Telling apes from humans

Excellent post! I can't tell you how many times I have asked creationist to describe how a transitional fossil between apes and humans should look and gotten no response. Their dogma doesn't allow for transitional fossils so they are incapable of recognizing or describing them.

Nice little post, Jim. Always good to revisit subjects like this every now and then, lest anyone get the idea that creationists have any idea what they're talking about.

However, I'm curious: why no link to your much more elaborate treatment of this topic at the talk.origins archive?

For the other teachers in the audience I highly recommend a similar activity to this in your biology classes. The talk origins archive has a wonderful image with a wide variety of hominid fossil skulls. I took the image, cut the skulls out erased the letters, and stuck them into a single power point slide for the students to then classify into different groups of the same and different species. It's a very organic way to have your students prove to themselves the difficulty and subtlety of grouping things into the same vs. a similar species.

This is a trick question, kind of like asking people to distinguish which fossils are tuna and which are fish. Hopefully, some astute reader will point out that humans ARE apes, generally positioned right in the middle of the ape clade. I suppose it might be possible from appearance alone to date a skull as closer or further from the branch from a common ancestor, but that's difficult enough so even experts don't agree.

IIRC, all of these hominids made and used stone tools. If the AIG quacks are going to insist that H. habilis is an ape, then it is an ape that makes and uses stone tools. Just like H. sapiens.

Hmmm, so did the H. habilis have their own god, Eden, and talking snake?

One of the minor absurdities of AIG is that there couldn't have been a stone age. In Genesis, the first city, Enoch, is founded by Caine, after he gets kicked out of the house. No ice ages either.

Of course, the earth's surface is littered with stone tools everywhere.

Okay, I'm embarrased. I counted 3 apes, but only 2 humans. (Based on those canines.)

You have to admit, the human skull is very impressive, the comparison must really upset people.

Flint said: This is a trick question, kind of like asking people to distinguish which fossils are tuna and which are fish. Hopefully, some astute reader will point out that humans ARE apes, generally positioned right in the middle of the ape clade. I suppose it might be possible from appearance alone to date a skull as closer or further from the branch from a common ancestor, but that's difficult enough so even experts don't agree.

My apologies! I made the same mistake I hate in other's posts. "loser", not "looser".

dpr

D. P. Robin said:

Flint said: This is a trick question, kind of like asking people to distinguish which fossils are tuna and which are fish. Hopefully, some astute reader will point out that humans ARE apes, generally positioned right in the middle of the ape clade. I suppose it might be possible from appearance alone to date a skull as closer or further from the branch from a common ancestor, but that's difficult enough so even experts don't agree.

Trick question? No, it is an absurd question, asked by Creationists of varied stripe. Agreed that if we are thinking about humans as we would other life, we would speak about humans as another example of ape specialization. However the question is not valueless if we pose it as "Which of these are on the lineage that include modern Homo as opposed to being on a lineage that led to some other modern ape?". For the Creationist the dilemma is that they've already lost the battle if they don't say that the top left skull is "human" and the other two skulls are "ape". Anything else looses their Fundamentalist base. Anything else also enmeshes them in a web of doublespeak that make them look foolish to all outsiders. dpr

Flint said: This is a trick question, kind of like asking people to distinguish which fossils are tuna and which are fish. Hopefully, some astute reader will point out that humans ARE apes, generally positioned right in the middle of the ape clade. I suppose it might be possible from appearance alone to date a skull as closer or further from the branch from a common ancestor, but that's difficult enough so even experts don't agree.

Apes? I thought we were primates-but apes?

(Primates also include monkeys, lemurs, and some others.)

Yes, humans are still apes. For the same reason that we're still mammals and still synapsids.

"Creationists are always very definite that there are absolutely, absolutely no transitional fossils between apes and humans."

Just for clarity, are we defining "transitional fossil" to be exactly the same as "something that appears like a transitional fossil"?

Henry J said:

Apes? I thought we were primates-but apes?

http://tolweb.org/Hominidae/16299 Hominidae is the taxonomic group that contains the apes (orangutan, gorilla, chimpanzee, human).

Joe Felsenstein said:

Henry J said:

Apes? I thought we were primates-but apes?

http://tolweb.org/Hominidae/16299 Hominidae is the taxonomic group that contains the apes (orangutan, gorilla, chimpanzee, human).

It has been a very common statement by evolutionary biologists, still said more often than you might think, that “humans are not descended from apes, although humans and apes did have a common ancestor”. It is supposed to reassure the listener. I have asked my classes about this statement and many of the students report having been told that. It seems to be based either on outdated notions of hominid phylogeny which had the lineage to humans as the sister lineage to the (other) apes. Or it is based on non-monophyletic taxonomies that are no longer widely accepted. It is more common for evolutionary biologists to announce that “we are not monkeys, but we have a common ancestor with monkeys.” This too is wrong, at least if New World monkeys (howler monkeys, spider monkeys, etc.) are allowed to be called monkeys. The last time I lectured on this, I announced that I was descended from apes because (in addition to my being an ape) my mother and father were apes. And we were all monkeys too. And for that matter, I am a monkey's uncle.

I have a copy of Lubenow 2004 that I just started reviewing for a friend of mine. I'm looking for the spot where he commits to calling H. habilis an ape. I see the table on p. 352, but that isn't very helpful, other than ER1813 is further down the table.

Yeah. I think the quote “humans are not descended from apes” is missing a critical qualifier - we aren't descended from currently living non-human apes - the last common ancestor is unlikely to be any of the still living species. But that ancestor (as I understand it) would have had enough characteristic ape features to be called an ape. (Similarly for the last common ancestor of monkeys and apes.)

Henry

You're using scientific jargon and vernacular English at the same time as if they were the same thing. We are primates because there's a clade called "Primates", just as birds ("Aves") are dinosaurs because they're included in a clade called "Dinosauria". We are catarrhines, too, and hominids-- but we're not apes. "Ape" is a common English word that doesn't mean to be phylogenetically accurate. It's used for tailless old world monkeys. To me, the word "ape" is like "fish" or "bug"- they only respond to some kind of animals' vague, common English description.

