New study: function found for beta-globin pseudogene that was labeled “junk” during Dover trial

Casey Luskin tells us about a new study in Evolution News.

Excerpt:

A new paper in Genome Biology and Evolution argues that the famous beta-globin pseudogene is functional. Why is this pseudogene famous?

Well, it’s been Exhibit A — literally, offered as evidence in a court case — for critics of intelligent design who argue that our genome is full of useless, functionless junk, and therefore can’t be a product of design. Near the beginning of his testimony on the very first day of the 2005 Kitzmiller v. Dover trial, Brown University biology professor Kenneth Miller testified to the court that the beta-globin pseudogene is “broken, and it has a series of molecular errors that render the gene non-functional.” (Day 1 AM, p. 79.) He further told the court:

And the fact that all three of these species have matching mistakes leads us to just one conclusion, and that’s the same conclusion that Charles Darwin predicted almost a century and a half ago, and that is that these three species share a common ancestor. Matching mistakes are evidence of common ancestry. (Day 1 AM, p. 81)

In his 2008 book Only a Theory, Miller is even more explicit in asserting that this pseudogene refutes intelligent design. He writes that “A detailed analysis of the beta-globin pseudogene shows a series of mutations have rendered it nonfunctional” (p. 102). In Miller’s view, that takes care of ID:

The gorilla and chimpanzee pseudogenes have exactly the same set of molecular errors [in their beta-globin pseudogene] … There’s no escaping the implication of these matching mistakes, and there’s no point in arguing that six identical mistakes could have turned up independently in three unrelated species. The only sensible interpretation is that the original errors developed at random in a single common ancestor of these three species. In a court of genetic copyright law, any motion that a designer could claim originality for the human genome would be tossed out in a flash. (pp. 102-103)

Now a new paper in Genome Biology and Evolution, “Evolutionary Constraints in the β-Globin Cluster: The Signature of Purifying Selection at the δ-Globin (HBD) Locus and Its Role in Developmental Gene Regulation, argues that the beta-globin pseudogene is not broken, but in fact performs an important function in regulating gene expression.

Remember, Darwinists are still reeling from the ENCODE study that found that the non-coding DNA that they said was 100% junk was actually 80% functional. The trouble is that they are always letting their philosophy of naturalism get in the way of their science. They assume that nature is all there is. They assumed that everything is not designed. Then they are quick to say that things that aren’t junk are junk, in order to confirm their assumption. Problems occur later when good science comes along and proves their philosophical assumption of naturalism wrong. Do they then give up the philosophical assumption? Heck no – that’s their religion! But they ought to give it up if they were honest, and stick with the science instead. Too much bad religion among the Darwinists – that’s the problem.

Filed under: News, Atheism, Darwin, Darwinian, Darwinism, Design, Dogma, Evidence, Evolution, Experiment, Junk, Junk DNA, Naturalism, Religion, Science

New study: formation of life-permitting elements carbon and oxygen is fine-tuned

First, let’s review the structure of the fine-tuning argument.

The argument goes like this:

1. The fine-tuning of the universe to support life is either due to law, chance or design
2. It is not due to law or chance
3. Therefore, the fine-tuning is due to design

Here are the facts on the fine-tuning:

• 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, a universal solvent, 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 ratios between the constants, will result in a universe inhospitable to life.
• The range of possible values spans 70 orders of magnitude.
• The constants are selected by whoever creates the universe. They are not determined by physical laws. And the extreme probabilities involved required put the fine-tuning beyond the reach of chance.
• 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).

Carbon is that element that can serve as a hub, and oxygen is also a vital element, since it is a component of water, which is required for life. So both carbon (the hub of large molecules) and oxygen (a building block of water) are required for complex life of any imaginable kind.

Now for the new study.

Reader Jen who blogs at Victory Rolls and V8s sent me this amazing article on Science Daily about a new peer-reviewed study that supports the fine-tuning argument.

Here’s an excerpt:

Life as we know it is based upon the elements of carbon and oxygen. Now a team of physicists, including one from North Carolina State University, is looking at the conditions necessary to the formation of those two elements in the universe. They’ve found that when it comes to supporting life, the universe leaves very little margin for error.

