Phylogenetic tree

Can we really map the macroevolution of species, including human from common ancestor of chimpanzee, by looking at each species’ genome and deducing which animal came from which by understanding common gene insertions and where they appeared (a similar technique with the way we study which manuscripts came after others) because I just had a Christian woman who had studied both biology and theology tell me so?

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This is an interesting statement. Perhaps you could ask your friend at what point in the phylogenetic tree did man become morally accountable before God?

Were archaic humans such as Neanderthalensis, Rhodesiensis, Floriensis and Habilus morally accountable before Creator God, or were they animals?

If we know that all humans today are morally accountable for their actions before God, whereas animals are not, at what point in the historical timeline did these pre-Adamic races become morally accountable. The Fall account states that Adam and Eve sinned, and death passed upon all man, for all have sinned. (Romans 5:12)

According to what I can find,
" A phylogenetic tree is a diagram that represents evolutionary relationships among organisms. Phylogenetic trees are hypotheses, not definitive facts."

You might find this video and discussion interesting?

Also a couple of articles that might be of interest?


Hello Graceful Deer,

First, please permit a minor correction, contemporary evolutionary theory does not teach that man derived from chimpanzees, it teaches that both man and chimps derived from a common ancestor, the genera Hominini.

Second, I can’t directly answer your main question as it’s very complex (and this is not my field). But, the concept is that evolution has an apparent direction (whether guided or unguided), from simpler to more complex. As new species were developed (or are developed), the new genome and design were not from scratch but were just progressive elaborations of the parents’ [genome]–the exact and precise characteristic of intelligent design by the way. This means that the progeny will have the parent’s genome w/some slight modification, it is this fact that your friend is implying leads to a successful regressive evolutionary model

The evolutionary model does appear to be highly successful wrt demonstrating that the genomic view of the Phyla is very similar to the Phenotypic view. That is, the closer the subject species are in phenotype, the closer they are in genotype. This relationship seems to be quite general if not universal. So, your friend does have a solid basis for positing genotypic sequencing as means to explore common decent. But this reinforces the case of intelligent design, no human design (car, plane, computer, house, etc.) is completely divorced from it’s predecessor. In fact, most design are small progressive elaborations of previous design (eg, closely coupled). The point is that while genotypic and phenotypic expressions are highly correlated (and even causally related), that does not mean that man (or any other advanced species) is the product of unguided evolution. Rather, for me, it reinforces (strongly) that God as the Intelligent Designer progressively elaborated His teleological intent from prokaryote to man.

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Thanks Matt. Without having finished reading and watching everything here you’ve written, and thanks I am more inclined to agree with you rather than this speaker at a Christian conference (she is not a friend). It is just the first time I’ve felt the need to ask about something in a while, and I am thankful for this platform RZIM Connect, I am back. I will do some reading and thinking and may write my thoughts in this thread later.

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Thanks Eric. I’ll read everything later when I have time but do want to point out I did understand her point and that she believes chimpanzee and human are from a common ancestor, this is something that I’ve come across before, so I understand that if you read carefully how I have phrased the question. I have never believed that, and still do not find the phylogenetic tree credible, the new information she gave me was about gene insertions. I’ll have a read what you have written soon, but right now I’m inclined to stay with the position I have always had, which is the same as Matthew’s.

I think what I’m getting at, is can that conclusion (the phylogenetic tree) really be made without significant assumptions?

Would you please spell out genotypic and phenotypic. Also, I certainly believe in intelligent design, just not macroevolution. And would you please tell me whether the “solid basis” you describe is free of assumptions?

