Intelligent Reasoning

Promoting, advancing and defending Intelligent Design via data, logic and Intelligent Reasoning and exposing the alleged theory of evolution as the nonsense it is. I also educate evotards about ID and the alleged theory of evolution one tard at a time and sometimes in groups

Friday, December 29, 2017

Biological Information in 3 Dimensions- Evidence for Life's Software, Again

Up to now biological information has always been related to the DNA sequence (sequence related). IOW the information depended on the sequence.

I do not believe this is a tenable position. I say that because in biology we observe that DNA just doesn't replicate itself, it does so with the help of other molecules in the cell. Those molecules are constructed by the information stored in the DNA. That's right- stored in- as in the data that is stored in a computer's hard drive, ROM and RAM.

And this is my point- that DNA, RNA and other cellular components are actually data carriers just like the computer components I just mentioned.

IOW the sequence is not the information. The sequence is important to carry out the instructions, that is the information embedded in the DNA (and perhaps other cellular components).

As I said in an earlier entry- Just for a eukaryotic cell to make an amino acid (polypeptide) chain-

Transcription and Translation:

You start with a tightly wound piece of DNA. Enzymes called RNA polymerases, along with transcrition factors, begin the process by unwinding a portion of DNA near the start of a gene, which is specified by sequences called promoters. Now there are two strands exposed. One strand is the coding strand- it has the correct sequence information for the product- and the other strand is the non-coding strand. That strand contains the complimentary layout.

At this point decisions have to be made. Where to start, where to stop and although it may seem counterintuitive the mRNA goes to the non-coding strand in order to reconstruct the proper codon sequence (nucleotide triplets which code for an amino acid) for the protein to be formed. Both sides of the parent DNA are exposed yet the mRNA "knows" to only form on one.

This process is unidirectional (5’-3’). There is only one start codon which also codes for an amino acid (met) and therefore all amino acid sequences start with methionine. The stop codons don’t code for an amino acid. Transcription actually starts before the “start” codon and continues past the stop codon. Before the mRNA leaves the nucleus any/ all introns are cut out and the remaining exons spliced together. A chemical cap is added to the 5’ end, the non-coding stuff at the end is cut off by a special enzyme (endonuclease) and a string of A’s is added in its place. You now have a processed mRNA.

So now we have this piece of processed mRNA which leaves the nucleus and has to rendezvous with a ribosome-the protein factory within the cell.

A ribosome consists of over 50 proteins and 3-4 different kinds of rRNA (ribosomal), plus free-floating tRNA (transfer). Each tRNA has a 3 nucleotide sequence- the anti-codon to the mRNA’s codon plus it carries the appropriate amino acid molecule for its anti-codon. To attach the appropriate amino acid to the correct anti-codon an enzyme called amino-acid synthase is used.

There, large workbenches made of both protein and nucleic acid grab the mRNA so the correct amino acids can be brought up to the mRNA. Each amino acid is escorted by a module called tRNA or transfer RNA. It is important to note that the escort molecules have three bases prominently exposed on their backsides and that these molecules also use the base U instead of T. The kind of amino acid is determined precisely by the tRNA escort’s anticodon, or triplet set of bases on the escort’s backside.-pg 23

And then the chain starts forming until the stop codon terminates the process.

Next is the folding process. That is what allows the protein to be useful- its spatial configuration.

That is just the basics of what one is introduced to when reading biology textbooks. And it doesn't include the proof-reading and error correction that accompanies the process.

So this is how I envision DNA- both sides of the ladder carry redundant information. One side does the work, that is transfers programming data to other molecules it contacts (mRNA for example) and the other side is a template for DNA replication.

Once DNA replication is complete the program is transferred to the newly constructed side via the hydrogen bonds that connect the two sides.

When other molecules are made- mRNA for example- they are given their instructions via the same hydrogen bonds. That information consists of editing instructions, as well as configuration/ assembly instructions and destination instructions.

These instructions are not the sequence, rather they are embedded on the sequence, just as computer data is embedded on the disk.

The ribosome is a genetic compiler!

