Intelligent Design

[JDaniel]

No, because there is actually evidence and reasoning for the Big Bang.

I think buffalo cited Kenneth Miller earlier. Why would you do that? He testified in court against intelligent design in the Kitzmiller v Dover case, and rejects this rubbish book and the Discovery Institute as much as any other scientist can. His only contention with Coyne was that Kenneth supports the ability to accommodate religion while having a scientific materialistic mindset that is required in order to do good science. Coyne believes it’s a contradiction and is an anti-accommodationist, and doesn’t believe people should say that religious thought is compatible with the scientific method. I agree with Coyne because science has to do with evidence, logic, and reason, and religion has to do with faith. They are two different standards that are the exact opposite of each other.

But yeah, agreeing with Miller doesn’t help you. Miller agrees with the whole European Council thing you guys are quoting. He does not think ID should be at all taught in schools because it is not scientific, and it threatens to confuse children as to what is the best method of obtaining real knowledge. Most people would prefer the scientific method over faith any day.

To answer the question of “does design exist.” Not being nit-picky about the definition of the term design, yes it exists, but it must assume a designer. In other words, in order to determine if something is designed, you must first know of a designer. Behe said in his book Darwin’s Black Box that Intelligent design is the “purposeful arrangement of parts.” It assumes a purpose and an arranger, which is why it is circular when used to try to point to God, among other fallacies in the argument.

Question: Why is it OK to postulate that “…science has to do with evidence, logic and reason, and religion has [only] to do with faith”?, when evidence, logic and reason have as much to do with religion as they do with science?

Of the four types of logical discourse, the primary two types employed by science are dialectical and demonstrative. (The other two, rhetorical and literary, don’t have a suitable scientific value.) Interestingly, the first two mentioned are the same two that are employed by religious reasoning for many Christian beliefs, including the belief in God’s existence. I suppose it’s acceptable to employ them in reasoning for the truths of science, but, not for the truths of religion.

Almost all – except for those very few deductive demonstrations that were discovered by pre-scientific men and, in time, were commandeered by modern scientists, and turned into scientific truths - scientific thought is the result of, first, a dialectic process, and second, a logically demonstrative process to a probably provable conclusion. This seems strangely related to Scholastic, and, perhaps, ontological logic.

I am religious, yet, I do believe that evolution may be a method that has been employed to move the earth, and its creatures, in the direction of greater evolutionary progress. I believe evolution to be a “guided” process. I do not believe that “chance” can possibly be the guiding force of the entirety of evolution. However, I believe that pure chance can be an occasional cause for some of life’s wins – some, but, not all. Real “chance” is causal in the sense that two or more efficient causes may be brought together so that they result in something quite unpredicted and unexpected in the effect.

Further, in the business that I am in – working directly with fossils – I know that some of what I see, from time to time, is nonsense that is often the result of overly enthusiastic pseudo-science in the form of legitimate scientific claims. On the other hand, I have first-handedly seen strata with fossils that are clearly over 6,000 years old. It appears to me that there are perhaps too many people who are too easily taken in on either the side of religion or the side of science. But, there is – or, should be - at least one test of the veracity of things that we can all count on: whatever logic and reason that is good for science is good for religion, too. And, though it is nice that science has some theories and laws that can be verified by repeatable experimentation, a great deal of it can only be postulated by logic and reason.

In demonstration alone is the middle term certain. For, only in the demonstrative syllogism is the middle term certain of the causality involved. In the dialectical syllogism the middle term is “tentative”. So the conclusion can be no more or less causally provable, but, not fully proved. (St. Thomas Aquinas, Commentary on the Metaphysics, Bk. 4, les. 4)

Thus, the only chance that scientistic anti-theism has for a refutation that holds is to deny causation. It does not really matter that Christianity cannot produce “repeatable experiments” to prove God, or spirituality, or the soul, or the verisimilitude of the testimony of historical men and women. Christianity has the all of the other ratification tools necessary to arrive at proof(s), particularly from causality. And, they’re primarily those same tools used by modern science.

jd

 

[buffalo]

If you don’t believe in ID after this you will… a killer video.

