phenomena. Others, like me, think that random genetic drift is far more interesting than natural selection because drift is responsible for junk DNA, molecular phylogenies, molecular clocks, and DNA fingerprinting.

On Darwinism, he writes,

Technically, Darwinism can be construed to mean only evolution by natural selection so this is an acceptable way of avoiding the topic of drift. However, if you read closely, you'll see that these writers are often very sloppy about using ""Darwinism" to describe their interests. The term often fills in for all of evolution in a sort of rhetorical sleight of hand. Thus, this group of chance-deniers tends to eliminate chance from evolution by re-defining evolution so that it only applies to natural selection. As you might expect, those who choose to eliminate chance by redefinition are usually the same people that are only interested in natural selection (see above).

All of which reminds me of the huge uproar last year when Stu Pivar, a friend of the late Steve Gould, told me that Gould was rather an indifferent Darwinist, and Darwinists charged in to protect Gould's reputation from the imputation of heresy.

I wonder if some evo bios can only allow themselves the luxury of questioning a given dogma as long as they all close ranks when attacked. A sort of angry religion without God or good music or Jesus kitsch? Sounds like Hull to me.

Evolution in the light of intelligent design - making evolution make sense

Here are the new additions to the Evolution and Intelligent Design Encyclopedia, from British physicist David Tyler. Why argue a point until you have checked the latest information?

Adaptation - adaptationist fantasies (Tyler)

Adaptationists have tended to develop lazy ways of thinking and rarely seek out ways to test their offered scenarios. "Glib generalizations [according to the author] come from the assumption shared by many biologists that natural selection is the only mechanism of evolutionary change, and hence every observed feature of organisms must have come about because of natural selection." This mechanism is highly prized because they think it can do anything. They claim it is the great creator of complexity. But the concept is qualitative, not quantitative, and there are inadequate checks to avoid the pathways to fantasy. "This conveniently licenses anyone to concoct any adaptive story about anything biological and put it forward as a serious contribution to the science of evolution."

Atheism and science (Tyler) Does science promote atheism?

"The first systematic analysis in decades to examine the religious beliefs and practices of elite academics in the sciences supports the notion that science professors at top universities are less religious than the general population, but attributes this to a number of variables that have little to do with their study of science."

Bacterial flagellum - no simple explanation (Tyler)

In a recent contribution to Current Biology, we read: "there are some caveats we evolutionists should consider before hailing Liu and Ochman as our next champions in the war against unreason." The caveats are to be welcomed. It was surprising to read the uncritical acclaim accompanying the publication of the original paper and a more measured assessment of its bold claims is to be welcomed. However, the reference to "war against unreason" is misguided. The authors are referring to ID, yet ID scientists are strong defenders of reason. Their reason leads them to make design inferences, and design inferences are totally unacceptable to scientists who have adopted the philosophy of naturalism.

Biomimetics (Tyler)

The reason why biomimetics has taken off is not because people are uncovering designs of the tinkering variety, but designs that are exquisite and holistic. This is particularly apparent in the integrative organism-driven biomimetics reviewed by Hesselberg. Biomimetics as an interdisciplinary discipline may well find that Intelligent Design is superior to Darwinism for underpinning its analytical framework.

Brain - anachronistic junk? (Tyler)
"According to David Linden, the brain is a product of the tinkering blind watchmaker espoused by Darwinist biologists. Unfortunately, few readers will realise that this "central thesis" is a deduction from dogma and not empirical evidence. The data that is discussed is perfectly capable of being understood within a design perspective, including the tendency for our minds to distort reality and to act foolishly."

Cell, metaphors,changing metaphors (Tyler)

Today, we are familiar with the metaphor of the cell as a factory, taking in raw materials and converting them, via elaborate processing equipment and complex chemistry, into usable products. But this metaphor is not the only one. The author of a recent review writes: "The history of cell theory offers a rich lesson in the use of metaphor and analogy in scientific thought. The first account of the cell likened it to an empty room, but it has also been conceptualized through the metaphors of a building stone (Baustein), an elementary organism (Elementarorganismus), a chemical laboratory or factory, a motor and a machine."

Chimp-human DNAcomparisons (Tyler)

For over 30 years, the public have been led to believe that human and chimpanzee genetics differ by mere 1%. This 'fact' of science has been used on innumerable occasions to silence anyone who offered the thought that humans are special among the animal kingdom. "Today we take as a given that the two species are genetically 99% the same." However, this "given" is about to be discarded. Apparently, it is now OK to openly acknowledge that those who are involved in this research have never been comfortable that the 1% figure was an accurate summary of the scientific information.