Semantics can get boring...

Henry J said: Yeah. I think the quote “humans are not descended from apes” is missing a critical qualifier - we aren't descended from currently living non-human apes

KP said: I have a copy of Lubenow 2004 that I just started reviewing for a friend of mine. I'm looking for the spot where he commits to calling H. habilis an ape. I see the table on p. 352, but that isn't very helpful, other than ER1813 is further down the table.

I don’t see why when you say “we come from apes” somebody has to think that you mean “we come from gorillas” or whatever other species of present-day apes.

KP said: Nevermind, I found it: "Homo habilis: The Little Man Who Isn't There" p. 299.

I suppose in the vernacular, "apes" refers mostly to gorillas - or possibly even to some cartoon parody of a gorilla.

But we are also without question "tailless old world monkeys". Granted many of us have migrated around the globe over the millennia.

I think the vernacular notion of an ape is associated with lots of body hair, unattractive (to us) faces and figures, low intelligence, lack of sophisticated language, and such. So the word refers to critters that kind of resemble us, so that the differences give them the appearance of being stupid and ugly. If only they were different enough, like (say) horses or cats, we wouldn't have nearly the motivation to disassociate ourselves from them and try to pretend we're not one of them.

RebusMaze said: "Creationists are always very definite that there are absolutely, absolutely no transitional fossils between apes and humans." Just for clarity, are we defining "transitional fossil" to be exactly the same as "something that appears like a transitional fossil"?

I am YEC.
Skulls mean nothing to me as its clear to me that the ape/man sameness is real.
God simply upon looking at his creations picked the best body type to put a being made in his image into. What else? What other type of body would suit a divine being like ourselves? A mouse, rhino. bear insect, bird??
All creatures show they come from a common design. Mostly we all have eyes, ears, legs, butt, etc.
So if god was going to have us on earth the only options are to pick a body so unlike the general theme or simply pick within the theme the best type of body.
This is the ape body.
So this creationist welcomes dead on sameness to monkeydom.
There is no need to seek differences.
The little difference in skulss is just for a practical container for the addition of this or that tool we use more then animals.

Its possible post flood humans did not need and therefore have as much of this or that tool in the brain. However probably we have pretty much the same skull.
so its easy to tell us from apes if apes have always lesser brains etc.

Once again this is all about weighing brains. Surely the computer age with its "small is smarter" should put to rest brain size as a factor in intelligence and so humanness.

Robert Byers

YEC = Young Earth Creationist. And yes, definitely avoid it. 99.9% (give or take .01%) of everything Byers says is utterly crazy.

Robert Byers said: I am YEC. Skulls mean nothing to me as its clear to me that the ape/man sameness is real. God simply upon looking at his creations picked the best body type to put a being made in his image into. What else? What other type of body would suit a divine being like ourselves? A mouse, rhino. bear insect, bird?? All creatures show they come from a common design. Mostly we all have eyes, ears, legs, butt, etc. So if god was going to have us on earth the only options are to pick a body so unlike the general theme or simply pick within the theme the best type of body. This is the ape body. So this creationist welcomes dead on sameness to monkeydom. There is no need to seek differences. The little difference in skulss is just for a practical container for the addition of this or that tool we use more then animals. Its possible post flood humans did not need and therefore have as much of this or that tool in the brain. However probably we have pretty much the same skull. so its easy to tell us from apes if apes have always lesser brains etc. Once again this is all about weighing brains. Surely the computer age with its "small is smarter" should put to rest brain size as a factor in intelligence and so humanness.

Flint said: ... I think the vernacular notion of an ape is associated with lots of body hair, unattractive (to us) faces and figures, low intelligence, lack of sophisticated language, and such. ...

Almost forgot: here's the Wiki on the taxonomy:

http://en.wikipedia.org/wiki/Human_taxonomy

Anon said: You're using scientific jargon and vernacular English at the same time as if they were the same thing. We are primates because there's a clade called "Primates", just as birds ("Aves") are dinosaurs because they're included in a clade called "Dinosauria". We are catarrhines, too, and hominids-- but we're not apes. "Ape" is a common English word that doesn't mean to be phylogenetically accurate. It's used for tailless old world monkeys. To me, the word "ape" is like "fish" or "bug"- they only respond to some kind of animals' vague, common English description. Semantics can get boring...

[quote]
To me, the word “ape” is like “fish” or “bug”- they only respond to some kind of animals’ vague, common English description.
[/quote]

If ape is a common word, and not a technical word, then should we really argue about what is included in the word? Are you telling me that [i]Lumbricus terrestris[/i] is not a bug?

Apparently I couldn't find that well hidden preview button....

Somewhere or other I have seen a table that lists various hominid fossils, and has columns showing what various creationist sources called them (human or ape), the takehome message being that there is no consistency about where different creationists draw the line -- almost as if the line were arbitrary.

Can anyone provide the actual reference here?

John Harshman said: Somewhere or other I have seen a table that lists various hominid fossils, and has columns showing what various creationist sources called them (human or ape), the takehome message being that there is no consistency about where different creationists draw the line -- almost as if the line were arbitrary. Can anyone provide the actual reference here?

Whoops forgot the rest of my comment...

Whatever you name these skulls and however you classify them, IMO the important point is that descent with modification predicts you will find a gradation of fossil forms for all species, even humans. In contrast any honest (non-weaselly) creationism which pays more than lip service to the concept that we are uniquely created would not; it would predict that we were, in fact, uniquely made in the image of God. Yet gradation of human-like forms over time is what we have discovered in nature.

Sure, you can force such square evidence into creationism's round hole, but those efforts are somewhat pointless because the only people who are going to be convinced by them are the people who were already convinced. No bystander is going to look at all the different hominid fossils and go "hmmm...clearly this series of hominid-type skeletons implies humans were uniquely and specially created."

I like to adapt an argument from the "intelligent design" folks.