Getting through your post amidst everything else…
Now on to your point about sin.
Never thought about that before. But as I go to bed thinking about such things, I do recall the biblical story being God created both male and female, and Eve then Adam sinned. With this whole phylogenetic tree idea, the mutation (also haven’t been convinced mutations really work to lead to the diversity of life forms on this planet) some two ancestors of both chimpanzee and human produced a mutant that was a human. Did it happen in one step? I mean one generation was ancestor-non-human and the next step was human? No, it can’t be for as it seems you need that one mutant-human to reproduce for several generations before it produces a new species that can no longer mate and hence define it as a new species. Or am I understanding something wrong, one generation to next defines it a new species? See it does not make sense, even if the first mutant human was Adam on this phylogenetic tree, where did Eve come from? She would have to reproduce with Adam, so it makes sense she was female
offspring of this non-human-ancestor, because Adam’s genes had not changed too much to allow him to reproduce with Eve. (I feel a bit banal saying mate and reproduced when it comes to humans but here I go using the scientific lingo befitting human beings who can write poetry.) And therefore you can’t really say there was one Adam and one Eve if you believe this phylogenetic tree thing, there would have to be a whole hoard of them geographically isolated to develop over however many generations to create a new species several generations later. And there I see your point, where did sin enter? Ok they may argue, the mutation occurred many many generations before the first Adam and Eve were conscious of sin. The first humans were the first beings conscious of sin on this tree, they may say. So do macroevolutionists do away with Eve coming from Adam, and “And He has made from one blood every nation of men” Acts 17:26 because according to this phylogenetic tree thing she’s got to come from somewhere else on this tree. You know even with democracy, we all well know that the majority isn’t always right, and many can come under the influence of a lie. I wish more than two people were listening and shedding some light. I have a right mind to ask the RZIM guest apologist to have a go. I haven’t done university (they call it university in New Zealand) level biology. I’ve never had to face up to it for challenge in my work but am also not amongst the data and research. But I am no climate change denier just because I don’t believe humans are derived from non-human life forms (that was one of the accusations at this Christian conference). I am science educated (physical sciences). I just wonder if there are many Christian biologists out there who survive against the tide and wish they would say something.

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I’ll look up words like phenotypic etc that I don’t understand tomorrow

Hi Grace,
yes, I’ve not had a satisfactory answer from the theistic evolutionist position yet about my question regarding sin.

I would also like to point out that the stated definition (either chimps to man, or a common ancestor genera Hominini to both chimps and man) is in contradiction to Genesis 2:7. God created man from the dust of the ground, not from previous animals. John Lennox, who holds to ‘day age’ position of creation, points this out in one of his lectures on the subject of his book ‘7 days that divide the world’. There is much debate about the length of ‘day’ in the Genesis account, but I’d agree with Lennox on this one that humans are a special creation. The question is at 1.05:16 in this discussion - the entire video is well worth a watch.

Did we descend from apes and hominids? the point I made earlier is this according to Genesis and God said let us make man the detailed story in chapter 2 and 3 of Genesis which says that God took the dust of the earth and made human beings. The Hebrew could have said very easily that God took an existing animal but that’s what it doesn’t say. If you were ever trying to get across the idea that human beings were a product of existing animals, Genesis is a very bad way to do it because it appears to go in the exact opposite direction, so my own feeling about it is that it is a special creation that human beings are utterly special, that God created them directly in his own image out of pre-existing material nature ,but as I said if you’re going by the story it seems to be to lead away from that I notice though which is interesting that some of my friends who do take the hominid view they still many of them have to say that God does something special to make up your hominid a human being, but then once you have admitted the principle that God does something special why not go the whole way.

you see what I mean by that ladies and gentlemen oh this is very important it’s this that the problem is singularity scientists don’t like them that is a place where the laws of nature appear to break down no physicists have got used to a spacetime singularity at the origin of the universe.

