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A Geneticist’s Journey

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September 23, 2011 Tags: Genetics

Today's entry was written by Darrel Falk. You can read more about what we believe here.

From the AAAS/Science Magazine Podcast (August 26, 2011). Posted with permission from AAAS.

These are mind-boggling times for a geneticist many years into his career. As a graduate student attending a conference at the University of California, Berkeley almost forty years ago, I remember watching with bated breath while another young graduate student, Nancy Maizels of Harvard, presented the DNA sequence of the lactose operator. Using amazing technology, she and Walter Gilbert had unraveled a little stretch of 24 units of code.

We were in awe—absolute awe—partly because the sequence was beautiful (it exhibited perfect twofold bilateral symmetry) and partly because we were incredulous that anyone could have done it—24 bases of DNA! A secret that had been locked inside of cells for millions of years was there on the screen in front of us. For a biologist, this was better than going to the moon. Twenty-four bases of the 4,600,000 bases in E. coli had been sequenced: one small step for a molecular biologist, but one giant leap for humankind!

It was Berkeley. It was 1973. Biology, we thought, had reached its zenith. The possibility of someday sequencing the other 4,600,000 bases of the E. coli genome or, heaven forbid, the 3,500,000,000 bases in the human genome, was like picturing the construction of a rocket ship that would take you to the outer reaches of the universe. No one dared dream of it.

I remember the February day in a San Francisco hotel in 2001 when Francis Collins, wearing a business suit (there were no business suits at Berkeley in 1973), showed his analysis of the just-completed first draft, not of another 24 base segment, but of the entire 3.5 billion bases in the human genome. Craig Venter, wearing a tuxedo (there were no tuxedos either), did the same the next night. We were dazzled with the two successive presentations. Indeed as the second evening came to a conclusion, it seemed like we had been on a trip—this time not to the moon, but now to the other side of the universe…and back.

Genetics had changed. No longer in a Berkeley classroom with shorts, sandals, long hair, and chalk board, we were now on the other side of the Bay in a fancy hotel in downtown San Francisco, where champagne corks were popping. Molecular biology had made the big time. Still, the simple awe of having unraveled the beauty of the molecule’s secrets was not dimmed by the hype or the glitz. The majesty of the molecule spoke for itself and I felt just like I had 28 years earlier.

What, I wondered, would be next? What could top a trip to the other side of the universe and back? We all had dreams, but no one dared dream of what actually happened.

Even as that excitement was wooing us all, the next unbelievable trip was already unknowingly underway. Svante Paabo and colleagues were working out the techniques to extract and sequence DNA from 30,000(+) year old Neanderthal bones. Never, in my wildest imagination in 2001, would I have pictured the possibility of obtaining enough nuclear DNA from our long extinct relatives to sequence their genome too. But now, ten years later we have a draft (1.3 fold coverage) of the DNA instructions for building the body of a Neanderthal.

It doesn’t stop there though. The molecule keeps revealing its secrets. No sooner had I caught my breath from reading the details of the Neanderthal sequence, when the biggest shock of all was released last December. Found in a Siberian cave were the fossilized bones of a single finger of a female hominin (human relative) who lived between 30,000 and 50,000 years ago. Paabo’s group was able to isolate enough high quality DNA from that one pinky finger to sequence her entire genome. (Listen to the fascinating discussion of the discovery in the accompanying audio.) We now have a better draft (1.7 coverage) of the DNA from the bones of one “pinky” finger than we do of the all of the fossilized Neanderthal remains put together.

Prior to analyzing her genome, investigators expected to find that either she was a human being like us, or she was a Neanderthal. What they found, however, no one was prepared for. No one! The DNA in that finger was not ours, nor was it Neanderthal. This single finger was from a different hominin altogether. Now it is clear that we had relatives—known as the Denisovans—roaming the earth in the recent past who were as different from us as Neanderthals were. There would likely have been at least hundreds of thousands of these individuals that lived on Earth from the time of their inception to the time of their extinction. Yet all we have identified so far is one finger, two molar teeth (found in the same cave, but from a different individual) and a piece of a knuckle bone. It was their genome, not a fossil, which has told us of their existence. Without that we would not have known.