Intelligent Design

 

[M0nkey]

The blood coagulation cascade involves of the order of thirty genes not 10,000 genes, so your argument fails at step 1. As for “pieces” what do you mean by “pieces”?

Really? Oh brother, you are either misunderstanding the proper context of the argument or being completely disingenuous. Are you (or they) confusing amino acids for genes? Let’s go back to basics, shall we. The human genome alone has 23 chromosome pairs, which give you a total of 46. Each of which have hundreds of genes which can then be divided into gene pieces. Think of DNA as the schematics for a self-autonomous building with security systems and automatic locking devices without the need for human intervention; it may sound like a thing of the future but that is exactly how these systems work. In light of these facts, pretty much the rest of your stuff crumbles.

By “TPA” I assume you mean tPA (tissue-type plasminogen activator). If you do, then what you write below is also gibberish in several different ways. The PLAT gene which codes for tPA has eight different transcripts formed by alternative splicing of the gene’s 14 exons. PLAT201, the protein that splices all exons, has five recognisable domains (a peptidase, two Kringle domains, an EGF-like domain and a fibronectin type 1 domain), but the “odds” you quote below are complete nonsense.

Actually, two are of the same type. But, if you want to use five domains go ahead it’ll only decrease your chances. Besides the calculation I showed you was pretty generous as there are other intricacies not accounted for.

As for mutations being catastrophic - although catastrophic mutations do occur, many mutations have a small or zero effect on the organism, and ones that provide a benefit are more likely to fix in a population.

Again, that is why it is called a duplication. Cells are designed to duplicate, but when large variations occur it results in a cataclysmic effect that can kill negating natural selection altogether.

Yes.

Good.

If you want a physical predecessor, then how about Sea Squirts: The evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes.

Let’s go through your beloved “evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes” shall we. I noticed the actual step-by-step evolution was way at the bottom in only two paragraphs.

It is thought that 50–100 million years separate the *appearances *of urochordates (which include the sea squirt) and vertebrates. During that time the machinery for thrombin-catalyzed fibrin formation had to be *concocted *by gene duplication and the shuffling about of key modular domains.

The first thing that pops up is no causative factors are cited. Language such as “the appearances” and “concocted” sounds very similar to stories of the tooth fairy when I was a kid. The incipient stages of how these proteins assembled are unaccounted for. To be honest, this doesn’t sound at all like science but myth. All it does is tell a story of how long ago “magic” appeared. If you want to believe in magic by all means but keep it to yourself as it doesn’t belong in science.

On the average, the two factors themselves (in this region) are 38% identical, implying that the gene duplication that led to them occurred only a relatively short while before the common ancestor of fish and mammals.

Again, total nonsense, a duplication is a duplication. Saying “that led to them occurred” is tantamount to believing in monsters in your closet.

A genome study devoted to the lamprey or hagfish would settle the point.

Alas! So at the end we are left with a “legendary story” that says nothing about nothing.

Natural selection has a great deal to do with what mutations survive from one generation to the next.

I think that perhaps you are too entrenched in your faith in Darwin or you don’t really understand natural selection as it is put forward. I already mentioned that without the incipient stage the theory falls to pieces.

The point, at the risk of repeating myself until I am hoarse, is that the methods that they use in evolutionary biology (regardless of where those ideas came from) actually work. Whereas the methods that ID proponents tout either don’t really exist, or don’t really work to detect intelligent design in testable, real-world situations.

Couple of things, I really hope you realize that computer software has nothing to do with the real world. I understand that being on the computer all day can blur reality in a way. Second, there in no such thing as a pure random number in mathematics as it is logically impossible. The best you are going to get is a pseudo random number generator. Third, probability theory doesn’t come from biology but mathematics and evolutionary biologists tend to use it to test their theories, however, this doesn’t prove macro-evolution.

 

[ricmat]

It turns out that computer viruses have a lot in common with biological viruses.

Well, uh, computer viruses are designed.

 

[Just_Lurking]

Well, uh, computer viruses are designed.

Exactly why one would expect that ID’s super-fantastic methods to detect design could be used to detect computer viruses. But ID is completely useless in this regard, and apparently has no uses at all other than to disprove macro-evolution.

