Introducing Babacar

First of all, thank you so much for sharing. I heard you on “Capturing Christianity” and I was challenged and intrigued. I went and bought the book, so I’ll be reading that amongst other things. I can’t help but want to use the opportunity to ask a scientist questions! I’m always wondering things so, may I ask you some questions? Please forgive my ignorance.

Regarding the interview on Capturing Christianity.

-I found your disillusionment with ID to be unclear. ID does push for science to confirm something that science can not currently confirm under naturalism. However, I think you were referring to fallacious proofs for ID. So could you clarify maybe using an commonly used example of ID? For example bacterial flagella.

-You gave a sort of rudimentary understanding for beginners on how to understand changes caused by evolution. “Rate x Time = Distance.” How DNA analysis works I don’t quite understand so I just have to take your word for it. The question I have regarding this is, how does this formula necessarily show parentage? Can you not take two things of separate origin and compare them for rate and distance and compute a time, despite the fact they are unrelated? Is there a danger of this becoming self-fulfilling? Perhaps a bad analogy would be two wax figures. You might compare the two and find them incredibly similar and also different. So you know the “distance” between the two, and perhaps you know the rate at which they can be remolded. Then you could calculate the time it would take for one to turn into the other, however this would not reflect the reality, if the one didn’t turn into the other. The reason I ask is that I figure I am missing something. A friend of mine did the evolution of “CD from a rock” in a class on evolution while in college just to beg this question. There may be a kind of relation that is not lineage. I suppose DNA somehow explains this, but I don’t know how.

Other stuff:

-Along those lines, why don’t we think that several evolutionary trees exist rather than just one leading back to one common ancestor? Don’t similar things evolve separately like fins, and stripes?

-Many times I read in ID arguments or other Christian sources that genetically there are limits for how much something can change. So there is a kind of ceiling an organism hits and can go no further. Is that true? If so, is there a limit for how much an evolutionary tree or branch can grow?

-If we know the difference between chimp and human DNA, can we not conceivably reprogram a chimp into a human?

-I have thought for a long while that somehow our behavior might write to our genes somehow, hence the way we live effects our descendants. I don’t know of any proof of this and I wonder if anybody knows if there is proof one way or another? If it happens, how does that happen?

Thanks so much,

Babs

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http://www.talkorigins.org/faqs/comdesc/section1.html#nested_hierarchy

There are certainly epigenetic effects on human behavior:

@swamidass, what did that mean? I presume that @Babs misunderstood it as referring to phylogeny. Where does it occur in the video?

However, that doesn’t “write to our genes”; I think @Babs is hinting at neo-Lamarckian ideas of behavior causing mutations that make the behavior heritable over the long term. That doesn’t happen. At most, epigenetic inheritance lasts for a generation or two.

Pleasuring meeting @Babs!

Looking forward to hearing your thoughts.

We welcome questions. Please excuse the gruffness of some of our scientists, that’s just how we sometimes are, but we genuinely enjoy questions from the public.

I’ve written on this elsewhere. Perhaps this will help:

That formula + common ancestry predicts a large range of patterns in DNA. Common ancestry is important because it means that all the clocks have the same starting point in the past. That is why scientists think common ancestry is true. To reject it we would need to see a mathematical theory of equivalent rigor that makes predictions this well or better.

This may take some time to sink in, so feel free to ask some questions.

There are host of reasons the trees computed in different ways are not exactly the same. But they are very close to one another, and that is surprising. It did not have to be that way. We can imagine other ways God could have created life independent, but this is what we expect with common descent. So it just looks like God created us by common descent.

I am familiar with the claim but unfamiliar with evidence supporting it.

Yes. Thankfully, there are ethical rules against even attempting this. Can you imagine?

There is some evidence of this in a non-durable way, that might last just one or two generations. It is much more difficult to see any examples that really change the AGTC’s of our code to create more lasting changes.

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This is highly condensed, and I’m not sure I understand what you’re saying. If I don’t understand, how likely is it that @Babs will? You seem to imply (“same starting point in the past”) that inference of common ancestry relies on a molecular clock, which of course it doesn’t.

I would really like to be able to find what you said in the video without going through the whole thing. Where does that equation happen, and what does it mean regarding evolution and phylogeny?

Nothing new to you on this @John_Harshman. I’m just being super brief here. I start explaining it at minute 36 in the video.

