Is homoplasy hidden from non-specialists?

The additional point that needs making about convergent evolution is that it applies to some characters, but not to even a large fraction of the characters in the organism. A moth may mimic a wasp in external appearance -- but that won't mean it converges in the fine details of external appearance (placement of individual bristles, for example). And when details of internal anatomy are examined they will be mothlike, as will the DNA and protein sequences. So once many characters, or many sites of molecules, are examined, the convergence does not mislead the reconstruction of the phylogeny.

Creationists typically fudge this, and try to persuade their audiences that the cases of convergence apply to all characters and would therefore mislead us when we make evolutionary trees.

That's exactly what Gauger did in the video with respect to the vertebrate and cephalopod camera eyes, to the extent that some creationists are now claiming that the DNA sequences of genes involved in the two sorts of eyes are identical.

Speaking of lineage sorting, Dennis Venema has nice post on it on the BioLogos forum site. In particular, Venema discusses the implications for reconstructing ancestral lineages, and hammers some misrepresentations Casey Luskin made about discordant phylogenetic trees. He also discusses some implications for estimates of ancestral population sizes, rebutting the Gauger/Axe/Luskin notion that there could have been an ancestral human population of just two individuals.

Convergent evolution was extensively covered in my most basic university biology courses, and I was already aware, as a not even very well informed lay person (at that age), that cetaceans are mammals that superficially resemble fish, that some marsupials have similar adaptations to some placental mammals, that bats and birds aren't very closely related even though both groups are flying vertebrates, that not terribly closely related plant and fungal species evolved use of similar toxic/psychoactive chemical defenses, etc.

Homoplasy/convergent evolution is well known and is strong evidence FOR evolution.

The argument that "whales look kind of like fish but aren't fish, so therefore humans and chimpanzees might not be closely related" is really silly.

Gauger wrote: 3. About homoplasy being a hidden secret: it’s hidden from non-specialists.

harold said: The argument that "whales look kind of like fish but aren't fish, so therefore humans and chimpanzees might not be closely related" is really silly.

I should clarify one point. "Homoplasy" refers to all sorts of noise that can complicate reconstruction of evolutionary trees. It does not just have to mean convergence. For example if, at site number 283 in a gene, a G changes to a C. and then later, in one of the descendant lineages, the C changes back to a G, that too is homoplasy. So homoplasy does not necessarily imply convergence.

To John's comment, even if it were true (as as far as I know it isn't) that the DNA sequences involved in making vertebrate and cephalopod camera eyes were absolutely identical, that would still leave all the rest of the genes (and intergenic sequences), overwhelmingly not involved in that convergence.

As for lineage sorting, Dennis's posts at Biologos are great -- I hope he collects them together someday, perhaps in a book entitled Mistakes People Make Talking About Evolution. I am also partial to my own post on coalescents and lineage sorting which needed a correction of the numbers here.

I posted this in the previous thread, but it seems more appropriate for this one:

I am a master’s student in evolutionary biology and teach a VERY introductory biodiversity and evolution lab class for non-biology majors. We talk about homoplasy in the first lecture of the semester and bring it up again many times thereafter. It was also discussed rather extensively in my undergrad courses as well.

I will be charitable and assume that Gauger simply has no idea what’s she is talking about…

IANABiologist, but it seems like she's playing with the unfamiliarity of the TERM 'homoplasy'. True, most laypeople would not have known it (I didn't)--which, in a very strained sense, perhaps makes it a 'secret'.

But a large proportion of lay people who know even a little about evolution would have heard of 'convergent evolution', and most--even some IDCs--would recognize that evolution can produce such apparently amazing similarities.

The DEFINITION of'homoplasy' is a "hidden secret" from NON-SPECIALISTS. Well, duhh. Then I wonder if she's concerned that the "hidden secret" of the overrunning sprag clutch is being kept from the public. What secrets are plumbers covering up with the innocent-seeming letters 'ASHRAE'?

Just Bob said:The DEFINITION of'homoplasy' is a "hidden secret" from NON-SPECIALISTS. Well, duhh. Then I wonder if she's concerned that the "hidden secret" of the overrunning sprag clutch is being kept from the public. What secrets are plumbers covering up with the innocent-seeming letters 'ASHRAE'?

Joe Felsenstein said: I should clarify one point. "Homoplasy" refers to all sorts of noise that can complicate reconstruction of evolutionary trees. It does not just have to mean convergence. For example if, at site number 283 in a gene, a G changes to a C. and then later, in one of the descendant lineages, the C changes back to a G, that too is homoplasy. So homoplasy does not necessarily imply convergence.

In some cases, it is difficult to tell whether a trait has been lost then re-evolved convergently, or whether a gene has simply been 'switched off' and then re-enabled later.