The location of the human species on the tree of life as the neighbor to chimps and other apes is something so complex, and moreover makes predictions (such as about DNA), so it certainly counts as "complex specified information" which cannot be just a matter of chance.

So, either it is due to some natural cause (such as common descent) or else it was purposefully designed to be that way.

Are we supposed to tell our kids that they were designed to be like chimps?

Robert Byers said: I am YEC. Skulls mean nothing to me as its clear to me that the ape/man sameness is real.

I am YEC.

— Robert Byers

So, either it is due to some natural cause (such as common descent) or else it was purposefully designed to be that way.

— TomS

Frank wrote:

"Behe thinks, and to my knowledge no major ID promoter has publicly disagreed, that it’s purposeful design and common descent. Though I doubt he’d phrase it that way, he seems to think it’s common descent with “unnatual” modification. But discovering the where (other than in-vivo somewhere), when, and how of those modifications are somehow not “important” for him, even though real scientists would consider that the research opportunity of a lifetime."

Yea, right. And we are 98.5% similar to chimps genetically because it is so great being a knuckle-walking hairy ape? The 1.5% sequence divergence couldn't possibly have occurred naturally without divine intervention? And all those intermediate forms were just god making mistakes?

This guy is just trying to tell everyone what they want to hear. The only reason I can think of to do that is to try to get everyone to buy your books. I guess you really don't have to make any sense at all.

Creationists are completely wrong in their interpretation of these fossils.

Yet is 100% true that there are no transitional fossils between apes and humans.

Humans are apes, and are probably not descended from other modern apes, although our relationship to the chimpanzee is so close that the most recent common ancestor may have been very chimp-like.

Yes, humans are apes; common English names of animal groups have been assigned biological meanings. Lions and house cats are both examples of "cats" and humans and gorillas are both examples of "apes". Some guy may think that "ape" implies body hair and lack of fully developed language. Some guy may also think that "cat" implies small domestic animals that tend to prey on even smaller animals, and display a characteristic aloof yet hedonistic and affectionate personality. However, humans are still apes and jaguars are still cats.

HOWEVER, there are many, many transitional fossils between our species, Homo sapiens sapiens, and earlier hominid species.

DS said: Yea, right. And we are 98.5% similar to chimps genetically because it is so great being a knuckle-walking hairy ape? The 1.5% sequence divergence couldn't possibly have occurred naturally without divine intervention? And all those intermediate forms were just god making mistakes?

harold said: Humans are apes, and are probably not descended from other modern apes, although our relationship to the chimpanzee is so close that the most recent common ancestor may have been very chimp-like.

Eric Finn said:

DS said: Yea, right. And we are 98.5% similar to chimps genetically because it is so great being a knuckle-walking hairy ape? The 1.5% sequence divergence couldn't possibly have occurred naturally without divine intervention? And all those intermediate forms were just god making mistakes?

I have seen also other percentages, e.g. 95 % similarity. To my (limited) understanding, assessment of genetic similarities is based on the protein coding parts of the DNA. The comparison of full DNAs may lead to other estimated percentages. I would appreciate, if you (or someone else) elaborated these percentages a bit. Thanks in advance

Jim Foley said: Yep, that's it. Isn't it remarkable that in 300+ pages of text, Homo habilis gets a measly two pages?

KP said:

Jim Foley said: Yep, that's it. Isn't it remarkable that in 300+ pages of text, Homo habilis gets a measly two pages?

No wonder it was so hard to find... In what is supposed to be an "assessment of the human fossils" he provides almost NO data, measurements or comparative analysis. Just long lists of fossils and where they were found. And of course 5 pages on Piltdown Man...

DS said: Gagneux and Varki (2001) Genetic differences between humans and Great Apes. Molecular Phylogenetics and Evolution 18(1):2-13. You can include only coding regions, only substitutions, only insertion/deletions, etc. You can count repetitive DNA, transposons, retroviruses, introns, alternative splicing, etc.

These might turn out to be mostly variations in regulatory regions.

Eric Finn said:

harold said: Humans are apes, and are probably not descended from other modern apes, although our relationship to the chimpanzee is so close that the most recent common ancestor may have been very chimp-like.

Is it overruled that our most recent common ancestor might have been more "human-like" than "chimp-like" ?

Anon said:

Robert Byers

Whoa, dude, your comment is really dumb. I don't even know where to start from. What's "YEC"? I'm asking cause I'd like to avoid it as much as possible, considering its effects.

Eric wrote:

"As far as I understand, these ‘regulatory regions’ are not ‘coding regions’. Still, they do seem to be important."

Well some regulatory sequences can also be coding regions, such as hox genes that code for transcription factors. However, most regulatory regions are promotors, promoter proximal elements and enhancers. These regions bind transcription factors and other proteins. Changes in these regions can have a profound impact on the spatio-temperal expression pattern of many different protein coding genes, which are potentially much more significant that most changes in the coding regions.

"I will rephrase my question: What do the percentages mean? What kind of similarities are compared?"

Say for example that you compared the nucleotide sequence of the hemoglobin alpha gene in chimps and humans. If you align the sequences and 985 out of 1000 nucleotides were identical in both species, that would constitute 98.5% similarity. Of course, the actual value will depend on whether you also count insertion and deletion events as mismatches or not. For humans and chimps, the mitochondrial control region might be a more appropriate region for comparison.

"What I do question is the use of three significant digits to describe the similarity of two species."

Well if you count enough nucleotides you can get any degree of accuracy you desire. More important is exactly what you count and how you count it. That might be more an issue of precision than accuracy. We could compare all three billion nucleotides, but no one is certain what the best type of comparison would be. Reducing all of the data to a single number means that you have to lose some information in the summary. That's why a description of the type of comparison is important for any estimate of divergence.

I hope that this more directly addresses your question.

DS said: Well some regulatory sequences can also be coding regions, such as hox genes that code for transcription factors. However, most regulatory regions are promotors, promoter proximal elements and enhancers. These regions bind transcription factors and other proteins. Changes in these regions can have a profound impact on the spatio-temperal expression pattern of many different protein coding genes, which are potentially much more significant that most changes in the coding regions.