The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist.

Think about it-

What happens to a newly written or modified computer code that has an error? All new and modified codes have to go through a compiler.

A compiler is nothing if not an editorial perfectionist!

I bet if we were to watch we would see the compiler doing its thing right up to the point the error occurs and then spits it out much faster than if the code was OK, ie error free.

Biologists need to be introduced to and experience computer science.

Then this sort of discovery wouldn’t be so “shocking”.

Compiler- source code in, object code out. Ribosome- mRNA in (string of nucleotides), polypeptide out (string of amino acids).

So where is the software? In the cell, meaning it is all throughout the cell- it isn't just in one place in the cell.

Thursday, December 28, 2017

Jerad the Broken Record

Ever try to have a discussion with someone who just lies and spews the same refuted shit over and over again? That is what it is like trying to have a discussion with UK Jerad. All Jerad has ever done here and anywhere else I have encountered him is lie and bluff. You can never get an answer from him. All you get is the same old shit over and over again as if his repeating hos shit is an actual argument. He never responds or actually addresses anything anyone actually says. He never supports any of his dumbass trope. He just repeats it ad nausea.

It's as if he is incapable of thinking. He attacks ID cuz ID isn't doing what ID was never meant to do. What the fuck is that besides ignorant desperation? He can't even read. I say that because some of his responses don't even follow from what he was responding to. He issues challenges that he hasn't even thought through and when his challenge is questioned he ignorantly claims victory. Typical for all evoTARDs.

EvoTARDs are so clueless and predictable. They harp and harp on ID all the while their own position remains untestable bullshit. Then they lie about that and yet never produce any methodology to test their claims! They ignorantly point to peer-review all the while peer-review never supports their position. When they do try to use peer-review it always blows up in their face and then they start accusing you of not understanding it all the while not being in able to make their own case.

That said it is time to say bye-bye to Jerad as I am sick of having my blog spammed with his cowardice and ignorance. If Jerad ever does actually ante up and start providing the evidence that supports his position and his claims I will post those. However given his track record that will never happen. All the while ID is growing stronger and stronger because the evidence for it is growing and growing. But Jerad wouldn't know because he is too stupid to assess the evidence.

Wednesday, December 27, 2017

The Blantant Stupidity of EvoTARDs

Yeah, yeah, I know- blatant stupidity is expected from evoTARDs. But this one takes the cake-

A shit-eating loser tat goes by Occam's Aftershave, ghostrider, and tiny timmy actually sed that the following page shows round stones as hand axes-

hand axe

Can anyone point to one round stone on that page? Anyone?

timmy's ignorant spewage

How pathetic are evoTARDs?

Tuesday, December 26, 2017

Doug Theobald is Ignorant of Nested Hierarchies

keiths continues to puke all over himself when it comes to nested hierarchies. And even though it has been proven that Doug Theobald is totally wrong keiths continues to reference him on nested hierarchies. Theobald wrongly spews:
The only known processes that specifically generate unique, nested, hierarchical patterns are branching evolutionary processes.

WRONG! Linnaean Taxonomy is an objective nested hierarchy and it doesn't have anything to do with branching evolutionary processes. Corporations can be placed in objective nested hierarchies and again they have nothing to do with branching evolutionary processes. The US Army is a nested hierarchy and it too has nothing to do with branching evolutionary processes.

Clearly Theobald is ignorant of nested hierarchies. He goes on to spew:
It would be very problematic if many species were found that combined characteristics of different nested groupings.
Umm, TRANSITIONAL FORMs have combined characteristics of different nested groups, Dougy. And your position expects numerous transitional forms.

But Doug's biggest mistake was saying that phylogenies form a nested hierarchy- they don't as explained in the Knox paper-  “The use of hierarchies as organizational models in systematics”, Biological Journal of the Linnean Society, 63: 1–49, 1998.

Wednesday, December 20, 2017

Intelligent Design, The Designer(s) and the Process(es)- again

Intelligent design begins with a seemingly innocuous question: Can objects, even if nothing is known about how they arose, exhibit features that reliably signal the action of an intelligent cause? Wm. Dembski
Yes, they can.