Darwinism - limits of Darwinism (Tyler) "The real issue is: will a debate within science be allowed? If Behe is not allowed the right of reply, this review should be treated as an exercise in polemics, designed to protect the world of science from ever having to face up to evidences of ID. If there is the opportunity to reply, readers will enjoy a genuine scientific debate. This review must backfire, because science has shown that there are limits to Darwinism and it is perfectly legitimate to ask what Darwinism can and cannot do." (Tyler)

Dover Trial (US) (Tyler)

The losers are variously portrayed as a scourge on society that the world is best rid of. The Warfare Thesis was invented towards the end of the 19th Century to replace the hegemony of the established church with the new hegemony of scientism, and ever since that time, the advocates of naturalism have been reinforcing the warfare myth and claiming victory for science against the forces of darkness (which generally means Christianity). The 1925 Scopes Trial in the US was slotted into this format and it now appears that the Dover trial is getting the same treatment.

Junk DNA - Framing the debate (Tyler)

... instead of equipping the public with the concepts and resources to make informed judgments, the objective appears to be to safeguard Darwinism to ensure the public do not revolt!

Human evolution, bipedalism

Taking all these characters into account means that the adaptive landscape looks like to very sharp peaks separated by a wide plain. We could call the peaks Mount Ape Improbable and Mount Human Improbable. The claim that there is an incremental route for an apelike animal to move from one peak to the other has so far eluded Darwinians. The authors comment: "why our unique two-legged gait evolved remains unknown."

Life - Vitalism theory (Tyler)

An Editorial in Nature deflects legitimate concerns about the ethics of a specific research project by interpreting these concerns as a luddite attack on science by vitalists who think the research is "an affront on God". The offence has been caused by the Venter Institute which is applying for worldwide patents on what they refer to as Mycoplasma laboratorium. This novel bacterium is claimed to have been made with synthetic DNA in the laboratory.

Methodological naturalism - Charles Lyell (Tyler)

There is a tendency for scholars in the Lyell tradition to think that empirical evidence can be gathered objectively and that analysis leads to robust knowledge. However, Lyell filtered the data available to him by an unarticulated interpretive principle. Anderson seeks to revise our perceptions of Lyell's contribution by focusing attention on his philosophical roots. "Just as the Aristotelians gathered huge amounts of data and yet because of false interpretive principles drew false conclusions about the world, so any other "science" is only as good as its interpretive principles." Lyell appeared to have been deeply influenced by the philosopher David Hume.

Mutation theory of phenotype evolution (Tyler)

The selectionist/neutralist controversy has continued for nearly 40 years, and a resolution is not in sight. NeoDarwinists like to think that Neutral Evolution is compatible with neoDarwinism, but this is a bit like their attitude to Punctuated Equilibrium: everything worth saying has to be compatible with neoDarwinism! Meanwhile, the controversy goes on. . . In a recent PNAS review paper, Masatoshi Nei argues that our knowledge of genetics is such that, as far as genes controlling phenotypic characters are concerned, conservation is a more applicable description than evolution.

Photosynthesis - extreme efficiency (Tyler) "Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated.” The problem has been one of understanding how 95%+ efficiencies are possible in a natural system."

Protein engineering - limits to Darwinian mechanism (Tyler)

In spite of the progress, we still do not have a general theory on how a sequence produces a specific structure and how a structure determines a function. Therefore, a blind Darwinian search within a known protein scaffold is often used to modify proteins. Unfortunately, blind searches have hard resource limits whereas insight has not. Therefore, in the long run, blind searches are of limited value in compensating our present ignorance."

Starlet sea anemone Unexpected genome complexity

Elizabeth Pennisi observes: "This implies that even very ancient genomes were quite complex and contained most of the genes necessary to build today's most sophisticated multicellular creatures." Eugene Koonin of the National Center for Biotechnology Information was interviewed about the research. He said that it is surprising to find such a "high level of genomic complexity in a supposedly primitive animal such as the sea anemone".

Natural vs. unnatural selection: Consider the ceaseless yap of the lap dog and be warned

In "Actually, the goal posts were just pulled up. Too much trouble to move...", I linked to Jonathan Well's comment on subtle attempts to change just what Darwinian evolution means, to avoid disconfirmation of any particular model. You know, first it's natural selection only, then, lo and behold, group selection is allowed, then Lamarckism (inheritance of acquired characteristics), then gene swapping ...

First junk DNA proved Darwin was right, then when it turned out not to be junk, you can be pretty sure, it will still prove Darwin was right. Darwinism has become a catch-all for a tired, worn-out theory, hysterically popular in the academic culture, with no real foundation for why.

Anyway, Mike Flannery, author of Alfred Russel Wallace's Theory of Intelligent Evolution, comments on my notes on the obviously unsupportable claim that artificial selection (= animal breeding) supports Darwinian evolution (random mutation acting on natural selection):

Anyone can breed a weird dog (I mean, assuming they have basic knowledge of canines).

But nature has a funnel.

There are only certain ways that dogs can really live in the wild.

For example, a greyhound can run faster than a wolf, because he doesn’t have heavy jaws - but what happens when he catches up with the prey?