 

[rossum]

You have failed to provide any backup for your claim of “10,000 genes” in the vertebrate clotting system. Your claim is false, so you should withdraw it. I would also be useful if you could refresh yourself on the meanings of ‘gene’, ‘intron’, ‘exon’ and ‘amino acid’, since you appear to me to be confusing them.

Let’s go through your beloved “evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes” shall we. I noticed the actual step-by-step evolution was way at the bottom in only two paragraphs.

The first thing that pops up is no causative factors are cited. Language such as “the appearances”

Shorthand for “first appearances in the fossil record” - the urochordates first appear in the fossil record 50 million years before the vertebrates. If you cannot understand the language of science then go and learn about it, otherwise you will have great difficulty in understanding scientific papers.

Again, total nonsense, a duplication is a duplication. Saying “that led to them occurred” is tantamount to believing in monsters in your closet.

We can observe gene duplications, present and past, in our own and other genomes. Duplications can be dated by looking at the number of differences between the two copies - globin genes and pseudogenes in humans are a classic example. This is basic genetics; if you do not understand genetics then you will find it difficult to make a sensible argument in this area.

I think that perhaps you are too entrenched in your faith in Darwin or you don’t really understand natural selection as it is put forward. I already mentioned that without the incipient stage the theory falls to pieces.

Mutations add variation to the genome of a population. Natural selection filters that variation on the basis of reproductive success so that only a subset of the initial mutations make it through the filter. Reproductive success entails more copies of those genes in the next generation. Any calculation that covers more than one generation needs to include the effects of natural selection if it is to be an accurate model of evolution. Any calculation that expects large changes in a single generation is not an accurate model of evolution.

Your model seems to make no allowance for natural selection so the results from your model appear worthless.

rossum

 

[hecd2]

hecd2:

M0nkey:

If you look at the numbers blood-clotting cascades have roughly 10,000 genes, each is divided into an average of three pieces giving you a total of 30,000.

This is gibberish. The blood coagulation cascade involves of the order of thirty genes not 10,000 genes, so your argument fails at step 1. As for “pieces” what do you mean by “pieces”? Really? Oh brother, you are either misunderstanding the proper context of the argument or being completely disingenuous. Are you (or they) confusing amino acids for genes? Let’s go back to basics, shall we. The human genome alone has 23 chromosome pairs, which give you a total of 46. Each of which have hundreds of genes which can then be divided into gene pieces. Think of DNA as the schematics for a self-autonomous building with security systems and automatic locking devices without the need for human intervention; it may sound like a thing of the future but that is exactly how these systems work. In light of these facts, pretty much the rest of your stuff crumbles.

You are the last person who should be attempting to patronise me about knowledge of molecular biology. The blood clotting cascade does not use 10,000 genes - it uses about 30 - I can even tell you what they are:

Prekallikrein, HMWK, fibrinogen, prothrombin, TF, Factor V, accelerin, proconvertin, Factor VIII, Christmas factor, Stuart-Prower factor, PTA, Hageman factor, Factor XIII, von Willebrand factor, Protein C, Protein S, Protein Z, thrombomodulin, antithrombin III, ZPI, plasminogen, tPA, urokinase, alpha2-antiplasmin and PAI1.

Why on earth do you think that I would have confused amino acids with genes? You need to learn a little molecular biology before you start copying and pasting other people’s arguments that you don’t understand. And you still haven’t told me what your gene “pieces” are: are they codons? Exons? Domains? All of these have precise meanings in molecular biology. So what do you mean by pieces? In any case the blood coagulation cascade involves about 30 genes, not 10,000 so you whole argument is nonsense.

Furthermore, you claim that the probability of creating the structure of tPA is 1/30,000^4 - in the other words, that it is the probability of randomly selecting four protein domains from 30,000 different things. But what are these 30,000 different things? They cannot be domains because comprehensive databases of domains such as PROSITE contain less than 1,000 different eukaryote-specific domains. Not only is your assumption wrong about how mammalian tPA came to be assembled (it did not occur in a single event), but your probability analysis is garbage.

