BioLogos Basics Video #7: How Evolution Works - Part 2 | The BioLogos Forum

Today we release the next video in our BioLogos Basics series. It is the second on the science of evolution. Last time we discussed small changes on relatively short time scales--what some people call “microevolution.” We’ve observed the development of new species in this way, but they are closely related species, like two different kinds of bird. This is not too difficult for most people to image. What is difficult is seeing how two very different kinds of organisms are related--like fish turning into land-dwelling creatures. This is sometimes called “macroevolution.” There is vigorous debate within the scientific community about the mechanisms for this, but there is no doubt that it takes lots of time. In this video we give a well-document transition that took about 10 million years. Thanks to Dr. Ryan Bebej from Calvin College, whose expertise is in this topic, for helpful feedback and resources.

Script: Jim Stump Video Production: Andrew DeSelm Narrator: Chris Stump

Next Steps for Exploring this Topic:

  • Evidence for Evolution. Two posts in this blog series give further details about whale evolution from the perspectives of DNA and comparative anatomy.

  • Understanding Evolution: Theory, Prediction, and Converging Lines of Evidence This blog series by Fellow Dennis Venema uses whale evolution as the example to explain evolution.

  • What is Evolution? Our common question entry on the topic, with many more resources.

  • Common Ancestry In this short video clip, Denis Alexander explains how he understands human common ancestry with other life forms as “very good”.

  • Does Science Disprove Faith? Video of a sermon by John Ortberg, which addresses science in general, but also evolution in particular.

  • Finally, consider several blog posts from 2012 by our former Senior Fellow of Arts and Humanities, Mark Sprinkle. These are artistic representations of whales, including a poem, a sculpture, and a song.

Script for “How Evolution Works - Part 2":

In the previous video we looked at microevolution—small changes in a population on relatively short timescales. Most critics of evolution accept this but are skeptical of macroevolution—the claim that small changes can add up to big changes over long stretches of time. While the particulars of the mechanisms for such change are not all fully understood, there is very little disagreement among biologists that we now have powerful models of macroevolutionary transitions. These models make testable predictions and are continuously being refined by new evidence.

Whales provide a clear example of macroevolution. They are superficially similar to fish, but are, in fact, mammals! Darwin himself wondered whether whales had evolved from mammals on land, but he had no real empirical evidence for such a claim. Now we have impressive evidence.

In 1978 a 49 million year old skull was discovered that belonged to a land-dwelling wolf-like creature whose inner ear structure was curiously similar to that of modern whales. This led to a search for transitional forms, and very quickly a series of fossils spanning about ten million years was found that showed clear signs of increasing adaptation to life in water. The spine and legs were modified to allow for more efficient modes of swimming; nostrils moved toward the top of the skull, later becoming a blow hole; and hind legs eventually shrank to where they could no longer support the animals on land.

Many more fossils fit into this picture of whale evolution—more than 1000 specimens have been discovered in the Valley of Whales in what is now Egyptian desert. Remember these are not necessarily direct ancestors of whales today. That’s not how evolution works. More likely is that these represent related species that were evolving over millions of years. And taken together, they form an impressive picture of significant change in this lineage of mammals. This picture is not the result of wishful thinking or driven by unwarranted assumptions. It has emerged as the result of careful observation of evidence, which leads to the formation of hypotheses; these make predictions of future finds and are tested by observable evidence which is open to the scrutiny of others.

At BioLogos we see this interconnectedness of life as a testimony to God’s creativity. He worked through simple natural processes to fashion dinosaurs and daisies, weevils and warthogs, and human beings in his own image. He could have snapped his fingers to do this instantaneously, but both scripture and the natural world reveal that God delights in working through processes to accomplish his will. Evidence from the fossil record and also in the distribution and comparison of species supports the claim that he worked through evolution. And today we find even more persuasive evidence in genetics. We’ll consider that in our next video.