Both carbon and oxygen are produced when helium burns inside of giant red stars. Carbon-12, an essential element we’re all made of, can only form when three alpha particles, or helium-4 nuclei, combine in a very specific way. The key to formation is an excited state of carbon-12 known as the Hoyle state, and it has a very specific energy — measured at 379 keV (or 379,000 electron volts) above the energy of three alpha particles. Oxygen is produced by the combination of another alpha particle and carbon.

NC State physicist Dean Lee and German colleagues Evgeny Epelbaum, Hermann Krebs, Timo Laehde and Ulf-G. Meissner had previously confirmed the existence and structure of the Hoyle state with a numerical lattice that allowed the researchers to simulate how protons and neutrons interact. These protons and neutrons are made up of elementary particles called quarks. The light quark mass is one of the fundamental parameters of nature, and this mass affects particles’ energies.

In new lattice calculations done at the Juelich Supercomputer Centre the physicists found that just a slight variation in the light quark mass will change the energy of the Hoyle state, and this in turn would affect the production of carbon and oxygen in such a way that life as we know it wouldn’t exist.

[...]The researchers’ findings appear in Physical Review Letters.

So that’s the latest research that supports the fine-tuning argument. But how effective is this argument really? Is it only admitted by theists, or do atheists accept the fine-tuning as well?

Is the fine-tuning real?

Yes, it’s real and it is conceded by the top-rank of atheist physicists. Let me give you a citation from the best one of all, Martin Rees. Martin Rees is an atheist and a qualified astronomer. He wrote a book called “Just Six Numbers: The Deep Forces That Shape The Universe”, (Basic Books: 2001). In it, he discusses 6 numbers that need to be fine-tuned in order to have a life-permitting universe.

Rees writes here:

These six numbers constitute a ‘recipe’ for a universe. Moreover, the outcome is sensitive to their values: if any one of them were to be ‘untuned’, there would be no stars and no life. Is this tuning just a brute fact, a coincidence? Or is it the providence of a benign Creator?

There are some atheists who deny the fine-tuning, but these atheists are in firm opposition to the progress of science. The more science has progressed, the more constants, ratios and quantities we have discovered that need to be fine-tuned. Science is going in a theistic direction. Next, let’s see how atheists try to account for the fine-tuning, on atheism.

Atheistic responses to the fine-tuning argument

There are two common responses among atheists to this argument.

The first is to speculate that there are actually an infinite number of other universes that are not fine-tuned, (i.e. – the gambler’s fallacy). All these other universes don’t support life. We just happen to be in the one universe is fine-tuned for life. The problem is that there is no way of directly observing these other universes and no independent evidence that they exist.

Here is an excerpt from an article in Discover magazine, (which is hostile to theism and Christianity).

Short of invoking a benevolent creator, many physicists see only one possible explanation: Our universe may be but one of perhaps infinitely many universes in an inconceivably vast multiverse. Most of those universes are barren, but some, like ours, have conditions suitable for life.

The idea is controversial. Critics say it doesn’t even qualify as a scientific theory because the existence of other universes cannot be proved or disproved. Advocates argue that, like it or not, the multiverse may well be the only viable non­religious explanation for what is often called the “fine-tuning problem”—the baffling observation that the laws of the universe seem custom-tailored to favor the emergence of life.

The second response by atheists is that the human observers that exist today, 14 billion years after the universe was created out of nothing, actually caused the fine-tuning. This solution would mean that although humans did not exist at the time the of the big bang, they are going to be able to reach back in time at some point in the future and manually fine-tune the universe.

Here is an excerpt from and article in the New Scientist, (which is hostile to theism and Christianity).

…maybe we should approach cosmic fine-tuning not as a problem but as a clue. Perhaps it is evidence that we somehow endow the universe with certain features by the mere act of observation… observers are creating the universe and its entire history right now. If we in some sense create the universe, it is not surprising that the universe is well suited to us.