Most, if not all, anti-IDists always try to force any theory of intelligent design to say something about the designer and the process involved BEFORE it can be considered as scientific. This is strange because in every use-able form of design detection in which there isn’t any direct observation or designer input, it works the other way, i.e. first we determine design (or not) and then we determine the process and/ or designer. IOW any and all of our knowledge about the process and/ or designer comes from first detecting and then understanding the design.

IOW reality dictates the the only possible way to make any determination about the designer(s) or the specific process(es) used, in the absence of direct observation or designer input, is by studying the design in question.

If anyone doubts that fact then all you have to do is show me a scenario in which the designer(s) or the process(es) were determined without designer input, direct observation or by studying the design in question.

If you can't than shut up and leave the design detection to those who know what they are doing.
This is a virtue of design-centric venues. It allows us to neatly separate whether something is designed from how it was produced and/ or who produced it (when, where, why):
“Once specified complexity tells us that something is designed, there is nothing to stop us from inquiring into its production. A design inference therefore does not avoid the problem of how a designing intelligence might have produced an object. It simply makes it a separate question.”
Wm. Dembski- pg 112 of No Free Lunch
Stonehenge- design determined; further research to establish how, by whom, why and when.

Nasca Plain, Peru- design determined; further research to establish how, by whom, why and when.

Puma Punku- design determined; further research to establish how, by whom, why and when.

Any artifact (archeology/ anthropology)- design determined; further research to establish how, by
whom, why and when- that is unless we have direct observation and/ or designer input.

Fire investigation- if arson is determined (ie design); further research to establish how, by whom, why and when- that is unless we have direct observation and/ or designer input.

An artifact does not stop being an artifact just because we do not know who, what, when, where, why and how. But it would be stupid to dismiss the object as being an artifact just because no one was up to the task of demonstrating a method of production and/ or the designing agent.

And even if we did determine a process by which the object in question may have been produced it does not follow that it will be the process used.

As a comparison no need to look any further than abiogenesis and evolutionism. Evolutionitwits make those separate questions even though life’s origin bears directly on its subsequent diversity. And just because it is a separate question does not hinder anyone from trying to answer either or both. Forget about a process except for the vague “random mutations, random genetic drift, random recombination culled by natural selection”. And as for a way to test that premise “forgetaboutit”. Also evolutionism is all about the how and when yet it cannot answer those questions scientifically. That must be what pisses them off and causes them to flail away at ID with their ignorance-if they could support their position's claims ID would be refuted.

Intelligent Design is about the DESIGN not the designer(s). The design exists in the physical world and as such is open to scientific investigation.

All that said we have made some progress. By going over the evidence we infer that our place in the cosmos was designed for (scientific) discovery. We have also figured out that targeted searches are very powerful design mechanisms when given a resource-rich configuration space.

Intelligent Design is the study of patterns in nature that are best explained as the result of intelligence. -- William A. Dembski

Suffice it to say, I have little patience with the "identify the designer" rhetoric. It's not just an example of sloppy thinking. It's a form of sloppy thinking that gunks up any sincere interest in design. It turns an attempt to adhere to logical, responsible thinking into a sinister motive. So perhaps, there is a better question to ask. Why do ID critics refuse to publicly acknowledge that it is illogical to identity the designer using the criteria of mainstream ID (IC and CSI)?- Mike Gene
IDists agree with Mike Gene. And no one can find any real fault with what Mike Gene said.

Tuesday, December 19, 2017

Neil Rickert is Confused, as Usual

Neil sez:
Changing topics: the most obvious issue with ID, is that for intelligent design to work would require an extremely mechanical design. So ID is, implicitly, an extremely materialistic and mechanistic theory. Yet the proponents of ID are anti-materialist and anti-mechanist. They somehow fail to see the contradictions in their own positions.
That is so wrong. That ID is not a mechanistic theory does not mean that IDists are anti-mechanists. That is just stupid talk, Neil. That the DESIGN is material and exists in this physical world has already been confirmed by IDists. That is how and why we can study it. It does not mean that materialistic processes produced it. That is what ID is against. And BTW, design is a mechanism.