Welcome to the forum, Babs!
Thank you for bringing your questions here. There are a lot of scientists on the forum, who I am sure would be happy to help indulge you in answering your questions. We come from many different backgrounds with different perspectives on creation (including young earth, old earth, intelligent design, atheist, agnostic, as well as Christians who affirm evolution). Thus, depending on your question, you could get different answers colored from those different perspectives. So it is a fun place to see how different people think and reason through some complex issues.

I’ll take a stab at one of your questions:

I am sure you are aware of the ethical issues surrounding such an idea. Setting ethics aside for a moment… in principle with new gene editing tools such as CRISPR one could theoretically conceive of the possibility of doing what you suggest. However, I do not think that even that technology is quite far enough along to succeed in such an attempt. First of all, the modifications would need to be made in germline cells, or at the embryo stage, to be able to affect all cells in the organism. While that could be done for a few genes, I think it would be hard to target more than a few genes in one attempt, and I think it would be hard to get cells to survive sequential attempts at introducing editing tools. Secondly, the technology is not perfectly targeted. Thus, any use of CRISPR technology can create new breaks in off-target sites, potentially creating multiple mutations, some of which could certainly be detrimental (just one of the ethical issues, among many). The only ethical use of CRISPR for therapeutic purposes would be modifying disease-causing genes in adult tissues. For example, the recent editing of the bone marrow of a patient with sickle cell anemia, which happened at the NIH last year. In that case, the bone marrow was removed from the patient, and a fetal hemoglobin gene was introduced into the patient’s bone marrow in the laboratory, then the bone marrow cells were transferred back into the patient.


Also this year, CRISPR was introduced into the eye of some patients to correct a rare genetic disease of the eye:

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Also, we don’t have a good idea which of the 40 million or so differences it’s important to change and which would have no effect. What if the chromosomal fusion turns out to have a phenotypic effect? CRISPR sure won’t do that for you.

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I’d also imagine any organism you tried to make this way (by modifying DNA of another species) would also be sterile (unable to produce offspring), right? Because the chromosomes would not be able to line up the right way during meiosis, or at least not in the second generation? This is the reason why mules, the offspring of a horse and a donkey, are sterile.

Not necessarily. Depends on the number and, more so, the nature of the differences.

I don’t think so. Human and chimp chromosomes probably line up just fine. There are species in which a Robertsonian fusion is polymorphic, and it doesn’t seem to cause problems. More problematic would be translocations, which could produce daisy chains in meiosis. I’d say that developmental incompatibility would be more likely to prevent human-chimp hybrids. Another potential problem is gene duplication with subsequent loss of different copies; in meiosis one could end up with two or (worse) zero copies of some critical gene.

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I’ll leave the biological details to the biologists, but assuming you could what would be the point? We already have a much easier way of making more humans.

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More fun too! :grin:

Dr. Moreau would beg to differ.

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But apparently it may also be unethical as it brings a person into existence without first obtaining their permission? This man is trying to sue his parents for giving birth to him - Vox

Now one of my interests is hominin evolution. There is so much conjecture and debate because of very flimsy evidence. If it didn’t face enormous technical and ethical challenges recreating some neanderthals or denisovans could teach us a lot. But spending a fortune to create another human (sorry Joshua, I meant anatomically modern Homo sapiens) when we already have about 8 billion of them? Seriously, I don’t see the point.

In regards to the link that you sent, I’m still slowly reading through things when I have free time. So far, the things I found most significant as it relates to common origin were the vestigial organs and DNA, as well as transitional like forms.

Regarding the first bit of the Talk Origins page you linked, what I understood was that everything has DNA made from the same polynucleotide. All DNA has the same composition in this sense. So this is a sign that all life is related. This is what one would expect if common descent is the process we’re observing. If you assume naturalism, it seems unlikely or near impossible for another evolutionary tree to exist of the same composition. I accept this as one sign of a common origin.

It sounds like the article is saying that if life didn’t have a common ancestor then it could have used different materials for these evolutionary processes. In that case a different composition could rule out a common ancestor. However, just because they do use they same materials doesn’t prove they have a common ancestor. It’s like four kids running a race. They all have their own starting points. Just because they are all using feet to run, doesn’t mean they started from the same point. Or, like if you walk in the room and find four colors of scribbles on the wall and your kids are looking at you guiltily, you know what crayons were used but not who the scribbler was, or how many scribblers there were.

