40% of peered reviewed scientific articles can't be reproduced

[Dan From Smithville]

Yes, only after we had to listen to how the proved evolution....


Husky produces Husky, Asian produces Asian. Tiny variation is not disputed. Nor is the fact that Asian mates with African and produces the variation Afro-Asian.....


You do realize it doesn’t mean it is either. It’s not my burden to prove punk unicorns exist.


You mean like misclassifying say the offspring of the Husky and Mastiff (the Chinook) as a separate species because you can’t tell what mated with what in the fossil record from a pile of bones when it suddenly appeared where it didn’t exist before????


No, we aren’t discussing claimed transitional, but your claimed “missing” common ancestors where every split exists.... not even one?


Says those that can’t discern imagination from facts and keep presenting imagination as fact....

Demonstrate using your vast database of Husky breeding that only Huskies have been produced by Husky breeders and that there is no need for them to weed out variations that are not true to the Husky model?

For that matter, provide the evidence that you must have for all your claims. It would be about time. No need to mention your awe at rabbit breeding proclivities this time around either.

 

[Dan From Smithville]

Says piltdown man, Nebraska man, etc, etc......

What facts?

Bacteria remaining bacteria despite the number of mutations?????

Fruit flies remaining fruit flies despite the number of mutations?????

Coelacanth being the claimed intermediary for 20 years until one was found alive? That fact? About the same as the other facts.

Fossils of every creature remaining the same until they go extinct? Connected to others with “missing” common ancestors for every single creature on every single tree for every single claimed split?

Facts? Wasn’t aware that imagination counted as facts....

Odd. Your imagination is being counted as facts and used against actual facts. I must learn this new science you preach. Tell me. If a woman weighs as much as a duck, and ducks float, does that mean she is a witch if she floats?

 

[Dan From Smithville]

Right here, right now.... I see no facts presented, just more avoidance.....

I brought those questions up on the other thread. You know. Those that you have been avoiding for days now.

Are you going to avoid them some more?

 

[Dan From Smithville]

Says piltdown man, Nebraska man, etc, etc......

What facts?

Bacteria remaining bacteria despite the number of mutations?????

Fruit flies remaining fruit flies despite the number of mutations?????

Coelacanth being the claimed intermediary for 20 years until one was found alive? That fact? About the same as the other facts.

Fossils of every creature remaining the same until they go extinct? Connected to others with “missing” common ancestors for every single creature on every single tree for every single claimed split?

Facts? Wasn’t aware that imagination counted as facts....

I am curious now. Obviously, you have access to a database on bacterial populations that no one else is even aware exists.

Does this include records of all bacteria ever examined and kept in culture?

Is that how you established that bacteria always remain bacteria. I did not know that anyone actually expected bacteria to magically change into something else. What do you think they would change into?

How long have people been looking to see bacteria change into something else? What kind of records were kept on that.

Should them be keeping colonies in strict conditions if they want them to change into something else? Wouldn't it be better to apply environmental stress to see changes? Wouldn't static conditions just result in stasis?

Gosh. So many questions and here I have you that knows everything to explain all this and set me straight.

Talk to me Goose.

 

[tas8831]

I brought those questions up on the other thread. You know. Those that you have been avoiding for days now.

Are you going to avoid them some more?

He's been doing a lot of avoiding of late - like my demolition of his absurd claim that courts of law compare entire genomes, "loci by loci"...

 

[tas8831]

Coelacanth being the claimed intermediary for 20 years until one was found alive? That fact? About the same as the other facts..

Intermediary... Allie... Genetic strand... the hits keep a' comin'!

 

[Dan From Smithville]

He's been doing a lot of avoiding of late - like my demolition of his absurd claim that courts of law compare entire genomes, "loci by loci"...

I saw that. You are right. I have seen nothing from him in response to that. Odd. He so hates avoidance too. Or so he says.

 

[ImmortalFlame]

Yes, only after we had to listen to how the proved evolution....

You have committed your first lie.

Nobody said that either "proved" evolution. In fact, piltdown man NEVER fit with evolutionary predictions. It was contrary to evolution.

