I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.
Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.
If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.
One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.
Since I think there is promising evidence for YFR, I don’t think too much about common design vs. common descent. If the Earth is old, but the fossil record is young, as far as I’m concerned the nested hierarchical patterns of similarity are due to common design.
That said, for the sake of this discussion I will assume the fossil record is old. But even under that assumption, I don’t see how phylogenetics solves the problem of orphan features found distributed in the nested hierarchical patterns of similarity. I should point out, there is an important distinction between taxonomic nested hierarchies and phylogenetic nested hierarchies. The nested hierarchies I refer to are taxonomic, not phylogenetic. Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).
Phylogeny is a nice superficial explanation for the pattern of taxonomic nested hierarchy in sets of proteins, DNA, whatever so long as a feature is actually shared among the creatures. That all breaks down however when we have orphan features that are not shared by sets of creatures.
The orphan features most evident to me are those associated with Eukaryotes. Phylogeny doesn’t do a good job of accounting for those. In fact, to assume common ancestry in that case, “poof” or some unknown mechanism is indicated. If the mechanism is unknown, then why claim universal common ancestry is a fact? Wouldn’t “we don’t know for sure, but we believe” be a more accurate statement of the state of affairs rather than saying “universal common ancestry is fact.”
So whenever orphan features sort of poof into existence, that suggests to me the patterns of nested hierarchy are explained better by common design. In fact there are lots of orphan features that define major groups of creatures. Off the top of my head, eukaryotes are divided into unicellular and multicellular creatures. There are vetebrates and a variety of invertebrates. Mammals have the orphan feature of mammary glands. The list could go on and on for orphan features and the groups they define. Now I use the phrase “orphan features” because I’m not comfortable using formal terms like autapomorphy or whatever. I actually don’t know what would be a good phrase.
So whenever I see an orphan feature that isn’t readily evolvable (like say a nervous system), I presume God did it, and therefore the similarities among creatures that have different orphan features is a the result of miraculous common design not ordinary common descent.
DNA_Jock,
Ha! 😀
stcordova,
‘The mechanism’ is the misidentification of sequence homology, which is ultimately mediated by Watson-Crick base pairing. If you identify the wrong pairing of sequences as homologous, you’ll get duplication/deletion. Nothing needs to single it out as such. Recombination is of course blind to gene boundaries.
Whether you get a fragment of the gene or the whole thing at one end depends on how far beyond the DSB site the gene extends in either direction ***. Gene conversion may conserve the lot. Even if you do get a terminal fragment, you still have intact copies in the middle, which can still be duplicated, so a gene fragment is not fatal to copy increase.
*** Thinking on, probably not even that.
Entropy,
LOL
D4Z4 repeats aren’t LCRs. 🙄
That’s at least the second time I pointed that out in this discussion.
That’s because genes don’t actually exist.
For the reader’s benefit since Dr. Entropy hasn’t yet acknowledge it,
LCR stands for low copy repeat (as in a 2 to a few copies, usually large units). The tandem repeats that were especially the focus of this discussion are high copy repeats.
Mung,
Or because recombination doesn’t have eyes, or any other such nonsense that pops into your head. I was using the term as it relates to transcriptional/translational boundaries. Go on, tell me they don’t really have boundaries either.
Exactly! That’s what I said Chava! They’re recurrent CNVs:
I must guess that maybe you also took two courses on reading for comprehension.
🤣
That’s also what I said Chava. Really. Way to make my point! You’re truly talented!
Entropy,
The GSWs to the foot continue.
😀
DNA_Jock,
No wonder they’re called IDiots.
So many books on cladistics and none so far with a definition of a clade. Weird.
However, I did find this:
Before I forget.
That was pretty good. Worth thinking about. Thanks.
Clade: a monophyletic taxon. And I would never say that nodes are defined by characters. That’s just a misuse of language. What point are you trying to make, if any?
stcordova,
Ta!
Mung,
That would be weird. They must be trying to keep it secret!
This, though.
Mung’s point is that no matter how much you might want to clarify concepts, Mung will find some way to muddle them back.
John Harshman,
Some general questions on molecular pylogeny of genes.
Recently I was constructing a primate phylogenetic gene tree on an interferon gene. I got one tree using the entire gene nucleotide sequences and another tree using the protein sequences (which obviously don’t reflect the introns) from the same gene. I could not get the same tree even trying to use the :
Maximum Likelihood (ML)
Neighbor Joining (NJ)
Minimum Evolution (ME)
UPGMA (whatever the acronym means)
Maximum Parsimony (MP)
Is that unusual?
We can work through the specific example here.