Rolf Aalberg said: Gorilla, Chimp and Man share a common ancestor. That ancestor shares its ancestor with the Orang-utan. And that ancestor shares his ancestor with the gibbon.

Eric wrote:

"Is there anything in the contemporary theory of evolution that denies the possibility of multiple origins?"

In my opinion, no.

"Or, is it “just the evidence” that points to that direction?"

In my opinion, yes.

DS said: Eric wrote:

"What I do question is the use of three significant digits to describe the similarity of two species."

Well if you count enough nucleotides you can get any degree of accuracy you desire. More important is exactly what you count and how you count it. That might be more an issue of precision than accuracy. We could compare all three billion nucleotides, but no one is certain what the best type of comparison would be. Reducing all of the data to a single number means that you have to lose some information in the summary. That's why a description of the type of comparison is important for any estimate of divergence. I hope that this more directly addresses your question.

Eric Finn said: No one is certain what the best type of comparison would be, I agree. I am complaining about the exact figures given. It does give the appearance of false accuracy.

I will rephrase my question: What do the percentages mean? What kind of similarities are compared?

Creationists are completely wrong in their interpretation of these fossils.

— harold

The 1.5% sequence divergence couldn’t possibly have occurred naturally without divine intervention?

— DS

Mike Elzinga said:

Eric Finn said: No one is certain what the best type of comparison would be, I agree. I am complaining about the exact figures given. It does give the appearance of false accuracy.

If I understand your objection, you seem to be saying that counting nucleotides - and this can be done with relatively high precision if the number of nucleotides is large - gives a false impression of how “close” two different species actually appear morphologically and behaviorally.

I think DS was noting that other considerations in regulatory regions account for those “larger differences”.

I was suggesting – perhaps incorrectly – that those other considerations “emerge” from those slight differences in the number of matching nucleotides. But I’m a physicist and I don’t really know; I should shut up and listen to the biologists here.

John Harshman said:

I will rephrase my question: What do the percentages mean? What kind of similarities are compared?

The 98.5% figure comes from DNA hybridization studies, which measure the mean similarity between short (500bp), homologous fragments in the bulk of the genome -- "bulk" because highly repetitive sequences were removed first. If you counted only protein-coding sequences, the figure would be about 99.5%. A more accurate average over the entire genome -- because it counts the entire genome base by base -- is 98.7%. The commonly quoted figure of 95% counts similarity in what I think is a bizarre way. If, for example, there is a 1000-base deletion in the human genome, that counts as 1000 differences, even though it's a single mutation.

John Harshman said: The commonly quoted figure of 95% counts similarity in what I think is a bizarre way. If, for example, there is a 1000-base deletion in the human genome, that counts as 1000 differences, even though it's a single mutation.

Robert Byers said: I am YEC. Skulls mean nothing to me as its clear to me that the ape/man sameness is real. God simply upon looking at his creations picked the best body type to put a being made in his image into. What else? What other type of body would suit a divine being like ourselves? A mouse, rhino. bear insect, bird?? All creatures show they come from a common design. Mostly we all have eyes, ears, legs, butt, etc. So if god was going to have us on earth the only options are to pick a body so unlike the general theme or simply pick within the theme the best type of body. This is the ape body. So this creationist welcomes dead on sameness to monkeydom. There is no need to seek differences. The little difference in skulss is just for a practical container for the addition of this or that tool we use more then animals. Its possible post flood humans did not need and therefore have as much of this or that tool in the brain. However probably we have pretty much the same skull. so its easy to tell us from apes if apes have always lesser brains etc. Once again this is all about weighing brains. Surely the computer age with its "small is smarter" should put to rest brain size as a factor in intelligence and so humanness.

DS said: Eric wrote: "Is there anything in the contemporary theory of evolution that denies the possibility of multiple origins?" In my opinion, no. "Or, is it “just the evidence” that points to that direction?" In my opinion, yes.

DS said: Eric wrote: "Is there anything in the contemporary theory of evolution that denies the possibility of multiple origins?" In my opinion, no. "Or, is it “just the evidence” that points to that direction?" In my opinion, yes.

Eric Finn wrote:

"Percentages are displayed everywhere. It seems to me that one reason might be that “evilutionist” try to use science to promote their evil dogma."

Well, what metric would you suggest for summarizing the data that two aligned sequences are identical at 985 positions and different at 15 positions? The important thing is not that the comparison is stated a s a percentage, the important thing is that evolutionary theory makes very specific predictions about the amount of genetic divergence that should be observed between any two individuals, populations or species. And by the way, the overall similarity is not the only important parameter. Sequence data can also be subdivided in many different ways:

substitution/insertion or deletion

transition/transversion

synonomous substitution/ nonsynonomous

position in the molecule (coding/intron/regulatory, stem/loop, binding site/transmembrane domain, etc.)

Evolutionary theory makes predictions about the patterns we should observe for all of these different types and many more. Just stating a percentage is a convenient way to summarize all of the data, but it is hardly exhaustive of the information in an aligned sequence. Retrotransposition events for example affect the overall percent similarity, but that is not the best way to present the data in making phylogenetic inferences. Of course other types of data, such as heterologous hyvbridization, can pretty much only be expressed as percentages.

Why on earth would any real scientist want anyone to believe anything, especially "evil dogma". Scientists are trained to collect and interpret data, why should they care where the data leads? You must have scientists confused with creationists.

"Trying to support common descent with percentages … that won’t work."

Actually, it has. This is known as molecular phenetics. It often recovers the same topology as that produced by cladistics. However, cladistics is considered to be a superior method in most cases. Still, the concept of a molecular clock is valid, given appropriate caveats.

"Is there a reason to use those figures in biology as a metric?"

Sure, because they are easy to understand and they summarize a great deal of data succinctly. If you don't like using percentages, you can always use number of informative sites, number of synapomorphies, consistency index in a cladogram, etc. These metrics can also be used to summarize data, but they tend to be a little harder for most non-experts to interpret.