So, no, Neil, there aren't any contradictions, just your confusion.

Monday, December 18, 2017

Common Design with respect to Biology

Common design. We see it and have experiences with it every day. Automobiles display varying degrees of common design. Personal computers display varying degrees of common design. Houses built to the same building codes display varying degrees of common design. The lost is very long,

With respect to biology Linnaean Classification lays out the pattern of common design expected. Linne based his scheme on the basis of "archetypes" with common design being part of that:

“One would expect a priori that such a complete change of the philosophical bias of classification would result in a radical change of classification, but this was by no means the case. There was hardly and change in method before and after Darwin, except that "archetype" was replaced by the common ancestor.”-- Ernst Mayr 
Simpson echoed those comments:

“From their classifications alone, it is practically impossible to tell whether zoologists of the middle decades of the nineteenth century were evolutionists or not. The common ancestor was at first, and in most cases, just as hypothetical as the archetype, and the methods of inference were much the same for both, so that classification continued to develop with no immediate evidence of the revolution in principles….the hierarchy looked the same as before even if it meant something totally different.” 
Common design is inherent in the concept of "archetypes".

To me it seems stupid to redesign a gene that will encode for the same protein for every different organism. To me it seems like a brilliant idea to be able to reuse similar sequences in organisms.

Friday, December 15, 2017

Why Common Descent Fails

Common Descent, the concept that all living organisms owe their collective common ancestry to some unknown population(s) of prokaryotes and/or archaea, is a failure because there aren't any mechanisms that can produce a eukaryote given populations of prokaryotes and archaea. And that means the concept is a non-starter.

And even given populations of single-celled eukaryotes there aren't any mechanisms that can produce metazoans. So again, it is a non-starter.

So the people who say there is evidence for Common Descent do so because their faith requires it. Science does not support the claim.

Tuesday, December 12, 2017

What Passes for "Logic" over on TSZ

This could also be titled "How to Erect a Strawman".

There is a recent post over on TSZ titled- The Fine-Tuning Argument – Kettle Logic on a Cosmological Scale. And yet it contains strawman after strawman and the "logic" is based on those.

For example the author has 3 premises:

1- An infinitely powerful being, God, created the Universe ex nihilo.
2- The same being carefully tuned a number of fundamental physical constants to extremely narrow ranges outside of which life as we know it would not be possible.
3- God’s creative hand is clearly visible in the structure of our Universe and its properties.
And somehow he thinks these three cannot all be true:
As with the Kettle Logic example above, any one of these three arguments might be true by itself.  However, also as with the previous example, I don’t see any way that all three can be true simultaneously.
Yet his "arguments" are all strawmen.
Scenario A: Assume statement 1 is true – If God is infinitely powerful and God created the Universe from nothing, then there can be no limit as to which values God could set physical constants to.  If he literally sets the rules, then he would be able to make any combination of values work for his desired outcome (If 1, then not 2).  And whatever set of values he chose, it should appear to any observers who might emerge within the Universe to be a brute fact (If 1, then not 3).
Yes, God could have picked any values but God also has to answer to the physical world God Created. It does not mean that God is not infinitely powerful just cuz God couldn't Create living organisms in a universe with any values for the laws and constants.

That is a huge strawman. And that brings us to:
Scenario B: Assume statement 2 is true – If there are only very narrow ranges of physical values that will allow life to emerge, then God could not have created the Universe from nothing.  In that case there must be a pre-existing substrate upon which reality is built which limits the creative actions of God (If 2, then not 1).  And similarly to Scenario A, if the constants were set at the beginning, they would appear to any observers in the Universe to be an unchanging brute fact (If 2, then not 3).
That doesn't follow at all and the author doesn't give any reasoning for it. The rules physical world is what limits the powers. God must adhere to those or be forced to be a baby-sitter for the Creation.