This is a companion discussion topic for the original entry at

we can also arrange cars in hierarchy ( a normal car–>a jeep–> a truck). but it doesnt prove commondescent but common design. even if cars was self replicating with DNA, the best conclusion is they was designed.

the hind “legs” are actually part of the reproduction system:

The fact that vestigial structures acquire different uses doesn’t show that they aren’t vestigial. It is quite a stretch to say the little legs on Dorudon were designed for reproduction–especially as you look later on the lineage to where the legs disappear (but a few pelvic bones remain), it’s pretty hard to see that as the sort of design you mean. And I don’t think we said “prove” anywhere… but putting thousands of different variations of cars, jeeps, and trucks into a hierarchy with their dates paints a picture of relationships between them of more than just wishful thinking. The evidence for this progression (we didn’t say anything about the mechanisms by which this happened) really is overwhelming.

hi jstump. first- dorudon dont have any legs but fins-like(like claspers in sharks). and they indeed was a part of the reproduction system even according to evolution scientists.

any series of animals cant be evidence for any macro-evolution. like any series of cars. and like i show before- even the phylogenentic tree isnt show hierarchy either.

Even modern cetaceans (e.g. dolphins) have four limbs at early embryonic stages, just like any mammal should have. The embryo develops forelimb and hindlimb buds, but later in development a second genetic pathway kicks in that overrides the first and causes hindlimb development to reverse and the hind buds to pull back into the body.

So, dcsccc, why does this take place? Why should a dolphin start developing hindlimbs only to reverse the process later in development?

hi dr venema.

“Even modern cetaceans (e.g. dolphins) have four limbs at early embryonic stages,”-

not realy. yes, they have a small “bump”. but they could be something different then limb. they could be a vestigial fin, or even somthing that have a conection to the embryo development.

embryo also have a gills like structure. but it never develop into a gills.

Hi Dcscccc,

It seems clear that we already have an entirely reasonable explanation for not only forelimb and hind-limb buds observed at early developmental stages, but for all such phenomena, including the gill-like structures you helpfully mentioned. The point is that no further explanation is necessary within the accepted evolutionary framework (either for why we see these early developments or for why they are overridden at later developmental stages). I think Dennis is suggesting that if you remove this framework, you remove all of it’s explanatory power as well and you are left with a number of unexplained phenomena. So again, what is the explanation for each?

Obviously it will have to be a bit ad hoc; you’ll need an explanation for each apparently vestigial structure and for why it just happens to look like and be in the position of the claimed homologous structure. Even if you offer more than just conjecture, an explanation that covers all such situations is far more convincing than a number of explanations tailored to each one. The tailored solutions may provide hedging to protect a cherished point of view, but they will not convince anyone who isn’t looking to protect the same view.

hi bren. the explanation is very simple: its a design trait, and we dont need to invoke any evolution theory to explain this.

“Obviously it will have to be a bit ad hoc; you’ll need an explanation for each apparently vestigial structure and for why it just happens to look like and be in the position of the claimed homologous structure.”

airplan and car both have wheels. doest it mean that they evolve from each other? the evolution explanation itself is ad hoc. when we see 2 similar structures, it may be because they both have the same designer.

evolution also doesnt explain how those structures evolve step wise. so the design option is the best option we have.

If anyone is interested in the actual science describing what we know about cetacean hindlimbs, there is a technical paper available freely here:

In a nutshell, the paper shows that the dolphin hindlimb bud develops with the correct properties for a mammalian limb bud until a certain point in development, and then stops developing. The authors investigate the reasons for the cessation, and find it is due to the loss of expression of a major signalling gene in the hindlimb. Studies in mice that remove the same gene produce a similar effect: hindlimb loss, but with some bone remaining in the body wall (just as we see in cetaceans).

Don’t forget that we have other lines of evidence that whales are descended from land-dwelling ancestors: they also have the remnants of hundreds of genes devoted to air-based olfaction (smelling). These gene fragments cannot be functional olfactory genes based on their structure. Should we postulate that each of these fragments has some other function but that each of them just happens to be in the right place in the genome and have a portion of the right sequence to merely look like the remains of genes we see in other mammals?

And on it goes… either we need to contrive an ad-hoc explanation for why whales have these features, or we fail to reject the hypothesis that all lines of evidence we have currently support - that whales evolved.

hi dr venema.

first- i already show that even a similar structure during embrio development can have different function in adult animals (aka gills- like stucture that become gills in fish but a part of the jaw in humans). so the bump during embrio development cant be evidence for commondescent. i also mention that it could be a vestigial fins.

your second claim is that whales cant smell. from designer prespective we can predict that this claim isnt true. and indeed, this is what we find:

we also know that whale cant evolve from a land mammal, because there is no step wise sequence from a land mammal to a whale.

again- all the evidences we have clearly show that a whale…always was a whale.