I don't really know exactly what your problem is, but hopefully I have addressed it. If not, you will have to be more specific about why you think that using percentages is a problem. We can all agree that there are other more important comparisons that can be made, but percent similarity is still a valuable parameter.

DS said: Evolutionary theory makes predictions about the patterns we should observe for all of these different types and many more. Just stating a percentage is a convenient way to summarize all of the data, but it is hardly exhaustive of the information in an aligned sequence. Retrotransposition events for example affect the overall percent similarity, but that is not the best way to present the data in making phylogenetic inferences. Of course other types of data, such as heterologous hyvbridization, can pretty much only be expressed as percentages.

I don't really know exactly what your problem is, but hopefully I have addressed it. If not, you will have to be more specific about why you think that using percentages is a problem. We can all agree that there are other more important comparisons that can be made, but percent similarity is still a valuable parameter.

Eric Finn wrote:

"If we were to compare the genomes of people in Europe with people living in Asia, what kind of percentual differences we might find?"

Probably less than 0.1% on average, at least for nuclear coding regions. Probably between 0.1 and 1.0% for mitochondrial DNA and microsatellites, since they tend to have higher mutation rates. Probably much less for ribosomal genes, since they are influenced by concerted evolution and strong selection. And yes, those would probably be significantly less than the average divergence between any two individuals in Africa. You would also expect more synonomous substitutions than nonsynonomous, a high transition to transversion ratio, and other patterns indicative of a short divergence time with continued gene flow. All of these studies have been performed, I can provide references if you like. The largest data sets are for protein electrophoresis, mitochondrial DNA and Y chromosome microsatellites.

"Human-apes and chimpanzee-apes are genetically very similar. I acknowledge that there are ways to quantify the genetic differences. However, stating that these two species are 95%, 98.5%, or 99.5% similar, does not carry much information. It always requires some expertise to interpret the figures."

Yes of course it does. But, with the proper qualifications, there is much information even in a single number. Still it is important to remember, as Mike pointed out, that percent sequence similarity is not always a reliable indicator of morphological similarity, nor should it be expected to be.

DS said: Probably less than 0.1% on average, at least for nuclear coding regions. Probably between 0.1 and 1.0% for mitochondrial DNA and microsatellites, since they tend to have higher mutation rates. Probably much less for ribosomal genes, since they are influenced by concerted evolution and strong selection. And yes, those would probably be significantly less than the average divergence between any two individuals in Africa. You would also expect more synonomous substitutions than nonsynonomous, a high transition to transversion ratio, and other patterns indicative of a short divergence time with continued gene flow. All of these studies have been performed, I can provide references if you like. The largest data sets are for protein electrophoresis, mitochondrial DNA and Y chromosome microsatellites.

Eric Finn,

Here are a few references if you want to take a look at them. I am not sure how accessible they are. I do not have access to the Y chromosome references right now, but I can try to get them for you later if you are interested. the Nature paper has a human phylogeny showing the divergence between human populations, including europe and asia.

Chromosome Banding: Science 215:1525-1530 (1982)

Mitochondrial DNA: PNAS 88:1570-1574 (1991)

Hemoglobin Genes: Mol. Phylo. Evo. 1(2):97-135 (1992)

SINE Insertions: J. Mol. Bio. 308:587-592 (2001)

Neanderthal mitochondrial DNA: Cell 90:19-30 (1997); Nature Genetics 26:144-146 (2000)

Human Microsatellites: Russian Journal of Genetics 40(10):1065-1079 (2004); Nature 368(6470):455-457 (1994);
PNAS 99(13):8748-8753 (2002)

I would be very surprised to hear of an ID advocate who would dare to suggest that there is a purpose behind designing humans to be the closest extant neighbors of chimps and other apes.

I don't know how they can deny that closeness. I don't know how they can deny that the relationship is "complex specified information".

But would they dare to apply their methodology to this case?

Robert Byers said: I am YEC. Skulls mean nothing to me as its clear to me that the ape/man sameness is real. God simply upon looking at his creations picked the best body type to put a being made in his image into. What else? What other type of body would suit a divine being like ourselves? A mouse, rhino. bear insect, bird?? All creatures show they come from a common design. Mostly we all have eyes, ears, legs, butt, etc. So if god was going to have us on earth the only options are to pick a body so unlike the general theme or simply pick within the theme the best type of body. This is the ape body. So this creationist welcomes dead on sameness to monkeydom. There is no need to seek differences. The little difference in skulss is just for a practical container for the addition of this or that tool we use more then animals. Its possible post flood humans did not need and therefore have as much of this or that tool in the brain. However probably we have pretty much the same skull. so its easy to tell us from apes if apes have always lesser brains etc. Once again this is all about weighing brains. Surely the computer age with its "small is smarter" should put to rest brain size as a factor in intelligence and so humanness.

I will rephrase my question: What do the percentages mean? What kind of similarities are compared?

Henry J said:

I will rephrase my question: What do the percentages mean? What kind of similarities are compared?

I think it's not so much the percentage between two specific species, but rather the pattern formed when percentage differences are computed between lots of species. The amount of difference between two species should have some correlation with the lowest taxonomic rank that contains both those species. If that makes sense. Henry

I suppose I should add, then when performing this type of analysis, in general, the higher the sequence similarity the shorter the time since two species last shared a common ancestor. At least that is usually the case, as long as the same type of comparison is made between all species. The relative values giver you as much, if not more, information than the absolute values.

Hope that helps.

Eric Finn said: Assume we compare two editions of a book letter by letter. Assume further that the only chance to the second edition is one letter in the very beginning. Obviously, we can get a result, according to which the editions are very different.

You gave figures between 98.5% and 99.5% on the genetic similarity between humans and chimpanzees. I think I got some idea, how comparisons are made, but could not figure out the reasons. Percentages are displayed everywhere. It seems to me that one reason might be that "evilutionist" try to use science to promote their evil dogma. Trying to support common descent with percentages ... that won't work. Is there a reason to use those figures in biology as a metric?

