Tag Archives: Junk

Polemics

Are Darwinists right to say that the appendix has no useful functions?

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Evolution News points to this Washington Post article.

Excerpt:

The appendix “acts as a good safe house for bacteria,” said Duke surgery professor Bill Parker, a study co-author. Its location — just below the normal one-way flow of food and germs in the large intestine in a sort of gut cul-de-sac — helps support the theory, he said. Also, the worm-shaped organ outgrowth acts like a bacteria factory, cultivating the good germs, Parker said. That use is not needed in a modern industrialized society, Parker said. If a person’s gut flora dies, it can usually be repopulated easily with germs they pick up from other people, he said. But before dense populations in modern times and during epidemics of cholera that affected a whole region, it wasn’t as easy to grow back that bacteria and the appendix came in handy.

Evolution News adds:

Additionally, Loren G. Martin, professor of physiology at Oklahoma State University, lists various likely functions for the appendix . Writing on Scientific American‘s website, he includes these examples:

  •  being “involved primarily in immune functions”
  • “function[ing] as a lymphoid organ, assisting with the maturation of B lymphocytes (one variety of white blood cell) and in the production of the class of antibodies known as immunoglobulin A (IgA) antibodies.”
  • helping with “the production of molecules that help to direct the movement of lymphocytes to various other locations in the body”
  • “suppress[ing] potentially destructive humoral (blood- and lymph-borne) antibody responses while promoting local immunity”
  • Additionally, it is “an important ‘back-up’ that can be used in a variety of reconstructive surgical techniques”

Likewise, a few months back David Klinghoffer reported that researchers in the journal Clinical Gastroenterology and Hepatology found:

Individuals without an appendix were four times more likely to have a recurrence of Clostridium difficile, [a pathogen common in hospitals,] exactly as Parker’s hypothesis predicted. Recurrence in individuals with their appendix intact occurred in 11% of cases. Recurrence in individuals without their appendix occurred in 48% of cases.

In other words, the appendix performs important immune-related functions. Thus, the appendix is not there to occasionally explode. With the appendix increasingly considered to be an important organ that you wouldn’t want to lose, researchers have also found that antibiotics can cure many cases of appendicitis (see Eriksson et al., 2006  ).

It just goes to show you that it’s a good idea to not decide your worldview by appealing to cartoons and funny one-liners. First of all, just because something is not perfect, it doesn’t mean that it isn’t designed. The Chevy Volt vehicle that Obama subsidizes with your tax dollars might burst into flames unexpectedly, but it’s still designed. Secondly, no designed object can be perfect in every way – every engineered object is a tradeoff of different, conflicting design goals. It might be nice to have a laptop that can last for 16 hours on a single charge, but then it’s either going to either weigh 12 pounds or cost $4000.

Junk DNA

This isn’t the only time that arguments of “poor design” are made by Darwinists, either – I also hear a lot about Junk DNA.

Look at what the peer-reviewed journal Nature says:

In 1961, French biologists François Jacob and Jacques Monod proposed the idea that ‘regulator’ proteins bind to DNA to control the expression of genes. Five years later, American biochemist Walter Gilbert confirmed this model by discovering the lac repressor protein, which binds to DNA to control lactose metabolism in Escherichia colibacteria1. For the rest of the twentieth century, scientists expanded on the details of the model, but they were confident that they understood the basics. “The crux of regulation,” says the 1997 genetics textbook Genes VI (Oxford Univ. Press), “is that a regulator gene codes for a regulator protein that controls transcription by binding to particular site(s) on DNA.”

Just one decade of post-genome biology has exploded that view. Biology’s new glimpse at a universe of non-coding DNA — what used to be called ‘junk’ DNA — has been fascinating and befuddling. Researchers from an international collaborative project called the Encyclopedia of DNA Elements (ENCODE) showed that in a selected portion of the genome containing just a few per cent of protein-coding sequence, between 74% and 93% of DNA was transcribed into RNA2. Much non-coding DNA has a regulatory role; small RNAs of different varieties seem to control gene expression at the level of both DNA and RNA transcripts in ways that are still only beginning to become clear. “Just the sheer existence of these exotic regulators suggests that our understanding about the most basic things — such as how a cell turns on and off — is incredibly naive,” says Joshua Plotkin, a mathematical biologist at the University of Pennsylvania in Philadelphia.