And I thought biology had gone to the moon when it revealed the 24 base sequence of the lactose operator! Now we have billions of bases sequenced and a draft of the instruction plans for building three different hominins, all of whom lived on this Earth at the same time, as recently as 30,000 years ago.

There are many ramifications of this discovery. First, we are in the unprecedented—and until now unimagined situation—of having the entire genome sequence of an organism for which we have virtually no fossil material. (One pinky, two molars and a part of a knuckle bone do not a full-fledged fossil make).

At BioLogos, we have said many times that we would expect to find significant gaps in the fossil record (see here for example). We understand the basis for the gaps. For one thing, fossilization is an exceedingly rare event, but there are other well-understood reasons as well. Paleontologists have scoured the world looking for hominin fossils. They are big and easy to spot should they be present in the area being searched, but the fossil record of these newest hominins was silent until recently. What ought that to tell us? How long will it take us to grasp that gaps in the fossil record are not surprising? The surprising thing is that we have as good a record of past events as we do. It’s that which should amaze us, not the absences.

Second, now that we have drafts of the instructions for building all three body types, we can determine how similar they are and when they would have last shared a common ancestor. Based on genetic analysis, the average gene difference points back to a common ancestor of all three groups who lived about 800,000 years ago.

The Neanderthal and the Denisovan are a little more closely related to each other than they are to modern humans. In their case, analysis of average gene difference suggests that they last shared a common ancestor about 400,000 years ago—though they are still very different from each other.

To give you a feeling for how similar and different they are from one another, consider human/chimpanzee differences. It’s been about 6,000,000 years since we had a common ancestor. On the other hand, our family tree is identical to that of the Denisovans and Neanderthals until about 800,000 years ago. We’ve only been diverging separately for a little over 10 percent of the time since the last common ancestor of chimps and humans. Of course, when one considers how different chimps are from humans, even ten percent of that for the human/Neanderthal or human/Denisovan comparisons is large. They were very different from us and it will be extremely interesting to analyze the differences gene by gene as the analysis continues in the coming years.

Third, we need to acknowledge that as the genetic and paleontological data keeps piling up, it is most important that the Church become engaged in thinking about its meaning. It is clear now that we can trace our lineage—in some cases gene by gene— with amazing precision. These are cousins of ours: the Neanderthals, Denisovans, and almost certainly others who occupied the Earth at the same time, some perhaps as recently as 17,000 years ago.

BioLogos exists to help Christians think carefully about the ramifications of these new data in light of long-standing traditional ways of viewing human creation. We have some re-thinking to do, but it can be done and will be done within the context of a Christian faith that is fully orthodox and thoroughly evangelical. Any time we draw closer to truth, to God’s truth, we have nothing to fear. There is still much to learn, but we can look back at what we have learned with awe—absolute awe.

I’m not at a Berkeley conference anymore, and I’m not in a cork-popping San Francisco hotel either. For me, however, this stage is the most thrilling of all because it takes us deeper—far deeper—than we could have ever imagined. Addressing the theological and philosophical questions that lie ahead will be rewarding to work through and will take us far outside the natural universe into the realm of the New Jerusalem—the supernatural world of heaven itself. This is God’s truth we are coming to understand. We must not leave this territory, which reveals so much about human nature, to the exploration of those who don’t believe there is a New Jerusalem. We as Christians ought to be at the forefront in thinking about the meaning of these new data and not turning our backs just because we find it so surprising (and to many, unsettling). As we begin an all-fulfilling journey across this new frontier together, I am confident we’ll go in the presence of God. The DNA molecule is God’s creation, after all, and the secrets it reveals to us are his truths, not ours.

The above audio, from the August 26th Science Magazine podcast, is a very engaging discussion of the science that has led to our current state of knowledge. We greatly appreciate the American Association of the Advancement of Science (AAAS) for granting us permission to post it here. Ann Gibbons, the interviewee, is a journalist at Science Magazine. For more about her work see http://www.anngibbons.com/bio/bio.shtml

Darrel Falk is former president of BioLogos and currently serves as BioLogos' Senior Advisor for Dialog. He is Professor of Biology, Emeritus at Point Loma Nazarene University and serves as Senior Fellow at The Colossian Forum. Falk is the author of Coming to Peace with Science.