You have addressed my questions diligently, many thanks for doing that. I do appreciate your effort. If we were to compare the genomes of people in Europe with people living in Asia, what kind of percentual differences we might find?

Trying to support common descent with percentages … that won’t work. Is there a reason to use those figures in biology as a metric?

Jim Foley said: Yep, that's it. Isn't it remarkable that in 300+ pages of text, Homo habilis gets a measly two pages?

Yep, that’s it. Isn’t it remarkable that in 300+ pages of text, Homo habilis gets a measly two pages?

Genesis 4:17 Cain lay with his wife, and she became pregnant and gave birth to Enoch. Cain was then building a city, and he named it after his son Enoch.

stevaroni said:

Robert Byers said: I am YEC. Skulls mean nothing to me as its clear to me that the ape/man sameness is real.

Lovely, Bob. So, for the record, are you saying these skulls are modern apes, or modern humans? Because, Bob, as a YEC, there can be no other category (don't forget, God commanded Noah to take all creatures, so if there was a 3rd option, "primitive ape-man or something", they one assumes they would have had space on the Ark and presumably, should be found either extant today, or somewhere in the recent historical record.)

There speaks a man who really does think that it's better to be pitied and laughed at than to get no attention at all.

Dave Luckett said: There speaks a man who really does think that it's better to be pitied and laughed at than to get no attention at all.

Robert Byers said: i didn't even look. It means nothing to me to compare skulls of people/apes. If a skull is so small that a normal human wouldn't fit then its not human. O don't know the difference between skull size/shape of the smalles human adult alive today and the largest ape/gorilla etc one. Yet it would change nothing as the intelligence/moral/identity of the smallest person would be light years ahead of the biggest monkeykind. its a false presumption to see people needing to be different from apes etc. If you were God and had a being (in your image ) what kind of body would you make for it on earth with the issues of natural laws on earth. I say that since all life is very alike in laws and a seeming common basic blueprint then you would pick the ape body as best. I saw ice skating over Christmas and can't imagine any other kind of body that could be so flexible and beautiful in that kind of dance. We got the highest order of a useful body that there is on earth relative to natural laws of what there can be. It seems to me all life is just a little different then its neighbour and apes are just more flexible then other animals. God picked the ape body as the best one for us. There is no reason to see relationshp based on same shapeness in this case. We are told and our unique intelligence nature should suggest strongly we were placed in this best equation of a common law of life on the planet.

This guy has caused trouble elsewhere:

http://scienceblogs.com/pharyngula/plonk.php

Robert Byers

Too stupid to be tolerated

Single-handedly bringing great shame to the good name of Canada. Incoherent, bigoted, insanely inane.

I don't know about Byers. He could be a genuine idiot grotesquely overdosed on hubris, or he could be demented, or he could be a troll whose only purpose is to seek attention. Since these are not mutually exclusive, he could be all three.

I vote for the third with overtones of the second, on the grounds that anyone who gets off that much on being derided must be crazy. But I don't know.

Robert qrote:

"i didn’t even look. It means nothing to me to compare skulls of people/apes. If a skull is so small that a normal human wouldn’t fit then its not human. O don’t know the difference between skull size/shape of the smalles human adult alive today and the largest ape/gorilla etc one. Yet it would change nothing as the intelligence/moral/identity of the smallest person would be light years ahead of the biggest monkeykind."

Well Robert, why don't you just give it a shot. We know that skulls mean nothing to you. We know that pottery shards mean nothing to you. For some reason, stone walls mean something to you, go figure. But now, about those skulls, the pictures are right there in front of you. Just give it your best shot, which in your opinion are human and which are ape? You are YEC remember, those are the only two possibilities, right?

Come on man, if you want to be taken seriously, just take a stab at it. You wouldn't want anyone to think your are ascared now would yas? If the intelligence of the smallest person is "light years" ahead of the biggest monkeykind, then this should be easy for you, right? You do know that "light years" is a measure of distance, right? Are you just ignorant, or are you an ignorant coward as well? If you want to have the opportunity to post here, you really should be willing to play along with those who have so graciously provided you with this opportunity, don't you think?

"dogmastic", I like that, Dale Husband.

A bone that's been chewed beyond all possible utility?

DS said: Here are a few references if you want to take a look at them. I am not sure how accessible they are.

From PNAS: The human genome is composed of 40–50% repetitive DNA, an important class being simple tandem repeats or microsatellite DNA sequences (1). Microsatellites are iterations of short (1–6 bp) sequence motifs, repeat numbers generally being less than 30 (2). [...] Microsatellites differ from most other DNA sequences in their high degree of polymorphism, with heterozygosities commonly exceeding 70%. As they generally seem to be free of selective constraints, it is evident that the extensive degree of genetic variability requires a high underlying mutation rate. [...]

John Harshman said:

Eric Finn said: Assume we compare two editions of a book letter by letter. Assume further that the only chance to the second edition is one letter in the very beginning. Obviously, we can get a result, according to which the editions are very different.

We can? I don't see how. One letter change is a tiny difference, however you count it.

You gave figures between 98.5% and 99.5% on the genetic similarity between humans and chimpanzees. I think I got some idea, how comparisons are made, but could not figure out the reasons. Percentages are displayed everywhere. It seems to me that one reason might be that "evilutionist" try to use science to promote their evil dogma. Trying to support common descent with percentages ... that won't work. Is there a reason to use those figures in biology as a metric?

Sure. They're most often a way to compare the amount of evolution that's happened. Rather than total number of mutations, you count percentage changes. Makes it easier to compare sequences of different sizes, for example, since presumably the amount of mutation is proportional to the length of the sequence.

I don't understand your paranoia about evilutionist misuse; was that a joke?

DS said:

Henry J said:

I will rephrase my question: What do the percentages mean? What kind of similarities are compared?

I think it's not so much the percentage between two specific species, but rather the pattern formed when percentage differences are computed between lots of species. The amount of difference between two species should have some correlation with the lowest taxonomic rank that contains both those species. If that makes sense. Henry

Exactly. that's one of the patterns I was talking about. Saying that the hemoglobin alpha gene is 98.5% similar between two species doesn't tell you all that much. But, if you make pairwise comparisons between many different species, you can start to get a lot of information about phylogenetic relationships.

