Apes and humans have different designs

[Loudmouth]

Single-base mismatches: median 3, mean 4.0 per 300 bp slice. Based on a mean substitution divergence of 1.3%, you'd expect a mean of 3.9.

That's about what I was seeing doing some random manual searches. The reason I ask is because of another article written by Tomkins found here:

Genome-Wide DNA Alignment Similarity (Identity) for 40,000 Chimpanzee DNA Sequences Queried against the Human Genome is 86–89% - Answers in Genesis

In it he claims:

" Depending on the BLASTN parameter combination, average sequence identity for the 30 separate experiments between human and chimp varied between 86 and 89%."

Once again, the difference is to to not allowing for gaps. As Tomkins explains:

"Gapping was disallowed for a variety of reasons. First, Altschul et al. (1990) determined that the addition of gapping strategies for alignments designed to locate regions of local similarity using BLAST was negligible. Secondly, an objective comparison among all queries negates the use of gapping with the algorithm. Finally, the top local pair-wise alignments that were obtained involved a variety of very liberal to very stringent matching parameters for word size and e-value."

Those are very, very poor arguments for excluding gapping strategies, as I am sure you are aware.

So when gapped strategies are used the identity goes from the high 80's to the high 90's as reported by the chimp genome paper. Go figure. What Tomkins was trying to do is find a strategy that returned the numbers he wanted no matter how dishonest the comparison really was.

Looking more closely at the results, I see another three matches with good scores but large numbers (> 40) of mismatches. These are probably bogus matches as well -- probably matching to the wrong repetitive sequence. The fact that the analysis is done with unmasked sequence (i.e. no filtering to remove repetitive elements) means that everything should be taken with a large grain of salt. But if you really want to do the job right, you don't use BLAST at all, but instead use alignment code tuned for the purpose, and you do a lot of work to make sure you're making sensible comparisons -- which is of course what was done in the chimpanzee genome paper. Reading the AiG paper reminds me of judging high school science fair projects. They really have no clue what they're doing.

That was my assessment as well. My one-by-one manual blastn searches did find regions of homology between multiple chromosomes, so I assumed they were repeats or other conserved features. Obviously, the honest approach is to compare orthologous DNA, or at least try to determine where recombination events have happened. I doubt that Tomkins is interested in such a honest approach.

 

[sfs]

"Gapping was disallowed for a variety of reasons. First, Altschul et al. (1990) determined that the addition of gapping strategies for alignments designed to locate regions of local similarity using BLAST was negligible. Secondly, an objective comparison among all queries negates the use of gapping with the algorithm. Finally, the top local pair-wise alignments that were obtained involved a variety of very liberal to very stringent matching parameters for word size and e-value."

Those are very, very poor arguments for excluding gapping strategies, as I am sure you are aware.

I don't even know what the second reason means. As for the first reason, what Altschul et al actually says is this: "We implemented a version of BLAST that uses dynamic programming to extend hits so as to allow gaps in the resulting alignments. Needless to say, this greatly slows the extension process. While the sensitivity of amino acid searches was improved in some cases, the selectivity was reduced as well. Given the trade-off of speed and selectivity for sensitivity, it is questionable whether the gap version of BLAST constitutes an improvement." Which is not the same thing as saying the improvement is negligible -- and it's of course out of date by a quarter century. (And the third reason is irrelevant: if you're looking for the wrong thing, it doesn't matter much whether you're being lenient or stringent in your search.)

They had to have tried gapped searches -- it's the default, after all, and it requires no extra work at all. Just run the command without that parameter in the command line and see what you get.

 

[Loudmouth]

I don't even know what the second reason means. As for the first reason, what Altschul et al actually says is this: "We implemented a version of BLAST that uses dynamic programming to extend hits so as to allow gaps in the resulting alignments. Needless to say, this greatly slows the extension process. While the sensitivity of amino acid searches was improved in some cases, the selectivity was reduced as well. Given the trade-off of speed and selectivity for sensitivity, it is questionable whether the gap version of BLAST constitutes an improvement." Which is not the same thing as saying the improvement is negligible -- and it's of course out of date by a quarter century. (And the third reason is irrelevant: if you're looking for the wrong thing, it doesn't matter much whether you're being lenient or stringent in your search.)