Hi Dcscccc,

Airplanes and cars are unfortunate examples for you to use, since they are full of features that most emphatically do not sort into the nested hierarchies that we see throughout the natural world. I can’t make sense of this as a counterpoint to the evolutionary explanation. Showing me two things that have a common feature (cars and planes) and then pointing out that they are not related only establishes the very obvious fact that a common feature does not guarantee relatedness. No one is claiming otherwise and this seems to rather miss the point being made!

When a theory fully explains a whole range of phenomena that otherwise seem unaccountably coincidental (see Dr. Venema’s very helpful points above), it seems that this theory gains support by this very fact (explanatory power), especially when no other hypothesis does anything close to the same explanatory work.

Given that a designer hypothesis does not seem to have a way to account for the specific coincidences and patterns for this range of phenomena (e.g. why do whales have so many sequences that have such an impressive amount of sequence homology with specific mammalian olfactory genes, and to clinch the case; why are they found in the same corresponding positions?!), it is obvious that it does not gain similar support by these observations.

There is a very stark difference in explanatory power here between our positions and the coincidences are wild enough that there is no reasonable way to overlook or explain them away on an ad hoc basis. This is what needs to be addressed.

Hi dcscccc,

I am a non-expert in the Biological Sciences (my training is in Philosophy), and we non-experts have no choice but to do our best to sort through the peer-reviewed literature in a given field that interests us, determine whether a consensus exists there, and then attempt to understand the consensus as well as we can. After that we may ask questions about the significance of the consensus for other fields in which we may or may not be experts. And so, as a philosopher, I have a special interest in surveying the biological sciences for consequences of philosophical significance. And as a Christian, I have an interest in doing likewise regarding consequences of spiritual significance. These are our limitations as non-experts, and they apply just as much to a scientist seeking to understand a scientific (or other) discipline that is not his or her own. We will often hear claims made by experts and find ourselves unable to evaluate them with confidence, simply because we lack the competence in the field that is a necessary condition for such confidence. We can listen in on dialogues that occur between experts, but we cannot confidently pronounce on who is right. But the problem is not hopeless, because a reasonably broad-based education does allow a non-expert to detect a consensus when it is there, and to understand it well enough to glean broader consequences from it. (Or so I say. If you don’t think so, please address that.)

I say all this in preparation for three questions, and I’ll get to them in the next paragraph. But please bear with a few more observations. When a non-expert surveys the biological sciences, it is very easy to discern that there is a powerful consensus regarding the common ancestry of life on earth (which includes the common ancestry of humans with other primates). When someone cites literature that questions or denies the consensus, it is likewise very easy to discern that it is representative of an extreme minority. It is not evidence of a significant debate within the field, but it is evidence that there is a strong consensus that is still being challenged by a few outliers. This conclusion is unavoidable if one carries out an honest assessment from a non-expert’s standpoint, and it seems to me that you can agree with that. But then one notices something else, which will immediately pique a philosopher’s interest. The outliers are all, without exception, religiously motivated. This is a striking correlation that requires an explanation. The fact that most of the outliers are motivated by a faith commitment that I happen to share is irrelevant to my judgment that they are in fact outliers, and that they are all religiously motivated, and that the latter fact requires an explanation. And a very good explanation presents itself effortlessly: they think their faith commitment requires them to be outliers. And I will tentatively agree that if they are correct, they should continue to be outliers (though there are limits to this). But if they should ever come to think that their faith commitment does NOT require them to be outliers, then they should cease to be outliers (this is an epistemological “should,” which may or may not turn into an ethical “should”). This will of course happen if one abandons one’s faith altogether, but it will also happen when one realizes that one’s deepest and most valued commitments do not require one to be an outlier, and that it was merely a peripheral commitment that was motivating one’s outlier status in the first place (I speak from some personal experience here).

So here are my three questions: If you were not a Christian, would you find your own anti-evolutionary sources persuasive? If a Christian does not think he/she has to deny common ancestry in order to be a faithful Christian, shouldn’t he/she refrain from denying common ancestry? And do you in fact think that Christians have to deny common ancestry in order to be faithful Christians?