How do we figure alternative splices into the gene/protein trees?
What about assembly quality and annotation? Many of the introns, and thus exons are predicted. The introns have donor and acceptor sites that define them, but the sequence is “GT” for donor and “AG” for acceptor. Seems gene predictions could miss the actual boundary. If mRNA data isn’t available, there maybe some noise in doing a protein comparison since this is really not a TRUE protein comparison, it is a comparison of predicted proteins which is contingent on the accuracy of the gene prediction which is contingent on the assumption of homology (by common ancestry). I don’t personally have an immediate problem with that since that is the best we can do, but it seems to me, until we have some really good sequencing depth of DNA, RNA, and actual proteins express (astronomically expensive), there could be enough noise to compromise a phylogenetic reconstruction, even assuming common descent is true.
My understanding is that very large scale genomic comparisons (say almost chromosome scale comparisons) though expensive, when they can be done have provided better tree reconstructions. Supposedly this resolved arguments whether we are more similar to chimps vs. other primates.
I know, right? It’s like they don’t want me to learn!
For example, the book I am looking at right now doesn’t even have apomorphy in the index, though it does have synapomorphies.
However, it does say:
.
This is the same sense in which I was speaking of what defines a clade.
Molecular Evolution and Phylogenetics
Yes. I would have to see the data to say more.
We can’t. Why would you want to?
You can choose to believe it or not. For DNA sequence comparisons it makes no difference. For protein sequence comparisons it seems to me that if you end up with major indels exactly matching splice sites that might be a clue that something is wrong.
Your understanding is in general wrong, though it may be correct in some cases. Not in the human/chimp case, though. Some questions can be answered using short sequences, others require long sequences. Whole genomes can provide the longest sequences, of course, but they have to be dealt with carefully; you can’t just slap together a bunch of genomes any which way and come up with the answer, unless the answer was already easy to get with much shorter sequences.
Thanks John.
You claimed that Darwin’s causal explanation for nested hierarchy was common descent. In support of that claim you directed me to Chapter 14 of the Origin.
Yet, the phrase “common descent” does not appear in that chapter at all. However, the phrase “descent with modification” appears repeatedly.
As I said, Darwin’s explanation was descent with modification, not “common descent.”
Care to try again? Did you mean to say “descent with modification”? Because that’s what Darwin said.
I mentioned earlier an interferon gene I was looking at. Well, technically it was a pseudo gene in some people and a functional one in others based on whether a premature stop codon is present in the exon 1 (TAC Tyrosine vs TAA stop). Amazing how much damage can be done by a single mutation in a specific location! Perhaps using a pseudo gene created a problem with the phylogenetic reconstruction I was trying to make.
So instead, how about starting afresh with another (but related gene).
This one:
https://www.ncbi.nlm.nih.gov/nuccore/849604769/
Now some funny things I can’t make heads or tails of in the entry. I’m told a lot of people ignore some of the data outside the sequence anyway like the “features” comments!
But first, depicted below are the exons highlighted starting at coordinates 1393 in exon 1 and then ending at 2839 in exon 5. This graphic is easily accessible by simply pressing “highlight sequence features” in the above link.
But then I see the following “features” data doesn’t seem to agree with the coordinates of the exons below as far as I can tell:
Why is this listed as a “gene/pseudogene”? The grammar of the gene section composed of 5 exons looks right, the intron exon boundaries look right. Why would the term “pseudogene” be applied to this section?
Also there are apparently 2 genes in this entry, and the exons of the other gene weren’t highlighted. Why are there 2 genes in an entry the looks like it’s describing only one gene?
The only thing that made sense is this section which agreed with the coordinates of the graph below and which looks like a grammatically correct eukaryotic gene:
So these are basic questions before even trying to build a phylogeny tree.
Thanks in advance to everyone.
Click for larger image:
http://theskepticalzone.com/wp/wp-content/uploads/2017/12/exon_template.png
We need to align the sequences and get rid of the things that don’t match up.
But tht’s not cherry picking!
It would help if you read for meaning rather than searching for particular words. I presume you are aware that the same idea can be communicated in many ways.
stcordova,
What you seem to have there is that the mature mRNA includes extensive 5′ and 3′ untranslated regions. That’s all.
I think it’s called a gene/pseudogene because it’s polymorphic. Of course a pseudogene doesn’t have to have a frameshift; it may just be unexpressed for some other reason. I don’t see any reason why a sequence that’s a gene in some taxa and a pseudogene in others would be a problem, as long as you aligned it properly. If you’re going for primates, incidentally, you should probably use the intron sequences as well as the exons, and DNA instead of protein sequence.
