P.Z. Myers vs Intelligent Design

The spokesperson for the modern intelligent design movement wrote a review on a NY Times article concerning some genes in fish which might give evolutionists ideas on how fins turned to feet. This prompted P.Z. Myers who uses evolution often to try and discredit the existence of God and creationism in general to respond to the review. Myers writes

“Stop, Casey, and think. Here’s this fascinating observation, that we keep finding conserved genes and conserved regulatory regions between mice and fish, which ought to tell you something, and your argument against a specific example is that it isn’t rare? It really tells you something when your critics’ rebuttal to a piece of evidence is that you’ve got so much evidence for your position that they’re tuning out whenever you talk about the detais.”

Here is what Casey Luskin who is the spokesperson for the modern intelligent design movement wrote in his review

“The real story isn’t quite that interesting. According to the Nature paper, a particular region of DNA associated with a Hox gene cluster in the coelocanth genome showed sequence homology with a stretch of Hox gene-related DNA in tetrapods. Hox genes are known to be widely conserved among vertebrates, so the fact that homology was found between Hox-gene-associated DNA across these organisms isn’t very surprising.”

“The authors aren’t sure exactly what this particular segment of DNA does, though it’s probably a promoter region. In mice the corresponding homologous region is associated with Hox genes that are important for forming the placenta. Ergo, we’ve solved the mystery of how the placenta evolved. Right?”

“Not really. Again, all that was found was a little homologous promoter region in Hox-gene related DNA in these two types of organisms. Given that we don’t even understand exactly what these genes do or how they work, obviously the study offered no discussion of what mutations might have provided an evolutionary advantage.”

No evolutionary pathway was proposed, or even discussed. So there’s not much meat to this story, other than a nice little region of homology between two shared, functional pieces of Hox-gene-related DNA. But of course, such shared functional DNA could be the result of common design and need not indicate common descent or Darwinian evolution.”

Casey Luskin is correct in this regard, there isn’t much to the discovery. No knowledge on how these genes work or why they work. All this paper claims is “homology” which isn’t hard evidence for evolution. Why? For one, similarities between organisms that evolutionists don’t believe are closely related!

Next Myers attacks intelligent design referring to it as “creationism”

“The Intelligent Design creationist explanation requires that every extant species was specifically and intentionally stocked with a set of genes hand-chosen by a designer. God magically inserted IgM into each vertebrate species, except that he missed the coelacanths, and he magically inserted IgW into each and every shark, ray, coelacanth, and lungfish, but he intentionally left them out of every tetrapod and teleost.” 

Of course the modern intelligent design movement denies any reference to God, because to them that wouldn’t be scientific. But they don’t define what an intelligent agent or agents is, thus anyone guessing what they mean by that would be considered an ad hominem argument. But when you use intelligent agent or agents within your framework in which you call science, it is reasonable to challenge or question who or what that is! Of course Myers assumes its God and labels it creationism because the courts outlawed it being taught in the public schools. Myers then also assumes how a mind (in this case, God) would create nature which is interesting.

Myers uses uniqueness as proof for a creator, because evolution uses “homology” for its framework or another words God wouldn’t have created that way so it was evolution. However, he is wrong! For example, a car company often times uses the same parts in different cars. Does that mean cars are not intelligently designed rather they naturally evolved? No! You can tell that Ford models are similar. The Ford company doesn’t make each model drastically different from other models that it produces in that same year. Conversely, most of the genetic code for all living things is universal, because for one, it indicates a lone designer not many different designers. Also, it has a purpose, this makes the code optimal for protecting against errors!

Here is a challenge for Myers! What scientific research has produced hard evidence that an intelligent designer would only produce each species using totally different parts? Didn’t you believe that creationism couldn’t be tested therefore not a science then how could you come up with such a conclusion on how God would create? Didn’t you believe only evolution could be tested therefore a science? Myers uses evolution exactly like a spiritual cult does in order to try and disprove in what he doesn’t want to believe in, and that is God! This is why his argument is a bluff of complexity rather than logical. Science has not disproved God neither has P.Z Myers version of evolution disproved God!        

Skeptics of ENCODE’s Discovery of Function

In 1972, geneticist, Susumu Ohno, was the first to coin the term “junk” DNA in reference to  pseudogenes but the meaning expanded to non-coding DNA as well. Ohno stated, “The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?

Out of a span of 30 years or so, scientists didn’t do much research on what was considered “fossil remains” of DNA.  Then a group of scientists called, ENCODE discovered something very interesting in 2007. DNA is transcribed into RNA!

Ewan Birney, a coordinator of ENCODE said, “The genome looks like it is far more of a network of RNA transcripts that are all collaborating together. Some go off and make proteins; [and] quite a few, although we know they are there, we really do not have a good understanding of what they do.” 

Then on September 5, 2012, the guardian reports…

“Long stretches of DNA previously dismissed as “junk” are in fact crucial to the way our genome works, an international team of researchers said on Wednesday.