Someone throws him a bag of Science Diet for Adult Working Dogs, right?

Human interventions almost always assume that we protect the life form from the normal routine of nature – otherwise there would be no reason to bother.

And nature is limited to certain routines. A wild animal that cannot feed itself will die.

But a Bassett Hound can live as long as its owner is willing to pay for advanced veterinary medicine, necessitated in part by the odd way the creature was bred.

If all the dogs in the world ran away, 50 years later, you would likely see only nature's usual wolfhound type.

Anyway, Flannery comments,

Jonathan revealingly quotes Mirsky in his excellent piece: "As Darwin did before him, Coyne noted that the development of new breeds through artificial selection is a good model for the evolution of new species by natural selection."

The model wasn't good when Darwin presented it and it cannot be improved in Coyne's re-telling. From the very beginning (even in the famous Ternate Letter of 1858), Alfred Russel Wallace pointed out, "in the domesticated animal all variations have an equal chance of continuance; and those which would decidedly render a wild animal unable to compete with its fellows and continue its existence are no disadvantage whatever in a state of domesticity. Our quickly fattening pigs, short-legged sheep, pouter pigeons, and poodle dogs could never have come into existence in a state of nature, because the very first step towards such inferior forms would have led to the rapid extinction of the race; still less could they now exist in competition with their wild allies. The great speed but slight endurance of the race horse, the unwieldy strength of the ploughman's team, would both be useless in a state of nature.

If turned wild on the pampas, such animals would probably soon become extinct, or under favourable circumstances might each lose those extreme qualities which would never be called into action, and in a few generations would revert to a common type, which must be that in which the various powers and faculties are so proportioned to each other as to be best adapted to procure food and secure safety,--that in which by the full exercise of every part of his organization the animal can alone continue to live. Domestic varieties, when turned wild, must return to something near the type of the original wild stock, or become altogether extinct." Wallace never would agree with Darwin on this point and it would lead to other more significant disagreements later.

Besides, AT BEST all domestic breeding examples merely established one thing: GUIDED and DIRECTED variation.

Maybe I am a Wallacist?

Evolution in the light of intelligent design

Evolution in the light of intelligent design: How would intelligent design advocates answer various questions about human evolution? Read here:

British physicist David Tyler, one of my co-bloggers at Access Research Network, blogs on a number of issues raised in the science literature that impact the intelligent design controversy. Here's an alphabetized list of the ones he's discussed to date. You will also find some of my own compilations from the media (animations, columnists discussing the issues, et cetera.).

The goal of this compendium of links is a one-stop shop if you are trying to track down information in the growing controversy, that is written from a design perspective.

Acritarchs - oldest known protists (Tyler)

The picture emerging of the Late Archaean is one that includes prokaryotes and eukaryotes, photosynthesis, an oxygenated atmosphere and lots of biological activity. This is a big contrast from the picture even 10 years ago. The significance for our thinking about origins is that the eons of time demanded by Darwinian processes are not available.

Adaptation - adaptationist fantasies (Tyler)

Adaptation - adaptationist paradigm (Tyler)

Adaptation(Tyler) - adaptive change and design in echolocation

Adaptive landscape(Tyler) Intermediate evolutionary forms and adaptive landscape

"Adult resistance to science" (Tyler) (a social science theory on doubt about Darwinism as rooted in childhood error)

Aldini, Giovanni, and virulent materialism, with John West (podcast)

Allegory of the Cave SciPhiShow with Jason Rennie (podcast)

Altruism (Tyler) Darwinian vs. intelligent design interpretation

Amber See Stasis

analogies in science interview with Jay Richards on analogies in science (podcast)

Animal evolution(Tyler) - central nervous system

Animal evolution (Tyler) multicellular animals and need for complex information

Animations of life inside the cell, indexed, for your convenience.

antibiotic resistance - problems for evolution theory (animation)

Anti-God crusade Recent series on anti-God books, teen blasphemy challenge, et cetera.

Apes and language (Tyler)

Appendix (human appendix) - despite it's name, no longer considered superfluous or rudimentary (Tyler)

Archaea - horizontal gene transfer - review of The Archaea's Tale (Tyler)

He presents evidence that Darwinian evolution does not go back to the beginning of life. When we compare genomes of ancient lineages of living creatures, we find evidence of numerous transfers of genetic information from one lineage to another. In early times, horizontal gene transfer, the sharing of genes between unrelated species, was prevalent. It becomes more prevalent the further back you go in time. - Freeman Dyson

astronomy and intelligent design interview with Guillermo Gonzalez, (podcast)

Atheism and science (Tyler) Does science promote atheism?



Ayala - Darwinian orthodoxy, beyond question (Tyler)

Azoic hypothesis (Tyler) How a deep-seated belief hindered science

Backwards eye wiring(Tyler) (The vertebrate eye does not have a compromised design.)