So, there are two choices for atheists. Either an infinite number of unobservable universes that are not fine-tuned, or humans go back in time at some future point and fine-tune the beginning of the universe, billions of years in the past.

Why the fine-tuning argument matters

We need to make a decision today about how we are going to live. The evidence available today supports the fine-tuning of the universe by a supernatural mind with immense power. The progress of science has strengthened this theory against determined opposition from rival naturalistic theories.

Those are the facts, and we must all choose what to do with them.

Further study

Here is a paper by Walter L. Bradley that contains many more examples of the fine-tuning, and explanations for what happens when you change the constants, quantities and rations even slightly.

Filed under: Polemics, Aliens, Amino Acid, Apologetics, Atheism, Carbon, Carbon-based Life, Chance, Complex Life, Constants, Cosmological Constants, Cosmology, Design, Fine Tuning, Habitability, Intelligent Design, Life, Liquid Water, Oxygen, Physical Laws, Physics, Probability Theory, Progress of Science, Protein, Solvent, Universal Solvent, Water

Stephen Meyer debates Peter Ward on intelligent design vs Darwinism

The speakers

Stephen C. Meyer is director of the Discovery Institute’s Center for Science and Culture (CSC) and a founder both of the intelligent design movement and of the CSC, intelligent design’s primary intellectual and scientific headquarters. Dr. Meyer is a Cambridge University-trained philosopher of science, the author of peer-reviewed publications in technical, scientific, philosophical and other books and journals. His signal contribution to ID theory is given most fully in Signature in the Cell: DNA and the Evidence for Intelligent Design, published by HarperOne in June 2009.

Graduating from Whitworth College in Spokane, Washington, in 1981 with a degree in physics and earth science, he later became a geophysicist with Atlantic Richfield Company (ARCO) in Dallas, Texas. From 1981 to 1985, he worked for ARCO in digital signal processing and seismic survey interpretation. As a Rotary International Scholar, he received his training in the history and philosophy of science at Cambridge University, earning a PhD in 1991. His thesis offered a methodological interpretation of origin-of-life research.

Peter D. Ward, Ph.D., is a paleontologist and professor in the Departments of Geology and Biology at the University of Washington in Seattle. He also serves as an adjunct professor of zoology and astronomy. His research specialties include the Cretaceous–Tertiary extinction event and mass extinctions generally. His books include the best-selling “Rare Earth: Why Complex Life Is Uncommon in the Universe” (co-author Donald Brownlee, 2000), “Under a Green Sky: Global Warming, the Mass Extinctions of the Past, and What They Can Tell Us About Our Future” (2007), and “The Medea Hypothesis: Is Life on Earth Ultimately Self-Destructive?” (2009).

The debate

Here’s the video of the debate:

The debate itself starts at around 8:19, after all the moderators have spoken.

There is a review of this debate here on Evolution News, and I include a snip to encourage you to watch it:

Last night, the Seattle Times Talk of the Times at Town Hall Seattle featured a debate over evolution and intelligent design between CSC Director Stephen Meyer and US paleontologist Peter Ward. The event was sold out with 800+ in attendance for what turned out to be a really good debate.

[...]The debate last night was almost ALL about science–from gene sequencing, to nanotechnology, to the Cambrian explosion, to the philosophy of science that decides how to define the terms in the first place. Both scientists are experts in their fields and the audience was eager to hear what they had to say. No matter how much Darwinists claim there is no debate, and that intelligent design somehow kills curiousity, you can’t argue with hundreds of people showing up to eagerly hear what both sides have to say about the issue. Clearly they were curious about the debate that doesn’t exist.

That article also includes a blow-by-blow summary by a person sympathetic to ID who attended the debate. This is probably the best debate on intelligent design out there, and it was only recently uploaded to Youtube in September last year. When I watch a great debate like this, it really makes me hope that we who do believe that life is designed are raising up the next generation of scientists who ask questions, and don’t assume this philosophical assumption of naturalism. Do the science first. Don’t assume anything religious. Don’t let the religion of naturalism determine what science can and cannot discover. That’s the burden of our side, anyway.