I’m not so sure about the idea that nested hierarchies only exist as a result for living organisms…because living organisms have a common point of origin??? By assuming common origin you get nested trees. As you mentioned, languages have them, and if you assume things to have common origin you can organize non-living things into them as far as I can tell. If you consider the model T the origin of all cars you can make a tree with nested hierarchies showing this. I don’t know how to agree with this statement, or perhaps I misunderstand it. However, I agree with the statement: “we are now in a position to begin construction of phylogenetic trees based on other independent lines of data, such as chromosomal organization. In a very general sense, chromosome number and length and the chromosomal position of genes are all causally independent of both morphology and of sequence identity. Phylogenies constructed from these data should recapitulate the standard phylogenetic tree as well.” So does it? How has comparing these trees changed “THE evolutionary tree”? What does the cytochrome c tree look like as opposed to the morphological and genetic trees?

Along those lines I read in the article: “When two independently determined trees mismatch by some branches they are called “incongruent”. In general, phylogenetic trees may be very incongruent and still match with an extremely high degree of statistical significance.” I take this to mean that the tree based on molecular studies (i.e. cytochrome c) doesn’t really match up just right, but as far as some statistics assuming common descent are concerned, it doesn’t matter. I don’t quite understand the logic here nor the significance of his calculations. I took these calculations to mean given how many possibilities of trees there are for our given taxa finding two trees based on different data that have “this much” in common is amazing. This could be misleading. It doesn’t solve the problem. The trees don’t match up, or show even how much discrepancy there is! It’s really like saying “oo we’ve almost got it…” What does that even mean? For example: Even, if one Pre-Denovion mammal was found it would be significant despite it being only one animal contradicting the current tree. How is not the case for incongruency? My dad was a statistician and he used to tell me you can get the statistics to say whatever you want. This seems a very weak point as I understand it, but perhaps I don’t.

I have the same problem with the computer languages example. All coding is based off machine code as far as I know like “10101011.” However, this doesn’t mean that all codes are related necessarily nor that all computer languages are related except that they are based on machine code. For example, let’s say Unix is the most secure operating system, so you have programs that written independently for different businesses because of the necessity of security. These Unix based systems all use the same code but are independent programs. The necessity for security might even put other unsecure systems out of use leaving only Unix based programs. You can map nested hierarchies of these systems, but there is no actual common origin for a say a Unix based banking program and the game Rusted Warfare. They developed independently in the sense of one did not produce the another. If some dude trying to keep his money safe in Holland makes a program for security’s sake, and some guy in America makes a goofy game for his kids, they are related in one sense (they use code) and not in another. This is because comparing shows likeness not lineage. Another example: Where we live I see what is called a “townay” sometimes. This happens when a seed falls into a nook or between two branches in a tree and takes root and grows out of that tree. It’s quite the phenomenon because it looks as if one tree has different kinds of branches, flowers, and leaves sometimes. If the seed of a baobab fell into a nook in another baobab, the two trees would look identical almost. You might consider them one tree at a glance when its actually 2 trees.

As it relates to phylogeny and the strata…If you found simple organisms at the top of a strata, that is normal because they exist throughout the strata. If you found a complex animal like a mammal lower in the strata would you not assume the strata are some how mixed up?

Thanks so much. Back to more reading…

Thanks for the warm welcome. I’m still reading through the book in my free time. I’ll write down any questions I have along the way. Also, I look forward to your next apperance on Capturing Christianity.

You said, “That formula + common ancestry predicts a large range of patterns in DNA. Common ancestry is important because it means that all the clocks have the same starting point in the past. That is why scientists think common ancestry is true. To reject it we would need to see a mathematical theory of equivalent rigor that makes predictions this well or better.”

First, so what I understand is that because when we assume common ancestry one can predict DNA patterns, thus common ancestry is viable, is that correct? What exactly do you mean by “a large range of patterns”?

Second, do I understand you to mean by “That formula + common ancestry” that if you assume the difference between two creatures being compared is accounted for by the observed rate of mutation, then the time of divergence was distance/rate = time? This could conceivably be done with creatures that do not have the same parentage and you still get an answer. That would suggest that your assumption determines your answer. Or do you maybe mean that the morphological chronology (found in fossils) and the DNA based time confirm one another?

-Here is my train of thought for correction. As it relates to molecular clocks. Are these clocks not calibrated by observing the mutations? I assume this is most effective with tiny creatures with quick life cycles and reproduction rates. However, for calibrating based on creatures that evolve more slowly, observing mutation is not an observable process except in a historical sense. (Am I wrong?) This seems to me to be problematic. I imagine calibration for these creatures is based on the fossil record, which is likely dated based on morphology patterns. Dates are approximate or even pliable to some degree. This seems to me to be self-fulfilling.