Mung,
That’s a very silly, even mendacious way of looking at matters. You think people do phylogenetics by looking only at fully aligned sequence, and ignoring all difference? You couldn’t do phylogenetics at all if that were the case.
That was IMMENSELY helpful. Thanks. I’ll post on this gene in subsequent comments. Thanks.
Yes, I know. I’ve been trying to make that very point. Without the differences you won’t get a nested hierarchy. Darwin’s theory of descent with modification tried to provide a causal explanation for both. But now there is apparently a competing theory called “common descent” which doesn’t even try to explain the differences.
Depicted below are some sequence coverage and similarity comparisons of the gene IFNL3/4. The technical terms are “coverage” and “identity.”
Each bar represents a segment that can be aligned with the human IFNL3/4 gene. In a couple cases it aligns with either a duplicate-type entry for humans or an actual similar duplicate paralog in the human genome.
The 4th row is interesting. The red bar on the left is Pan troglodytes Chimpanzee, the purple+red bar on the right is a Macaca mulatta (Rhesus monkey).
The coverage for the Rhesus monkey is 51% whereas for the Pan troglodytes it is only 24% to the human INFL4 gene. For the large 51% similar segment for Rhesus monkey there is 94% identity and for the Chimpanzees 24% similar segment there is 98% identity.
So let’s give and approximate score of similarity between human, Rhesus Moneky and Chimpanzee where the composite score is
Coverate x Identity = Overall Similarity
For INFL3/4
Human: 100% x 100% = 100%
Rhesus Monkey: 51% x 94% = 48%
Chimpanzee: 24% x 98% = 24%
The rest of the primates are even worse, with many composite scores less than 15%.
Now, I’m not saying we’re dissimilar to chimps, in fact I think we are far more similar to chimps than we are to lungfish. No question.
But the issue is that when we are doing comparisons even on the same gene, we tend to snip out large segments that aren’t shared. In the case of the INFL3/4 gene, yeah we can say one piece of the corresponding INF3/4 gene in chimps is 98% identical but fail to mention we had to exclude the 76% that definitely was dis-similar! So this is one example where we are closer to the Rhesus monkey than we are to chimps, but if we cherry pick identity scores without factoring in coverage scores, we could view ourselves closer to chimps.
That’s an example of the problem of cherry picking. We tend to do neighbor joining by discounting rather large segments of dis-similarity. We do enough of that we can come up with all sorts of forced similarity claims. The difference becomes more apparent when we compare longer sequences between species. Using shorter sequences invites systematic cherry picking, and it’s become such an industry standard now, it’s hardly given a second thought.
That’s why the phenotypic and morphological comparisons are in my opinion more representative. So Hennig and Linnaeus were on a better track since morphological comparisons are more wholistic.
Here is the search I did. The link expires in 2 days, but one can easily do the search themselves:
https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=2S98F0JJ014
Click for lager image.
http://theskepticalzone.com/wp/wp-content/uploads/2017/12/infl4.png
Slow down, or you’ll have overturned all of our current understanding of biology and then we’ll have to find something to do with the unemployed biologists now you’ve replaced their jobs with goddit.
Ok just for grins I did a search for INFL3/4 in giraffes:
Ok, so primates aren’t giraffes. I buy that.
And I also did a search for INFL3/4 in lungfish. This was the result:
Reasons why no significant similarity found? Because mammals aren’t fish Dab Gummit!
I find almost everything you post as an argument to be pointless playing about with words, and this is a fine example. All you’re doing here is fixating on the word “modification” as if that’s an explanation for the differences among species. “Descent with modification” isn’t an attempt to explain the modifications; it’s about the pattern of similarities and differences. In other words, common descent. The same theory, not a competing theory.
“Natural selection” was Darwin’s attempt to explain the modifications.
I think your comparisons here are unlikely to be between orthologous sequences. And your suggested similarity measure is a meaningless one.
What would be the correct way to find orthologous sequences specifically for this gene?
I can force-fit orthology by cherry picking out the “offending” nucleotide sequences, the introns, and using segments of predicted proteins from concatenated exons. But that is exactly the point I was making regarding cherry picking.
What would be the 5 best orthologs?
I don’t have to defend my approximation, the BLAST alignment algorithm put the rhesus monkey more similar to humans than to chimps for that particular sequence.
The order of best hits in terms of species:
Human
Rhesus Monkey
Chimp
Olive baboon (Papio Anubis)
Gorilla
Pongo abelii (Sumatran orangutan)
Chlorocebus sabaeus (green monkey)
Macaca nemestrina (pig-tailed macaque)
Mung,
If you know, why the insistence, in the comment to which I responded, that people discard differences, and ‘cherry-pick’ only identity?
stcordova,
Molecular comparisons cause you much more of a headache than morphological ones, so you want to pretend they are uninformative, and we should go back 50 years or so.