And now a surprise! There is actually a transcript of this debate that I found on the Discovery Institute web site. Isn’t it amazing that intelligent design has been out there for such a long time, yet almost no one can define it, and no one has ever seen a debate where both sides come out to debate it. You can download the audio here, but it’s 90 Mb.

Even though Peter Ward is an atheist, he has co-written a fabulous book that I own and have read called “Rare Earth: Why Complex Life is Uncommon in the Universe“. I really recommend getting this book, as it is a great book by two non-theists on the habitability argument. It’s sort of a secular precursor to Jay Richards’ and Guillermo Gonzalez’s “The Privileged Planet: How Our Place in the Cosmos is Designed for Discovery“. The habitability argument is a really neglected argument, but it’s a good one.

Filed under: Videos, Cambrian, Cambrian Explosion, Cell, Chance, Computer Science, Darwinism, Debate, Design, Education, Evolution, Fossil Record, Habitability, Intelligence, Intelligent Design, Michael Behe, Naturalism, Origin of Life, Peter D. Ward, Peter Ward, Philosophy of Science, Probability, Public Schools, Schools, Science, Stephen C. Meyer, Stephen Meyer, Teach the Controversy

Target acquisition and interception in dragonflies

Here is a fascinating post about some of the capabilities of dragonflies from Evolution News.

Selective attention

First, dragonflies have “selective attention” – the ability to focus on a single prey and ignore other distractions:

Dragonflies are among the best flyers in the insect world. Their twin pairs of paper-thin wings allow them to hover and move in all directions, even in mating. When the time comes to dart after prey at high speed, they rarely miss.

What’s their secret? One is “selective attention” — a trait previously known only in primates, according to new research from the University of Adelaide, Australia. Selective attention is the ability to focus on one object and exclude others. Just as a tennis player must focus on the ball and ignore the cheers of the crowd, a dragonfly must pick out one target from a swarm of insects and avoid being distracted by all the others.

Here’s a snip from the research paper:

Our data make a compelling case that CSTMD1 reflects competitive selection of one target. We emphasize “competitive,” because the attended target is not always the same between trials or even within a trial, as seen in strikingly perfect switches from one to the other…. Competition is further suggested by rare examples where the activity observed under Pair stimulation initially lags both T₁and T₂ responses… suggesting initial conflict in the underlying neural network before resolution of competition by a “winning” target.

We previously showed that CSTMD1 still responds robustly to a target even when it is embedded within a high-contrast natural scene containing numerous potential distracters. Taken together with recent evidence that the behavioral state of insects strongly modulates responses of neurons involved in visuomotor control, our new data thus suggest a hitherto unexpected sophistication in higher-order control of insect visual processing, akin to selective attention in primates.Perhaps the most remarkable feature of our data is that once the response “locks” onto a target (or following a switch), the second target exerts no influence on the neuron’s response: the distracter is ignored completely.

In order to succeed at the task of catching its prey, the dragonfly has to tune out all other distractions.

Target selection

In addition, dragonflies have the ability to intercept a target in mid-air – similar missile defense systems on AEGIS cruisers and destroyers.

The Evolution News article explains:

Another paper on dragonflies shows that these marvels of the insect world are equipped with navigational equipment that can do vector calculus. In the Proceedings of the National Academy of Sciences, Gonzalez-Bellido and a team at the Howard Hughes Medical Institute discerned “Eight pairs of descending visual neurons in the dragonfly [that] give wing motor centers accurate population vector of prey direction.“

Intercepting a moving object requires prediction of its future location. This complex task has been solved by dragonflies, who intercept their prey in midair with a 95% success rate. In this study, we show that a group of 16 neurons, called target-selective descending neurons (TSDNs), code a population vector that reflects the direction of the target with high accuracy and reliability across 360°. The TSDN spatial (receptive field) and temporal (latency) properties matched the area of the retina where the prey is focused and the reaction time, respectively, during predatory flights. The directional tuning curves and morphological traits (3D tracings) for each TSDN type were consistent among animals, but spike rates were not. Our results emphasize that a successful neural circuit for target tracking and interception can be achieved with few neurons and that in dragonflies this information is relayed from the brain to the wing motor centers in population vector form.