I broadly agree with your outlook, and as a Christian I am more puzzled by the arguments put forward regarding specifics of such matters as the “common” origin of life on earth. As a practicing research scientist (Physical Sciences) however, I find DETAILS of such matters as common ancestry of various species (including humans), and changes from one species to another, very dissatisfying. I cannot understand the acerbic positions taken by both religious and non-religious people when discussing such detail. I also note that consensus in the Sciences is better dealt with by considering paradigms and their shifts that have occurred in the Sciences.

To provide a rough answer to your questions, I do not think that faith is based on any particular view of the sciences, and when considered in this way, a Christian may find harmony between the Faith and Reason, including the non-controversial areas or settled conclusions provided by the Sciences. I am also aware of considerable controversy regarding the semantic Neo-Darwinian theoretical framework, including a considerable number of bio-scientists expressing a variety of views and doubts related to natural selection. Additionally, I am aware of great speculation regarding the origins of all of the bio-world, including universal common ancestry. Thus I conclude that a healthy scepticism regarding the Darwinian paradigm is a good position for both non-religious and religious people. Consequently these debates which often question people’s honesty and their competence, is an unfortunate aspect of a destructive argument that ultimately will have a minor aspect on the Christian faith, but yet may cause harm to some through its warfare mentality.

John M, interesting thoughts. First, as regards outliers, it is important to realize that these are not scientific outliers, but human outliers. From time to time, human outliers become mainstream. This is true in many different areas, whether music, exercise, philosophy, morality, and religion. Second, rarely do the “outliers” in this case differ on actual evidence or biological artifacts; rather they differ in the interpretation. Even if they are motivated by faith, or by historical accounts, this does not invalidate their conclusions of interpretation. We also know that consensus does not guarantee truth, just as might does not make right. The question could be asked, for which other theories do we have this type of “outlier”? How long do these outliers continue?

As a christian, I like the challenge posed by YEC. But occassionally I can see a stretch in the YEC argument. On the other hand, I see many more weaknesses in the OEE scenario (from a scientific perspective). Both sides have some valid arguments, but I personally find OEE more plastic, and less useful. I find that OEE has often made premature predictions. The answer to every bio question or discovery simply becomes: “evolution did it.” A new organ? Evolution. A missing organ? Evolution. Blindness? Evolution. Eagle eyes? Evolution. Genetic similarity? Evolution. Genetic dissimilarity? Evolution. If we were talking about gravity, it would be comparable to saying, that two masses attract? Gravity. Two masses separate? gravity. Radiation comes to earth? Gravity. Radiation leaves the sun? Gravity. The theory of evolution has nothing it can’t explain, because it explains everything… the theory will change until it does explain it. It’s too easy, and so becomes rather meaningless.

Your questions 2 and 3 involve making judgements about other people, so I hesitate to answer… in fact, I do not think it useful to answer those questions, because once you start looking at those questions, you stop looking at the science.

As one who obtained a philosophy degree many years ago, I fully understand the lure of speculation…

hi bren. acctually, there is no such hierarchy in the living world either. here is some examples:

even in micrna phylogeny:

so my claim about cars hold water.

the explanatory power of the evolution is actually very weak. because it doesnt explain its main claim- how a complex system evolve step wise. from the other side- we have a good answer from design prespective.

you said:

“Given that a designer hypothesis does not seem to have a way to account for the specific coincidences and patterns for this range of phenomena (e.g. why do whales have so many sequences that have such an impressive amount of sequence homology with specific mammalian olfactory genes,”-

like i show- they are ideed functional. and again- this is the similarity argument. .

i john t. like john said: consensus isnt a scietific claim. so its mean almost nothing from scientific prespective. now, a lots of scientists actually doesnt agree with the evolution theory. even biologists. so its question of prespective, not evidence. even if you are not a biologist, i think you can understand the arguments in both side, and choose for yourself what is the best explanation.

as for your question- im actually going after the scientific claims and not the religions one. the evolution theory is actually a natural explanation. so in the first place it doesnt need any designer. but i actually think it may be false either. because even a car in a car factory produce in a series of steps (evolution). but we all know that a car need a designer.