Nonetheless, there’s this process of template directed DNA polymerisation – that, ultimately, is how relationship is effected – and therefore sequence comparison is a very nifty way of getting at relationship.
stcordova,
I don’t know why you find anomalies based on one gene to be problematic for the whole methodology. After all, what persuades you that they are anomalous?
At issue is not the question of hierarchy in my mind. I already affirmed it’s obvious presence.
The question I’m raising is one of sampling. What is considered a representative sample of characters and/or DNA such that the sample comparison is representative of complete comparison.
I already have affirmed I believe we are more similar to chimps than any other creature. The sticking point for me is the notion, to paraphrase Axel Meyer, that mammals are fish. I’ve argued this claim of similarity is owing to the sampling techniques. If I chose the INFL3/4 gene, for example, clearly we would not be grouped nor neighbor joined with Sarcopterygiian’s like lungfish.
Furthermore, the INFL3/4 gene shows that the similarity claims suggesting it’s easy to evolve chimps and humans from a common ancestor because there genes are 98% similar. But really that is only saying the segments of DNA that are 98% similar are 98% similar. It doesn’t deal with the segments that are very dis-similar as shown with the INFL3/4 gene. There are huge differences, for example, in the centromeric regions — they don’t correspond between the chromosomes! Some how the centromeric regions got re-mapped and re-homogenized between chimps and humans?
Before I forget, there is something that troubled me about the lungfish. We have a monster of a time building an assembly for the lungfish because of the repetitive sequences and the fact our affordable sequencers like Illumina can only sequence short segments at a time (300 bases, and in some cases a lot less). So we take billions of short reads and try to reassemble them into a complete genome. It fails to work on the stretches of repetitive elements.
But this brought to mind a problem Henikoff could not resolve for the centromeric regions, but it really is problem elsewhere. The tandem repeats, and I would presume the dispersed repeats as well, are, to use Henikoff’s word, “homogenized”. They lack the level of expected variability over time.
That is to say, if the repeats accumulated slowly, one would expect point mutations to make them different over time. They are different, but not quite different enough.
The fact the sequencers are having problems with repetitive sequences in the lungfish are testament to the level of homogenization in the repetitive sequences and the absence of sufficient point mutation between them. This suggest to me the expansion of the repetitive sequences has been recent, if not part of the special creation which happened recently.
If one will invoke all these changes of sequence in the genes which are supposedly under selection, why then the absence of corresponding changes in repeats in the non-coding section? Something seems incongruent there.
stcordova,
Taxonomically, they nest neatly within the clade, so I don’t really see the problem, other than it offends your preference for nomenclature. Obviously genetic distances are greater, and so differences likewise greater, but it’s still the large numbers of genes with clear relationship that supports the placement.
You don’t have quite the retention of karyotype that we have with chimps that provides an additional layer of support among closer relatives. I’m not sure about centromeres – the centromere on our fused 2 certainly lines up with centromeres in the chimp homologues. But if even there were divergence in centromere position I wouldn’t see it as troublesome. Nothing anchors centromeres in a fixed position other than the other chromosome copies in the population; the ‘mean’ position can clearly drift over time.
I don’t think so. Fish don’t have placentas like placental mammals. There are egg laying mammals like the duck-billed platypus, but these strange creatures have mammary glands which fish don’t have.
Additionally, if we consider the gene lists, the fish in question don’t have as close a list of genes as mammals share with one another. Hence the mammals and fish are sister groups, and the fish aren’t the parent group of mammals — taxonomically speaking.
To quote Nick Matzke:
These sister group relationships are approximated by the Neighbor Joining methods which approximate least squares for the DNA grouping. But as I said, the morphological, though superficially seeming more subjective than DNA sequences, strikes me as the superior comparison.
Some will say DNA is better. Well, if were talking phylogeny between members of a species, DNA is superior — as in paternity testing. But between species that are substantially different, it seems the morphological comparisons are much better. For example, I can clearly see a giraffe is not a lungfish, not even close. I don’t need DNA testing for that.
Speaking of the platypus, it’s more amazing than Ray Comfort’s crockoduck.
From wiki:
“they locate their prey in part by detecting electric fields generated by muscular contractions”. Friggin amazing how God’s creatures work.
Darwin calls it “common parentage/parent”, or “common progenitor”, or “community of descent”.
“Summary.