What did I make of this? Well, evidence like this always causes me to think aboutthe reality of God, and the disturbing thought that we do not live in an accidental universe where I can do whatever I want and be accountable to no one. It’s easier to believe that – it requires less work and it frees us to be our own boss and make our happiness the first priority. As individuals, it’s very tempting for us to think that we are number one, and to resent our obligations to anyone else. The problem is that the scientific data doesn’t support that worldview. The facts are what they are and it is up to us, now, to try to find out who the designer is and what he wants from us.

Filed under: News, Biology, Biomimetics, Darwinism, Design, Dragonflies, Dragonfly, Engineering, Evolution, Intelligent Design, Naturalism, Research, Theism

How biological convergence falsifies Darwinian evolution

Cornelius Hunter, a software engineer / biologist with a Ph.D in bioinformatics from UIUC explains the latest discovery of biological convergence on his blog. (H/T Tweet from J. Warner Wallace)

Excerpt:

The theory of evolution states that the species arose spontaneously, one from another via a pattern of common descent. This means the species should form an evolutionary tree, where species that share a recent common ancestor, such as two frog species, are highly similar, and species that share a distant common ancestor, such as humans and squids, are very different. But the species do not form such an evolutionary tree pattern. In fact this expectation has been violated so many times it is difficult to keep track. These violations are not rare or occasional anomalies, they are the rule. Entire volumes have been written on them. Many examples are the repeated designs found in what, according to evolution, must be very distant species. Such evolutionary convergence is biology’s version of lightning striking twice. To explain this evolutionists must say that random mutations just happened to hit upon the same detailed, intricate design at different times, in different parts of the world, in different ecological niches, and so forth. The idea that the most complex designs we know of would spontaneously arise by themselves is, itself, not scientifically motivated and a real stretch of the imagination. But for the same intricate designs to arise independently by chance is even more of a stretch. That is why evolutionist’s claim this week that they have found evidence for convergent evolution was so intriguing.

[...]Though evolutionists sometimes deny biological convergence, it is a scientific fact. And a paper from this week added yet another example:

In mammals, hearing is dependent on three canonical processing stages: (i) an eardrum collecting sound, (ii) a middle ear impedance converter, and (iii) a cochlear frequency analyzer. Here, we show that some insects, such as rainforest katydids, possess equivalent biophysical mechanisms for auditory processing. Although katydid ears are among the smallest in all organisms, these ears perform the crucial stage of air-to-liquid impedance conversion and signal amplification, with the use of a distinct tympanal lever system. Further along the chain of hearing, spectral sound analysis is achieved through dispersive wave propagation across a fluid substrate, as in the mammalian cochlea. Thus, two phylogenetically remote organisms, katydids and mammals, have evolved a series of convergent solutions to common biophysical problems, despite their reliance on very different morphological substrates.

It is another curious example of biological convergence, so rather than attempt to deny the undeniable, evolutionists now claim it as another confirmation of evolution.

I’m a software engineer, and we re-use components all the time for different programs that have no “common ancestor”. E.g. – I can develop my String function library and use it in my web application and my Eclipse IDE plug-in, and those two Java programs have no common ancestry, but they do have a common designer. So you find the same bits in two different programs because I am the developer of both programs.

Previously, I blogged about another example of convergence reported by Science Daily. One of the predictions of intelligent design theory is that examples of convergence, which is really just re-use of common code by the designer, will be everywhere in nature. And that predictions just keeps getting confirmed as science marches forward, and the primitive religion of naturalism retreats.

Filed under: News, Ancestor, Ancestry, Bioinformatics, Biological Convergence, Biology, Common Ancestry, Common Design, Common Designer, Computer Science, Convergence, Convergent Evolution, Convergent Trait, Darwinism, Design, Design Patterns, Designer, DNA, Evolution, Feature, Gene, Genetics, Information Theory, Intelligent Design, Mutation, Phenotype, Phylogeny, Selection, Structure, Trait