Husky produces Husky, Asian produces Asian. Tiny variation is not disputed. Nor is the fact that Asian mates with African and produces the variation Afro-Asian.....

Small changes over time add up to big changes. Hence how huskies are a variation of dog, which is variation of wolf, which is a variation of a mammal, which is a variation of a vertebrate, which is a variation of a eukaryote.

You do realize it doesn’t mean it is either. It’s not my burden to prove punk unicorns exist.

Correct. What DOES indicate it is an investigation of the evidence.

You mean like misclassifying say the offspring of the Husky and Mastiff (the Chinook) as a separate species because you can’t tell what mated with what in the fossil record from a pile of bones when it suddenly appeared where it didn’t exist before????

Nope, that's not even remotely like what I wrote. It's quite simple: if you believe all the fossil record shows is "species staying the same before going extinct", then you MUST believe species suddenly pop into existence fully formed without changing for thousands of years and then go extinct, and then another species pops into existence fully formed that - for no apparent reason - shares many physiological similarities with the previous species despite being entirely unrelated and then going extinct, and that this process happened thousands of times for every species we have ever discovered in the fossil record.

So, is that what you believe?

No, we aren’t discussing claimed transitional, but your claimed “missing” common ancestors where every split exists.... not even one?

What are you talking about?

Says those that can’t discern imagination from facts and keep presenting imagination as fact....

Please stop projecting. You've already outright lied once in this post.

 

[tas8831]

Husky produces Husky, Asian produces Asian. ... Nor is the fact that Asian mates with African and produces the variation Afro-Asian.....

So which two taxa interbred to produce the Asian in the first place?
So which two taxa interbred to produce the African in the first place?
So which two taxa interbred to produce the Husky in the first place?

 

[Dan From Smithville]

Intermediary... Allie... Genetic strand... the hits keep a' comin'!

Living Coelacanths were discovered in the 1930's. I have yet to understand how finding a member of a group that was thought extinct somehow erases everything that has been observed about evolution?

It makes no sense to follow that line of reasoning. Well, not unless you have no other lines and your favorite wish will not come true in your mind otherwise.

 

[Dan From Smithville]

So which two taxa interbred to produce the Asian in the first place?
So which two taxa interbred to produce the African in the first place?
So which two taxa interbred to produce the Husky in the first place?

Why it is just like the oodles and oodles of never ending poodles that stretch forward and backward into time for eternity. It is like this. Dog kind was poofed into existence all at once just like all other kinds were created. Do not ask me what I mean by kind. It can mean anything. That is the beauty of it. Anyway. Dog kind contained all the variation that is necessary for poodles, huskies, chihuahuas, afghan hounds, foxes, coyotes and all that there stuff. But for dogs, all that variation was held back until people noticed and magically pulled it out. My question in all of this is "Who let the dogs out".

 

[tas8831]

It's quite simple: if you believe all the fossil record shows is "species staying the same before going extinct", then you MUST believe species suddenly pop into existence fully formed without changing for thousands of years and then go extinct, and then another species pops into existence fully formed that - for no apparent reason - shares many physiological similarities with the previous species despite being entirely unrelated and then going extinct, and that this process happened thousands of times for every species we have ever discovered in the fossil record.

So, is that what you believe?

It has to be - and this, of course, is in DIRECT opposition to Scripture.

Whatever shall he do?

 

[tas8831]

Living Coelacanths were discovered in the 1930's. I have yet to understand how finding a member of a group that was thought extinct somehow erases everything that has been observed about evolution?

It makes no sense to follow that line of reasoning. Well, not unless you have no other lines and your favorite wish will not come true in your mind otherwise.

What - you mean all of your living relatives from previous generations did not all die the instant you were born? Mom, dad, grandma, all cousins, aunts, uncles - all poof! the second the cord was cut?

 

[tas8831]

Why it is just like the oodles and oodles of never ending poodles that stretch forward and backward into time for eternity. It is like this. Dog kind was poofed into existence all at once just like all other kinds were created. Do not ask me what I mean by kind. It can mean anything. That is the beauty of it. Anyway. Dog kind contained all the variation that is necessary for poodles, huskies, chihuahuas, afghan hounds, foxes, coyotes and all that there stuff. But for dogs, all that variation was held back until people noticed and magically pulled it out. My question in all of this is "Who let the dogs out".