Altschul is also talking about amino acid sequence for open reading frames where ungapped analyses can actually be helpful:

"You can avoid stop codons only by using ungapped alignment in addition to highly negative stop scores. Doing so segments the alignment in Figure 8-6 into three short alignments with insignificant E-values."
8.14 Consider Using Ungapped Alignment for BLASTX, TBLASTN, and TBLASTX :: Chapter 8. 20 Tips to Improve Your BLAST Searches :: Part III: Practice :: Basic local alignment search tool (blast) :: Misc :: eTutorials.org

When comparing nucleotide sequence across coding and non-coding regions, it makes no sense at all to use an ungapped alignement. They were obviously digging deep to find any justification for using an ungapped strategy because the gapped strategy returned numbers that were not to their liking.

They had to have tried gapped searches -- it's the default, after all, and it requires no extra work at all. Just run the command without that parameter in the command line and see what you get.

Indeed.

 

[Shemjaza]

When I read stuff from Ken Ham or Kent Hovind I get the impression that they will just say anything, regardless of if it is consistent to keep on their message.

But this weird twitching of real science seems a whole lot more calculated. This seems to be people who understand the science sculpting the results in a way that I find very difficult not to label a lie.

I can see why Christians get so upset. (I can empathise having read vile misogynistic and racist filth framed as skeptical and atheist).

 

[mindlight]

Ummmm. No. You are trying to say "well, they are the same, but not exactly the same". Every animal is filled with "re-used" design. Again, all of this is sub-optimal and thus does not reflect a creator at all.

There is a certain pattern in the coding for life that reoccurs in slightly different ways in each creature according to its type and even further on occasions to specific creatures (as sometimes genes are on or off on an individual rather than collective basis)- that shows uniquely considered configuration. To me that reflects a common designer of an order of intelligence and with a work rate way beyond our own. It requires much more effort to try and cram the same facts (and we agree on these) into an all emcompassing theory of development that goes back billions of years which was initiated by accident and has acquired its own logic by trial and error.

 

[mindlight]

I must have missed where you demonstrated that DNA could not come about by evolution. Care to point to that evidence?

You have theories about how DNA might have developed by evolution. But I think it requires more faith to believe in the kinds of timespans you are talking about and that the results we see to day were a result of an undirected process that has its own naturalistic logic than to believe in a creator God. Also the complexity of DNA and the essential nature of each aspect of that complexity (which I believe we agree on) fits better with the notion that it was designed rather than developed naturalistically by trial and error.

 

[mindlight]

Then why create species so that they fall into a nested hierarchy? Why did the Creator limit himself to a very restrictive pattern of divergence and homology that only evolution produces?

There are similarities that help us classify groups of creatures together- this is a fact and can be proven by observation and experiment. What is not factual or provable is the evolutionary explanation of how they arose and the time spans that would be required for this to be so. These are in effect matters of speculative theorising. If this study is correct and the methodology valid (in arguing that a difference makes all the difference and that only 100% matches are actually optimally aligned) then even the ways in which nested hierarchies have been categorised needs to be questioned. Slight differences in the DNA can potentially produce very different results and better illustrate a common Designer than a common ancestor from which their evolutionary development occurred.

 

[mindlight]

No it isn't. You are anthropomorphizing.

My focus is on something way beyond human so anthropomorphizing is the wrong word.

 

[mindlight]

I checked: the low percentage of matches does in fact result from only looking for ungapped alignments. I downloaded the human and chimpanzee genomes and the BLAST executable. As a test set, I pulled 500 randomly sampled, non-overlapping slices from chimpanzee chromosome 12, each 300 base pairs long. After dropping any slices that contained unknown sequence (i.e. 'N's), I had 471 test sequences. I fed these into BLASTN against human chromosome 12, using the parameters specified by Tomkins, with and without allowing gaps in the alignment. With no gaps, 68% of my queries yielded matches, in good agreement with Tomkins's finding. With gaps allowed, 100% of queries matched; of these, one or two were of poor quality and likely represent random matches. So the actual matching rate, when doing a proper alignment, was 99.6%.

I could add some sarcastic comments about the quality of creationist research, but it doesn't seem worth the trouble.

So you have assumed that the gaps in the alignment are not significant.

Also (as a matter of interest, and I am asking cause I do not know the answer)- what is the significance of the unknown sequences(N's)? Are these not yet understood, unobservable or what?

 

[mindlight]

My one-by-one manual blastn searches did find regions of homology between multiple chromosomes, so I assumed they were repeats or other conserved features. Obviously, the honest approach is to compare orthologous DNA, or at least try to determine where recombination events have happened. I doubt that Tomkins is interested in such a honest approach.