I have a PhD in genetics and have been doing research and teaching genetics and molecular biology for over 30 years, and I don't recall ever having read the jargon "homoplasy." Of course, I'm quite familiar with the idea of convergent evolution. Just sayin'.

Joel: I have to admit I'm surprised. It's a term commonly used in systematics. It's just the companion term to "homology". And I can see how you might not use it, but doesn't anyone in your department do any phylogenetics?

Thanks for the nods, Richard and Joe. Funny you should mention a book, Joe - I've just found out that I won a grant to assist with writing one. The intended audience will be evangelical laypersons and pastors. It will be co-authored with a colleague who has theological expertise.

kai.extern said: So I went and looked for the Wikipedia article on homoplasy. OK, that redirects to convergent evolution. Then there's this:

In some cases, it is difficult to tell whether a trait has been lost then re-evolved convergently, or whether a gene has simply been 'switched off' and then re-enabled later.

This sounds to me as if Wikipedia thinks what you describe is convergent evolution. (Or just switching off and on again, depending on what the changed sequence does.)

Joel Eissenberg said: I have a PhD in genetics and have been doing research and teaching genetics and molecular biology for over 30 years, and I don't recall ever having read the jargon "homoplasy." Of course, I'm quite familiar with the idea of convergent evolution. Just sayin'.

So Gauger’s claim about the issue being hidden from non-specialists is just flatly false. It’s right out there in plain site in books by professional scientists that are specifically aimed at non-specialists.

Damn evilutionists! They constantly hide stuff in places like books and libraries where no red blooded American can find it!

John Harshman said: Joel: I have to admit I'm surprised. It's a term commonly used in systematics. It's just the companion term to "homology". And I can see how you might not use it, but doesn't anyone in your department do any phylogenetics?

Joe Felsenstein said:

Joel Eissenberg said: I have a PhD in genetics and have been doing research and teaching genetics and molecular biology for over 30 years, and I don't recall ever having read the jargon "homoplasy." Of course, I'm quite familiar with the idea of convergent evolution. Just sayin'.

I looked your University up. I see you are in the Biochemistry and Molecular Biology Department in the Medical School. The Biology Department has a number of people who list their interests as "molecular phylogenetics" and will certainly know about homoplasy and tell you that they do talk about it in their courses. In addition your University has a formal connection with the Missouri Botanical Garden which has many people who know all about homoplasy. Peter Raven, a quite distinguished systematist, is there and he will know a lot about homoplasy.

Joel Eissenberg said: Has anyone else on this thread besides me considered the possibility that fettishizing jargon only makes you look foolish?

Joel Eissenberg said: ... Yes, I'm familiar with the faculty in our department. I know several personally (though not Peter Raven). We also have a theology department, and I'm afraid I lack a working knowledge of most of the jargon of Islam. And we have an engineering school, but I still can't give you a good working definition of "Young's modulus." Has anyone else on this thread besides me considered the possibility that fettishizing jargon only makes you look foolish?

Joe Felsenstein said: Fetishizing jargon? I don't complain when your department uses terms like "N-terminus' or "alpha helix" or "membrane protein". You're not "fetishizing" when you use phrases like that, and I think we all respect that. "Homoplasy" is another useful descriptive phrase. It is better than saying "you know, the case where there are at least one more change in the site (or character) on the phylogeny than the minimum number you would need to have on a tree to get that number of states". Having a single word does shorten the dialog.

Joe Felsenstein said:

Joel Eissenberg said: ... Yes, I'm familiar with the faculty in our department. I know several personally (though not Peter Raven). We also have a theology department, and I'm afraid I lack a working knowledge of most of the jargon of Islam. And we have an engineering school, but I still can't give you a good working definition of "Young's modulus." Has anyone else on this thread besides me considered the possibility that fettishizing jargon only makes you look foolish?

Fetishizing jargon? I don't complain when your department uses terms like "N-terminus' or "alpha helix" or "membrane protein". You're not "fetishizing" when you use phrases like that, and I think we all respect that. "Homoplasy" is another useful descriptive phrase. It is better than saying "you know, the case where there are at least one more change in the site (or character) on the phylogeny than the minimum number you would need to have on a tree to get that number of states". Having a single word does shorten the dialog.

Joel Eissenberg said:

Joe Felsenstein said:

Joel Eissenberg said: ... Yes, I'm familiar with the faculty in our department. I know several personally (though not Peter Raven). We also have a theology department, and I'm afraid I lack a working knowledge of most of the jargon of Islam. And we have an engineering school, but I still can't give you a good working definition of "Young's modulus." Has anyone else on this thread besides me considered the possibility that fettishizing jargon only makes you look foolish?

