Tag Archives: Darwin

News

New peer-reviewed paper in Nature falsifies Darwinian junk DNA prediction

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First, let’s see what Darwinian evolutionists say about junk DNA, before we look at what the experiments show.

Here’s biologist John Timmer to explain the orthodox Darwinian view of DNA from 2007:

Personally, I fall into the “it’s all junk” end of the spectrum. If almost all of these sequences are not conserved by evolution, and we haven’t found a function for any of them yet, it’s hard to see how the “none of it’s junk” view can be maintained. There’s also an absence of support for the intervening view, again because of a lack of evidence for actual utility. The genomes of closely related species have revealed very few genes added from non-coding DNA, and all of the structural RNA we’ve found has very specific sequence requirements. The all-junk view, in contrast, is consistent with current data.

Got that? According to Darwinists, DNA is almost entirely junk – this is what is consistent with the view that creatures have evolved through a process of random mutation and selection. The estimates that I’ve seen from evolutionary biologists range from 95% to 99% junk. Now let’s compare the religion with the lab experiments and separate myth from fact.

Now let’s compare that with intelligent design theorist William Dembski’s view of “junk” DNA, from 1998:

Even if we have a reliable criterion for detecting design, and even if that criterion tells us that biological systems are designed, it seems that determining a biological system to be designed is akin to shrugging our shoulders and saying God did it. The fear is that admitting design as an explanation will stifle scientific inquiry, that scientists will stop investigating difficult problems because they have a sufficient explanation already.

But design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term “junk DNA.” Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as “junk” merely cloaks our current lack of knowledge about function… Design encourages scientists to look for function where evolution discourages it.

Now let’s look at the experimental evidence and see whose prediction was right.

Evolution News reports on a new peer-reviewed paper published in Nature, the top peer-reviewed science journal. (H/T ECM)

Excerpt:

A groundbreaking paper in Nature reports the results of the Encyclopedia of DNA Elements (ENCODE) project, which has detected evidence of function for the “vast majority” of the human genome. Titled “An integrated encyclopedia of DNA elements in the human genome,” the paper finds an “unprecedented number of functional elements,” where “a surprisingly large amount of the human genome” appears functional. Based upon current knowledge, the paper concludes that at least 80% of the human genome is now known to be functional:

The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation.

(The ENCODE Project Consortium, “An integrated encyclopedia of DNA elements in the human genome,” Nature, Vol. 489:57-74 (September 6, 2012) (emphasis added))

If you doubt Evolution News, we can always turn the ultra-leftist Los Angeles Times, reporting on the same study. (H/T Wes from Reason to Stand)

Excerpt:

The $123-million effort involved more than 400 scientists and more than 1,600 experiments during five years of work. If presented graphically, the data generated so far would cover a poster 30 kilometers wide and 16 meters high, Birney has estimated.

This is still just a start — akin to “grainy images beamed back to Earth by the first satellite,” said Dr. Eric Green, director of the National Human Genome Research Institute, which funded ENCODE. But already, it’s throwing up surprises.

Strikingly, the data overturn old ideas that the bulk of DNA in our cells is useless — albeit inoffensive — junk just carried along for the evolutionary ride. Back in 2003 when the human genome was published, scientists estimated that less than 2% of it carries instructions for making proteins, and many of them thought the rest didn’t do very much.

But the new analysis shows that more than 80% of the human genome is active in at least one biological process that the ENCODE team measured. Nearly every part of it could end up being active when the data are more complete.

Here’s the ultra-left-wing New York Times, confirming the statement I made earlier about the dogma of the Darwinians:

The discoveries were published on Wednesday in six papers in the journal Nature and in 24 papers in Genome Research and Genome Biology. In addition, The Journal of Biological Chemistry is publishing six review articles, and Science is publishing yet another article.

[…]The thought before the start of the project, said Thomas Gingeras, an Encode researcher from Cold Spring Harbor Laboratory, was that only 5 to 10 percent of the DNA in a human being was actually being used.

The big surprise was not only that almost all of the DNA is used but also that a large proportion of it is gene switches. Before Encode, said Dr. John Stamatoyannopoulos, a University of Washington scientist who was part of the project, “if you had said half of the genome and probably more has instructions for turning genes on and off, I don’t think people would have believed you.”

It’s just another prediction of Darwinian orthodoxy falsified by experimental evidence published in the top scientific peer-reviewed journal. Will this cause Darwinians to revise their theory to fit the evidence? Not likely. Their motivations for clinging to naturalism, the religion that undergirds Darwinism, are entirely beyond correction by evidence.

I wonder what people like P.Z. Myers and Larry Moran do when their religion comes into conflict with scientific evidence from lab experiments? Do they bitterly cling to their mythology from the 19th century? Or do they adjust their worldview to be in line with the progress of science?