Let’s not be too hasty when making these “bad design” arguments – let’s be guided by the progress of science, and not just by cartoons and snarky terms like “junk DNA”.

Commentary

Is the presupposition of naturalism a science stopper?

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UPDATE: Welcome readers from 4Simpsons! Thanks for the link Neil!

In cosmology, we had to wait decades for the theism-friendly big bang theory to beat out atheism-friendly theories like the eternal universe model, the steady-state model, the oscillating model, etc. Piles of taxpayer money wasted trying to prove atheistic flights of fancy. But in the end, the evidence for the big bang was too much for the atheistic theories, and we beat them out.

Junk DNA

And here is another example of how atheism is bad for scientific inquiry: “Junk DNA”.

The purpose of the genome is to contain the instructions that allow the cell to build functional sequences of smaller components. If the sequences are done right, you get a folded-up protein that can be used for all kinds of things.

But what those parts of the genome that don’t code for proteins? Well, atheists have been calling them “Junk DNA” and hailing it as proof that there is no designer to life. I can remember Christian groups like Reasons to Believe predicting that a purpose for “Junk DNA” would be found. But atheists pooh-pooh’d that idea. Gee, I wonder who was right? The same people who are always right: THEISTS.

Denyse O’Leary cites this Princeton University press release on Post-Darwinist:

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.

…The term “junk DNA” was originally coined to refer to a region of DNA that contained no genetic information. Scientists are beginning to find, however, that much of this so-called junk plays important roles in the regulation of gene activity. No one yet knows how extensive that role may be.

She’s got a stack of other related links at the bottom of the post.

Commenter ECM also sent me this story from Cornelius Hunter’s new blog.

Excerpt:

One problem with evolution is its strong bias toward viewing everything in biology as a kludge. When a newly discovered structure is examined, evolutionists take one look and conclude it is leftover junk. After all, blind, unguided mutations and other processes just happened to produce everything we see. The evolutionist’s going in position is that biology is a fluke. We’re lucky anything works.

Hunter then cites this passage from some naturalist researchers who study “junk DNA”:

Here we have a molecule that serves an important role in how cells function and survive, but it contains these puzzling ‘junk’ sequences that don’t seem to have any apparent purpose. Our work suggests that this disorder is really a way of creating flexibility, allowing the protein to function as a molecular switch, a process that is thought to go wrong in certain diseases.

Evolution has provided researchers with convenient modular structures, areas that are repeated over and over again to make up proteins, and so we tend to dismiss the interspersed disordered sequences that don’t seem to have any definable structure. Here we show that the weak molecular interactions in a disorganized protein sequence are essential in giving this protein its unique attributes.

Know what? If you substitute “Flying Spaghetti Monster” in there for “Evolution”, it makes just as much sense! Try it! Evolution causes toothpaste to come out of the toothpaste tube when you squeeze it, and Shakespearean rhyming couplets to rhyme, and my Java code to compile. It’s all evolution!

Conclusion

Atheists, always remember this quote from agnostic NASA astronomer Robert Jastrow, regarding the progress of science:

For the scientist who has lived by his faith in the power of reason, the story ends like a bad dream. He has scaled the mountains of ignorance; he is about to conquer the highest peak; as he pulls himself over the final rock, he is greeted by a band of theologians who have been sitting there for centuries.

In the 1920s, there was no theory about a universe that begins to exist out of nothing, no fine-tuning, no DNA, no Cambrian explosion, nothing. Then science progressed, reducing atheism to a kind of childish delusion, still believed by ignorant snake-handlers and people with certain persistent moral, … ah… issues. But that’s what psychiatrists are for!