Fetishizing jargon? I don't complain when your department uses terms like "N-terminus' or "alpha helix" or "membrane protein". You're not "fetishizing" when you use phrases like that, and I think we all respect that. "Homoplasy" is another useful descriptive phrase. It is better than saying "you know, the case where there are at least one more change in the site (or character) on the phylogeny than the minimum number you would need to have on a tree to get that number of states". Having a single word does shorten the dialog.

Uh, Joe, neither I nor anyone in my department has made an entire blog post that rests on the use/misunderstanding of "N-terminus' or "alpha helix" or "membrane protein." Your analogy is a false one. The words "convergent" and "evolution" are parts of the lexicon of most modestly educated English-speaking people. Thus, the phrase "convergent evolution" at least conjures something like its actual definition in the mind of an educated English-speaking person. I heard it for the first time without a definition and I got it. Homoplasy doesn't immediately suggest its meaning to someone unfamiliar with Greek etymology. Thus, I regard it as jargon, and I regard its use for the purposes of diminishing others or their arguments as a type of fettishizing. YMMV. I will not reply to further discussion on this point. I was making a personal observation from the POV of a highly trained life scientist and teacher who is sympathetic to the goals of teaching evolution. Take it or leave it. I'm not interested in making this thread about me.

By the way, I forgot this on another thread - if the person who is using my list of questions around the web is reading - THANK YOU.

Here they are for anyone. These are 100% "open source". Some of them I invented, but others, plausibly most, were good questions I saw asked individually in threads.

1) Could any evidence convince you of the theory of evolution, and if so, what type of evidence is now lacking, that would convince you if present?

2) The Supreme Court ruled against the direct teaching of Biblical Young Earth Creationism as science in public schools; however, if that ruling were overturned, which would you support more, teaching of ID, or direct teaching of Bible-based YEC?

3) Do you think it is important for opponents of the theory of evolution to fully understand the theory of evolution? If so, can you explain it, and if not, can you explain why not?

4) Who is the designer? How can we test your answer?

5) What did that designer do? How can we test your answer?

6) How did the designer do it? How can we test your answer?

7) When did the designer do it? How can we test your answer?

8) What is an example of something that was not designed by the designer?

9) Some parts of the Bible suggest that pi equals exactly three, and that the earth is flat and has four corners. Do you accept these as facts of physical reality, and if not, why do you deny the theory of evolution on the grounds of Biblical literacy, if it can be symbolic about other scientific issues?

Not to throw more gasoline on the fire, but it does seem to speak to the unfortunate compartmentalization of science that a professional biologist can have avoided hearing the term "homoplasy" for his entire career. After all, nothing in biology makes sense except in the light of evolution, and homplasy is an important concept in evolution, right up there with homology, fitness, etc. I'm less concerned that the general public doesn't know the word. They probably don't know "homology" either.

John Harshman said: After all, nothing in biology makes sense except in the light of evolution, and homplasy is an important concept in evolution, right up there with homology, fitness, etc. I'm less concerned that the general public doesn't know the word. They probably don't know "homology" either.

It is worth noting that the basics of evolution are critical to all of biomedical science, and, although somehow counter-intuitive to many people, fairly easy to understand. (By counter-intuitve I do not mean that people intuitively come up with ID/creationism nonsense, they don't, but that people often tend to be "Lamarckist" and project conscious intent onto molecular processes.)

There are also a variety of sub-specialized fields which deal with phylogenetic relationships and/or detailed mechanisms of evolution at a very granular layer. These fields have their own terminology, like any other fields.

As I noted before, some members of the community that pays attention to evolution denial are from such specialized fields.

However, others are from other fields of biomedical science, and others still are interested people from the physical sciences or mathematics/computing, and many are merely well-informed people who have no formal scientific credentials, basic or applied, whatsoever.

The reason "homoplasy" has come up is not because Joe Felsenstein or anyone else is belittling biomedical scientists who don't work directly in a field like population genetics, it is because professional ID/creationist Ann Gauger misused the term to try to create public confusion and advance the sectarian/authoritarian agenda of those who fund the DI.

If anyone who defends sound science wasn't aware of the term 'homoplasy' before - I was aware of it but thought of it as pretty much synonymous with convergent evolution, which in one sense, it is - then they should take this opportunity to learn what it really means and why Gauger's comments are misleading.

Well, I don't know that Gauger actually misused the term. Her definition, which if I recall was something like "similarity not due to common ancestry", is a pretty good one. She's just taking that correct definition and concluding that if there is any such similarity, we can't believe there is any true homology, i.e. similarity that *is* due to common ancestry. And therefore Jesus.