Let Richard Dawkins explain evolution and the role of evidence:

“My argument will be that Darwinism is the only known theory that is in principle capable of explaining certain aspects of life. If I am right it means that, even if there were no actual evidence in favour of the Darwinian theory (there is, of course) we should still be justified in preferring it over all rival theories.” — p. 287, Blind Watchmaker” (1986)

Or Richard Lewontin:

“Our willingness to accept [naturalistic]  scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world but, on the contrary, that we are forced by our own a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, not matter how counterintuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a divine foot in the door.” (Richard Lewontin in New York Review of Books, January 9, 1997, p. 28)

Junk DNA isn’t the only battle in the long war between atheism and scientific evidence. Naturalists fought the Big Bang tooth and nail, trying to save their eternal universe from the progress of science. Naturalists invented the now discredited oscillating model of the universe in order to “explain” the evidence for a cosmic beginning. Naturalists invented the unobservable, untestable multiverse to “explain” the cosmic fine-tuning. Aliens are posited in order to “explain” the origin of life. Precursor fossils are invented without evidence in order to “explain” the Cambrian era explosion in complexity. And so on.

Evidence doesn’t matter to people who are motivated by naturalistic faith. Like belief in a flat-Earth, the delusion of naturalism is not accountable to scientific evidence. They believe what they want to believe. It’s not up for debate. For some people like Richard Dawkins, a prior lifestyle commitment makes theism (and the moral law!) an impossibility a priori. But rational people know that believing something just so that your actions are “justified” doesn’t make what you believe true.

For the intelligent design take on junk DNA, check out this article. To see who was right about predicting whether “vestigial organs” like the appendix have function, check out this post. You can find more predictions that follow from intelligent design right here.

Polemics

Can a materialist question Darwinism without having his career ruined?

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From Uncommon Descent, the abstract of a paper by Alex Rosenberg, warning even materialists not to question Darwinism.

Excerpt:

Abstract

There is only one physically possible process that builds and operates purposive systems in nature: natural selection. What it does is build and operate systems that look to us purposive, goal directed, teleological. There really are not any purposes in nature and no purposive processes ether. It is just one vast network of linked causal chains. Darwinian natural selection is the only process that could produce the appearance of purpose. That is why natural selection must have built and must continually shape the intentional causes of purposive behavior. Fodor’s argument against Darwinian theory involves a biologist’s modus tollens which is a cognitive scientist’s modus ponens. Assuming his argument is valid, the right conclusion is not that Darwin’s theory is mistaken but that Fodor’s and any other non-Darwinian approaches to the mind are wrong. It shows how getting things wrong in the philosophy of biology leads to mistaken conclusions with the potential to damage the acceptance of a theory with harmful consequences for human well-being. Fodor has shown that the real consequence of rejecting a Darwinian approach to the mind is to reject a Darwinian theory of phylogenetic evolution. This forces us to take seriously a notion that otherwise would not have much of a chance: that when it comes to the nature of mental states, indeterminacy rules. This is an insight that should have the most beneficial impact on freeing cognitive neuroscience from demands on the adequacy of its theories that it could never meet.

This might have been written by a Catholic Inquisitor at the height of the Spanish Inquisition. “Don’t demand that our theory be empirically adequate, or you’ll be sorry”. We have only to look at the stories documented in the movie “Expelled” to see how sorry. You can watch it on Youtube here, in full.

And more from a later post by Casey Luskin, on Uncommon Descent.

Excerpt:

the true purpose of Rosenberg’s piece is to warn people not to challenge Darwin or they’ll suffer the same castigation as Darwin-critic (and atheist) Jerry Fodor. Rosenberg writes: “When a philosopher advances a purely a priori argument to show that a well-established scientific theory is fatally defective, it is usually safe to assume that the problem is the philosopher’s and not the theory’s.” Translation: If you question Darwin, expect trouble–and the trouble will come from me and other defenders of Darwinism. Given the logic we see being used to defend Darwinian theory, perhaps the philosopher isn’t the problem after all.

And of course, a major part of Rosenberg’s warning is to claim that Fodor’s arguments against Darwinism lead to “damage with harmful consequences for human well being.” And just what is that damage? Well, as Rosenberg puts it, it is lending support for religion (though he can’t bring himself to put it that nicely).

[ … ]In any case, this tarring and feathering of Fodor is just the latest frustrated attempt by hardline Darwinians to discourage people from using design terminology. It’s a hopeless effort, because try as they might to impose speech codes on each another, they can’t change the fact that nature is infused with purpose, which readily lends itself to, as Rosenberg calls it “teleosemantics.”