This reads to me like a prior acceptance of the theories which you are trying to affirm. If the difference makes all the difference the attempt to smooth over the margins of error is what is dishonest here.

 

[Loudmouth]

This reads to me like a prior acceptance of the theories which you are trying to affirm.

Not at all. There is no prior theory as to the genome sequence of the chimp genome. This is the first attempt at putting the chimp genome together.

If the difference makes all the difference the attempt to smooth over the margins of error is what is dishonest here.

I think we have already exposed the dishonesty in this thread, and it doesn't look good for Tomkins. He actually excludes a whole class of differences from his comparison. He excludes indels.

Indel - Wikipedia, the free encyclopedia

Why is this important? Let's take a look. Here are two made up sequences that are separated by a single indel (*=match):

seq A: ATATTGCGAT-ATTCGTA
.......**********.*******
seq B: ATATTGCGATGATTCGTA

Using a gapped analysis you would find that they are the same at 17 out of 18 bases. If I did an ungapped analysis that ignores indels, what would the comparison return? Let's take a look:

seq A: ATATTGCGATATTCGTA
.......**********..*
seq B: ATATTGCGATGATTCGTA

By removing the gap we ignore the indel mutation. Now the homology is just 11/18. This is the dishonesty that Tomkins is guilty of. He knowingly leaves out indels to get artifically lower numbers. No honest geneticist would do this.

 

[Loudmouth]

So you have assumed that the gaps in the alignment are not significant.

No, Tomkins has assumed that they are not important when they are extremely important for measuring sequence identity.

Also (as a matter of interest, and I am asking cause I do not know the answer)- what is the significance of the unknown sequences(N's)? Are these not yet understood, unobservable or what?

It means that the data is poor or missing for that section of the genome.

 

[Loudmouth]

There are similarities that help us classify groups of creatures together- this is a fact and can be proven by observation and experiment.

So how does creationism explain this fact? Why do we see the very pattern we would expect from evolution, but unlike the pattern of similarity we see between known designs?

Did God go out of his way just to make it look like life evolved? Was God incapable of creating a species with feathers and mammary glands, or a species with fur and flow through lungs?

What is not factual or provable is the evolutionary explanation of how they arose and the time spans that would be required for this to be so.

The evolutionary explanations are testable. Evolution predicts that we should see a nested hierarchy, and we do. Creationism makes no such predictions. A nested hierarchy makes no sense with respect to creationism since a creator would not be restricted to a nested hierarchy.

These are in effect matters of speculative theorising.

It is a matter of testing hypotheses, otherwise known as doing science.

If this study is correct and the methodology valid (in arguing that a difference makes all the difference and that only 100% matches are actually optimally aligned) then even the ways in which nested hierarchies have been categorised needs to be questioned. Slight differences in the DNA can potentially produce very different results and better illustrate a common Designer than a common ancestor from which their evolutionary development occurred.

We observe that mutations produce slight differences in DNA. We have never observed a supernatural designer making changes to DNA. So why is a common designer a better explanation? Please explain.

 

[Loudmouth]

There is a certain pattern in the coding for life that reoccurs in slightly different ways in each creature according to its type and even further on occasions to specific creatures (as sometimes genes are on or off on an individual rather than collective basis)- that shows uniquely considered configuration.

How so? How did you determine that these are uniquely considered configurations?

 

[Loudmouth]

If you want to check out a real result, you can check out this megablast result:

NCBI Blast:Nucleotide Sequence (884 letters)

You can find the chunk of chimp DNA that I used here:

Pan troglodytes chromosome 1 genomic scaffold, Pan_troglodytes-2.1.4 - Nucleotide - NCBI

You will notice that there is just one gap in the sequence. By my count, there are 45 bases on one side of the indel (an ungapped analysis would weigh the comparison on the negative strand to produce the most identity). If we did an ungapped alignment those 45 bases would no longer line up like they do in the gapped comparison. I have looked very closley, but let's say that 1 out of 4 randomly line up for a total of 32 differences that will exist in the ungapped alignment that do not occur in the gapped alignment.

In the gapped alignment we have 634/648 bases that match for 98% identity and 1 gap. In the ungapped alignment we would have 602/648 bases that match for 93% identity. Obviously, gapped vs. ungapped makes a huge difference contrary to Tomkins' claims.

 

[sfs]

Note: there's something funny going on with my ungapped alignments. Further investigation is underway.