Ha!

I do wonder where all those poodle alleles are hiding out in the wolf genome...

 

[Dan From Smithville]

What - you mean all of your living relatives from previous generations did not all die the instant you were born? Mom, dad, grandma, all cousins, aunts, uncles - all poof! the second the cord was cut?

Well...uh...hmm...

How about that Avengers movie? What a thing.

Gotta go.

Stop avoiding me.

You don't know physics and stuff like that.

 

[Dan From Smithville]

Ha!

I do wonder where all those poodle alleles are hiding out in the wolf genome...

Me too. I also wonder why we do not see the occasional poodle running with wolves. Poodle-Wolf? I wonder what causes those alleles to suddenly turn on. Is it Timmy caught in the well?

 

[tas8831]

Me too. I also wonder why we do not see the occasional poodle running with wolves. Poodle-Wolf? I wonder what causes those alleles to suddenly turn on. Is it Timmy caught in the well?

He is not the first person to put forth this "fully front loaded" genome idea - YECs have been floating it about for years. The last guy I encountered who made this argument (probably 6 years ago?) also could not explain how alleles 'created' for modern day critters were kept off yet in functional condition and then, for no apparent reason, turned on.

That guy was more of a cat person, based on a NYT article he had read (but had not bothered to look up the actual scientific paper - which I used to great effect in undermining his claims). Also started ignoring me when I called his bluff. He had also claimed that the "Iceman's" genome was "pure" (being closer in time to the creation, after all) and mysteriously fell silent when I linked to his genome and provided a number of quotes outlining his several alleles associated with diseases and the like.

One of the big problems with creationists - they don't bother to look before they leap, then get indignant when we point out the fact that they are shouting up from the bottom of the hole they believed they had cleared.

 

[Justatruthseeker]

Hilarious!
From the thread you've been ignoring...

It has been claimed/implied by a creationist that the type of DNA analyses used in Courts of Law are more stringent and rigorous than those used in evolutionary biology - that such tests (those used in court) have been tested and are accurate. It has been indicated by this creationist that, in fact, these tests used in court are far better than those used in actual molecular biological analyses of phylogeny because they do not employ algorithms to assess the data, and further, that in courts of law, "genomes are compared side by side, loci by loci, not by matching by algorithms."


I will show unequivocally that this creationist's position is premised entirely on abject ignorance of the techniques employed; this creationist is uninformed and uneducated on these topics and has no business making such assertions on these and related topics.


1. DNA analysis techniques used in court.

For this segment I will rely primarily on the National Institute of Justice's "DNA Evidence Basics" page and the relevant links on that page, as well as the book "DNA Technology in Forensic Science". Any quotes used will come from one or the other of these sources.


There are generally 5 types of DNA analysis/analytical techniques employed by courts of law. Which type is used depends on a number of factors - cost, questions being asked, condition of biological material, etc.

They are:

Restriction Fragment Length Polymorphism (RFLP), Polymerase Chain Reaction (PCR), Short Tandem Repeats (STR, aka microsatellite), Y-Chromosome, and Mitochondrial DNA (mtDNA). The last 2 rely on analyses of specific markers found in these sources, so they basically fall under STR/RFLP anyway.

A brief explanation of each technique follows:

1. PCR - this technique can be used in and of itself, or in generating additional ‘raw material’ on which other analyses can be used. It makes copies of a target sequence, the end points of which are determined by the use of short DNA sequences called primers. In some cases, the length of the fragment produced by using the same pairs of primers can be used in a similar fashion to what is described below for RFLP. By definition, this does not use the entire genome.

2. RFLP – this technique uses bacterial restriction enzymes (enzymes that recognize specific DNA sequences, bind to them, and ‘cut’ the DNA at that point) to cut larger DNA fragments (or whole genomes) into smaller fragments. These smaller fragments are then run through a gel material using an electric current, and the fragments are separated by their length. Fragments of differing lengths, indicating the presence of indels, are the ‘length polymorphisms’ referred to in the RFLP moniker. These polymorphic fragments are heritable (or, rather, the DNA sequences that produce them are), so individuals sharing a certain number of them do so via ‘common ancestry’, so to speak. This technique may use an entire genome as raw material, but it is only the lengths of a set amount of fragments that are considered in the analysis – so, this is not the whole genome being compared ‘loci by loci.’.