Hi dcscccc,

For the first article you offer, it is a well known fact that there are means other than descent by which genetic information may be transferred, and that this complicates the tree/ bush of life to some extent. But to what extent? Darwin was wrong in that the tree of life did not give a complete picture, but he was not wrong in that a tree or a bush is a good representation of the discernible evolutionary relationships (this is especially true of eukaryotes, which is all that he really had in mind, given when he lived). As is also well know, the limited horizontal genetic transfer is not nearly significant enough to mask the nested hierarchy pattern that can be traced by the genetic material (converging on the same pattern that can be traced using morphological traits). The all or nothing claim is often made by creationists and it goes something like this; since Darwin was not completely accurate with respect to the evolutionary tree, he was wrong about everything else. By that reasoning, we can dismiss anything we’d like. This is obviously not logical, and the far more temperate claim (actually supported by the science) would be the following: evolutionary relationships may be traced by various means, converging on high-likelihood phylogenies using multiple independent data-set, but there is a degree of horizontal gene transfer, particularly in prokaryotes, that complicates, while not actually masking the data that is necessary to trace these relationships. Especially given that hgt is far less pervasive in Eukaryotes, it is absurd to claim that it somehow invalidates the entire evolutionary tree/bush. It simply doesn’t. If you wish to oppose this, it is best done not by discussing specific cases of hgt and endosymbiosis, but by addressing the faulty logic of assuming that the phylogenetic tree is invalidated when a layer of complexity is added to it (just as Newton’s discoveries were not rendered invalid or false when they were complicated or found to be special or limiting cases of relativity/QM).

For the second article, this is about a novel form of data being used to generate phylogenies. The claim that it accomplishes the opposite, supporting the idea that evolution did not occur is not-comprehensible to me.

I’m afraid you have misunderstood the articles, or have been misled to thinking they say something that they don’t.

“the explanatory power of the evolution is actually very weak. because it doesnt explain its main claim- how a complex system evolve step wise. from the other side- we have a good answer from design prespective.”

I thought the whole point of Darwin’s theory, especially now that we understand the genetic mechanisms, was that we actually do know how stepwise change and increased complexity can occur. This is the pith and marrow of the theory, so I have trouble understanding this point. I suspect you have been bamboozled by the common creationist claims about information, which have never made much sense to me and which have always relied on an idiosyncratic and self-serving definition of information (involving the built in claim of how information “must” come about and using this to make claims about how it couldn’t have come about!!). Anyway, you are diverting, please focus on the specific data-set for which explanatory power is being claimed, I made no other claims for the time-being.

In relation to sequence homology with specific mammalian olfactory genes, you said: “like i show- they are ideed functional. and again- this is the similarity argument.”

So all of the mutated, fragmentary, frame-shifted, but otherwise homologous whale sequences that apparently relate to and are in the position of mammalian olfactory genes have been proven to be functional after all?! It is, of course, entirely beside the point (secondarily acquired functionality has nothing at all to do with whether or not there is obvious homology), but I’m nevertheless interested to see how this claim was made and supported. Again, it is totally beside the point, but in the past the argument has looked something like this; since we have now discovered that there are some (mostly regulatory) functions for some sequences of DNA that were previously thought to have no functions, it should be assumed that ALL such sequences have a function. Therefore so do these apparently homologous ones. An argument with a convenient conclusion (though one that doesn’t actually address the real argument), but its not really a very good syllogism at all. It is similar to: Some places on earth that were previously thought to be uninhabitable were found to be colonized by extremophiles; therefore all places thought to be uninhabitable on earth should be assumed to have life. Some to all isn’t even an argument. It doesn’t follow and I hope this wasn’t the reasoning you had in mind. And if I hadn’t mentioned it previously; it misses the point anyway;-). Not sure what you mean by similarity argument.

I know it was in response to Dr. Venema and not to myself but when I read the following line: “your second claim is that whales cant smell…”, I was concerned by it. The actual take-home message was far more obvious and far more interesting that that, and it leads me to suggest that you consider the comments a little more carefully, you don’t seem to really be addressing or even considering the reasoning that is being carefully laid out for your benefit. You don’t obviously need to agree, but if your responses show that you at least worked through the arguments before rejecting them, it would make the exercise of presenting them worthwhile.

