Are there transitional fossils?

[xianghua]

I have explained probability to you so many times, I've run out of ways to do it. That you can't understand the difference between the probability of 70 base pairs occurring as a result of convergent evolution versus 8000 base pairs (the average length for a mammalian gene, near as I can find) is on you.

but if you agree that we can get say 100 bases by convergent evolution we can also get 200. right? so there is no real evolutionery limit.

 

[tas8831]

Yea the Laetoli footprints certainly indicate a bipedal gait. As does the endocast from the Taung child. The only problem is it's two million years ago and the cranial capacity is still near 3 times smaller. Throw in some tools and some mix and match the specimens and you have everything but the accelerated evolution of the human brain from that of apes. A million year previously there is only Paranthrapos, which cannot be mistaken for a hominid so the split between gorrils and chimpanzee is identifiable.

Yeah, yeah whatever -

What do you think about creationist pshun totally misrepresenting a paper?

 

[mark kennedy]

Yeah, yeah whatever -

What do you think about creationist pshun totally misrepresenting a paper?

The same thing I think of scientific american, talk origins, Time and Nature magazine's web focus lying about the divergence between Chimpazee and human DNA.

 

[PsychoSarah]

but if you agree that we can get say 100 bases by convergent evolution we can also get 200. right? so there is no real evolutionery limit.

*Shakes head* NO. You once again fail to understand that the decreases in probability are on an exponential scale. 200 bases (not 100, like you are bringing up now for whatever reason) is not about 1/3 as likely as 70 bases (not 100, not sure why you changed the number).

Genome-wide signatures of convergent evolution in echolocating mammals
Also, in regards to the nature article about convergent evolution between bats and dolphins when it comes to echolocation, not once is it ever stated that these groups have any genes that have a block of 70 base pairs or codons which match exactly. They never even say anything in that regard.

In fact, the best one can tell from the paper, they are referring to genes with very similar protein products. Given that nearly all codons are redundant, very similar proteins can be produced utilizing very different sequences. Not to mention that this study can't account for alternative splicing; that is, despite any similarity in proteins that could be derived from these sequences, that doesn't mean that all the proteins produced in the cells of these organisms which are derived from these sequences are particularly similar.

The article says that the echolocation relevant genes in bats and dolphins are more similar than the rest of their genomes are to each other, but that doesn't actually mean much other than there isn't much variety to what proteins can aid in echolocation.

If you read closer, you'll note that they relied on sequences which weren't necessarily complete. Heck, I have used BLAST before, and trust me, most of the sequences for genes on there are not complete, and plenty of those that are have never been confirmed independently (they've only been sequenced once). This also means that they didn't account for the position of the genes within their respective genomes much, if at all. Now, what have I claimed in the past? Allow me to summarize:
1. Aside from very short genes, no gene IN ITS ENTIRETY will occur in independent lineages. Note that I never said that similar genes can't arise independently, only that the exact same ones won't appear twice, assuming that they aren't 50 base pairs or something.
2. Codons are highly redundant, so it is entirely possible for two genes with different sequences to produce the same protein. Like the bat and dolphin genes.
3. It is technically possible for even long sequences to appear twice, but the longer they are, the more improbable it is to occur. The average mammalian gene is 8000 base pairs; far too large to regularly independently appear in different lineages.

Note that the sequences these people compared were as short as 450 base pairs, and that not a single one was a perfect match between bats and dolphins. So, using your own logic, if there isn't any evidence showing that 450 base pairs can be the same between separate lineages, why assume that the average mammalian gene, more than 10 times that length, could plausibly appear in unrelated lineages?

 

[xianghua]

*Shakes head* NO. You once again fail to understand that the decreases in probability are on an exponential scale. 200 bases (not 100, like you are bringing up now for whatever reason) is not about 1/3 as likely as 70 bases (not 100, not sure why you changed the number).

i actually aware about this. but again: if evolution is ok with 100 bases by convergent evolution (4^100) it will also be ok with 200. agree?

 

[doubtingmerle]

i actually aware about this. but again: if evolution is ok with 100 bases by convergent evolution (4^100) it will also be ok with 200. agree?

Huh?