Eric Finn wrote:

"They did not state the distance between humans and chimpanzees based on the microsatellites. Somehow, I doubt that a single figure would be meaningful in this case. Anyway, a single figure would, most likely, be different from the distance between e.g. hemoglobin genes. This is the main reason I am uneasy about describing the genetic difference between two species using only one figure without any qualifiers."

Exactly. This type of data is not usually analyzed in that way. It is usually used more at the population level. For interspecific comparisons, other parameters are probably more important. For example, total size variation per locus and measures of genetic distance are more appropriate than percent similarity comparisons for this type of data. The point is that humans and chimps still come out as sister groups which is consistent with all of the other data sets.

"Even then, we get different distances based on our selection of the parts of DNA we are comparing. It is my understanding that some genes are very similar in otherwise very different species. http://pandasthumb.org/archives/200[…]on-vs-f.html."

Absolutely. That is why one must specify what is being compared and how the comparison is made, especially when using percent similarity. This is especially true for molecular clocks which are only valid for certain parts of certain genes in certain species over certain time frames. Inappropriate use of a molecular clock will give you an answer just as wrong as inappropriate use of a radiometric dating technique. Of course, they are unlikely to give the same wrong answer. That is the power of independent data sets.

I must say Eric, it is a real pleasure to have an intelligent discussion with someone who honestly wants to learn and is willing to read the primary literature. So often we are wasting out time here on trolls and we forget that we have a real opportunity to learn from each other. I know I appreciate the expertise and insightful comments of many of the participants here. I just can't understand why the bathroom wall is not a more poplar destination for trolls.

Eric wrote:

"Now, if the trees are almost identical for many selections of genes, and if the trees are supported by the fossil data, then that would be a strong evidence in favour of common descent."

And indeed it is. In fact, there are even statistical methods for analyzing the degree of confidence that one has in any tree or part of a tree and for analyzing the congruence of different tree topologies. This all gets rather technical, but the bottom line is that there has been a virtual revolution in molecular phylogenetics as more and more comparative molecular data has become available. We are now capable not only of confirming common descent but in reliably reconstructing the branching order of the tree of life.

That is why modern biologists find it so hard to understand why some people still refuse to believe in evolution. It isn't a matter of honest scientific differences any more. Now it usually boils down to willful ignorance. It's not that we have all of the answers already, it's that some people still refuse to believe the answers we do have.

We are now capable not only of confirming common descent but in reliably reconstructing the branching order of the tree of life. That is why modern biologists find it so hard to understand why some people still refuse to believe in evolution.

— DS

It isn’t a matter of honest scientific differences any more. Now it usually boils down to willful ignorance.

— DS

I know that I don't have to convince Frank J, but as long as we don't keep their feet to the fire, they can continue to ignore the fact that they don't have anything positive to offer, only unreasonable doubts, mostly doubts about things that have no more to do with evolution than with just about any other aspect of reality.

harold said: Humans are apes, and are probably not descended from other modern apes, although our relationship to the chimpanzee is so close that the most recent common ancestor may have been very chimp-like.

Is it overruled that our most recent common ancestor might have been more “human-like” than “chimp-like” ?

My question about the importance of this, or similar figure to biology still stands.

Eric Finn said: Yes, we can. Books can be represented as ordered sequences of letters and we can compare letters position by position. Not that it seems worthwhile of comparing editions that way...

Even then, we get different distances based on our selection of the parts of DNA we are comparing. It is my understanding that some genes are very similar in otherwise very different species.

John Harshman said: I still don't see how changing one letter at the beginning, out of many thousands, makes a big difference. What counting method are you using that does this? The simple method would give you 1/booklength. How short a book were you thinking of?

If you want a measure of overall genetic similarity between humans and chimps, it’s 98.7%.

John Harshman said:

Eric Finn said: Yes, we can. Books can be represented as ordered sequences of letters and we can compare letters position by position. Not that it seems worthwhile of comparing editions that way...

I still don't see how changing one letter at the beginning, out of many thousands, makes a big difference. What counting method are you using that does this? The simple method would give you 1/booklength. How short a book were you thinking of?

harold said: Technically, Eric Finn has a decent point of sorts.

harold said: Having said that, the approximate meaning is always that if we take almost any reasonably defined region of the human genome and compare it to the same region of the chimp genome, we will find a very high degree of similarity in nucleotide sequences.

Eric Finn said: Assume a book starts with abcd... Then add z in the beginning zabc...

Say we have three genome sequences A, B, C, each of the same length N. Take A as the reference, and let’s consider only a single change in each of B and C. Genome B differs from A in the ith position, and genome C differs from A in the kth position.

Now, f I understand this correctly, B and C each have the same percentage difference from A but have a greater percentage difference from each other.

However, it could conceivably be the case that B and C each have large phenotypic differences from A but could be closer to each other in phenotype. This would depend on what regulatory differences were implied by the positions of those single changes.

harold said: This looks like a lot of information but it's actually very simplified :)...

Eric Finn said: This is not leading anywhere, and I'm not sure, if it is all my fault. Assume a book starts with abcd... Then add z in the beginning zabc... A position by position comparison produces no matches in the region displayed. I do not imply that this is the method used.

I think my question was a valid one. What is the method of comparison? What parts of the DNA are compared?

Are presumably neutrally evolving parts (e.g. microsatellites or other repetitive sections) excluded or included?

Is the quoted distance 98.7% an arithmetic mean, weighted average, or how it was obtained?

Mike Elzinga said:

harold said: This looks like a lot of information but it's actually very simplified :)...

Thanks harold. The importance of mRNA and tRNA “finding” and latching onto those sequences is obviously extremely important in expression, as is further “downstream processing”. Your explanation is very clear.

John Harshman said: Apparently not clear enough, because I'm not sure what you're trying to say there.