Christians believe of course that God is behind that. now Christian’s also believed that there was a spacetime singularity around 20 centuries ago, the Virgin conception the life the resurrection of Jesus the Incarnation, that isn’t a result of physical processes going on in the womb of Mary that is God’s deliberate intervention whether we believe it or not that is what the text says. Now where I come in is this Genesis says I am God said it doesn’t save many times it’s not saying that God did billions and billions and special creations but it does say I am God said so if you admit that the original creation was a singularity the resurrection was a singularity what is the in principle difficulty in admitting that the origin of life and the origin of humanity say are equally singularities in principle I see no difficulty you have to face the in principle question now I try to face that in my book God and Stephen Hawking and also in my recent book gunning for God so I can’t go into that tonight but it seems to me that that is where the real issue lies and as I say scientists don’t like the idea and I’m accused of it all the time but they say oh well all you’re doing is saying you can’t explain it therefore God did it the god of the gaps they say that’s the lazy way right yes it is sometimes but not if the gap tells you what the thing is you’re studying if I see that the gap so to speak is the taxes written on the sand I don’t think that saying that an intelligence wrote that on the sand is just saying an intelligence of the gaps because it’s the nature of the writing that tells me there’s an intelligence behind it that’s a totally different matter so that’s how I’d approach that question

The biblical term ‘after it’s kind’ doesn’t mean there are no changes;

Various Types

From this passage we see that the Bible recognizes various types of owls, as well as various types of other living creatures. Therefore, the biblical word “kind” is not limited to our modern term “species.” There are many varieties of fish, plants, cattle, as well as men and women. John Klotz comments further:

We also need to recognize that the language of the Bible is the commonsense, everyday language of our newspapers. This language does not change; technical scientific language does change . . . . We may have new ‘species’ of tomatoes, but they are still the same ‘kind.’ There may be changes within the species, yet tomatoes have not developed into cantaloupes or watermelons. There may also have been changes within the dog ‘kind,’ but these have not developed into lions or bears (John Klotz, Studies in Creation, St. Louis: Concordia Publishing House, 1985, p. 76).

The Bible teaches “the fixity of the species” in that each biblical kind can only reproduce within certain fixed boundaries. Change within a kind, however, is consistent with the biblical teaching.

I see no reason that God would not have ‘reused’ the basic building blocks of life in different kinds at the genetic level. If you’ve got a good design at the cellular/genetic level, why not reuse it elsewhere when creating something entirely different that cannot reproduce such as a cat and a dog or a fish or a bird?

Your quote of Acts 17:26 is very interesting. Paul was talking to the Greek philosophers, and I would suggest that ‘God creating every nation from one blood’ is consistent with God creating Adam and Eve from the dust, and the confusion of languages at the tower of Babel accounts for the genetic variations in the one human race. There is a very ‘thick line’ dividing animals and humans (created in God’s image).

Contrast what Darwin wrote when his explained that his evolutionary thinking applied to human races as well as to animal species:

The Western nations of Europe . . . now so immeasurably surpass their former savage progenitors [that they] stand at the summit of civilization. . . . The civilized races of man will almost certainly exterminate and replace the savage races through the world.


lots to think about… I don’t have all the answers, I just like to question things… :slight_smile:


Thanks Matthew. More good things to pour over, over the next while.

I picked up this though while skimming your reply: “I see no reason that God would not have ‘reused’ the basic building blocks of life in different kinds at the genetic level. If you’ve got a good design at the cellular/genetic level, why not reuse it elsewhere when creating something entirely different that cannot reproduce such as a cat and a dog or a fish or a bird?” That’s where I think the biologists have made the contrary and wrong assumption, I think they’ve just mapped this gene insertion information into a tree to satisfy their own hypothesis without thinking about the here quoted from your last reply.

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Ok so phenotype and genotype you are basically saying if they look about the same they will have more common gene sequencing. I myself am training to be an architect and understand design process. Both the last two sentences don’t necessarily have me conclude in the validity of the phylogenetic tree. God is not limited and has no need to create out of an iterative design process and just because they look similar and have similar gene sequencing doesn’t necessarily mean one species is derived from another, I think people are still jumping to conclusions. I wonder if any biologist would say they don’t believe Darwinian macroevolution is true based on their research and face career-suicide. Well they can be anonymous here, so please do.