[Shaking head in sorrow]

This reminds me of a quote: “The greatest shortcoming of the human race is our inability to understand the exponential function.” --Al Bartlett

 

[PsychoSarah]

i actually aware about this. but again: if evolution is ok with 100 bases by convergent evolution (4^100) it will also be ok with 200. agree?

Lol, how about giving a legitimate example of 100 bases happening before bothering with that question? It does not help you at all when you don't quote the part of the post that's shows your 70 base pair example doesn't exist. Not only that, but you've used a source before that depicts any sequence longer than 50 base pairs occurring independently is extremely improbable.

 

[xianghua]

Lol, how about giving a legitimate example of 100 bases happening before bothering with that question? It does not help you at all when you don't quote the part of the post that's shows your 70 base pair example doesn't exist. Not only that, but you've used a source before that depicts any sequence longer than 50 base pairs occurring independently is extremely improbable.

in the example above they are talking about 200 genes with convergent events. so if its only about a single bp we are talking about 4^200. but evolutionists have no problem to argue for adaptive mutations. so even if it was about a full gene as the result of convergent evolution evolution has no problem.

 

[PsychoSarah]

in the example above they are talking about 200 genes with convergent events. so if its only about a single bp we are talking about 4^200. but evolutionists have no problem to argue for adaptive mutations. so even if it was about a full gene as the result of convergent evolution evolution has no problem.

Yes, they are talking about CONVERGENT genes. The genetic sequences are NOT identical. How many times do I have to tell you that it is IDENTICAL genes that cannot arise independently once they exceed a specific length (about 50 base pairs)?

The fact that they aren't identical is why we can tell that they arose independently to begin with. Different genes with similar functions are not a means by which, say, mammals can arise independently multiple times, because that's not what we observe in actual mammalian genomes. That is, this explanation for the origin of mammals doesn't fit with the genetic evidence we have.

Are you done being constantly focused on this?

 

[xianghua]

Yes, they are talking about CONVERGENT genes. The genetic sequences are NOT identical. How many times do I have to tell you that it is IDENTICAL genes that cannot arise independently once they exceed a specific length (about 50 base pairs)?

what is the difference in terms of probability? if we are talking about 100 same bases on 100 genes or 100 bases in a single gene its basically the same sequence space. of course its not identical because several reasons but its still close.

 

[PsychoSarah]

what is the difference in terms of probability? if we are talking about 100 same bases on 100 genes or 100 bases in a single gene its basically the same sequence space.

-_- no, it isn't the same sequence space at all. Just because there are only 4 different nucleotide bases, about 25% of the bases in genomes with equal numbers of base pairs in them would be the same, purely by chance. If we were comparing a human genome to an equal sized yet entirely unrelated genome, there should still be about 750000000 bases that line up the same despite that lack of relatedness. Hence why 100 shared bases across 100 different genes would be negligible. Heck, for 100 different genes to only have 100 base pairs match up would make them MORE genetically dissimilar than what would normally occur in entirely independent lineages that utilized the same bases. Especially considering the fact that every gene starts with ATG.

Now I will try, one last time, to get through to you. In a lottery in which tickets have 4 different numbers, ranging from 0-100, are you not more likely to draw a winning ticket than in a lottery in which tickets have 10 different numbers, each ranging from 0-100? If you can understand that, you should realize why how long shared sequences are is relevant to their probability of occurring independently.

of course its not identical because several reasons but its still close.

Close is not the same, get that through your head. Plus, your source didn't even say that the genes were overall super similar, only that they were more similar than generally seen in lineages that distant from each other.

 

[xianghua]

-_- no, it isn't the same sequence space at all. Just because there are only 4 different nucleotide bases, about 25% of the bases in genomes with equal numbers of base pairs in them would be the same, purely by chance. If we were comparing a human genome to an equal sized yet entirely unrelated genome, there should still be about 750000000 bases that line up the same despite that lack of relatedness. Hence why 100 shared bases across 100 different genes would be negligible. Heck, for 100 different genes to only have 100 base pairs match up would make them MORE genetically dissimilar than what would normally occur in entirely independent lineages that utilized the same bases. Especially considering the fact that every gene starts with ATG.

Now I will try, one last time, to get through to you. In a lottery in which tickets have 4 different numbers, ranging from 0-100, are you not more likely to draw a winning ticket than in a lottery in which tickets have 10 different numbers, each ranging from 0-100? If you can understand that, you should realize why how long shared sequences are is relevant to their probability of occurring independently.