And finally, a word from the master of Darwinish debate-avoidance, Richard Dawkins:

“My argument will be that Darwinism is the only known theory that is in principle capable of explaining certain aspects of life. If I am right it means that, even if there were no actual evidence in favour of the Darwinian theory (there is, of course) we should still be justified in preferring it over all rival theories.” — p. 287, Blind Watchmaker” (1986)

Again, these are the words of a fundamentalist. You better agree with his theory, whether the evidence is for it or not.

Here is Richard Dawkins in a video clip explaining that even if life were designed, then he knows without any evidence that aliens who evolved by Darwinian processes are the ones who did the designing:

How does he know that the aliens evolved without being able to see their fossil record and run experiments on their genetic coding? Because when it comes to Darwinism, no evidence is needed. And if you don’t buy into his little religion, then he’ll “destroy” you. And he doesn’t mean destroy you by debating, because we know that the coward refuses to debate his religion in public.

And what about Darwinist Richard Lewontin: (and by “science” he means “naturalistic science”)

“Our willingness to accept [naturalistic]  scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world but, on the contrary, that we are forced by our own a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, not matter how counterintuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a divine foot in the door.” (Richard Lewontin in New York Review of Books, January 9, 1997, p. 28)

This is what Darwinism really amounts to: a faith commitment. A fundamentalist faith commitment, that allows no dissent. It is absolute.

Darwinism beyond the level of simple micro-evolution has never been observed or tested experimentally. And what’s more – the proponents of Darwinism do not want their theory to be subjected to criticism or testing. It fulfills a religious purpose, and therefore they are very concerned that it not be taken away from them. They are fighting against having to care what God thinks, and they will strangle any good experimental science that shows that their religion is wrong. You can see the same fundamentalism at work in the atheistic war against the experimental science that confirms the Big Bang theory, which describes the origin of the universe out of nothing.

Podcasts

Walter Bradley: three scientific phenomena that point to a designed universe

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Dr. Walter L. Bradley
Dr. Walter L. Bradley

Dr. Walter L. Bradley (C.V. here) is the Distinguished Professor of Engineering at Baylor.

Here’s a bio:

Walter Bradley (B.S., Ph.D. University of Texas at Austin) is Distinguished Professor of Engineering at Baylor. He comes to Baylor from Texas A&M University where he helped develop a nationally recognized program in polymeric composite materials. At Texas A&M, he served as director of the Polymer Technology Center for 10 years and as Department Head of Mechanical Engineering, a department of 67 professors that was ranked as high as 12th nationally during his tenure. Bradley has authored over 150 refereed research publications including book chapters, articles in archival journals such as the Journal of Material Science, Journal of Reinforced Plastics and Composites, Mechanics of Time-Dependent Materials, Journal of Composites Technology and Research, Composite Science and Technology, Journal of Metals, Polymer Engineering and Science, and Journal of Materials Science, and refereed conference proceedings.

Dr. Bradley has secured over $5.0 million in research funding from NSF grants (15 yrs.), AFOSR (10 years), NASA grants (10 years), and DOE (3 years). He has also received research grants or contracts from many Fortune 500 companies, including Alcoa, Dow Chemical, DuPont, 3M, Shell, Exxon, Boeing, and Phillips.

He co-authored The Mystery of Life Origin: Reassessing Current Theories and has written 10 book chapters dealing with various faith science issues, a topic on which he speaks widely.

He has received 5 research awards at Texas A&M University and 1 national research award. He has also received two teaching awards. He is an Elected Fellow of the American Society for Materials and the American Scientific Affiliation (ASA), the largest organization of Christians in Science and Technology in the world. He is President elect of the ASA and will serve his term in 2008.

You can read more about his recent research in this article from Science Daily.

Below, I analyze a lecture entitled “Is There Scientific Evidence for an Intelligent Designer?”. Dr. Bradley explains how the progress of science has made the idea of a Creator and Designer of the universe more acceptable than ever before.

The MP3 file is here.

Evidence #1: The design of the universe

1. The correspondence of natural phenomena to mathematical law

  • All observations of physical phenomena in the universe, such as throwing a ball up in the air, are described by a few simple, elegant mathematical equations.

2. The fine-tuning of physical constants and rations between constants in order to provide a life-permitting universe

  • Life has certain minimal requirements; long-term stable source of energy, a large number of different chemical elements, an element that can serve as a hub for joining together other elements into compounds, etc.
  • In order to meet these minimal requirements, the physical constants, (such as the gravitational constant), and the ratios between physical constants, need to be withing a narrow range of values in order to support the minimal requirements for life of any kind.
  • Slight changes to any of the physical constants, or to the rations between the constants, will result in a universe inhospitable to life.
  • The range of possible ranges over 70 orders of magnitude.
  • Although each individual selection of constants and ratios is as unlikely as any other selection, the vast majority of these possibilities do not support the minimal requirements of life of any kind. (In the same way as any hand of 5 cards that is dealt is as likely as any other, but you are overwhelmingly likely NOT to get a royal flush. In our case, a royal flush is a life-permitting universe).

