Monkeys in the cow shed.

[Micaiah]

In a recent thread the chance of convergent mutation was discussed. Several examples were considered. Spetner (Ref 1) cites the results of a study that compared versions of the same enzyme found in several mammals (Ref 2). Lysozyme is an enzyme which is found in the stomach of ruminating animals. This includes cows, sheep, goats, girrafes, and other animals that have hooves and chew the cud.

The Langur monkey is a primate, and yet has a stomach that is similar to the ruminants. The two animals are obviously not related, so this is a clear case of convergence.

Spetner notes that in the study, it was concluded that there were seven amino acids that converged in the cow and lemur. He concludes that this convergence is not the result of evolution, since the chance of it happening is so low it is impossible.

1. Spetner L. "Not by chance", The Judaic Press Inc, pg 114, 1998

2. Stewart C.B., Schilling J.W., and Wilson A.C., "Adaptive evolution in the stomach lysozyme of foregut fermenters," Nature, < http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=1987Natur.330..401S&amp;db_key=GEN&amp;data_type=HTML&amp;format=>
Nov 1987

 

[Tomk80]

As pointed out in the previous thread, similar=/=the same. What is the structure of the enzyme in monkeys? What proteins does it derive from?

My guess is, but feel free to point out that I'm wrong, that this is the same case as with the echolocation example or the wing example. That the function is the same, but how it works and looks is different.

 

[Tomk80]

For anyone interested, here is the abstract of the nature article:

[font=times, times new roman, serif]The convergent evolution of a fermentative foregut in two groups of mammals offers an opportunity to study adaptive evolution at the protein level. The appearance of this mode of digestion has been accompanied by the recruitment of lysozyme as a bacteriolytic enzyme in the stomach both in the ruminants (for example the cow) and later in the colobine monkeys (for example the langur). The stomach lysozymes of these two groups share some physicochemical and catalytic properties that appear to adapt them for functioning in the stomach fluid1,2. To examine the basis for these shared properties, we sequenced langur stomach lysozyme and compared it to other lysozymes of known sequence. Tree analysis suggests that, after foregut fermentation arose in monkeys, the langur lysozyme gained sequence similarity to cow stomach lysozyme and evolved two times faster than the other primate lysozymes. This rapid evolution, coupled with functional and sequence convergence upon cow stomach lysozyme, could imply that positive darwinian selection has driven about 50% of the evolution of langur stomach lysozyme.

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I'm trying to download the article, but that doesn't seem to work from home. I'm going to the university tomorrow to get the full article. Looks interesting.

 

[Micaiah]

I agree that in the previous thread it was hard to draw out the specific points I wanted to demonstrate in a quantitative sense because the research was not readily available. In this case the similarity in the DNA of the animals has been analysed.

I have to take the researchers word for the number of amino acids mentioned. I'm not a biologist, as you probably gathered. So this is a good starting point. I think the basic argument from Spetner is that we have here one of those examples of convergences that everyone agreed could not happen in the previous thread. It is a phenotypic trait that has arisen independently more than one is separate animal populations. It was previously agreed that if we found one of these examples it would prove very difficult for evolution if Spetners' methodology was correct.

 

[Micaiah]

For anyone interested, here is the abstract of the nature article:
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I'm trying to download the article, but that doesn't seem to work from home. I'm going to the university tomorrow to get the full article. Looks interesting.

Thankyou. It would be good if we can access the article.

 

[Numenor]

He concludes that this convergence is not the result of evolution, since the chance of it happening is so low it is impossible.

The chance of all the events happening which lead to your birth are so low, your existance is impossible. Take your logical fallacies elsewhere.

 

[Karl - Liberal Backslider]

Seven amino acids? That's only 21 base pairs that are the same. This is a far cry from what we were talking about in the other thread, which was an entire gene that has independently arisen in two lineages.

I hope Spetner's not doing a simplistic "odds against this are 4^21=4,398,046,511,104 to one against can't have happened ner ner ni ner ner", is he?