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Will have to have a read of that post “Giving Up Darwin” and see the video there too soon. But noticed the article after it concerning racism, wow, true but that was more to the point than I might ever dare to put it, at least to someone’s face. I actually posited that question to that Christian biologist theologian evolution workshop speaker at the Christian conference when I sought her to ask her point of view as I actually missed most of her workshop, softening it with, “I’ve got another point, you might find it offensive, so be prepared.” The conversation went something to like this…She has me understand everything in my original question, the phylogenetic tree, common genes showing up in different species and biologists “logically” mapping out the tree by deducing in the same way theologians would derive which manuscripts came after others. I said, I can’t see macroevolution before my very eyes, or new species emerging today. She said of course you can’t see it, it takes billions of years. I said well doesn’t that take faith to believe then? And then she actually talks about the gene insertions mapping, sorry got that out of order. Then I do the whole softening what I am about to say, and say what about WWII, we’ve got to be careful how we think. Eugenics. And she says yes, but that was old school evolutionary thinking, when it was in its earlier days (she and her co speaker and the father in law of the co speaker were like Christians need to understand contemporary evolutionary thinking or whatever). I’m starting to not like her. But you know what really tops off me not liking her? She’s continues, as we understand more about genes we become more God-like. Technology can be used for good and for evil. It doesn’t mean we shouldn’t invent technology and become more God-like. Wow! That thought is starting to get dangerous I’m thinking. Aren’t we meant to know our very humble place before God and doesn’t that Tower of Babel story teach you anything? So, I ask her, have you heard of CRISPR? She said oh yes, the technology that will give parents the ability to erase the genes of their children that will give them a disability before they are born. I said yes, I had had a talk with a post-graduate Catholic law student whose thesis was on the ethics of that. Ethics. Precisely what we need around technology so someone’s manic desire to be God-like has limitations don’t you think. He gave the example of muscular dystrophy, I told her. I was like yes of course muscular dystrophy is painful who would want their child to have that. But I’ve seen a video of a man with Downs Syndrome say don’t abort me, and he probably would have said don’t erase the gene that gave me this, I am at university, thriving, I think he was doing a PhD on his condition, anyway you can look it up on YouTube. Which reminds me of the verse, His disciples asked him, “Rabbi, who sinned, this man or his parents, that he was born blind?” 3 “Neither this man nor his parents sinned,” said Jesus, “but this happened so that the works of God might be displayed in him. John 9:2-3. Her response (more I don’t like you points and don’t think you should get a speaking platform at this Christian conference), I just don’t understand why these deaf parents want their children to be born deaf, they could erase the gene with CRISPR and the child could hear. I myself have a disability and I am thankful I have it, I wouldn’t want my parents to have erased it. I have learnt to live with it and God displays his power through my weakness. And you know what, I am so pleased to be close to God because of it.

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This is a verse I like to give people when they ask me about my faith when they have trouble believing in Jesus because of science-faith conflict. I find it comforting myself, maybe there is knowledge that just belongs to God.

“He has made everything beautiful in its time. He has also set eternity in the human heart; yet no one can fathom what God has done from beginning to end.” Ecclesiastes 3:11

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Hi Caitlyn,
it just occurred to me I called you ‘Grace’, instead of Caitlyn. My apologies. I looked at your username instead of your real name in the previous post. Oopsies. :slight_smile:

I was a bit curious about this topic, so did a little reading trying to find something other than high school level material. I must confess I struggle to understand anything other than things written in everyday language. This article was interesting; it suggests that ‘tree-makers’ expect a lot from gene comparisons, there seems to be lateral gene transfer (from what I understand this is the point that the creation article is making that I shared in the first post entitled ‘creationist orchid’), and that representations other than a single tree should be considered.



Since Darwin’s Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes) likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes.


Heat map analyses were used to investigate the congruence of orthologues in four datasets (archaeal, bacterial, eukaryotic and alpha-proteobacterial). We conclude that we simply cannot determine if a large portion of the genes have a common history. In addition, none of these datasets can be considered free of lateral gene transfer.