Science is always for us, it’s never for you. You have faith. Blind faith. We have all the evidence. We invented science, and every new discovery makes your materialism look more silly and naive… you bravely hold out hope for some hopeful Flying Spaghetti Monster to swoop in and rescue your atheism from the big, bad mind-independent reality. When will you grow up?

There is no Flying Spaghetti Monster!

News

Round-up of stories about intelligent design, from the Discovery Institute

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The Discovery Institute is the headquarters for ID research and advocacy in the United States. They send out a newsletter by e-mail and I though this week’s hit on all cylinders. Below are some of their stories from the newsletter. Thanks to commenter ECM for an earlier tip on the Junk DNA story.

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.

Also at ENV, Dr. Sternberg takes a look at the old Darwinian tripe that biological systems couldn’t possibly have been designed because they exhibit “shoddy engineering”:

We often hear from Darwinians that the biological world is replete with examples of shoddy engineering, or, as they prefer to put it, bad design. One such case of really poor construction is the inverted retina of the vertebrate eye. As we all know, the retina of our eyes is configured all wrong because the cells that gather photons, the rod photoreceptors, are behind two other tissue layers. Light first strikes the ganglion cells and then passes by or through the bipolar cells before reaching the rod photoreceptors. Surely, a child could have arranged the system better — so they tell us.

The problem with this story of supposed unintelligent design is that it is long on anthropomorphisms and short on evidence. Consider nocturnal mammals. Night vision for, say, a mouse is no small feat. Light intensities during night can be a million times less than those of the day, so the rod cells must be optimized — yes, optimized — to capture even the few stray photons that strike them. Given the backwards organization of the mouse’s retina, how is this scavenging of light accomplished? Part of the solution is that the ganglion and bipolar cell layers are thinner in mammals that are nocturnal. But other optimizations must also occur. Enter the cell nucleus and “junk” DNA.

Jerry Coyne Recycles: Why Darwinism Is False

Jonathan Wells is reviewing Jerry Coyne’s Why Evolution Is True over at ENV, and already the list of problems with Coyne’s book is mounting:

On Earth Day 2009, we are reminded of the ecological importance of recycling. As a professor in the Department of Ecology and Evolution at The University of Chicago, Jerry A. Coyne must be keen on recycling: He even recycles worn-out arguments for Darwinism.

If “evolution” meant simply that existing species can undergo minor changes over time, or that many species alive today did not exist in the past, then evolution would undeniably be true. But “evolution” for Coyne means Darwinism — the theory that all living things are descendants of a common ancestor, modified by unguided natural processes such as DNA mutations and natural selection.

Coyne discusses the fossil record, embryos, vestigial structures, the geographic distribution of species, artificial and natural selection, and the origin of species. In the process, (1) he ignores the Cambrian explosion — which Darwin considered a “serious” problem — and he rearranges the fossil record to fit Darwin’s theory; (2) he defends Ernst Haeckel — who faked some drawings of vertebrate embryos to provide support for Darwinism — and he dredges up the doctrine that ontogeny recapitulates phylogeny; (3) he claims that much human DNA is useless junk — despite abundant recent evidence that this is not true — and he relies on theological arguments that have no legitimate place in natural science; (4) he invokes “the well-known process called convergent evolution” to explain many cases of the geographic distribution of species — even though the “well-known process” is merely speculation — and he again falls back on theology to justify a supposedly scientific theory; and (5) he describes examples of natural and artificial selection — none of which show anything more than minor changes within existing species — and he misrepresents experimental evidence to make it sound as though the origin of species by natural selection has been directly observed.

Part 1
Part 2
Part 3
Part 4

Other stuff

The newsletter also discussed historian A.N. Wilson’s return to faith from atheism, which is really interesting because he seems to be well-rounded in his reasons for rejecting atheism. And the newsletter mentions that Jay Richards’ forthcoming book, “Money, Greed, and God: Why Capitalism Is the Solution and Not the Problem” is out May 6th! Jay gave a great lecture on basic economics for Christians and another great lecture on what Christians should think about global warming.