Bacterial flagellum - no simple explanation (Tyler)

Bacterial flagellum(Tyler) - sequence similarities

Bats (Tyler) - echolocation, adaptive change and design

Beetle (Tyler) White beetle as optimally designed

Biomimetics (Tyler)

Bipedalism See Human evolution, bipedalism

Birds - bird song(Tyler) Female song neglected due to sexual selection bias

Brain - anachronistic junk? (Tyler)

Brain(Tyler) Mechanistic assumptions and criminal law

Butterfly sex ratios in Samoa - and natural selection (Tyler)

Sex ratios are distorted by the presence of a maternally inherited bacterium which has the effect of selectively killing male embryos. The authors report ratios of >99% female to nearly 1:1. These were different on different islands and at different times. The genetics of this shift of sex ratios is summarised in one paragraph with some supporting online data. There is not enough information here for anyone to either confirm or challenge their conclusions.

Cambrian era (Tyler) Ancestors largely missing

Cambrian era(Tyler) Comb jellies well developed

Cambrian era (Tyler) Pattern of diversity in the marine fossil record

Cambrian explosion - jellyfish in Cambrian as representatives of modern jellyfish (Tyler)

Campagna, Joey C., Intelligent design - research Wiki Web site for research (podcast)

Canada - intelligent design controversy in Canada - Cultural differences between Canada and the United States, interview with Denyse O'Leary (podcast)

Catholic Church A summary of the Catholic Church's actual teachings on evolution

Cell development (Tyler) and complex specified information

Cell, metaphors,changing metaphors (Tyler)

Cell - molecular recognition - advantages of cellular key-lock not being an exact fit. (Tyler)

So, something that could have been interpreted as evidence for tinkering evolution is discovered to have advantages after all. Furthermore, it has potential for the design of human systems operating in noisy environments. By invoking "evolutionary selection", the authors suggest an evolutionary context for their work. However, there is no evidence that evolutionary selection was involved, and the link with evolutionary theory is gratuitous.

Central dogma (Tyler)

Casual observers might say they find chaos in the emerging picture of the genome, but systems biology is tracking down extraordinary sophistication at the molecular biology level, indicating that theories (like Darwinism) that are undirected and stochastic have little to offer 21st Century biology.

Central nervous system - animal evolution(Tyler)

Chambers, Scott, "Cosmological Fine-Tuning and the Multiverse Model" interview (podcast)

Chimpanzees(Tyler) Common ancestor with humans - dating disputes

Chimp-human DNAcomparisons (Tyler)

Chimpanzees (Tyler) Differ from humans by six percent of genes

Chimpanzees(Tyler) Tool use of late Stone Age chimps and evidence of design, intelligent causation

Chimpanzees See also Apes

Ciencia Alternativa - intelligent design interview with Mario Lopez (podcast)

Coelacanth Devonian coelacanth find fills gap. "The find is significant for consigning an extensive discussion of coelacanth and lungfish fins to the filing cabinet of history." (Tyler)

Collins, Francis My review of Francis Collins' book The Language of God

Columnists weigh in on the intelligent design controversy A summary of recent opinion columns on the ID controversy

Comb jellies(Tyler) in Cambrian era

Compsocidae - an example of stasis. (Tyler) See also Stasis

Consciousness Douglas Hofstadter attempts to deconstruct consciousness:

... the materialist approach to consciousness is commonly dignified by the name "science". Other approaches, which are likely to be linked to Theism, are labelled "religion" and are excluded, on demarcation grounds, from science. This is an unacceptable situation, for as metaphysics, materialism has a philosophical standing that is entirely equivalent to Theism. It is simply that people choose to build their thoughts on different foundations. The paradox is that materialistic science wants to be realist and to have truth as a goal, but its approach to human consciousness can only support a post-modern philosophy which emphasises the socially constructed nature of reality and substitutes relativism for truth. And, for materialists, individuals have to seek for meaning and self-worth in existential experiences (an escape from reason) because the universal acid of rationalism has completely corroded realism and truth in human psychology.

Common ancestor of all life(Tyler) Assumptions vs. evidence

Common ancestor of all life(Tyler) Hagfish and common ancestor

Common ancestor of humans and chimps (Tyler)

cosmological fine tuning "Cosmological Fine-Tuning and the Multiverse Model", interview by Casey Luskin with Scott Chambers (podcast) See also Fine tuning

CO2 sensors (Tyler) as wonders of natural engineering

Cypher's choice Jason Rennie explains the Matrix crux (podcast)

Darwinbots Denyse O'Leary vs. the Darwinbots (podcast)

Darwin Day in America - West, John, on Darwin Day in America (podcast) John West reads from his book Darwin Day in America (podcast)

Darwin exhibition (Tyler) American Museum of Natural History - historical errors

Darwinism and its Discontents(Tyler) Comments by David Tyler on Michael Ruse's book

Darwinism - Ayala's Darwinian orthodoxy, beyond question (Tyler)