Examples of finely-tuned constants and ratios: (there are more examples in the lecture)

a) The strong force: (the force that binds nucleons (= protons and neutrons) together in nucleus, by means of meson exchange)

  • if the strong force constant were 2% stronger, there would be no stable hydrogen, no long-lived stars, no hydrogen containing compounds. This is because the single proton in hydrogen would want to stick to something else so badly that there would be no hydrogen left!
  • if the strong force constant were 5% weaker, there would be no stable stars, few (if any) elements besides hydrogen. This is because you would be able to build up the nuclei of the heavier elements, which contain more than 1 proton.
  • So, whether you adjust the strong force up or down, you lose stars than can serve as long-term sources of stable energy, or you lose chemical diversity, which is necessary to make beings that can perform the minimal requirements of living beings. (see below)

b) The conversion of beryllium to carbon, and carbon to oxygen

  • Life requires carbon in order to serve as the hub for complex molecules, but it also requires oxygen in order to create water.
  • Carbon is like the hub wheel in a tinker toy set: you can bind other elements together to more complicated molecules (e.g. – “carbon-based life), but the bonds are not so tight that they can’t be broken down again later to make something else.
  • The carbon resonance level is determined by two constants: the strong force and electromagnetic force.
  • If you mess with these forces even slightly, you either lose the carbon or the oxygen.

3. Fine-tuning to allow a habitable planet

  • A number of factors must be fine-tuned in order to have a planet that supports life
  • Initial estimates predicted abundant life in the universe, but revised estimates now predict that life is almost certainly unique in the galaxy, and probably unique in the universe.
  • Even though there are lots of stars in the universe, the odds are against any of them supporting complex life.
  • Here are just a few of the minimal requirements for habitability: must be a single star solar system, in order to support stable planetary orbits, the planet must be the right distance from the sun in order to have liquid water at the surface, the planet must sufficient mass in order to retain an atmosphere, etc.

The best non-theistic response to this argument is to postulate a multiverse, but that is very speculative and there is no experimental evidence that supports it.

Evidence #2: The origin of the universe

1. The progress of science has shown that the entire physical universe came into being out of nothing (= “the big bang”). It also shows that the cause of this creation event is non-physical and non-temporal. The cause is supernatural.

  • Atheism prefers an eternal universe, to get around the problem of a Creator having to create the universe.
  • Discovery #1: Observations of galaxies moving away from one another confirms that the universe expanded from a single point.
  • Discovery #2: Measurements of the cosmic background radiation confirms that the universe exploding into being.
  • Discovery #3: Predictions of elemental abundances prove that the universe is not eternal.
  • Discovery #4:The atheism-friendly steady-state model and oscillating model were both falsified by the evidence.
  • And there were other discoveries as well, mentioned in the lecture.

The best non-theistic response to this argument is to postulate a hyper-universe outside of ours, but that is very speculative and there is no experimental evidence that supports it.

Evidence #3: The origin of life

1. The progress of science has shown that the simplest living organism contains huge amounts of biological information, similar to the Java code I write all day at work. This is a problem for atheists, because the sequence of instructions in a living system has to come together all at once, it cannot have evolved by mutation and selection – because there was no replication in place prior to the formation of that first living system!

  • Living systems must support certain minimum life functions: processing energy, storing information, and replicating.
  • There needs to be a certain amount of complexity in the living system that can perform these minimum functions.
  • But on atheism, the living system needs to be simple enough to form by accident in a pre-biotic soup, and in a reasonable amount of time.
  • The minimal functionality in a living system is a achieved by DNA, RNA and enzymes. DNA and RNA are composed of sequences of proteins, which are in turn composed of sequences of amino acids.

Consider the problems of building a chain of 100 amino acids

  • The amino acids must be left-handed only, but left and right kinds are equally abundant in nature. How do you sort out the right-handed ones?
  • The amino acids must be bound together using peptide bonds. How do you prevent other types of bonds?
  • Each link of the amino acid chain needs to be carefully chosen such that the completed chain with fold up into a protein. How do you choose the correct amino acid for each link from the pool of 20 different kinds found in living systems?
  • In every case, a human or other intelligence could solve these problems by doing what intelligent agents do best: making choices.
  • But who is there to make the choices on atheism?

The best current non-theistic response to this is to speculate that aliens may have seeded the Earth with life at some point in the past.

The problem of the origin of life is not a problem of chemistry, it is a problem of engineering. Every part of car functionality can be understood and described using the laws of physics and chemistry. But an intelligence is still needed in order to assemble the components into a system that has the minimal requirements for a functioning vehicle.