That was strawman #2. Then he finally gets it right:
Assuming that statement 3 is true brings me back to Joe Felsenstein’s comment that I quoted above.  The chemical properties of water are indeed exceptional.  However, as Joe points out, changing anything about the properties of water would necessarily change the nature of all of chemistry since water is made up of components which are common to all elements.
That is true! And guess what? Your position doesn't have an explanation for the existence of water. All you have is sheer dumb luck to explain what we observe. And seeing that science can only allow so much luck then your position is out of it and not science.

Look, if you want to refute the fine-tuning argument as evidence for some Intelligent Designer then start with science and show us how your position explains what we observe. But we all know that you have nothing and so you are forced to erect strawmen arguments and attack those.


Sunday, December 10, 2017

EvoTARDs are Still Choking on Tiktaalik

The Skeptical Zone is home to some of the most ignorant evolutionists around. Now they are still talking about Tiktaalik as if it was some kind of prediction for evolutionism. Too bad evolutionism doesn't even have a mechanism capable of getting beyond populations of prokaryotes and that is given starting populations of prokaryotes.

But I digress- there is a moron named Rumraket, who spews the following nonsense:

No, it wasn’t. Rather, it is you who is mistaken about what the fossil represents.
You think it represents the first transition to land, rather than a transitional tetrapod.
It had actually been suspected for a while, even prior to the discovery of tiktaalik, and the later discovered tetrapod trackways from poland, that the first transition to land took place before the ages of known transitional fossils, because there were already numerous trackways known exhibiting transitional morphology, predating the fossil “series” incorporating tiktaalik, panderichtus, acanthostega and so on.
Reality refutes that bit of ignorance:

First, the set-up:
"In a nutshell, the 'fish–tetrapod transition' usually refers to the origin, from their fishy ancestors, of creatures with four legs bearing digits (fingers and toes), and with joints that permit the animals to walk on land. This event took place between about 385 and 360 million years ago toward the end of the period of time known as the Devonian. The Devonian is often referred to as the 'Age of Fishes,' as fish form the bulk of the vertebrate fossil record for this time."- Jennifer Clack, The Fish–Tetrapod Transition: New Fossils and Interpretations; "Evolution: Education and Outreach", 2009, Volume 2, Number 2, Pages 213-223

Got that- "the transition" refers to an event, a specific event that occurred between two specified time periods, a time when there were fish and no tetrapods and the time when there were fish and tetrapods. (as I said Here and again here- just can't get enough of RichTard's cowardice and ignorance)

With that now firmly established we return to "Your Inner Fish" chapter 1 where Shubin discusses what he was looking for- hint: evidence for the transition, ie the event:

Let's return to our problem of how to find relatives of the first fish to walk on land. In our grouping scheme, these creatures are somewhere between the "Everythings" and the "Everythings with limbs". Map this to what we know of the rocks, and there is strong geological evidence that the period from 380 million to 365 million years ago is the critical time. The younger rocks in that range, those about 360 million years old, include diverse kinds of fossilized animals that we would recognize as amphibians or reptiles. My colleague Jenny Clark at Cambridge University and others have uncovered amphibians from rocks in Greenland that are about 365 million years old. With their necks, their ears, and their four legs, they do not look like fish. But in rocks that are about 385 million years old, we find whole fish that look like, well, fish. They have fins. conical heads, and scales; and they have no necks. Given this, it is probably no great surprise that we should focus on rocks about 375 million years old to find evidence of the transition between fish and land-living animals.- Neil Subin pages 9-10 (bold and italics added)
OK he did it just exactly as described, bracketed the dates. However his dates were wrong, which means he did not find evidence for the transition, which occurred many millions of years earlier.

In order to find what he was looking for, evidence of the transition, he needed to focus on rocks 400 million years old, as the new data puts terapods in existence about 395 million years ago.

Tetrapod trackways from the early Middle Devonian period of Poland

Shubin et al., made a very specific claim and it is obvious that Rumraket is totally ignorant of that claim. Rumraket's ignorance is neither an argument nor a refutation of the facts. But it does expose the fact that evos are ignorant asses and apparently very proud of it.