Actually, two are of the same type. But, if you want to use five domains go ahead it’ll only decrease your chances. Besides the calculation I showed you was pretty generous as there are other intricacies not accounted for.

So you can read and copy Michael Behe’s chapter notes too. Since the “calculation” you showed us was complete nonsense from start to finish, why should we believe anything else you say about this subject?

As for mutations being catastrophic - although catastrophic mutations do occur, many mutations have a small or zero effect on the organism, and ones that provide a benefit are more likely to fix in a population.

Again, that is why it is called a duplication. Cells are designed to duplicate, but when large variations occur it results in a cataclysmic effect that can kill negating natural selection altogether.

Talk about a non-sequitur. You even seem to be confusing normal DNA duplication during cell replication with mutational duplication events that increase the gene count within a germ line. Did you know that humans commonly carry different counts of the same gene in their genome - and so do other vertebrates (it’s called copy number variation or copy number polymorphism - you should look it up). You need to learn a whole lot more about molecular biology if you are to make a convincing argument.

Alec
evolutionpages.com

 

[M0nkey]

Wow, are we reading the same stuff? The 10,000 genes come from the the *genome *which has the blood-clotting system. Duplications occur at the eukaryotic level therefore all genes must be accounted for. No where in the evolutionary literature does it say gene mutations just happened to come together at random, that would make it even more unbelievable. We can observe duplications and variations, which is where the pseudo science comes in and says that a lucky variation gave us the system we see today. The gene pieces are sub-strands that contain functional information which is where the genes of the cascade come from. Again, DNA: Chromosome Pairs: Gene Strands: Gene Pieces. Enough said.

 

[M0nkey]

rossum:

Mutations add variation to the genome of a population.

Not if a mutation kills, or you never get the right one like I showed you through the calculation. Do you see how natural selection doesn’t get to go to work here?

 

[M0nkey]

If you don’t believe in ID after this you will… a killer video.

Intelligent Design

So:

• From Glass et at., the minimal genome is thought to require at least 382 protein-coding genes.
• At an average of 700 Fits/average protein, the minimal life form I(Ex) ~ 267,000 Fits
• Using Inat = 140 Fits, I(Ex)>Inat
• It is about 10^80,000 times more probable, that ID was required to produce the simplest life form, than mindless natural processes.

What a wonderful video, I really enjoyed it.

 

[rossum]

Not if a mutation kills, or you never get the right one like I showed you through the calculation. Do you see how natural selection doesn’t get to go to work here?

You have about 150 mutations. I have about 150 mutations. Every one of the six billion people alive today has about 150 mutations. 150 x 6,000,000,000 = 900,000,000,000 mutations. I think that natural selection is not short of mutations to work on.

You need to learn a lot more about science if you want to avoid making such obvious errors.

rossum

 

[buffalo]

You have about 150 mutations. I have about 150 mutations. Every one of the six billion people alive today has about 150 mutations. 150 x 6,000,000,000 = 900,000,000,000 mutations. I think that natural selection is not short of mutations to work on.

You need to learn a lot more about science if you want to avoid making such obvious errors.

rossum

Which means every generation is degenerating.

 

[rossum]

Wow, are we reading the same stuff?

No. The stuff I read tells me that the vertebrate blood clotting systems use up to about 30 genes. Can you give a source for your 10,000 figure please.

The 10,000 genes come from the the *genome *which has the blood-clotting system.

Yes, all genes are part of the genome. The blood clotting genes are part of the genome just as all the other genes are. The human genome has about 30,000 genes in it. What does your figure of 10,000 genes refer to?

Duplications occur at the eukaryotic level therefore all genes must be accounted for.

This has no meaning. If you mean that the entire genome can duplicate then that happens in eukaryotes, eubacteria and archaea - it is not confined to eukaryotes only. Are you aware that chromosomes (which are present in eukaryotes only) can duplicate without duplicating the entire genome? Are you aware that portions of a chromosome can duplicate without duplicating the entire chromosome? Are you aware that a single gene can duplicate without duplicating the entire chromosome? Are you aware that a single exon can duplicate without duplicating the entire gene? Duplication can happen at many levels in the genome.

No where in the evolutionary literature does it say gene mutations just happened to come together at random, that would make it even more unbelievable.