Also, are the dates for fossils not also dated in the same manner? If so, this is what I think confuses me. It seems as if the mutation rate, is based on a sample of mutation over time, and for more slowly evolving creatures this is determined by the fossil record (by nodes or tips). In such a case, the dates of the fossils help determine the rate of change, and these dates may be determined by that rate of change. That is self-fulfilling: The date determines the rate of mutation and hence that rate confirms that same date and vice versa. This is obviously circular. I’m confused.

In addition to that, it occurs to me that by choosing what you are comparing (in DNA or morphology) to determine distance you could conceivably, choose data that matches what you are looking for. You can prove whatever you want in this manner. This is something done in statistics sometimes. I conclude that I must be missing something.

" Common ancestry is important because…scientists think common ancestry is true."

Yes, but what I think you mean logically sounds circular to me. I’m having trouble understanding it.

“To reject it we would need to see a mathematical theory of equivalent rigor that makes predictions this well or better.”

So, do you mean to say that this formula represents accurately what we find in the fossil record, and/or predicts accurately the projection of evolution? (Future or past predictions?) It certainly seems less complex to assume common descent. However, it seems feasible, off the cuff, that one could come up with a new form of the theory to account for diversity. Like I said, I’m not sure what kinds of predictions you are referring to.

In light of the fact things evolve similarly yet separately like seals and sea lions, what if there were primordial oozes rather than just one? Or imagine if single celled life forms piggy backed on a meteorite and landed on earth and began evolving alongside life on earth for billions of years how might we distinguish them?

“I am familiar with the claim but unfamiliar with evidence supporting it.”

Regarding examples of genetic limitations: So, “since we know the number of alleles in the genetic code is limited and the natural variation that occurs as a part of reproduction is limited, therefore the variation a species can experience is not unlimited. It is limited by the number and type of alleles in the species genetic code…( if) a life form has unlimited ability to change it means that some process must exist to add information. There are only a certain number of genes and alleles of those genes there is therefore only a certain number of possible variations in genotype, and therefore a limited number of phenotypes.”-Wiles and Durnell

Different criteria give different relations, so if you look at one particular point in the code you might get a different looking evolutionary tree. For example, there are different ways of making an amino acid- case and point, Cytochrome C production. “Certain proteins are common to many species like cytochrome C, but each individual species has its own sequence to make cytochrome C. The cytochrome C that is in a bacterium is sequenced a bit different from the one in a human. The sequence is a little different for each species. One would assume the process of evolution would show that the sequences with the least amount of differences would be the species that are more closely related. Most of the time this is not the case” -paraphrase of pg 285 of Exploring Creation with Biology by Wiles and Durnell.

Other questions I had while reading:

As I understand it so far, ubiquitous genes are genes in common between all life forms. Do ubiquitous genes make making an evolutionary tree based off DNA easier or more difficult? What I mean to say is if everything is related, how do you know what gave rise to what?

Would you personally describe evolution as a random process? If so, what do you mean by random?

Can the evolutionary tree not be reformed based on different criteria? How can there be consensus then?

Why don’t we see other evolutionary processes popping up on earth from a different (molecular) composition?

Is it feasible to make DNA using different polymers and make a different kind of life?

How can you even compare DNAs with different numbers of chromosomes? For example crawdads have 200 and people have 46.

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@babs this are really great questions. Some of them will be split into other threads, and others will take some time for me to answer. Your thoughtful engagement is great, and I look forward to the exchange.

Might I suggest that creationist literature is not the best source for scientific information? If you’re familiar with the term “word salad”, those two quotes are excellent examples. The genetic code is the mapping between DNA triplets and amino acids. The code does not have alleles; genes have alleles. Natural variation is not limited; any mutation can happen, and any series of mutations can happen. There are in principle a number of alleles equal to all possible sequences, though of course most of them would be selected against.

I don’t know what “different ways of making an amino acid” is supposed to mean. Cytochrome-c is not an amino acid; it’s a peptide, a chain of amino acids. Cytochrome-c is produced in the same way in every species, by translation of a messenger RNA on a ribosome. The messenger RNAs vary in sequence, but “sequenced” doesn’t mean that; it refers to human efforts to find out the sequence, as in “I sequenced ADH in D. simulans yesterday”. One might assume that smaller differences means more closely related species, but that’s true only if there’s a uniform rate of evolution across the tree of life, which is not the case. Fortunately, most methods of phylogenetic analysis do not assume this uniform rate. Still, the assumption does indeed hold in many cases, so I don’t know where “most of the time” comes from.

Based on your quotes, Wiles and Durnell seem grossly ignorant of biology, and you should probably get your information elsewhere.

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