It is the most significant shift in scientists’ understanding of the way our DNA operates since the sequencing of the human genome in 2000, when it was discovered that our bodies are built and controlled by far fewer genes than expected. Now the next generation of geneticists have updated that picture.”

80 percent of the genome is now regarded to having function which is a major shift considering most of it was considered junk. The discovery has caused quite a stir with those who advocate “junk DNA” being necessary for evolution (having a critical role in ensuring the survival of biological lineages) while using it for evidence against creationism or intelligent design.

P.Z Meyers has been a skeptic of ENCODE and a huge advocate of junk DNA, (but admires their work) here he writes the following in his blog called, “The ENCODE Delusion.” 

“The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type.”

“That isn’t function. (says PZ Myers) That isn’t even close. And it’s a million light years away from “a critical role in controlling how our cells, tissue and organs behave”. All that says is that any one bit of DNA is going to have something bound to it at some point in some cell in the human body, or may even be transcribed. This isn’t just a loose and liberal definition of “function”, it’s an utterly useless one.”

Nick Matzke in Panda’s Thumb, reiterates what Myers spewed out…

“The science media exploded today with the claim from the ENCODE project that 80% of the genome is “functional”. The creationists are already beside themselves with joy. And the problem cannot be blamed on the science media, although I wish they were quicker to exercise independent skepticism – the 80% claim is right there in the abstract of the Nature article.”

“However, skepticism has arisen spontaneously from all over the scientific blogosphere, facebook, and twitter. You see, most of us scientists know that (a) ENCODE is using an extremely liberal and dubious definition of “function”, basically meaning “some detectable chemical activity”.

“People have pointed out that randomly generated DNA sequences would often be “functional” on this definition. (b) All the evidence for relative nonfunctionality which has been known for decades is still there and hasn’t really changed – lack of conservation, onion test, etc. But I’m beginning to think that certain parts of molecular biology and bioinformatics are populated with people who are very smart, but who got through school with a lot of detailed technical training but without enough broad training in basic comparative biology.”

ENCODE defines function by activity meaning, the transcription into RNA which makes 80% of our DNA functional which is a perfectly logical conclusion. However, PZ Myers suggests in his sarcasm…”Oh, jeez, straining over definitions—ultimately, what he ends up doing is redefining “functional” to not mean functional at all, but to mean simply anything that their set of biochemical assays can measure.” 

ID proponent and scientist says…”Non-protein-coding DNA even provides spacers to regulate the timing of protein production; and focusing light in rod cells in the retinas of nocturnal mammals.”  –Biologist Jonathan Wells.

Skeptics of ENCODE, are just one angry bunch of men because one of their weapons they have used for many years is being taken away from them as a result of better science. There is nothing to suggest that the majority of scientists even agree with them just rumblings on facebook and twitter. That is not to say the majority in the science community is always right, (many times they are wrong concerning evolution) but they have always advocated the majority to creationists as being logically conclusive and right in science. But we know that is nothing more than a straw man’s argument along with circular reasoning.

Most Ambitious Human Genetics Project To Date

New science is putting the so-called leftovers from our supposed evolutionary past to shame! When the first study of the genome was published about 11 years ago, scientists were surprised to find that only about 3% of it coded for proteins and the rest was considered, “junk DNA.”

Then of course new science discoveries came to be where researchers discovered coded information in the “epigenome,” which includes RNAtranscripts that regulate the code.  New results from the most ambitious human genetics project to date,  show at the least, 80 percent of the genome has a function! A remarkable turnaround in slightly over a decade.

The turnaround has become one of the major stories for science discoveries this year and could be the best breakthrough study out of them all in science for this year as well! Numerous publications have been writing about it. Over 20 papers were published in various publications like Genome Research and Genome Biology, along with reviews in The Journal of Biological Chemistry. Even my local newspaper made this front page news and described what it means for possible future medical uses.

It also has Darwinists putting to rest the notion of  leftovers from our supposed evolutionary past which had been heavily promoted by militant evolutionists who lobby hard against creationism and intelligent design such as  P.Z. Myers, Nick Matzke, Jerry Coyne, Kenneth Miller and British atheist, Richard Dawkins.

It has been part of the creationism model and ID proponents who have argued for years that function will be discovered for much of our DNA that was once considered to be useless with better science and indeed it has!

In an article in Nature

“The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. 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 newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation.

“Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.”  

Was the evolutionary explanation helpful with this discovery? Nope.  In this article in Nature, it says…“Why evolution would maintain large amounts of ‘useless’ DNA had remained a mystery, and seemed wasteful,” Barroso wrote.  “It turns out, however, that there are good reasons to keep this DNA.”

Language like  “evolutionary constraints” and “evolutionarily conserved” used in many of the articles is another indication that evolution was useless when it came to this discovery. Both of those terms of course refer to lack of evolution rather than showing evolution which is why the likes of P.Z. Myers, Nick Matzke, Jerry Coyne, Kenneth Miller and Richard Dawkins advocate junk DNA very heavily! Perhaps it will modify their position, anything left which is considered “junk DNA” they will begin to focus on. Or they could hold the position what New Scientist is now advocating with their skepticism of finding function with non-coding DNA.