John Harshman said: Well, I don't know that Gauger actually misused the term. Her definition, which if I recall was something like "similarity not due to common ancestry", is a pretty good one. She's just taking that correct definition and concluding that if there is any such similarity, we can't believe there is any true homology, i.e. similarity that *is* due to common ancestry. And therefore Jesus.

John Harshman said: Well, I don't know that Gauger actually misused the term. Her definition, which if I recall was something like "similarity not due to common ancestry", is a pretty good one. She's just taking that correct definition and concluding that if there is any such similarity, we can't believe there is any true homology, i.e. similarity that *is* due to common ancestry. And therefore Jesus.

That's pretty much how ID works, you know. I prefer the recently coined term (by whom?) "carge cult science", because it fits so well. IDiots adopt the surface trappings of science: lab coat, lab background, fancy technical terms, even the occasional research paper, in hopes that much cargo will come their way.

Interesting: the term "cargo cult science" was apparently coined by none other than Richard Feynman, and not so recently: 1974. Or so says Wikipedia.

John Harshman said: Interesting: the term "cargo cult science" was apparently coined by none other than Richard Feynman, and not so recently: 1974. Or so says Wikipedia.

“Discovery Institute's Center for the Renewal of Science and Culture seeks nothing less than the overthrow of materialism and its cultural legacies. Bringing together leading scholars from the natural sciences and those from the humanities and social sciences, the Center explores how new developments in biology, physics and cognitive science raise serious doubts about scientific materialism and have re-opened the case for a broadly theistic understanding of nature.”

Mike Elzinga said: Another alternative for “cargo cult science” would be a Potempkin village of science.

Good science will come Your editorial asks a reasonable question: can the theory of intelligent design (ID) lead to good science (16 December 2006, p 5)? Researchers at the Biologic Institute are convinced it can. ID sceptics, of course, want proof. We take that challenge seriously, which is why we insist on completing our research projects before talking about them. What you have interpreted as conspiratorial "caginess" is just scientific caution. Your description of ID as doing nothing more than questioning Darwinism is incomplete. Cells process digital information. Humans have also developed this technology. Cells make molecular machines and complex materials by nano-fabrication. So do humans. Cells do complex chemistry, signal transduction and process control. So do humans. But Darwinism prevents what we have learned as engineers from illuminating biology, by insisting that the two modes of invention are fundamentally different. What humans accomplish only by intellectual effort, nature puts to shame by mindless accident, we are told. If that is wrong -- and we think it is -- whole new fields open up, waiting to be explored. Perhaps neurobiologists would learn something from computer designers and network whizzes. Maybe systems biologists would start hanging out with systems engineers. We don't know where all this would lead, but we are confident that good science will come out of it. ~~~~~~~~ By Douglas Axe; Brendan Dixon and Ann Gauger Redmond, Washington, US

I guess it depends on how cynical you think they are. If they honestly believe that their science-like activities are real research that will shed a genuinely scientific light on “design,” then Cargo Cult would be appropriate. If they secretly know that ID isn’t amenable to scientific investigation and are just going through the motions to make it look like they have a viable research program, it’s a Potemkin Village.

I just looked at the Wikipedia article on "Convergent evolution" (to which one is directed from "Homoplasy"). There is this interesting sentence: "Convergence has been associated with Darwinian evolution in the popular imagination since at least the 1940s."

Piotr Gąsiorowski said: Their letter to New Scientist (13 Jan 2007). Emphasis mine.

Good science will come What humans accomplish only by intellectual effort, nature puts to shame by mindless accident, we are told. ~~~~~~~~ By Douglas Axe; Brendan Dixon and Ann Gauger Redmond, Washington, US

Words, words, words. It was six years ago. Where's the bloody science?

Healthy: Are you a native English speaker? If not, you will need to improve your English before you can become comprehensible. If so, I don't see any hope for you. Still, you might try to explain what the heck you were talking about.

He appears to be a spammer pretending to be interested in the discussions going on here.

The incoherent patter is just an excuse to get us to look at some “non-profit” organization called Aging Portfolio. Presumably he wants us to Google it.

Mike Elzinga said: He appears to be a spammer pretending to be interested in the discussions going on here. The incoherent patter is just an excuse to get us to look at some “non-profit” organization called Aging Portfolio. Presumably he wants us to Google it.

when I get near a computer I'll do something about Healthy.

It occurs to me (and this probably isn't that revolutionary) that one could develop a curriculum that uses Intelligent Design/OEC/YEC and by doing nothing but have students expose the flaws, have a pretty comprehensive biology program... and get some good training in critical thinking.

ogremk5: It occurs to me (and this probably isn’t that revolutionary) that one could develop a curriculum that uses Intelligent Design/OEC/YEC and by doing nothing but have students expose the flaws, have a pretty comprehensive biology program… and get some good training in critical thinking.