Close is not the same, get that through your head. Plus, your source didn't even say that the genes were overall super similar, only that they were more similar than generally seen in lineages that distant from each other.

fine. here is an example in a single protein:

Structure and Organization of Lamprin Genes: Multiple-Copy Genes with Alternative Splicing and Convergent Evolution with Insect Structural Proteins | Molecular Biology and Evolution | Oxford Academic

"If this is the case, then sequence similarities between lamprin and oothecin, which share a 28/30 amino acid sequence identity, may represent one of the best examples of primary sequence convergence so far identified"

again: evolution has no problem to explain it.

 

[tas8831]

The same thing I think of scientific american, talk origins, Time and Nature magazine's web focus lying about the divergence between Chimpazee and human DNA.

No idea what you are referring to, but it sounds like a major diversion.

 

[tas8831]

"If this is the case, then sequence similarities between lamprin and oothecin, which share a 28/30 amino acid sequence identity, may represent one of the best examples of primary sequence convergence so far identified"

How similar do the exons for these 30 amino acids have to be to in 2 converged genes?

From the context of your last couple of exchanges with psycho, I get the impression that to you, convergence means 2 100% different sequence become nearly 100% identical.

Is this accurate?

If so, I have to wonder if you read the abstract for that paper:

"...Lamprin is noncollagenous in nature but shows sequence similarities to elastins and to insect structural proteins. Here, we characterize the structure and organization of lamprin genes, demonstrating the presence of multiple similar but not identical copies of the lamprin gene in the genome of the lamprey. In at least one species of lamprey, Lampetra richardsoni, the multiple gene copies are arranged in tandem in the genome in a head-to-tail orientation. Lamprin genes from Petromyzon marinus contain either seven or eight exons, with exon 4 being alternatively spliced in all genes, resulting in a total of six different lamprin transcripts. All exon junctions are of class 1,1. An unusual feature of the lamprin gene structure is the distribution of the 3′ untranslated region sequence among multiple exons. A TATA box and cap sequence have been identified in upstream sequences in close proximity to the transcription start site, but no CAAT box could be identified. Sequence and gene structure comparisons between lamprins, elastins, and insect structural proteins suggest that the regions of sequence similarity are the result of a process of convergent evolution.

 

[PsychoSarah]

fine. here is an example in a single protein:

Structure and Organization of Lamprin Genes: Multiple-Copy Genes with Alternative Splicing and Convergent Evolution with Insect Structural Proteins | Molecular Biology and Evolution | Oxford Academic

"If this is the case, then sequence similarities between lamprin and oothecin, which share a 28/30 amino acid sequence identity, may represent one of the best examples of primary sequence convergence so far identified"

again: evolution has no problem to explain it.

1. still not identical, even within the amino acids. What part of "identical" do you not understand?
2. Having the same amino acids and having the same sequence are two different things. Remember how I've told you before that codons are highly redundant? Leucine alone has 6 different codons that can signal it to be added to a protein. Thus, even if those 28 codons were in a row, that doesn't mean that 84 base pairs are identical in a row.
3. This article is specifically about a repeating sequence found in lamprin that is also seen in entirely unrelated genes in insects and at least 1 species of spider. The repeating sequence is GGLGY (shorthand of the proteins produced, not the base pairs, meaning the repeating sequence is 15 base pairs long). It's not the entire gene.
4. One of the insect proteins compared is also a tandem repeat (the 21/24 one), and the other (the 28/30 one) is not. This means that the latter, despite being a region of comparable size, is not the same throughout, meaning that it's base pairs MUST be partially different within those 28 to the lamprin protein
5. Not going to bother acknowledging your entire source? "While such sequence similarities might suggest descent from a common ancestral protein, there are several difficulties with arguments based on sequence conservation. For example, outside these regions of identity, the sequences of the proteins show essentially no other similarity. Although these regions of identity could reflect a common exon that has been shuffled between genes over time, a second explanation for the appearance of such isolated sequence identity is a mechanism dependent on sequence convergence."

I know you aren't illiterate, so why do you play these games with me? You must either be choosing not to read articles after they say a bit you think supports your position, or you read the whole thing but opt to ignore what doesn't support your position, which is detrimental to your arguments because I DO READ THE WHOLE THING. Torturous though it is to get through one that long.