“The ENCODE project has revealed that 80 per cent of our genome does something, but doing something is not the same as doing something useful…there are still very good reasons for thinking that most of our DNA is far from essential.”

You can tell that this discovery is not good for evolution when you have a publication like New Scientist that confuses “essential” with “adaptive” and then begs the question whether something useful must be essential. On the other side, ID proponents are jumping for joy, Casey Luskin writes

“We will have more to say about this blockbuster paper from ENCODE researchers in coming days, but for now, let’s simply observe that it provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called “junk” DNA. ENCODE researchers use words like “surprising” or “unprecedented.”

“They talk about of how “human DNA is a lot more active than we expected.” But under an intelligent design paradigm, none of this is surprising. In fact, it is exactly what ID predicted.” 

While this breakthrough in science has caused a problem for the story of evolution, Darwinists have pushed back the idea of forcing the data into their evolutionary framework for future researchers such as in this article, “Evolution and the Code” where one scientist mentions it, but the other three did not which doesn’t mean they didn’t go along with the assumption in the same paper in which they co-wrote together.

Here is a video, where it suggest there might be more than 80 percent function with the genome. “There are probably things that we have no idea what they’re doing and yet they’re going something important.” A logical assumption considering the pattern of discoveries being made so far!

 

Evolution has hurt this part of research for years with its assumption of junk DNA but not anymore. Now researchers are looking for more functions than ever before! Here is more quotes by scientists…

“I don’t think anyone would have anticipated even close to the amount of sequence that ENCODE has uncovered that looks like it has functional importance,” says John A. Stamatoyannopoulos, an ENCODE researcher at the University of Washington, Seattle.  He is referring to researchers who believe in evolution, other scientists have anticipated a lot more sequence that ENCODE.

“It’s a treasure trove of information,” says Manolis Kellis, a computational biologist from Massachusetts Institute of Technology (MIT) in Cambridge who analyzed data from the project.

“Regulation is a 3D puzzle that has to be put together,” Gingeras says. “That’s what ENCODE is putting out on the table.”

What an amazing time we live in! Wow! Unless there is a cure for cancer or someone lands on Mars, this is no doubt the science breakthrough for 2012 which confirms creationism and will also help improve the health of mankind!

P.Z. Myers Asserts The Mediocrity Principle

The “anthropic argument” which is used for creationism which includes the existence of God is based on the tight values taken on by certain constants in the world of physics thus making our own existence unique and implies intent produced by intelligence. Albert Einstein was the first to propose the cosmological constant.

Cosmic microwave background (CMB) measurement not only demonstrate the existence of the cosmological constant, but also the value of the constant which makes up the lack of matter in the universe. It’s alternative explanation to the invisible dark matter, many secular scientists have embraced. Now there are also various other constants, here are few examples…

1) An electromagnetic force constant, if this is greater, it would cause chemical bonding to be disrupted; elements more massive than boron would be unstable to fission. Now if it was lesser: the chemical bonding would be insufficient for life chemistry.

2) Ratio of electron to proton mass, regardless of greater or lesser, the results would be the same, chemical bonding would be not sufficient enough for life chemistry.

3) The sun, earth’s closest star. It’s made up mostly of hydrogen and helium. Surface temperature is an incredible 6,000 degrees Kelvin. The Bible talks about the sun being, “the greater light” which governs the day. All life on earth depends on the sun. If the sun would burn out one day, it would cause the earth to freeze, the atmosphere would condense, liquefy and freeze, rendering the earth’s temperature to deep space.  The sun is unique, the light and heat from most stars is very variable but the Sun is relatively constant.

PZ Myers is a biologist and associate professor at the University of Minnesota, Morris. Some regard him as a militant atheist who presents very anti-christian viewpoints in his blog. Recently, he wrote about how he teaches students at his University about the “Mediocrity Principle” which he regards it as a must for science. What is it?  He describes it this way…

1) “The mediocrity principle simply states that you aren’t special.”

2) “What the mediocrity principle tells us is that our state is not the product of intent, that the universe lacks both malice and benevolence, but that everything does follow rules — and that grasping those rules should be the goal of science.”

3) “Everything that you as a human being consider cosmically important is an accident.”

4) “Most of what happens in the world is just a consequence of natural, universal laws”

P.Z. Myers claims that “Opposition to the mediocrity principle is one of the major linchpins of religion and creationism and jingoism and failed social policies.” He fails directly to answer, why is that “essential” to science?  Why would accidents be compelled to follow any rules? ““Everything that you as a human being consider cosmically important is an accident.” How could your kids be considered nothing special but just an accident? Many people plan with their intelligence (not instincts) on having kids and many also accomplish those goals.

PZ is clearly advocating atheism while attacking Christianity and other religions by calling them a “cognitive ill” which can be done a way with if only people would have faith in the Mediocrity Principle which has no foundation on what is observed in the real world and attempts to tell us that this is required in science. We are special, we live in a special place, with tight constants that have been designed in such a way that allows us to live our lives in, kids are a blessing to us, not an accident!