3. STR (aka microsatellite) – In many areas of the genome, there are regions that are comprised of short tandem repeats – for example, 10s or hundreds of copies of TA (i.e., TATATATATATA…). Such areas are prone to polymorphisms, which again are heritable. The FBI has established a 13-locus strategy for DNA forensics (“For example, the likelihood that any two individuals (except identical twins) will have the same 13-loci DNA profile can be as high as 1 in 1 billion or greater.”). STRs are not the whole genome.

4. Y-chromosome – this only works with males, of course, so is often used in rape cases. It also relies on a set of markers (specific DNA sequences) on the Y chromosome (not the whole genome).

5. mtDNA – More useful in, say, identifying old remains in which the nuclear DNA has decayed sufficiently that RFLP or other analyses are not likely to work well. Regardless of why it is used, it, too relies on specific markers, not the whole mtGenome.

As to whether or not “algorithms” are used in these analyses in courts of law, a few link clicks from the NIJ site linked above shows us things like:

STR (Short Tandem Repeat) Data Analysis and Interpretation Software. Learn the basics of data analysis software, become familiar with the purpose of GeneScan® and Genotyper® software, learn the difference between GeneScan® and Genotyper® software and GeneMapper ID® software, and become aware of the unique features of GeneMapper ID® software, and understand FMBIO® Analysis software and STaRCallTM software as related to GeneScan® and Genotyper® software.​

RFLP and PCR forensic analyses do not necessarily require software for analysis – it is just a matter of comparing band sizes in a gel (not whole genomes, not ‘loci by loci’), but it is probably the case that some analytical software is used, especially for searching databases and the like.

Just looking at these main techniques used by courts of law for doing various DNA analyses negates, 100%, the creationist’s claim that whole genomes are compared “side by side, loci by loci”.


2. As to how phylogentic analyses are done…*

Regarding phylogenetic analyses, PCR is a staple component.

RFLP - As I have previously documented, RFLP analyses have been used to assess Primate phylogeny, and the results were congruent with other DNA-based analyses (see, for example, this).

Strike 1.


STR – these have been used to assess modern human phylogeny:

“Reconstructing recent human phylogenies with forensic STR loci: A statistical approach”

Reconstructing recent human phylogenies with forensic STR loci: A statistical approach

as well as primate phylogeny:

“Microsatellite polymorphisms reveal phylogenetic relationships in primates”

Microsatellite polymorphisms reveal phylogenetic relationships in primates

Strike 2.


Y-chromosome – “A Molecular Phylogeny of Living Primates”
From the abstract:

“Gene partitions were analyzed separately, as well as combined, for genome comparison and phylogenetic reconstruction. Six gene partitions were created, corresponding to X-chromosome, Y-chromosome, autosome, intron, exon and UTR segments.”

A Molecular Phylogeny of Living Primates

Strike 3.

mtDNA – “Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes”

Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes

It should be noted that the human mtGenome is only on the order of 16kb



Strike 4.



3. Regarding the use of ‘matching algorithms’, it is hard to know what the creationist is actually referring to. It is the case that in his related rants, he brings up claims apparently made by disgraced hack Jeff Tomkins regarding his use of BLAST in assessing % sequence identity in humans and chimps (despite the fact that what Tomkins described, as relayed by the creationist in question, is not how such numbers are typically produced). The initial assessments of the % identity between humans and chimps was done using the entire single-copy genome of each in 1984, and while the analysis of those data was criticized by many, the values obtained were in the 90+%, so no ‘random matching’ involved. When the chimpanzee genome paper came out, there, too, a large proportion of both genomes were used, but not via ‘random matching’:

Best reciprocal nucleotide-level alignments of the chimpanzee and human genomes cover ∼2.4 gigabases (Gb) of high-quality sequence, including 89 Mb from chromosome X and 7.5 Mb from chromosome Y….