Darwinism Darwinian reductionism and Darwinism(Tyler) Alex Rosenberg's views
Darwinism, Judaism, and Christianity with Jonathan Rosenblum (podcast)

Darwinism moral relativism and Darwinism John West (podcast)

Darwinism and dissent(Tyler) - defenders of Darwinism propose ways to deal with dissent from current consensus in science

Darwinism dissent Lists of theoretical and applied scientists who doubt Darwin

Darwinism, limits of Darwinism Reviews of Michael Behe's Edge of Evolution "The real issue is: will a debate within science be allowed? If Behe is not allowed the right of reply, this review should be treated as an exercise in polemics, designed to protect the world of science from ever having to face up to evidences of ID. If there is the opportunity to reply, readers will enjoy a genuine scientific debate. This review must backfire, because science has shown that there are limits to Darwinism and it is perfectly legitimate to ask what Darwinism can and cannot do." (Tyler)

Darwinism (Tyler) and molecular clocks

Davies, Paul(Tyler) and design inference

Dawkins, Richard, information challenge Casey Luskin's response (podcast)

Dembski, William, on intelligent design and the church, in conversation with Russell Moore (podcast)

Descartes's demon SciPhiShow with Jason Rennie (podcast)

Design(Tyler) Can self-organization explain design?

design - unintelligent design - A discussion between Sheirdan Voysey (host), Robyn Williams, and Denyse O'Leary (science journalists) (podcast)

Dinosaurs(Tyler) Horned dinosaurs and evolutionary predictions

Dissent(Tyler) - defenders of Darwinism propose ways to deal with dissent

Doan, Andy, interviewed by Jason Rennie, "Miracles and the Q" (podcast)

Dover Trial (US) (Tyler)

Dover Trial (US) Montana Law review articles (podcast)


Ear evolution(Tyler) Yanoconodon

Ears (Tyler) Moth ears show design sophistication

Earth as privileged planet "Theories of how planetary atmospheres formed will need to be reappraised. The findings create yet more problems for OOL research. In other contexts, finding water outside the Earth has been used to raise expectations of finding life, but at least that does not arise here. However, it is worth contrasting this point with some of the more sensational media reports ... " (Tyler)


Earth-like planet (Tyler) Found in 2007

Echolocation(Tyler) - Adaptive change and design

Emergent evolution (Tyler) Can self-organization explain design?

Enzymatic PH activity profiles(Tyler) Fine tuning

Eozoon - a claimed fossil strenuously defended by the 19th century science establishment

Eozoon was not a fossil and the dissenters were correct to challenge the consensus. Clearly there are parallels with today: the role of scientific elites, the status of peer publication, the protocols required to be accepted as members of the scientific community, the way debated issues can be presented as fact to the public, the disdain shown to dissenters, the lobbying of editors to restrict access by critics of the Establishment, and the exploration of alternative ways of communicating minority views to peers and the public. This is the very human face of science. We are seeing these characteristics today in numerous areas where scientists have reached different conclusions.

(Tyler)

eukaryotes, origin Reason for flood of speculation in 2007: "According to Poole and Penny, there has been far too much speculation about the origin of eukaryotes. "The conflicting hypotheses currently on offer show a curious disregard for mechanism." (Tyler)

Eukaryotic cell (Tyler) enigmas

Eukaryotic cells (Tyler) Irreducibility issue

Evolution - animal evolution (Tyler) multicellular animals and need for complex information

Evolution(Tyler) And long periods of no change (stasis) See also Stasis

Evolutionary Informatics Lab Robert Marks's explanation (podcast)

Evolutionary Informatics Lab and Banned Items (podcast)

Evolutionary Informatics Lab - Web site suppressed at Baylor Report by Anika Smith (podcast)

Evolutionary Informatics Lab See also Marks, Robert

Evolution - Evolutionary transformations - Darwinism does not have the answers(Tyler)

Evolutionary psychology - Altruism (Tyler) Darwinian vs. intelligent design interpretation

Evolutionary psychology - grandmothers who care

This is 'black box' biology, with natural selection being asked to do an amazing number of things in a short period of time to achieve the (relatively small) fitness benefits. It should be noted that genetic changes are not directly passed on to offspring, as in the normal portrayal of the way Darwinism works. We are dealing here with complex changes in females that marginally affect the survival of grandchildren. Additionally, one wonders how many caring grandmothers there actually were in the hypothetical social groups of early man where life expectancies were low.

Exoplanets - atmospheres (Tyler)

Exoplanets See also Hot Jupiters

Expelled movie, with Ben Stein - interview with Bruce Chapman (video podcast)

Explore Evolution information, textbook (podcast)

Eye - squid's eye lens (Tyler) Fine tuning

Eye, vertebrate eye (Tyler) (It does not have a compromised design.)