Mike Elzinga said: What I think I understand is that whatever sequences there are in various parts of a genome, they ultimately have “downstream” implications for such things as morphology and other characteristics.

John wrote:

"Short answer: the homologous parts. The comparison has three steps. First, sequence the complete genomes of a human and a chimps. Second, align those genomes. That means you compare sequences with their counterparts."

John makes an excellent point. Before doing any sequence comparisons, you must first perform an alignment. The alignment algorithm is just as important, if not more important, than how the comparison is performed. You can set gap penalties, include information on secondary structure, etc. This amounts to the determination of homology between nucleotides. Just more information that should accompany any estimate of percent similarity.

DS said: The alignment algorithm is just as important, if not more important, than how the comparison is performed.

John Harshman said: Correct, with one addition: some of those sequences have implications, but most of them don't. Most of the genome is junk (conservative estimate: 90% or more), and has no effect on phenotype whatsoever.

Mike Elzinga said: It may be a personal quirk with me (although I suspect most physicists feel the same way), but I have always found fields like organic chemistry and biology considerably more complicated and difficult to navigate than physics and mathematics.

Apparently not clear enough, because I’m not sure what you’re trying to say there. Neither mRNA nor tRNA “finds” or “latches on to” any sequence.

When a gene is expressed, the DNA sequence is “transcribed” into an mRNA sequence (which may then undergo a fair amount of post-transcriptional processing, or not),

and ultimately, “translation” occurs - tRNA molecules (bound to individual amino acids) which contain regions complementary to the triplets of the mRNA sequence are recruited in correct sequence, and the amino acids form peptide bonds to one another, ultimately leading to the production of the protein (which may undergo a fair amount of modification during and after translation, or not).

Mike Elzinga said:

John Harshman said: Correct, with one addition: some of those sequences have implications, but most of them don't. Most of the genome is junk (conservative estimate: 90% or more), and has no effect on phenotype whatsoever.

Ok; I think I understood that part. But my blunder did jog something that I had momentarily forgotten. I, like many in the science community, tend to forget that our attempts to communicate across fields, and especially to laypeople, are fraught with all sorts of difficulties in translation and insufficient knowledge of terminology. It may be a personal quirk with me (although I suspect most physicists feel the same way), but I have always found fields like organic chemistry and biology considerably more complicated and difficult to navigate than physics and mathematics. With complex areas such as organic chemistry and biology, I tend to lose track of terminology and start confusing names of things. There doesn’t seem to be the compact linkages among concepts in biology that there are across all the subfields of physics and math. Biology seems more difficult to learn than physics because it really is more complicated; and I think Leon Lederman’s “physics first” idea for the secondary science curriculum is based on this notion. One of my, perhaps mistaken, perceptions about why ID/creationists go after biology more than they do physics and chemistry is that it is easier to bamboozle people in biology because biology really is more difficult; not just because it is the science that strikes at the heart of their sectarian dogma. ID/creationist physics just as wrong, but it is easier to shoot them down there. ID/creationists tend to stay away from physics not because it is harder, but because they are more vulnerable there. In biology there are more opportunities to change subject and nit-pick over details, concepts and terminology in order to keep a “debate” going. A number of of us in the physics community have tried to put a lot of thought into simplifying explanations for laypeople, but maybe we are deluding ourselves when it comes to dealing with ID/creationist misconceptions. The battle won’t ever really take place on physics turf; that’s too easy for them to lose. ID/creationists are going to go where they can make the biggest mess. Does this make any sense to the biologists or chemists here?

Yec here. Physics hardly matters to creationism save in a few areas. Math nothing.

— Robert Byers

Creationists often imagine that evolutionary biology equals paleontology, and that all the evidence for evolution comes from the fossil record. No matter how many times you tell them otherwise.

But hey, let's try again. Most of the evidence for evolution comes from living organisms, especially, these days, from their genomes. Most evolutionary biologists work with living organisms.

Physics hardly matters to creationism save in a few areas. Math nothing.

John Harshman said:

[...] What is the method of comparison? What parts of the DNA are compared?

Short answer: the homologous parts. The comparison has three steps. First, sequence the complete genomes of a human and a chimps. Second, align those genomes. That means you compare sequences with their counterparts. Now about 2% of the human genome consists of sequences that don't have counterparts in the chimp genome, and the chimp genome has about the same percentage of sequences with no human counterpart. (These arise through insertions and deletions.) What the comparison does is ignore those sequences, because you can't compare something to nothing. Third, having aligned all the homologous sequences, you count differences. That ends up with about 35 million such differences. 35 million out of 3 billion is about 1.2%, or 98.8% similarity. Now back to the insertions and deletions. There are about 5 million of them. If you wanted, you could add them to the total, which gives about 1.3% difference. Some estimates have added each individual base without a counterpart into the total, i.e. if there's a 10,000-base deletion in the chimp genome, you count that as 10,000 differences. I would consider that a biologically meaningless way to do it, but that gives a 95% similarity figure.

Robert Byers said: Physics hardly matters to creationism save in a few areas. Math nothing.

Robert Byers said: I also see the fact of these subjects so able to be equations and so understood by children, retarded people (Idiot savant )(sp) etc that math requires less thinking or weighing of concepts.

Mike Elzinga said:

Robert Byers said: Physics hardly matters to creationism save in a few areas. Math nothing.

No one expects that you would know any of this...

Robert Byers said: Creationists do not address much biology but rather evolutionary biology which is not about biology but origins of it. Biology is a subject of blood and guts and tools to hold the same. Evolutionary biology is about casts of former life and ideas of life that is not before ones eyes. Real biology uses dissecting tools. Evolutionary biology uses pick axes. Creationists address evolutionary 'biology" because it attacks the truth of origins in Genesis or God. Clear motivation .

Robert Byers said: Yec here. ... Physics and math are simple ideas in comparison and thats why they advanced quicker in the old days.

I’m not sure whether its because creationists realized they were rubbish

Robert Byers said: Physics and math are simple ideas in comparison and thats why they advanced quicker in the old days. Physics hardly matters to creationism save in a few areas. Math nothing.

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