For one thing, there are any number of different codons that code for the same amino acid. A fairer calculation, even without taking into account natural selection, would be 22^7=2,494,357,888. But I won't accuse Spetner on that account because I don't know what particular figures he did use.

For another, we should remember the old Yahtzee game. If ruminants and lemurs need the same functionality, the same mutations in their lysosyme are going to be selected for. It's not like the lemurs could have had any old sequence of 21 base pairs compared with the ruminants. And it's not like a mutation had to get all 21 right at once. A single amino acid change towards the same solution as used by the ruminants would have a selective advantage. And there are a lot of lemurs playing Yahtzee here.

 

[Tomk80]

Spetner can also only draw the conclusion he does if he completely neglects natural selection. That is what I would call a strawman.

 

[Micaiah]

Seven amino acids? That's only 21 base pairs that are the same. This is a far cry from what we were talking about in the other thread, which was an entire gene that has independently arisen in two lineages.

I hope Spetner's not doing a simplistic "odds against this are 4^21=4,398,046,511,104 to one against can't have happened ner ner ni ner ner", is he?

For one thing, there are any number of different codons that code for the same amino acid. A fairer calculation, even without taking into account natural selection, would be 22^7=2,494,357,888. But I won't accuse Spetner on that account because I don't know what particular figures he did use.

For another, we should remember the old Yahtzee game. If ruminants and lemurs need the same functionality, the same mutations in their lysosyme are going to be selected for. It's not like the lemurs could have had any old sequence of 21 base pairs compared with the ruminants. And it's not like a mutation had to get all 21 right at once. A single amino acid change towards the same solution as used by the ruminants would have a selective advantage. And there are a lot of lemurs playing Yahtzee here.

Spetner states there would be no less than 9 similar nucleotides had to mutate to change those seven amino acids. I believe this is based on the article in question though it would be good to check that point.

Spetner, has a PHD in physics from MIT in the 1950's and has since worked and lectured in the areas of physics, biophysics, and information and communication theory. I'd be interested to know your qualification in mathematics KTB since you so confidently denigrate Spetner's work. Perhaps you could explain your method to us so it can be scrutinised.

 

[Tomk80]

Spetner states there would be no less than 9 similar nucleotides had to mutate to change those seven amino acids. I believe this is based on the article in question though it would be good to check that point.

Spetner, has a PHD in physics from MIT in the 1950's and has since worked and lectured in the areas of physics, biophysics, and information and communication theory. I'd be interested to know your qualification in mathematics KTB since you so confidently denigrate Spetner's work. Perhaps you could explain your method to us so it can be scrutinised.

But somehow, he misses that evolution consists of mutation + natural selection. Why? Why does he do that, if he's so smart?

 

[Micaiah]

That is incorperated in the first three steps of the calculations. In the previous thread I outlined the steps Spetner takes in doing the calculations. That was where the multiplier of 1,000,000 came from. It actually wasn't just plucked from out of the air.

 

[Loudmouth]

It would seem that colobine monkey lysozyme is still more closely related to other primates, followed by carnivorae (dogs, seals), then ruminants, then rodents. The langur lysozyme sequence is mkaltilglvllsvtvqgkifercel. You can do a comparison of known sequences through a Blastp search. Just cut and paste the sequence into the window at the top.

 

[Jet Black]

it would be nice to see Spetner's calculation in more detail, to see why he is claiming that the convergence of seven amino acids is effectively impossible. It seems as if all he is talking about is active site convergence, and that can happen. There are a number of enzmes that appear very different, but have the same active sites.

 

[Jet Black]

Spetner states there would be no less than 9 similar nucleotides had to mutate to change those seven amino acids. I believe this is based on the article in question though it would be good to check that point.

very nice, but can we see the actual calculations?

Spetner, has a PHD in physics from MIT in the 1950's and has since worked and lectured in the areas of physics, biophysics, and information and communication theory. I'd be interested to know your qualification in mathematics KTB since you so confidently denigrate Spetner's work.

He could be a genetically engineered splice of Steven Hawking, Albert Einstein, Charles Darwin and every Nobel Prize winner ever for all I care.