Genome-wide rates. We calculate the genome-wide nucleotide divergence between human and chimpanzee to be 1.23%, confirming recent results from more limited studies12,33,34. The differences between one copy of the human genome and one copy of the chimpanzee genome include both the sites of fixed divergence between the species and some polymorphic sites within each species….​

..

Yes, because you fail to understand......

“For example, following the discovery of a previously unknown gene in the mouse, a scientist will typically perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST will identify sequences in the human genome that resemble the mouse gene based on similarity of sequence.”

Not location in the genome, but random similarity regardless of where it exists in the genome....

And everyone here should know, IF they understand anything about biology, that two identical sequences located in different positions in the genome can have entirely different functions and not actually be similar at all.....

But keep ignoring the facts to preach your pseudoscience. There are those who understand similarity of sequence does not mean similarity of function or even relatedness.

It is randomly matching similar sequences regardless of their actual position or function in the genome. This is becoming evident even from within the same genome, let alone across species...

Same Gene, Different Functions

But go ahead, continue to preach your pseudoscience that similar sequences mean ancestors when it is placement within the genome that defines function, not just similarity between random sequences...

Is pseudoscience all you got?????

Random matching. What part of aligning sequences regardless of position do you fail to comprehend?

 

[Justatruthseeker]

I am curious now. Obviously, you have access to a database on bacterial populations that no one else is even aware exists.

Does this include records of all bacteria ever examined and kept in culture?

Is that how you established that bacteria always remain bacteria. I did not know that anyone actually expected bacteria to magically change into something else. What do you think they would change into?

How long have people been looking to see bacteria change into something else? What kind of records were kept on that.

Should them be keeping colonies in strict conditions if they want them to change into something else? Wouldn't it be better to apply environmental stress to see changes? Wouldn't static conditions just result in stasis?

Gosh. So many questions and here I have you that knows everything to explain all this and set me straight.

Talk to me Goose.

Go actually read them.... but then that’s why you just make rhetorical claims and fail to support your assertions

 

[tas8831]

So cool how you totally IGNORED the fact that I blew your idiotic claim that courts compare the entire genome "loci by loci" out of the water.. Poor fellow...

Yes, because you fail to understand......

“For example, following the discovery of a previously unknown gene in the mouse, a scientist will typically perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST will identify sequences in the human genome that resemble the mouse gene based on similarity of sequence.”

Not location in the genome, but random similarity regardless of where it exists in the genome....

LOL!

Well... if the sequences matched, it isn't really random, is it, genius? You have never done a BLAST search, have you?

Here - give it a try:

BLAST: Basic Local Alignment Search Tool

Here is the FOXP2 gene in mice:

Foxp2 forkhead box P2 [Mus musculus (house mouse)] - Gene - NCBI

You can see that it is on Chromosome 6 in the mouse.

Here are mRNA transcript sequences for the mouse:

RefSeq RNA Links for Gene (Select 114142) - Nucleotide - NCBI

On the right side of that page, there is a menu, one of the buttons of which is "Run BLAST".

Click on it. Don't worry about all the options, just click the button "BLAST" on the bottom left.

In about 15 seconds, you will get your results. Since I doubt you will do this, I will provide a few observations -
There are hundreds of returns. Keep in mind that the search sequences are all 6k or so in length - since you know so much about genome sequences, how often do you think a 6k sequence will randomly match another taxon's sequence by 80% or more?

You must believe it is very common to write the things you do.

Here is another one - human msx1 gene:

human msx1 - Nucleotide - NCBI

Let's pick the complete cds (this is the DNA sequence), about 5K:

Homo sapiens muscle segment homeobox 1 (MSX1) gene, complete cds - Nucleotide - NCBI

Again, on the right, click "Run BLAST"

When you get the results, mouse over the red lines - the 4th one down is to a gibbon. Click on it. Click 'Alignment'. It shows that there is a 97% identity.

Looking for the chimp version, 98%.

With your vast understanding of genetics and statistics and the like, what are the odds, do you think, that a 5 kilobase human sequence would just randomly match - at 98% identity - a sequence in a chimp? And at but a single locus?