Falsifiability - Intelligent design - philosophical criticisms (Tyler)

falsifiability - intelligent design and falsifiability interview with Jay Richards (podcast)

fine tuning of the universe Discovery Institute's Casey Luskin discusses Newsweek's Sharon Begley's take on fine-tuning (podcast)

fine tuning of the universe "Cosmological Fine-Tuning and the Multiverse Model", interview by Casey Luskin with Scott Chambers (podcast)

Flagellum - See Bacterial flagellum

Flight - Flightless birds (Tyler) Design in ostriches

Flight - insect flight (Tyler) Hawk moth gyroscope

Form, theory of form The modern synthesis (neo-Darwinism) has not given us a theory of form. (Tyler)


Foundation for Thought and Ethics Dover Trial (podcast) Casey Luskin and Seth Cooper ask, was justice done?

Framing information(Tyler) for public consumption

Galactic habitable zone - Earth-like planet (Tyler) Found in 2007

Galactic habitable zone- hot Jupiters (Tyler) Hot Jupiters lack water

Gecko - feet a standard for adhesion (Tyler)

... the gecko does not demonstrate just a single trait with enhanced performance. There are issues of adhesion and delamination, self-cleaning, and achieving a sustained adhesive performance. What we have in the gecko is exquisite design and, for that, biomimetics needs a methodology that can relate well to intelligent engineering design concepts.

Gene regulatory networks(Tyler) and design

Genetic code(Tyler) Optimal features

Genetic code(Tyler) Silent mutations and design inference

Genetic information(Tyler) and design inference

Gilder, George A summary of tech guru George Gilder's arguments for ID and against Darwinism

Gilder, George, on information theory, at Bar-Ilan University (podcast)

Gnosticism Ben Witherington III interviewed by Jason Rennie of the SciPhiShow, on Gnosticism and Christianity (podcast)

Gnosticism Edwin Yamauchi interviewed by Jason Rennie of the SciPhiShow, on who Gnostics were and what they believed (podcast)

Goldilocks Principle(Tyler) Pau Davies and design inference

Gonzalez, Guillermo - and academic freedom (Tyler)
See also Galactic habitable zone

Gonzalez, Guillermo, interview on the Privileged Planet hypothesis (podcast)

Gonzalez, Guillermo, astronomy and intelligent design interview with Guillermo Gonzalez, (podcast)

Gonzalez, Guillermo - denied tenure - documents, interview with John West (podcast)

Gonzalez, Guillermo - denied tenure - tenure appeal (podcast)

Habitable zone See Galactic habitable zone

Haeckel, Ernst (Tyler) doctored embryo images

Haeckel's embryos - use in textbooks, interview with Casey Luskin (podcast)

Hagfish(Tyler) and common ancestor

homology - intelligent design and homology (video podcast)

Hot Jupiters (Tyler)

Human evolution, bipedalism (Tyler)

Human evolution (Tyler) Common ancestor with chimps - dating disputes

Human evolution 1470 man deemed an ape - deemed ape (Tyler)


Human evolution (Tyler) Little Foot and the time gap problem

Human evolution(Tyler) Lucy - former icon currently deemed gorilla

Human evolution - Neanderthals(Tyler) Neanderthals not so primitive as once thought

Human genome (Tyler) Differs from chimpanzees by six percent of genes

Human genome(Tyler) Diversity of human genome

Hunter, George Cornelius - interview on his recent book, Science's Blind Spot (podcast)

information theory - George Gilder at Bar-Ilan University (podcast)


Insect evolution(Tyler) Speculation vs. evidence

Insects - beetles (Tyler) White beetle as optimally designed

Insects - CO2 sensors (Tyler) as wonders of natural engineering

Insects - ears (Tyler) Moth ears show design sophistication

Insects - insect flight(Tyler) Biorobotics and insect flight See also Flight

Insects - insect muscles(Tyler) remarkable adaptations

Intelligent design - and academic freedom (Tyler) Guillermo Gonzalez

Intelligent design academic publications.

Intelligent design - controversy timeline An ID Timeline: The ID folk seem always to win when they lose.

intelligent design - definitions, Crowther, Robert: "Defining what intelligent design is" (podcast)

intelligent design - definitions, Luskin, Casey: "Confronting misrepresentative definitions of intelligent design" (podcast)

ntelligent design - falsifiability interview with Jay Richards (podcast) See also falsifiablity

intelligent design - origin of term by Rob Crowther (podcast)

Intelligent design - philosophical criticisms (Tyler)

intelligent design - research Wiki Web site for research (podcast)

Intelligent design(Tyler) Self-organization and design

Intelligent design - refusal to engage arguments (Tyler)

Intermediate evolutionary forms(Tyler) and adaptation as explanation

In the Light of Evolution conference(Tyler)

Jellyfish - reinforcing challenge created by Cambrian explosion

New fossils from the Middle Cambrian of Utah "have very well preserved soft tissue, which the authors interpret as evidence that representatives of modern jellyfish existed by the middle Cambrian period."