Our phylogenetic analyses do not support tree-thinking. These results have important conceptual and practical implications. We argue that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading.

I do wonder if evolutionary biologists are forced by their paradigm pressure to always try to find a single tree solution; to support Darwin. To think otherwise, like you said would incur the wrath of the collective. This is also what I found interesting in that ‘Giving Up Darwin’ video; David Gelernter (who is not a Christian) noticed this and asked why do people get so upset when questioning the science?

I do agree with your line of questioning that the lady suggesting that gene mapping is the same as the study of old manuscripts. I think it’s logically flawed to compare the two. We have the old historical manuscripts (at the time they were written) to study and can match things up. The question I would ask is do we have the the genetic material at the time they were alive billions of years ago in order to match them up, or is the gene matching taking place on current living creatures and extrapolating backwards? I do not know, but logic would suggest we don’t have the original material today.

yes you are absolutely right on ethics and eugenics. Science can only tell you what is, it cannot tell you what you ought to do. You cannot get morality from science. To want to become more ‘godlike’ sounds a little like the temptation in the garden of Eden.

Thankyou for sharing that verse about the disciples asking who sinned; the disciples assumed like a lot of us today that suffering happens because of sin; and Jesus plainly told them that wasn’t the case. (not to mention, how can the man sin when he was in his mothers womb! :slight_smile: ). I love how Vince Vitalie talks about suffering in this article. It’s a great comfort to know that God is not distant but entered into our suffering. Vince also talks about ‘what it takes to be us’; and the part that suffering plays in our lives. I think there is the promise in the verse too you have mentioned, as well as the verse in Romans 8 ‘all things work together for good to them that love God’.

I also like the second verse you shared; ‘God makes everything beautiful in it’s time’. We can rest in Him knowing he has our lives in his hands and that He’s promised to bring us to become more like Jesus over our lifetimes; for His Glory… This is great encouragement when life is hard.

in reference to your mention of science-faith conflict; I thought you might find this little quote interesting. Darwin himself struggled with thought that “if his mind was the product of mindless unguided processes, how could he rely on it to do science and logic”. :slight_smile: See the thread below, which is from Lennox’s book ‘Can science explain everything?’. He would suggest it’s not a faith-science conflict; but a conflict of worldviews; materialistic atheism vs monotheism; and there are scientists on both sides. Richard Dawkins in his books is trying to force a decision of a false alternative.

May we focus on Jesus the author and finisher of our faith (Hebrews 12)…
Kind regards

Thanks for the research and this comprehensive answer.

And yes faith and science are not in conflict. This is a worldview conflict, that has entered the echelons of the academic world. Universities should be a free place to question so it is a sad thing there is this vitriol. And sadder still that there are Christians trying to convince Christians that they need to accept this tree.

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Hello Caitlyn,

Thank you for the questions and discussions. It seems you’re passionate about certain subjects, and that’s almost invariably a good thing.

You have multiple ASKs going on in your communication: 1) Phylogenetic Tree; 2) gene insertion; and 3) proposing the literal interpretation of Scripture and doctrine viz. the origin and evolution (if any) of life.

Wrt the Phylogenetic Tree, you are correct that science can’t prove that just because the phenotype and genotype are casually related and that there appears to be very substantial and universal gene reuse that the only viable, reasonable, and warranted explanation is that of unguided evolution from common decent. However, neither can science prove that the moon isn’t made of green cheese. This statement is directed at the philosophic and mathematical definition of the term “proof” rather than reflective of any real deficit in science or the objective methodology of empirical observation. Science can approach a solid, rational, and warranted conclusion concerning evolution from common decent and the nature of the moon.

My point about the correlation between phenotype and genotype, and especially my proposition that the phenotype is casually derived from the genotype, means that the likelihood of the Phylogenetic Tree being a substantially accurate representation of reality is high. This is because gene sequencing (the reading of the genotype of each creature) shows the very substantial and universal reuse of parental gene in progeny. There is a corollary, how many genetic code are there? There are bacteria, fungi, plants, reptiles, animals, mammals, etc. So how many genetic codes are there? There is exactly and precisely one. The significance of this fact is astounding and it points to intelligent design–design reuse. God created one genetic code for ALL life (because that was all that was needed).