Plus, if you look at the images, the most number of times that GGLGY lines up within these compared unrelated genes is 3 times. Since GGLGY is derived from 15 nucleotide bases, that times 3 is 45. Oh, what do you know, that's below the 50 I told you is the length of a sequence that can be reasonably expected to appear in independent lineages. So even if those were completely identical in terms of their bases (we only know that the amino acids in that bit are the same, which does NOT tell us that the nucleotides are the same), that's well within the realm of probability.

You seem to be grasping at straws. Where are your 100 base pairs which are identical in a row, much less entire average sized genes? Why are you using a paper from the year 2000, in which we barely had sequences to compare? Why are you considering comparisons of genes that are in no way similar in length yet share a tiny bit of sequence with each other the same as 100+ base pairs being identical IN A ROW?

 

[xianghua]

1. still not identical, even within the amino acids. What part of "identical" do you not understand?
2. Having the same amino acids and having the same sequence are two different things. Remember how I've told you before that codons are highly redundant? Leucine alone has 6 different codons that can signal it to be added to a protein. Thus, even if those 28 codons were in a row, that doesn't mean that 84 base pairs are identical in a row.
3. This article is specifically about a repeating sequence found in lamprin that is also seen in entirely unrelated genes in insects and at least 1 species of spider. The repeating sequence is GGLGY (shorthand of the proteins produced, not the base pairs, meaning the repeating sequence is 15 base pairs long). It's not the entire gene.
4. One of the insect proteins compared is also a tandem repeat (the 21/24 one), and the other (the 28/30 one) is not. This means that the latter, despite being a region of comparable size, is not the same throughout, meaning that it's base pairs MUST be partially different within those 28 to the lamprin protein
5. Not going to bother acknowledging your entire source? "While such sequence similarities might suggest descent from a common ancestral protein, there are several difficulties with arguments based on sequence conservation. For example, outside these regions of identity, the sequences of the proteins show essentially no other similarity. Although these regions of identity could reflect a common exon that has been shuffled between genes over time, a second explanation for the appearance of such isolated sequence identity is a mechanism dependent on sequence convergence."

I know you aren't illiterate, so why do you play these games with me? You must either be choosing not to read articles after they say a bit you think supports your position, or you read the whole thing but opt to ignore what doesn't support your position, which is detrimental to your arguments because I DO READ THE WHOLE THING. Torturous though it is to get through one that long.

Plus, if you look at the images, the most number of times that GGLGY lines up within these compared unrelated genes is 3 times. Since GGLGY is derived from 15 nucleotide bases, that times 3 is 45. Oh, what do you know, that's below the 50 I told you is the length of a sequence that can be reasonably expected to appear in independent lineages. So even if those were completely identical in terms of their bases (we only know that the amino acids in that bit are the same, which does NOT tell us that the nucleotides are the same), that's well within the realm of probability.

You seem to be grasping at straws. Where are your 100 base pairs which are identical in a row, much less entire average sized genes? Why are you using a paper from the year 2000, in which we barely had sequences to compare? Why are you considering comparisons of genes that are in no way similar in length yet share a tiny bit of sequence with each other the same as 100+ base pairs being identical IN A ROW?

i think you missed the main point. if there is no problem for evolution to get about 28 amino acids by convergent evolution, it will not be a problem at the genetic level too. so its doesnt matter if we are talking about DNA or amino acids. the only thing matter is the sequence space. the sequance space for 28 aa is about 20^28. and if such a chance can happen according to evolution i see no problem for even a lower chance.

 

[PsychoSarah]

i think you missed the main point. if there is no problem for evolution to get about 28 amino acids by convergent evolution, it will not be a problem at the genetic level too. so its doesnt matter if we are talking about DNA or amino acids. the only thing matter is the sequence space. the sequance space for 28 aa is about 20^28. and if such a chance can happen according to evolution i see no problem for even a lower chance.