 

[Micaiah]

very nice, but can we see the actual calculations?

You were previously given the method and should be able to work this out.

 

[Tomk80]

You were previously given the method and should be able to work this out.

You mean this?

Step 1. - Spetner estimated that at each step of the development of a certain trait, there were a million possible sites at which a base pair substitution could be made that would meet the requirements of the NDT. (Please don't ask me to repeat those requirements - again).

Step 2. - Estimate the total number of steps required for the development of a new species.

Step 3. - Determine the probability of this same path being taken twice, which models convergence in two animals.

The calculation is really quite straight forward. (If it wasn't, I probably wouldn't follow the argument.)

P(Step 1.) = 1/1,000,000
P(Step 2.) = (1/1,000,000)^2
P(Step 3.) = (1/1,000,000)^3
.
.
.
P(Step n.) = (1/1,000,000)^n

You can do the calculations to model what happens in the genome, or in the physical characteristics of the animal. Spetner notes that there would be fewer steps with the latter approach, but even if you reduced the number of steps by a third, you would still get extremely low probabilities.

You may claim that there is more than one order for the supposed evolution of the trait, and while that may be the case, Spetner states it does not substantially reduce the probabilities.

 

[Micaiah]

That is correct.

 

[notto]

I think the basic argument from Spetner is that we have here one of those examples of convergences that everyone agreed could not happen in the previous thread.

What was discussed in the previous thread was the following:

For example two animals with identical genes that cannot be explained in terms of the evolutionists basal genes.

You've got a long way to go to get there from a few amino acids that are common among animals that are plant eaters.

Chemistry and natural selection as a solution to this would need to be eliminated before claims of intelligent design need to be made.

Animals need certain things to digest the ways rudiments do (or if you are going to digest a high cellulose diet). These amino acids are one of those things. Natural selection would select for them and they would become fixed. It is not a surprise to see similar digetive chemistry and biology evolve in animals with a similar diet. Show us a monkey with 4 stomachs and you might be on to something. Show us a monkey with the same gene as the cow and you would fulfill your claim from the previous thread.

What you have uncovered here is far different than an entire gene or 'trait' as you referenced in the other thread coming about through covergent evolution. This is not a gene, an organ, or a trait in any sense of the word. Don't shift the goalposts.

 

[notto]

An additional study
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=1960739&dopt=Abstract

Genomic blotting and enzymatic amplification show that the genome of the langur monkey (like that of other primates) contains only a single gene for lysozyme c, in contrast to another group of foregut fermenters, the ruminants, which have a multigene family encoding this protein. Therefore, the langur stomach lysozyme gene has probably evolved recently (i.e., within the period of monkey evolution) from a conventional primate lysozyme. The sequences of cDNAs for the stomach lysozyme of langur and the conventional lysozymes of three other Old World monkeys were determined. Identification of the promoter for the stomach gene and comparison to the human gene, which is expressed conventionally in macrophages, show that both lysozyme genes use the same promoter. This suggests that the difference in expression patterns is due to change(s) in enhancer or silencer regulatory elements. With the cDNA sequences the hypothesis that the langur stomach lysozyme has converged in amino acid sequence upon the stomach lysozymes of ruminants is tested. Consistent with the convergence hypothesis, only those sites that specify amino acids in the mature lysozyme are shared uniquely with ruminant lysozyme genes. None of the silent sites at third positions of codons or in noncoding regions support a link between the langur and ruminants. Statistical analysis based on silent sites rules out the possibility of horizontal transfer of a stomach lysozyme gene between the langur and ruminant lineages and supports the close relationship of the langur lysozyme gene to that of other monkeys.

 

[Micaiah]

If Spetner can demonstrate that the supposed convergence of the 9 nucleotides is impossible, that is an adequate. It should be kept in mind that in the many cases of convergence in the animal kingdom, the genetc similarities of convergent traits would include significantly more that an isolated aspect of the trait. Any additional similarities just add weight to the argument. Once something is impossible, it is impossible.