In this chapter I have attempted to show that the arrangement of all organic beings throughout all time in groups under groups — that the nature of the relationships by which all living and extinct organisms are united by complex, radiating, and circuitous lines of affinities into a few grand classes,— the rules followed and the difficulties encountered by naturalists in their classifications — the value set upon characters, if constant and prevalent, whether of high or of the most trifling importance, or, as with rudimentary organs of no importance,— the wide opposition in value between analogical or adaptive characters, and characters of true affinity; and other such rules,— all naturally follow if we admit the common parentage of allied forms, together with their modification through variation and natural selection, with the contingencies of extinction and divergence of character.
(…)
Finally, the several classes of facts which have been considered in this chapter, seem to me to proclaim so plainly, that the innumerable species, genera and families, with which this world is peopled, are all descended, each within its own class or group, from common parents, and have all been modified in the course of descent, that I should without hesitation adopt this view, even if it were unsupported by other facts or arguments.” – Charles Darwin, The Origin of Species (1872), Chapter XIV: Mutual Affinities of Organic Beings: Morphology, Embryology, Rudimentary Organs
Mung, your word-searchings are pathetic.
stcordova,
They do though. Fish don’t have placentas or eyelids, of course, nor do mammals have scales and gills. Nonetheless, the significant numbers of related genes show a clear nesting of mammals within the clade, using exactly the same criteria as apply to human/chimp.
stcordova,
This is silly. No-one is saying that modern fish are the ancestors of modern mammals. But the genetic relationship of modern fish and modern mammals is hard to deny – even if you don’t think it is a real genetic relationship, but a bizarre commonality introduced by a Designer for some obscure reason. And it’s pretty clear that the common ancestor of modern mammals and modern fish, if such existed, would be declared ‘a fish’, due to its swimmy, gill-festooned ways placing it neatly in that mental pocket.
Why do we mostly have bones that are homologous with theirs (like fin and arm bones)? There’s no design reason why this should be so.
Why do mammal testes develop roughly the same place as fish testes develop and remain, while in most mammals they make a significant (and not always complete) journey to end up outside the body cavity?
I suppose this gets back to the need for any kind of reason to believe in common design, the false dilemma thrown at us only indicating how pathetic that case is.
Glen Davidson
Well, a fair number of them do, though of course they aren’t homologous to mammalian placentas.
Quite a few fish have placentas, and as you note some mammals don’t. More importantly, why are you using differences to refute relationship? Can’t differences arise in the course of evolution? What shows relationship are synapomorphies, or shared, derived characters. Mammary glands are a synapomorphy of mammals, evidence that mammals have a common ancestor, though you don’t believe that. Bones in the pelvic and pectoral appendages is a synapomorphy of sarcopterygians, and there are quite a few others, and that’s evidence that sarcopterygians have a common ancestor, though you don’t believe that. But what I can’t figure is why you think Mammalia is a more legitimate group than Sarcopterygii. I also can’t figure out what you think Mammalia is, if it isn’t a “kind”, or why you think there are nested groups within and without Mammalia.
What gene lists? Do you even have any sort of list for lungfish or coelacanths? Surely you aren’t trying to use the zebrafish as a proxy for them; that would be really silly. It isn’t clear what you mean when you say “fish”. If you refer to all those gilled vertebrates, then yes, they’re paraphyletic and a parent group of mammals.
I’m unclear why you quoted Matzke saying a commonplace of systematics. What point were you trying to make about it? I suspect some bizarre and counterfactual creationist interpretation. Also, I don’t understand your obsession with neighbor-joining and your need to constantly repeat that it’s an approximation of least-squares fit.
What does that have to do with phylogeny? I can clearly see that a giraffe isn’t a cow either, but how does that show that giraffes aren’t artiodactyls? Similarly, how does a giraffe not being a lungfish show you that they aren’t sarcopterygians? It seems that you don’t understand descent with modification.
So what explains its presence? Do you have any sort of hypothesis?
I would suggest that a dozen or so unlinked loci ought to be a good sample. A bigger problem is figuring out how to analyze the data.
You haven’t argued, you have just claimed on the basis of a poor sample of one mitochondrial gene. You have demonstrated nothing about the INFL3/4 gene except that you are unable to get a valid sample of mammals using BLAST. You have certainly not shown anything about sarcopterygians. Incidentally, “neighbor joined” isn’t a word, and it’s unclear what you think it means.
A one-paragraph Gish gallop, starting with INFL3/4 and ending up with centromeres. What the heck? You haven’t shown anything with either of these. You merely allude to something you think you know, but I suspect what you know is illusory.