(Tyler)

Jensen, Lyle, neo-Darwiism skeptic (podcast)

Junk DNA (Tyler)

Junk DNA - Framing the debate (Tyler)

Keller, Rebecca, on "Real Science for Kids" (podcast)

Kelvin "As a physicist, Kelvin sought to develop quantitative, rather than qualitative, science and he found himself in conflict with geologists who wanted an Earth with "no vestige of a beginning." (Tyler)

Lactose intolerance (Tyler) and design perspective

Language (Tyler) Apes and language

Life - Vitalism theory (Tyler)

Light of Evolution conference(Tyler)

Linnaeus(Tyler) Tree of life, evolution, and intelligent design

Living fossils(Tyler) (Life forms that change little over long periods of time) - stasis

Living fossils - Jurassic shrimp (Tyler) Challenge to Darwinism

Lucy(Tyler) Former icon currently deemed merely gorilla

lungfish Why lungfish have the best of both worlds.

Lungfish do not demonstrate a transitional physiological system, but employ two developed systems side-by-side. They have an air-breathing system for controlling acidity (respiratory compensation) and they use their gills and kidneys to reduce excess base (metabolic compensation). In other words, the ability to operate in both watery and land environments requires two complex systems to be in place: one for living in water and the other for living in air. The case of lungfish shows that biological information precedes and permits biological function.

(Tyler)

magic - SciPhiSHow with Jason Rennie, on science, rreligion, magic, and technology (podcast)

Mammals - mammal evolution(Tyler) early Cretaceous mammal specialized - not the neo-Darwinian view

Marks, Robert - Evolutionary Informatics Lab Web site suppressed at Baylor Report by Anika Smith (podcast)

Marsupial genome - what we have learned(Tyler) (the opposum)

Matrix SciPhiShow with Jason Rennie (podcast)

Methodological naturalism - Charles Lyell (Tyler)

Microbes(Tyler) as complex in real world

Microbes(Tyler) How microbes don't fit reductionist Darwinian thinking

Microtubules (Tyler) Molecular zipper and complex specified information

mind - mind as illusion - Is the mind just an illusion. Anika Smith interviews Denyse O'Leary (podcast)

miracles, Doan, Andy, "Miracles and the Q" (podcast)

Molecular clocks(Tyler) Darwinism assumed, never tested

Molecular clocks (Tyler) Telling the wrong time

Molecular motors (Tyler) Structural similarity and intelligent design

Molecules(Tyler) small molecules, medicine, and design

Molecular recognition in the cell (Tyler)

moral relativism moral relativism and Darwinism John West (podcast)

Multicellular animal evolution (Tyler) multicellular animals and need for complex information

multiverse "Cosmological Fine-Tuning and the Multiverse Model", interview by Casey Luskin with Scott Chambers (podcast)

Mutation theory of phenotype evolution (Tyler)

Mutations as mostly harmful (Tyler) Challenge for Darwinism

Neanderthals(Tyler) Not so primitive as once thought

Neanderthals - language and FoxP2 (Tyler)


Non-coding DNA (Tyler)

Orchids "on the basis that the "rate of orchid evolution" exhibited by the subtribe Goodyerinae is almost zero, the comment of the lead author is probably correct: "The dinosaurs could have walked among orchids." (Tyler)

Origin of life research - examples of flawed thinking (Tyler)

Origin of life (Tyler) Need for design perspective

Origin of life Why origin of life is such a difficult problem. (O'Leary)

Ostriches (Tyler) design in ostriches

Peppered Moth controversy
"Is it scientifically defensible to find an example of natural selection within a population of an animal, and then use this as an evidence for evolutionary transformation from the first single cell to the extraordinary diversity of life that we find in the biosphere?" ( Tyler)

Phenotype variations(Tyler)

Photosynthesis(Tyler) - its efficiency

Photosynthesis(Tyler) Irreducible complexity and photosynthesis evolution

Photosynthesis - extreme efficiency (Tyler) "Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated.” The problem has been one of understanding how 95%+ efficiencies are possible in a natural system."

Platypus's complex electrolocation sense evolved early.

... there are extreme constraints on time for any evolutionary story of the origin of platypuses and their electrolocation device. We appear to have a situation where intelligent design is demanded by the evidence of short timescales and the complexity of the "implausible" electrosensory system.

(Tyler)

Polls relevant to the intelligent design controversy A summary of recent polls of US public opinion on the ID controversy

privileged planet hypothesis interview with Guillermo Gonzalez, on the Privileged Planet hypothesis (podcast)

Protein engineering - limits to Darwinian mechanism (Tyler)

Protists - oldest known protists (Tyler)

Pycnogonids - pycnogonids (sea spiders) (Tyler)

Real Science for Kids - Keller, Rebecca, on "Real Science for Kids" (podcast)

Reductionism(Tyler) How microbes don't fit

Reductionism(Tyler) Why it doesn't work in medical research

Reductionism - Darwinian reductionism(Tyler) Alex Rosenberg

Retraction - Homer Jacobson's retraction of 1950s origin of life quotes to prevent use by creationists.