You make it very, very obvious that you have no experience whatsoever in doing any of these sorts of analyses.

And everyone here should know, IF they understand anything about biology, that two identical sequences located in different positions in the genome can have entirely different functions and not actually be similar at all.....

Amazing. How do YOU know if these things are found in multiple places in the genome?
And isn't it odd that when I did that BLAST for the human genes, that there were not multiple returns to the human genome?

Kind of blows your made-up claims out of the water.

But keep ignoring the facts to preach your pseudoscience.

Like how you just ignored the fact that I DESTROYED your ignorant claim about courts and and DNA testing?

Anyway - what did I ignore, exactly? You have made these charges but all you ever do is repeat them - you have never once provided any rationale for your claim, no sources that support them, and you've never made an attempt to demonstrate them at all.

There are those who understand similarity of sequence does not mean similarity of function or even relatedness.

Yes - those people are called morons.

People that actually understand these issues and have backgrounds and experience in such things can tell when poseurs are pretending to know things that not only can they not know, but are in fact rather foolish and naive.
Your lame repetitious assertions may impress the simpletons at the water cooler, but to anyone with a biology background, you just come across as desperate and uninformed.

But no, you go ahead and embarrass me - prove that you are right and I am wrong.

SHOW that sequence matches of hundreds or thousands of bps in length just pop up haphazardly all over the genome. SHOW that these identical sequence has different functions. SHOW that we cannot use such sequences to infer phylogeny - to do so, you will have to show that all of those papers that I paste now and then are demonstrably wrong, and that all of the hundreds of other such papers are also demonstrably wrong, and so on. I'm sure you can do it!


SHOW that courts really do compare complete genomes "loci by loci", thus negating all of the information available from the FBI and the National Institute of Justice - I am sure they will want to update their records based on your documentation!


Can't wait!

It is randomly matching similar sequences regardless of their actual position or function in the genome. This is becoming evident even from within the same genome, let alone across species...

Really? Tell me more!

Same Gene, Different Functions

Interesting - the sub-title is:

"Proteins encoded by the same gene can play very different roles in the cell, scientists show."

Hmmm... Did you read beyond the title? Or how about the keywords at the bottom - did you see them:


Keywords: alternative splicing, protein, protein isoforms

Nothing about being randomly placed around genomes?

If I were you, I would immediately contact the publisher and let them know that the subtitle and the keywords counter your 100% correct implication and interpretation that this is about and supports the notion that this is really about how random matching sequences show up all over the genome, and that there are multiple gens or something, not sure what you mean.


Oh and the content, too - because it talks about alternative splicing and how a gene's [protein can be altered in different tissues and such, and nothing about how the gene cannot be used to infer phylogeny or anything like that, as it really must since you implied it does.

But seriously - as far as you reading it beyond the title, it seems not, because the subtitle kind of shoots down your implication that this brief news release somehow supports your repeated and unsupported notion that there are "randomly matching similar sequences regardless of their actual position or function in the genome".

But go ahead, continue to preach your pseudoscience that similar sequences mean ancestors when it is placement within the genome that defines function, not just similarity between random sequences...

Cool distraction, champ!

Looking forward to you DEMONSTRATING any of your claims for once:


- placement within the genome that defines function
- courts compare entire genomes
- phylogenetics relies on randomly matching sequences that are apparently all over the genome

Is pseudoscience all you got?????

Random matching. What part of aligning sequences regardless of position do you fail to comprehend?

I comprehend entirely that you are so spectacularly clueless re: genetics and evolution and biology that you cannot even tell how completely naive and, frankly, idiotic you sound when you keep repeating these claims that you have never once even attempted to justify or support.

I did my first alignment in 1996, and there was nothing 'random' about it at all. You've never taken a biology class.

And it is so cool how you just totally ignored my complete demolition of your sheer stupidity re: courts and DNA testing all so you could just regurgitate your laughably naive nonsense about which you are clueless.

I hope you are fooling yourself, because you are not fooling anyone else.

But do keep it up - I enjoy watching the farce that is creationism crumble due to the ignorance of its adherents.