Hi John T Mullen,

I appreciate your well considered and careful approach to dealing with any field where you consider yourself a non-expert. Looks like good general policy to me. From what I can see, the main criticisms being offered are

(a) that consensus doesn’t count in science.
I have trouble seeing what else is supposed to count in it’s place for a non-expert (this criticism seems to miss the context; we are specifically discussing people who are not in a position to judge for themselves); the whole point is that you are not qualified to disagree with the majority opinion of the experts in a field where there as a strong consensus unless you understand the issues as well as they do, in which case you would be qualified after all.

(b) it isn’t really a consensus since there are a lot of dissenting voices.
The expert dissenting voices, except on issues which are not related to whether or not evolution occurred or common descent is true, seem to be to be very obviously outliers (it doesn’t make sense to list ongoing controversies when all parties agree on the central facts we are considering), and more importantly, as you pointed out, they correlate very exactly with religious commitments - a correlation that is extremely significant and which no one seems to want to address. Any takers?

© every consensus starts as an outlier and every outlier might be correct
Questionionable reasoning at best, since every single incorrect, ridiculous and mildly insane idea also starts as an outlier. And yes, every outlier may be correct, but given that the outlier opinion view in question started as the religiously blustered majority opinion, and only lost ground as the science progressed over multiple generations, this is a pretty weak hope to hold on to.


I don’t think I communicated very well.

Regarding (a), I think that consensus does count in science. In fact, I was trying to say that a consensus is the only thing a non-expert can rely on to tell him/her what the results of a given scientific inquiry are. I also said that a non-expert is at least able to discern when a consensus exists. And so a consensus within a field should be authoritative for a non-expert. There is a consensus among experts regarding the common ancestry of life on earth, and so all non-experts should regard common ancestry as the authoritative result of scientific inquiry into biological origins.

Regarding (b), I think there can be a consensus even if there are a few remaining dissenting voices. A few dissenters do not negate a consensus. I called such dissenters “outliers” because they lie outside an established consensus, and those who deny common ancestry are indeed outliers. Admittedly, the percentage of dissenters is significant for the existence of a consensus, so “a lot” of dissenting voices is some evidence that no consensus exists. Unfortunately, there is no numerical threshold that can serve as an exact indicator of a consensus. We will have to live with some vagueness regarding how many dissenters it takes to negate a consensus. The same goes for the exact time a consensus is established. But in any case, those who deny common ancestry are definitely outliers now.

Regarding ©, I don’t think that every consensus starts out as an outlier. In every inquiry there is a time prior to the establishment of a consensus (a Kuhnian pre-paradigm stage, if you like), but the various competing views in that situation cannot be called outliers precisely because there is no consensus (yet) for them to deny. Because it is possible for a consensus to be wrong, it is likewise possible for an outlier to be correct. But such cases are so rare and improbable that it is not rational for a non-expert to deny a consensus. Non-experts really are rationally required to defer to the consensus of experts when there is one. And non-experts can tell when there is one.

My three questions were intended to suggest to those who deny common ancestry (e.g., JohnZ and dcscccc) that they should examine their motives for doing so. My hope is that those who are inclined to deny common ancestry will grant that they would not be so inclined if they did not think that the Christian faith requires it of them. And the last question was intended to suggest that the Christian faith does not, in fact, require it of them.


Yes, the warfare mentality cannot do any good, and likely does a lot of harm. I hope I didn’t question anyone’s honesty when I suggested that religious motives are at work in those who deny common ancestry. I didn’t intend to question anyone’s honesty. I was only trying to point out that religious beliefs do in fact play a major role in that judgment. That can be true even if everyone is being completely honest.

I think we may disagree about what is now an established consensus, and which details are part of that consensus. I can agree that a healthy skepticism is appropriate regarding abiogenesis (life from non-life), and perhaps also for some other transitions that must have occurred in natural history. That’s because there is no consensus yet regarding how some of those transitions might have occurred. Perhaps the Darwinian paradigm will prove inadequate for a few of them. Who knows? We’ll have to wait and see. But I do take it that a consensus now exists, and has existed at least since the completion of the human and chimpanzee genome projects (and probably even before that), regarding the common ancestry of humans and other primates. And that alone requires a sober and thoughtful response from Christians, and most other religious believers as well.