 

[mindlight]

Not at all. There is no prior theory as to the genome sequence of the chimp genome. This is the first attempt at putting the chimp genome together.



I think we have already exposed the dishonesty in this thread, and it doesn't look good for Tomkins. He actually excludes a whole class of differences from his comparison. He excludes indels.

Indel - Wikipedia, the free encyclopedia

Why is this important? Let's take a look. Here are two made up sequences that are separated by a single indel (*=match):

seq A: ATATTGCGAT-ATTCGTA
.......**********.*******
seq B: ATATTGCGATGATTCGTA

Using a gapped analysis you would find that they are the same at 17 out of 18 bases. If I did an ungapped analysis that ignores indels, what would the comparison return? Let's take a look:

seq A: ATATTGCGATATTCGTA
.......**********..*
seq B: ATATTGCGATGATTCGTA

By removing the gap we ignore the indel mutation. Now the homology is just 11/18. This is the dishonesty that Tomkins is guilty of. He knowingly leaves out indels to get artifically lower numbers. No honest geneticist would do this.

The idea of idel mutation e.g. insertions or deletions that determine phylogenetic direction assumes evolution. It may well be that species A has 4Gs at a locus where species B has 5Gs but that does not have to mean that B underwent a frameshift from the A like arrangement. This seems highly speculative to me and also contradicts the notion that each creature was created according to its kind. A creationist is not going to accept an evolutionary perspective and understanding of idels by default (nor is that a dishonest approach) and anyway as your links states it would be impossible to prove if species were gaining or losing sequences so the notion of phylogenetic direction is actually nonsensical.

 

[mindlight]

No, Tomkins has assumed that they are not important when they are extremely important for measuring sequence identity.

It means that the data is poor or missing for that section of the genome.

Thanks for clarifying that. I am just trying to understand this bit.

But the idea of sequence identity is itself quite controversial as noone really knows if insertions or deletions have occurred historically and the notion of progression from one species to another would be rejected by default by creationists anyway.

Also we are still missing , for whatever reason,significant sections of the data

 

[sfs]

The idea of idel mutation e.g. insertions or deletions that determine phylogenetic direction assumes evolution. It may well be that species A has 4Gs at a locus where species B has 5Gs but that does not have to mean that B underwent a frameshift from the A like arrangement. This seems highly speculative to me and also contradicts the notion that each creature was created according to its kind. A creationist is not going to accept an evolutionary perspective and understanding of idels by default (nor is that a dishonest approach) and anyway as your links states it would be impossible to prove if species were gaining or losing sequences so the notion of phylogenetic direction is actually nonsensical.

You don't have to assume anything about phylogeny or evolution. The question is simply, how similar are two pieces of DNA? We can decide what similarity implies later (or not at all). According to Tomkins's approach, the two pieces in Loudmouth's post are only 60% similar. Do you really think that's a sensible measure of similarity?

Or consider two pages from two different books. Suppose they each have 1000 characters, and are identical except that one has an extra space in the middle of the page. According to Tomkins, those two pages are 50% similar. In fact, if that page is in the middle of the book, and every other page is identical, then the two books are still 50% similar, if you happen to be looking at the whole book. Seriously, do you think this is a good measure of similarity?

 

[mindlight]

So how does creationism explain this fact? Why do we see the very pattern we would expect from evolution, but unlike the pattern of similarity we see between known designs?

Did God go out of his way just to make it look like life evolved? Was God incapable of creating a species with feathers and mammary glands, or a species with fur and flow through lungs?

God created species pretty much as we find them , each according to their kind. We agree on the facts it is the explanations that differ and evolution is just a theory not a fact.

The evolutionary explanations are testable. Evolution predicts that we should see a nested hierarchy, and we do. Creationism makes no such predictions. A nested hierarchy makes no sense with respect to creationism since a creator would not be restricted to a nested hierarchy.

I see similarities in the work of the creators hand and groups of creatures that share comon features and yet are all uniquely configured when considered holisitically. The small differences in their coding here and there producing radically different results. The evidence supports this view better in my view

We observe that mutations produce slight differences in DNA. We have never observed a supernatural designer making changes to DNA. So why is a common designer a better explanation? Please explain.

But no type to type evolutionary jumps have ever been observed and even by evolutionists own arguments would be unobservable because of the vast timespans in which these changes are supposed to have occurred. Microevolution does not prove macroevolution- it only proves the flexibilty of the Makers design to adapt to changing conditions.