They did not come together at random. Natural selection had an impact on the process as different alleles passed down the generations. If you do not know what ‘allele’ means then look it up; you need to know what the word means in order to understand that sentence.

Natural selection is not a random process. Any model of evolution that does not include natural selection is broken and will not produce reliable results.

rossum

 

[tjm190]

Which means every generation is degenerating.

Changing≠degenerating

 

[buffalo]

Changing≠degenerating

Hmmmm!

Let’s see - most mutations are deleterious. Each generation has 200-300 more. The math is obvious.

 

[hecd2]

Hmmmm!

Let’s see - most mutations are deleterious. Each generation has 200-300 more. The math is obvious.

You are wrong as usual. Most mutations are neutral and some drift to fixation. Severely deleterious ones are selected out. Beneficial ones are positively selected. There is no generation by generation loss of fitness in humans or other species. The maths was developed by population geneticists but you can’t be bothered to learn it.

Alec
htp://www.evolutionpages.com

 

[buffalo]

You are wrong as usual. Most mutations are neutral and some drift to fixation. Severely deleterious ones are selected out. Beneficial ones are positively selected. There is no generation by generation loss of fitness in humans or other species. The maths was developed by population geneticists but you can’t be bothered to learn it.

Alec
htp://www.evolutionpages.com

Right - I should have said neutral or deleterious.

So how many positive ones do I have? My kids?

 

[M0nkey]

What does your figure of 10,000 genes refer to?

The genome.

Are you aware that chromosomes (which are present in eukaryotes only) can duplicate without duplicating the entire genome? Are you aware that portions of a chromosome can duplicate without duplicating the entire chromosome? Are you aware that a single gene can duplicate without duplicating the entire chromosome? Are you aware that a single exon can duplicate without duplicating the entire gene? Duplication can happen at many levels in the genome.

Are you aware it’s called RNA? (gasp) I mean really this is basic knowledge.

Natural selection is not a random process. Any model of evolution that does not include natural selection is broken and will not produce reliable results.

Exactly my point. However, the only rebuttal I would add to your notation is that it is *blind *as it is currently being presented. Which in my opinion negates certain aspects of causality that are critical in science.

You have about 150 mutations. I have about 150 mutations.

And as far as I can tell you pulled that number out of your hoo-ha. What exactly is the point of this anyway? I don’t see how it helps your argument.

Changing≠degenerating

Second law of thermodynamics: entropy.

 

[M0nkey]

So how many positive ones do I have? My kids?

Well, that depends according to Darwin. Are you looking at the next generation, or your next de-generation?

 

[tjm190]

Second law of thermodynamics: entropy.

I’m sure the Earth-organism system lost some energy to entropy with each and everyone of those mutations.

(and now for some self quoting-)

For this exercise, imagine a society with a currency. There are two entities- the traders and the government. Initially, the traders have access to all the currency, the government none. Also, the traders have an interest in moving around the currency- the reasons are various and irrelevant to the discussion. And let’s say that every time there was an exchange of currency, the government would tax it- taking a share of the currency traded. The money taken by the government could not be regained by the trading sector by any means- the money still exists and still affects the goings on of the world in some way, but it can not be directly controlled by the trading sector.

Now let’s say instead of currency, we’re talking about energy. There’s energy everywhere- all around us even. And we, as well as most of nature, like to move it around for various reasons. But with (nearly) every exchange, some energy is lost to friction and the like. That energy is, for all intents and purposes, gone. If you rub your hands together, you “loose” that energy to friction- the energy which started in a reaction in the sun, was stored in food, and broken down by your digestive system just entered a state called “entropy”- the energy is out there, but can no longer be brought to order.

Now think about both cases- in both, whenever a transfer is made some of the unit transferred is removed from the control of those doing the transferring permanently- the amount varies highly, it may even be very small, but (essentially) all transactions suffer some loss. In physics, we use the second law of thermodynamics to state that as time goes on, more and more is lost to the “tax.” Does this mean that individual entities can not make gains? Of course not! If i give you ten dollars and the government takes one, did you make money? Yes. Did the you-me system loose money? Yes.