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Roger A. Sawtelle - #64915

September 22nd 2011

Variation, based largely on genetic change, is one key to evolution. 

However, we should not be overwhelmed by the miracles of DNA to overlook the other key process, which is natural selection, as neoDarwinists have done. 

Evolution is not understood until both variation and natural selection are understood.  Dawkins’ gene based evolution is only half of the story.

S. Scott Mapes - #64932

September 23rd 2011

Thank you, Darrell, for a well-written and accessible piece.  For those of us with minimal background in the biological sciences, it is very helpful to get a quick read regarding significant developments on things as complex as “paleo-genetics” and to not feel totally lost in other discussions and research.  This new discovery appears to be quite significant and ought to give greater opportunities for the Biologos perspective to be considered.

David Evarts - #65203

September 28th 2011

Wow.  Absolutely wow!  It’s time for some worship and the most obtuse anti-evolutionist cannot take that away.

Menno van Barneveld - #65388

October 4th 2011

My comment is not that of a biologist but of a servant of Jesus Christ our lord.
Jesus Christ revealed to me the following facts, that you do not think that I am so clever: God created Adam, who is the father of mankind, a little less than one million years ago. Both the Neanderthals and the Denisovans belong to the human kind.
The difference between humans and mammal animals is that God created humans with spoken language and with an indestructible soul. When the human body dies, the soul gets out of the body and has everlasting life.
When a mammal animal dies the soul falls apart in little soul particles and retreates in the blood to leave the body. This is why the animal has to be slaughtered fully conscious by cutting the neck, and let the blood flow out of the body (Acts 15:19-20). In that way we cannot steel the soul of the animal from God (Ex. 22:1).
The scientist cannot detect the soul nor God nor the holy spirit. This is the reason why the atheist supposes that everything evolves from itself. He cannot see the holy spirit at work. The truth is that God is at the stearingwheel of creation and the holy spirit is doing the work.
Therefor I prefer to speak about intelligent design, because God made His plan and He is making His plan come true.

Roger A. Sawtelle - #65395

October 4th 2011

As a Servant of our Lord Jesus Christ you should know that He is the Logos of God sent by the Father to reconcile the world unto God through the Holy Spirit.

What does your private revelation have to do with God’s revelation of Jesus the Messiah, the Chosen One of YHWH? 

Menno van Barneveld - #65416

October 5th 2011

Dear Roger,

The statement that Jesus Christ is the Logos of God sent by the Father is a philosophical thought taken from Plato and it is heretic.
The truth is that Jesus was born as a human male and that when he was baptized by John the Baptist the holy spirit descended upon him which made him godly, the Christ. In the second century the bisshops did stop giving gifts of the holy spirit to the followers of Jesus Christ, to moderate the persecution. And in 325 on the coucil of Nicea under the pressure of Ceacar Consatntine the bisshops addopted the church dogma of the holy trinity, also to moderate persecution. Changes had to be made in the Bible text to support this dogma.
Now John 1:1 was changed into
1:1 εν αρχη ην ο λογος και ο λογος ην προς τον θεον και θεος ην ο λογος.
from the originaly revealed text
1:1 εν αρχη ην ο λογος και ο λογος ην προς τον θεον και θεος λογος προφητην υμιν αναστησει ο θεος εκ των αδελφων υμων ως εμε.
This original text translates to
1:1 In the beginning was the word and the word was with God and the word of God prophecies you the resurrection of the god out of the brothers of you as saviour.
This verse proofs that ‘the word’ is the prophetic word of God and disproofs that Logos is Christ. It also proofs that Jesus was born out of the brothers, that means he is a Jew by birth.

As a sevant of Jesus Christ our lord he gave me a gift of the holy spirit that gives me his answers on my questions. So my private revelation is is a direct revelation from Jesus Christ through the holy spirit.


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