In therms of gene insertion, that’s just a known fact of biology. There are multiple mechanisms of gene insertion (always or almost always across species lines). These include plasmids and viruses.

Wrt your third proposition, this is a matter of personal choice. However, I will cautiously and respectfully mention that science indicates an allegorical hermeneutic rather than a literal one is most appropriate.

Thank you again for your questions and discussion sister.

Hello Caitlyn,

Congratulations on becoming an architect, it’s a worthy profession. Btw, John Denver was studying to be an architect too (he designed his home in Starwood CO.).

So let’s talk design, even architecture. Design reuse is one of the foundational tenets of intelligent agency. Why? Would an architect design a building from scratch, ignoring all of what is known? Known about building codes, electrical codes, plumbing codes? Material strengths? Static forces? and many other variables, standards, and knowledge? Of course not. Such an architect would be immediately fired, and he/she should be. An architect, engineer, designer, scientist, physician, teacher, etc. always starts from first understanding what is already known then they try to improve upon prior art by trying to do more with less. This is the hallmark of intelligent agency. God made man an intelligent agent, why would not God practice the same teleological imperative in His designs?

Wrt whether or not God is limited, there are a couple other threads in the RZIM Academy exploring that question. It is generally conceded by almost all RZIM Academy participants that God does indeed have limits (eg, God can’t sin). And the question of just how limited God might be is interesting; my personal belief is that God is more limited than most of us consider. The reason is because God is operate by laws and not randomness, fiat, or contradiction. This restricts reality.

Hi Eric, thanks for providing a balanced view, and for responding. And sorry, if I’ve sounded disrespectful, that has not been my intention. And it’s probable you are older than me so, again without any disrespect for an older Christian. I am not an architect yet, I only graduated last year and it will be a few years til I’m registered. I am quite a passionate person, and I have found myself back on here asking questions because I am obvious bothered by the interaction with this woman. But forgive me, I will try to keep this about the discussion, and by using reason. So please forget my saying I didn’t like this woman, I didn’t, but that is a personal viewpoint I didn’t need to share.

I’ll respond to two points. The first is, science can prove the moon is not made of green cheese. They have made it to the moon and can bring a sample back. As you say science has not proven the phylogenetic tree, thank you. It could very well be wrong.

The second is, and as for how much should we hold to the Word of God, where do you draw the line? I think the line is in a different place for you and I. But the line is in a different place for me and a Calvinist, or maybe it isn’t but we are certainly interpreting things differently. I have come to value the words in the Bible as gold (yes, out of 20 years of a life lived in faith and experiencing it this way) and hold to it as the benchmark. I cite these verses about His Word, just like God swears by Himself and God’s name is I AM, he kind of has to refer to Himself because there is nothing higher, I can’t see how a Christian can do anything but back him or herself up by citing scripture.

“How sweet Your word is to my taste— sweeter than honey in my mouth. I gain understanding from Your precepts; therefore I hate every false way.” Psalm 119:103-104 HCSB

“For the word of God is alive and active. Sharper than any double-edged sword, it penetrates even to dividing soul and spirit, joints and marrow; it judges the thoughts and attitudes of the heart. Nothing in all creation is hidden from God’s sight. Everything is uncovered and laid bare before the eyes of him to whom we must give account.” Hebrews 4:12-13 NIV

“35 Heaven and earth will pass away, but my words will never pass away.” Matthew 24:35 NIV

Ok, what I mean is God is not limited in His creativity. I know that they teach us iterative design process because we are so limited in our creativity, it is a method for generating ideas. Now I haven’t quite got my head around the word “singularity” which one of Matthew’s post mentioned, but I think this might be the word discussing the same idea.