1. No, you have constantly argued that you think mammals could, according to what is known about genetics and evolution, feasibly evolve independently from each other as the result of genes arising independently. Acting as if 28 amino acids matching up in entirely unrelated proteins of completely different lengths and purposes is somehow the same thing is silly. It doesn't even account for the introns in the genes or alternate splicing. That is, proteins that have animo acids line up can be derived from very different sequences. You have consistently failed to give an example in which 100 or more base pairs are identical which couldn't reasonably have arose via shared ancestry. Not once.
2. your 20^28 thing is entirely incorrect. For one thing, it assumes that codons for each amino acid are equally likely, and that isn't true. Leucine can be signaled by 6 different codons while methionine can only be signaled by 1. You also neglect to acknowledge that the length of the genes being compared is not the same. Lamprin is less than a 7th of the length of the genes it is being compared to. With so many genes in so many organisms, I think it'd be weird if there weren't any that shared a few amino acids in a row at random. The positions of these shared amino acids in the proteins are not the same, nor do they generally appear the same number of times in each gene.
3. My statement: it is unreasonable to expect a sequence longer than 50 BASE PAIRS to arise independently. This isn't more than 50 base pairs in a row being identical, and 28 amino acids makes for 84 base pairs, which isn't even a match for the 100 base pairs you keep trying to claim. You ignore introns and alternative splicing entirely. You don't get to neglect the actual base pairs of the gene. Your whole position demands that we shouldn't be able to determine shared ancestry by sequencing genomes, because you think significant numbers of genes could hypothetically arise in independent lineages. We use both exons AND introns when determining ancestry, so to ignore the actual genetic sequence in favor of the amino acids, which in and of themselves aren't a good representation of the overall sequence they are derived from, makes absolutely no sense. Show that 100 BASE PAIRS in a row are shared which are not explained by shared ancestry. Do it or drop the claim. Not amino acids in proteins of entirely different lengths, actual base pairs. Defend your actual claim. It absolutely matters if we are talking about DNA or amino acids, because the same amino acids can be derived from very different sequences. My claim that more than 50 base pairs won't appear identically in a row is a DNA claim; use DNA to challenge me.
4. You know that when you can't even find an example of a gene the size of lamprin expressed in independent lineages that your claim that, say, mammals could arise independently according to our understanding of genes and evolution is flawed. The average gene is more than 1,000 base pairs, and you can't even come close.
5. Lol, why would, say, a 1/10 event mean that a 1/100000000 event was just as reasonable to anticipate? To use your own math against you, even though it is wrong, based on the math you have done before, I can infer that you'd calculate the probability of, say, 8000 amino acids being the same in a row as 20^8000. Do you know what an online calculator calls that number? INFINITY. You know what it calls 20^28? 2684354560000000000000000000000000000. 20^50 is a number so much larger than that my calculator can hardly handle it, and yet you think something you personally would calculate as being an event occurring with a 1/(20^8000) chance is something reasonable to expect to happen? How?! 1/infinity is effectively 0% chance of an event occurring.

 

[xianghua]

My claim that more than 50 base pairs won't appear identically in a row is a DNA claim; use DNA to challenge me.

fine. lets say that we will find such an identical gene between two far species. we can solve this problem by several possibilities. so lets stick with the convergent option. we can simply argue that those iidentical bases are the result of similar selection pressure. therefore they arent the result of a random process. this is why the numbers are meaningless since they are talking about random event.

 

[PsychoSarah]

fine. lets say that we will find such an identical gene between two far species. we can solve this problem by several possibilities. so lets stick with the convergent option. we can simply argue that those iidentical bases are the result of similar selection pressure. therefore they arent the result of a random process. this is why the numbers are meaningless since they are talking about random event.

Uh uh uh, reply to my entire post #1777. I didn't go through all of that for you to reply to only 1 sentence. The whole thing, address each numbered point in full to the best of your ability. I'm not doing this out of spite or anything, it is just that there was too much in my post for you not to account for it in your response.

 

[xianghua]

Uh uh uh, reply to my entire post #1777. I didn't go through all of that for you to reply to only 1 sentence. The whole thing, address each numbered point in full to the best of your ability. I'm not doing this out of spite or anything, it is just that there was too much in my post for you not to account for it in your response.

i actually assume (for the sake of the argument) that you are right at every point in your claims. some of your points may be actually true. but the problem is that i need more data to confirm (data that i dont think we have) this so i just skip this and focus on the main point. and the main point is that if we consider the natural selection then the whole calculaion is meaningless.