This response recalls the Miller-Urey experiments (which are currently regarded as peripheral by most OOL researchers). The element of conjecture is apparent here also, as Jacobson can only argue that the right conditions "could have existed under early Earth conditions". The empirical support for this is highly controversial. More generally, it is worth noting that evolutionists are very reluctant to calculate probabilities - because some regard it as very high (but we don't yet know the mechanism) whereas others regard it as very very low (but think it was a lucky chance anyway). Based on what we know, the probabilities are extraordinarily low, as Koonin has demonstrated. For more on this, go here.

Jacobson is perfectly entitled to make a retraction, but the issues are not going to go away. Jacobson may gain some personal satisfaction, but the challenge of IC systems remains and the improbability of chemical evolution appears insuperable. Far better for Jacobson and those who think like him to face up to these challenges and address the data as we know it (rather than indulge in fantasies about "might well have occurred" and what conditions "could have existed").

(Tyler)

Ribosome(Tyler) and design inference (Ribosome as an AMT cell)

RNP Complexes(Tyler) - remarkable complexity

Rosenblum, Jonathan, interview on Deniable Darwin (podcast)

Ruse, Michael - Darwinism and its Discontents(Tyler) Comments by David Tyler

science journals - double standard re intelligent design interview with Paul Nelson re Michael Behe's work (podcast)

Science - and pursuit of truth (Tyler)

Science teaching (Tyler) Culture of conformity vs. culture of enquiry

SciPhiShow, featuring Australia's Jason Rennie, offers podcasts featuring major players pro and con intelligent design (O'Leary)

Self-organization (Tyler) Can self-organization explain design?

Sensory perception - advanced perception in Permian amniotes (Tyler)

The discovery of a highly-evolved auditory apparatus in Middle Permian parareptiles even further emphasizes that the entire groundplan for the impressive evolutionary history of amniotes was already largely in place by the end of the Paleozoic; what followed was in fact only a subsequent tinkering of earlier inventions." Darwinism needs time, but the fossil record no longer provides it.

Silent mutations(Tyler) Genetic code and design inference

"Small molecules(Tyler) medicine from nature and design

Squid's eye lens (Tyler) Fine tuning

Starlet sea anemone Tyler Unexpected genome complexity

Stasis - amber preserved insects(Tyler) Evidence shows mostly stasis, not evolution - a challenge to Darwinism.

Stasis - amber-preserved insects (Tyler) Midges show little change over time - why stasis should be considred more important than it is.

Stasis Compsocidae as an insect example of stasis from Cretaceous era (Tyler)

Stasis(Tyler) Darwinian attempts to account for stasis (little change in life forms over time)

Stasis - and Jurassic shrimp (Tyler) Challenge to Darwinism

Stasis - and leaf insects (Tyler) Stasis in their fossil record

Stasis - pycnogonids (sea spiders)

Here is yet another life form, stretching from the lower Palaeozoic to the present, that displays stasis in its morphology with relatively minor differences over time. Why is it that the dominant feature (stasis) gets so little attention, when "evolutionary history" gets so much?

(Tyler)

Stasis - trilobites (Tyler)

Stove, David O'Leary's intro to non-Darwinian agnostic philosopher David Stove's critique of Darwinism.

Taste (Tyler) evolution and design

Teleology - "promiscuous teleology" and design inferences (Tyler)

Tool use (Tyler) in chimpanzees, and intelligent causation

Transitional forms (Tyler) Intermediate evolutionary forms begin to be studied

Tree of life (Tyler) Bush or forest of life better explanation? Alternatives to common ancestry

Tree of life (Tyler) - force fitting explanations to defend an orthodoxy

Tree of life (Tyler) as unnecessary concept that cannot be justified by empirical data

Trilobites - variation and stasis as a pattern

The research documented both rapid morphological variation and subsequent stasis. ... One hypothesis is that radiations occur because organisms are designed to vary, but the process results in genetic impoverishment that leads to stasis.

(Tyler)

Type III secretory machines(Tyler) challenge to gradualism

Unfalsifiability (Tyler)

Variation - trilobites (Tyler)

Vertebrate eye (Tyler) (It does not have a compromised design.)

Von Baer's law - interview with Paul Nelson (podcast)

Walking(Tyler) intelligent design and evolution

Wells, Jonathan, an interview with Doug Giles at AudioClash on his book, The Politically Incorrect Guide to Darwinism and Intelligent Design (podcast)

West, John, on Darwin Day in America (podcast)

West, John, Darwinism moral relativism and Darwinism John West (podcast)

Wing morphology and intelligent design (Tyler)

Yanoconodon(Tyler) Ear evolution